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Sample records for anaerobic methane-oxidizing archaea

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

    DEFF Research Database (Denmark)

    Lloyd, Karen; Teske, Andreas; Alperin, Marc J.

    2011-01-01

    Uncultured ANaerobic MEthanotrophic (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. Anaero...

  2. Anaerobic methane oxidation in a landfill-leachate plume.

    Science.gov (United States)

    Grossman, Ethan L; Cifuentes, Luis A; Cozzarelli, Isabelle M

    2002-06-01

    The alluvial aquifer adjacent to Norman Landfill, OK, provides an excellent natural laboratory for the study of anaerobic processes impacting landfill-leachate contaminated aquifers. We collected groundwaters from a transect of seven multilevel wells ranging in depth from 1.3 to 11 m that were oriented parallel to the flow path. The center of the leachate plume was characterized by (1) high alkalinity and elevated concentrations of total dissolved organic carbon, reduced iron, and methane, and (2) negligible oxygen, nitrate, and sulfate concentrations. Methane concentrations and stable carbon isotope (delta13C) values suggest anaerobic methane oxidation was occurring within the plume and at its margins. Methane delta13C values increased from about -54 per thousand near the source to > -10 per thousand downgradient and at the plume margins. The isotopic fractionation associated with this methane oxidation was -13.6+/-1.0 per thousand. Methane 13C enrichment indicated that 80-90% of the original landfill methane was oxidized over the 210-m transect. First-order rate constants ranged from 0.06 to 0.23 per year, and oxidation rates ranged from 18 to 230 microM/y. Overall, hydrochemical data suggest that a sulfate reducer-methanogen consortium may mediate this methane oxidation. These results demonstrate that natural attenuation through anaerobic methane oxidation can be an important sink for landfill methane in aquifer systems.

  3. Ultrastructure and viral metagenome of bacteriophages from an anaerobic methane oxidizing methylomirabilis bioreactor enrichment culture

    NARCIS (Netherlands)

    Gambelli, Lavinia; Cremers, Geert; Mesman, Rob; Guerrero, Simon; Dutilh, Bas E.; Jetten, Mike S M; den Camp, Huub J M Op; van Niftrik, Laura

    2016-01-01

    With its capacity for anaerobic methane oxidation and denitrification, the bacterium Methylomirabilis oxyfera plays an important role in natural ecosystems. Its unique physiology can be exploited for more sustainable wastewater treatment technologies. However, operational stability of full-scale bio

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

    DEFF Research Database (Denmark)

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

    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...

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

    OpenAIRE

    Li-Dong eShen; Bao-lan eHu

    2012-01-01

    Nitrite-dependent anaerobic methane oxidation (n-damo), which couples the anaerobic oxidation of methane to denitrification, is a recently discovered process observed in 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 ga...

  6. Combined anaerobic ammonium and methane oxidation for nitrogen and methane removal.

    Science.gov (United States)

    Zhu, Baoli; Sánchez, Jaime; van Alen, Theo A; Sanabria, Janeth; Jetten, Mike S M; Ettwig, Katharina F; Kartal, Boran

    2011-12-01

    Anammox (anaerobic ammonium oxidation) is an environment-friendly and cost-efficient nitrogen-removal process currently applied to high-ammonium-loaded wastewaters such as anaerobic digester effluents. In these wastewaters, dissolved methane is also present and should be removed to prevent greenhouse gas emissions into the environment. Potentially, another recently discovered microbial pathway, n-damo (nitrite-dependent anaerobic methane oxidation) could be used for this purpose. In the present paper, we explore the feasibility of simultaneously removing methane and ammonium anaerobically, starting with granules from a full-scale anammox bioreactor. We describe the development of a co-culture of anammox and n-damo bacteria using a medium containing methane, ammonium and nitrite. The results are discussed in the context of other recent studies on the application of anaerobic methane- and ammonia-oxidizing bacteria for wastewater treatment.

  7. Simultaneous enrichment of denitrifying anaerobic methane-oxidizing microorganisms and anammox bacteria in a hollow-fiber membrane biofilm reactor.

    Science.gov (United States)

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

    2017-01-01

    In this study, the coculture system of denitrifying anaerobic methane oxidation (DAMO) microbes and anaerobic ammonium oxidation (anammox) bacteria was successfully enriched in a hollow-fiber membrane biofilm reactor (HfMBR) using freshwater sediment as the inoculum. The maximal removal rates of nitrate and ammonium were 78 mg N/L/day (131 mg N/m(2)/day) and 26 mg N/L/day (43 mg N/m(2)/day), respectively. Due to the high rate of methane mass transfer in HfMBR, the activity of DAMO archaea continued to increase during the enrichment period, indicating that HfMBR could be a powerful tool to enrich DAMO microorganisms. Effects of partial methane pressure, temperature, and pH on the cocultures were obvious. However, the microbial activity in HfMBR could be recovered quickly after the shock change of environmental factors. Furthermore, the result also found that DAMO bacteria likely had a stronger competitive advantage than anammox bacteria under the operating conditions in this study. High-throughput sequencing 16S rRNA genes illustrated that the dominant microbes were NC10, Euryarchaeota, Proteobacteria, Planctomycetes, and Chlorobi with relative abundance of 38.8, 26.2, 13.78, 6.2, and 3.6 %, respectively.

  8. Diversity and enrichment of nitrite-dependent anaerobic methane oxidizing bacteria from wastewater sludge.

    Science.gov (United States)

    Luesken, Francisca A; van Alen, Theo A; van der Biezen, Erwin; Frijters, Carla; Toonen, Ger; Kampman, Christel; Hendrickx, Tim L G; Zeeman, Grietje; Temmink, Hardy; Strous, Marc; Op den Camp, Huub J M; Jetten, Mike S M

    2011-11-01

    Recently discovered microorganisms affiliated to the bacterial phylum NC10, named "Candidatus Methylomirabilis oxyfera", perform nitrite-dependent anaerobic methane oxidation. These microorganisms could be important players in a novel way of anaerobic wastewater treatment where ammonium and residual dissolved methane might be removed at the expense of nitrate or nitrite. To find suitable inocula for reactor startup, ten selected wastewater treatment plants (WWTPs) located in The Netherlands were screened for the endogenous presence of M. oxyfera using molecular diagnostic methods. We could identify NC10 bacteria with 98% similarity to M. oxyfera in nine out of ten WWTPs tested. Sludge from one selected WWTP was used to start a new enrichment culture of NC10 bacteria. This enrichment was monitored using specific pmoA primers and M. oxyfera cells were visualized with fluorescence oligonucleotide probes. After 112 days, the enrichment consumed up to 0.4 mM NO(2)(-) per day. The results of this study show that appropriate sources of biomass, enrichment strategies, and diagnostic tools existed to start and monitor pilot scale tests for the implementation of nitrite-dependent methane oxidation in wastewater treatment at ambient temperature.

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

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Pancost, R.D.; Lint, S. de; Maarel, M.J.E.C. van der; Gottschal, J.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 Medite

  10. Archaea in biogeochemical cycles.

    Science.gov (United States)

    Offre, Pierre; Spang, Anja; Schleper, Christa

    2013-01-01

    Archaea constitute a considerable fraction of the microbial biomass on Earth. Like Bacteria they have evolved a variety of energy metabolisms using organic and/or inorganic electron donors and acceptors, and many of them are able to fix carbon from inorganic sources. Archaea thus play crucial roles in the Earth's global geochemical cycles and influence greenhouse gas emissions. Methanogenesis and anaerobic methane oxidation are important steps in the carbon cycle; both are performed exclusively by anaerobic archaea. Oxidation of ammonia to nitrite is performed by Thaumarchaeota. They represent the only archaeal group that resides in large numbers in the global aerobic terrestrial and marine environments on Earth. Sulfur-dependent archaea are confined mostly to hot environments, but metal leaching by acidophiles and reduction of sulfate by anaerobic, nonthermophilic methane oxidizers have a potential impact on the environment. The metabolisms of a large number of archaea, in particular those dominating the subsurface, remain to be explored.

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

    Science.gov (United States)

    Dong, Jun; Ding, Linjie; Wang, Xu; Chi, Zifang; Lei, Jiansen

    2015-03-01

    Anaerobic methane oxidation (AMO) is considered to be an important sink of CH4 in habitats as marine sediments. But, few studies focused on AMO in landfills which may be an important sink of CH4 derived from waste fermentation. To show evidence of AMO and to uncover function anaerobic methanotroph (ANME) community in landfill, different age waste samples were collected in Jinqianpu landfill located in north China. Through high-throughput sequencing, Methanomicrobiales and Methanosarcinales archaea associated with ANME and reverse methanogenic archaea of Methanosarcina and Methanobacterium were detected. Sulfate-reducing bacteria (SRB) (Desulfobulbus and Desulfococcus) which could couple with ANME-conducting AMO were also found. But, the community structure of ANME had no significant difference with depths. From the results of investigation, we can come to a conclusion that sulfate-dependent anaerobic methane oxidation (SR-DAMO) would be the dominant AMO process in the landfill, while iron-dependent anaerobic methane oxidation (M/IR-DAMO) process was weak though concentration of ferric iron was large in the landfill. Denitrification-dependent anaerobic methane oxidation (NR-DAMO) was negative because of lack of nitrate and relevant function microorganisms in the landfill. Results also indicate that CH4 mitigation would have higher potential by increasing electron acceptor contents and promoting the growth of relevant function microorganisms.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Li-Dong eShen

    2012-07-01

    Full Text Available Nitrite-dependent anaerobic methane oxidation (n-damo, which couples the anaerobic oxidation of methane to denitrification, is a recently discovered process observed in 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 bacterial shapes. 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 an ecological 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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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)).

  16. Regulation of anaerobic methane oxidation in sediments of the Black Sea

    Directory of Open Access Journals (Sweden)

    N. J. Knab

    2008-05-01

    Full Text Available Anaerobic oxidation of methane (AOM and sulfate reduction (SRR were investigated in sediments of the western Black Sea, where methane transport is controlled by diffusion. To understand the regulation and dynamics of methane production and oxidation in the Black Sea, rates of methanogenesis, AOM, and SRR were determined using radiotracers in combination with pore water chemistry and stable isotopes. On the shelf of the Danube paleo-delta and the Dnjepr Canyon, AOM did not consume methane effectively and upwards diffusing methane created an extended sulfate-methane transition zone (SMTZ that spread over more than 2.5 m and was located in formerly limnic sediment. Measurable AOM rates occurred mainly in the lower part of the SMTZ, sometimes even at depths where sulfate seemed to be unavailable. The inefficiency of methane oxidation appears to be linked to the limnic history of the sediment, since in all cores methane was completely oxidized at the limnic-marine transition. The upward tailing of methane was less pronounced in a core from the deep sea in the area of the Dnjepr Canyon, the only station with a SMTZ close to the marine deposits. Sulfate reduction rates were mostly extremely low, and in the SMTZ were even lower than AOM rates. Rates of bicarbonate-based methanogenesis were below detection limit in two of the cores, but δ13C values of methane indicate a biogenic origin. The most depleted δ13C-signal was found in the SMTZ of the core from the deep sea, most likely as a result of carbon recycling between AOM and methanogenesis.

  17. Immunological detection of enzymes for sulfate reduction in anaerobic methane-oxidizing consortia.

    Science.gov (United States)

    Milucka, Jana; Widdel, Friedrich; Shima, Seigo

    2013-05-01

    Anaerobic oxidation of methane (AOM) coupled to sulfate reduction (SR) at marine gas seeps is performed by archaeal-bacterial consortia that have so far not been cultivated in axenic binary or pure cultures. Knowledge about possible biochemical reactions in AOM consortia is based on metagenomic retrieval of genes related to those in archaeal methanogenesis and bacterial sulfate reduction, and identification of a few catabolic enzymes in protein extracts. Whereas the possible enzyme for methane activation (a variant of methyl-coenzyme M reductase, Mcr) was shown to be harboured by the archaea, enzymes for sulfate activation and reduction have not been localized so far. We adopted a novel approach of fluorescent immunolabelling on semi-thin (0.3-0.5 μm) cryosections to localize two enzymes of the SR pathway, adenylyl : sulfate transferase (Sat; ATP sulfurylase) and dissimilatory sulfite reductase (Dsr) in microbial consortia from Black Sea methane seeps. Both Sat and Dsr were exclusively found in an abundant microbial morphotype (c. 50% of all cells), which was tentatively identified as Desulfosarcina/Desulfococcus-related bacteria. These results show that ANME-2 archaea in the Black Sea AOM consortia did not express bacterial enzymes of the canonical sulfate reduction pathway and thus, in contrast to previous suggestions, most likely cannot perform canonical sulfate reduction. Moreover, our results show that fluorescent immunolabelling on semi-thin cryosections which to our knowledge has been so far only applied on cell tissues, is a powerful tool for intracellular protein detection in natural microbial associations.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2013-08-01

    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

  1. Anaerobic nitrite-dependent methane-oxidizing bacteria - novel participants in methane cycling of drained peatlands ecosystems

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    Kravchenko, Irina; Sukhacheva, Marina; Menko, Ekaterina; Sirin, Andrey

    2014-05-01

    Northern peatlands are one of the key sources of atmospheric methane. Process-based studies of methane dynamic are based on the hypothesis of the balance between microbial methane production and oxidation, but this doesn't explain all variations in and constraints on peatland CH4 emissions. One of the reasons for this discrepancy could be anaerobic methane oxidation (AOM) - the process which is still poorly studied and remained controversial. Very little is known about AOM in peatlands, where it could work as an important 'internal' sink for CH4. This lack of knowledge primarily originated from researchers who generally consider AOM quantitatively insignificant or even non-existent in northern peatland ecosystems. But not far ago, Smemo and Yavitt (2007) presented evidence for AOM in freshwater peatlands used indirect techniques including isotope dilution assays and selective methanogenic inhibitors. Nitrite-dependent anaerobic methane oxidation NC10 group bacteria (n-damo) were detected in a minerotrophic peatland in the Netherlands that is infiltrated by nitrate-rich ground water (Zhu et al., 2012). Present study represents the first, to our knowledge, characterization of AOM in human disturbed peatlands, including hydrological elements of artificial drainage network. The experiments were conducted with samples of peat from drained peatlands, as well as of water and bottom sediments of ditches from drained Dubnensky mire massif, Moscow region (Chistotin et al., 2006; Sirin et al., 2012). This is the key testing area of our research group in European part of Russia for the long-term greenhouse gases fluxes measurements supported by testing physicochemical parameters, intensity and genomic diversity of CH4-cycling microbial communities. Only in sediments of drainage ditches the transition anaerobic zone was found, where methane and nitrate occurred, suggested the possible ecological niche for n-damo bacteria. The NC10 group methanotrophs were analyzed by PCR

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

    Science.gov (United States)

    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.

  3. Trace methane oxidation and the methane dependency of sulfate reduction in anaerobic granular sludge

    KAUST Repository

    Meulepas, Roel J.W.

    2010-05-01

    This study investigates the oxidation of labeled methane (CH4) and the CH4 dependence of sulfate reduction in three types of anaerobic granular sludge. In all samples, 13C-labeled CH4 was anaerobically oxidized to 13C-labeled CO2, while net endogenous CH4 production was observed. Labeled-CH4 oxidation rates followed CH4 production rates, and the presence of sulfate hampered both labeled-CH4 oxidation and methanogenesis. Labeled-CH4 oxidation was therefore linked to methanogenesis. This process is referred to as trace CH4 oxidation and has been demonstrated in methanogenic pure cultures. This study shows that the ratio between labeled-CH4 oxidation and methanogenesis is positively affected by the CH4 partial pressure and that this ratio is in methanogenic granular sludge more than 40 times higher than that in pure cultures of methanogens. The CH4 partial pressure also positively affected sulfate reduction and negatively affected methanogenesis: a repression of methanogenesis at elevated CH4 partial pressures confers an advantage to sulfate reducers that compete with methanogens for common substrates, formed from endogenous material. The oxidation of labeled CH 4 and the CH4 dependence of sulfate reduction are thus not necessarily evidence of anaerobic oxidation of CH4 coupled to sulfate reduction. © 2010 Federation of European Microbiological Societies.

  4. The potential for biologically catalyzed anaerobic methane oxidation on ancient Mars.

    Science.gov (United States)

    Marlow, Jeffrey J; Larowe, Douglas E; Ehlmann, Bethany L; Amend, Jan P; Orphan, Victoria J

    2014-04-01

    This study examines the potential for the biologically mediated anaerobic oxidation of methane (AOM) coupled to sulfate reduction on ancient Mars. Seven distinct fluids representative of putative martian groundwater were used to calculate Gibbs energy values in the presence of dissolved methane under a range of atmospheric CO2 partial pressures. In all scenarios, AOM is exergonic, ranging from -31 to -135 kJ/mol CH4. A reaction transport model was constructed to examine how environmentally relevant parameters such as advection velocity, reactant concentrations, and biomass production rate affect the spatial and temporal dependences of AOM reaction rates. Two geologically supported models for ancient martian AOM are presented: a sulfate-rich groundwater with methane produced from serpentinization by-products, and acid-sulfate fluids with methane from basalt alteration. The simulations presented in this study indicate that AOM could have been a feasible metabolism on ancient Mars, and fossil or isotopic evidence of this metabolic pathway may persist beneath the surface and in surface exposures of eroded ancient terrains.

  5. Evidence for Anaerobic Methane Oxidation Under Iron-Reducing Conditions in a Crude-Oil Contaminated Aquifer

    Science.gov (United States)

    Bekins, B. A.; Amos, R. T.; Cozzarelli, I. M.; Voytek, M. A.; Kirshtein, J.; Jones, E. J.; Delin, G. N.

    2008-12-01

    Although anaerobic methane oxidation (AMO) under iron reducing conditions is energetically feasible, its existence is still an open question. At a crude oil spill site near the town of Bemidji, MN, methanogenic degradation of entrapped oil floating at the water table has been occurring for more than 20 years. In the anaerobic portion of the hydrocarbon plume there is evidence for AMO under iron-reducing conditions between 75 m and 120 m downgradient of the oil body. In this zone, dissolved methane concentrations decrease steadily from over 0.6 mmol/L to less than 0.06 mmol/L. Decreases in dissolved methane are accompanied by an increase in δ13C-CH4 indicating that methane attenuation occurs through microbially mediated oxidation. The dissolved methane decrease of ~0.5 mmol/L occurs where dissolved sulfate is below 0.06 mmol/L, dissolved oxygen is below 3 μmol/L, and nitrate is below 0.02 mmol/L. Together these electron acceptors can account for degradation of only 0.07 mmol/L of methane. Moreover, hydrocarbon contaminants contribute an additional ~1 mmol/L total organic carbon in this area. Active iron- reduction is indicated by dissolved iron concentrations exceeding 0.15 mmol/L. To investigate the sediment bioavailable iron and microbial populations, 2-m-long cores were collected at four locations spaced 15 m horizontally and sampled at 50-cm-depth intervals. Values of bioavailable Fe(III) averaged 8 mmol/kg (n=16), which is over eight times the amount required to degrade 0.5 mmol/L methane. Geobacter detected by qPCR averaged over 2,600/g, while sulfate reducing bacteria were detected in only four samples with 100/g being the highest abundance measured. Laboratory incubations were performed with eight sediment samples from these cores. For each location, 1 g of sediment was added to 10 mL anaerobic medium and amended with amorphous FeOOH, Fe(III)NTA, sulfate, or nitrate. Loss of methane occurred in 33% of the iron-amended treatments, 25% of the nitrate

  6. Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

    Directory of Open Access Journals (Sweden)

    B. Orcutt

    2008-11-01

    Full Text Available Anaerobic oxidation of methane (AOM is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal were examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species can cause the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007, none of the potential intermediates considered here is able to support metabolic activity matching the measured rates.

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

    Energy Technology Data Exchange (ETDEWEB)

    Orphan, Victoria Jeanne [California Inst. of Technology (CalTech), Pasadena, CA (United States). Division of Geological and Planetary Sciences

    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

  8. Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

    Directory of Open Access Journals (Sweden)

    B. Orcutt

    2008-05-01

    Full Text Available Anaerobic oxidation of methane (AOM is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism, substrate affinity and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal was examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species causes the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007, neither hydrogen nor formate is exchanged fast enough between the consortia partners to achieve measured rates of metabolic activity, but that acetate exchange might support rates that approach those observed.

  9. 硫酸盐还原型甲烷厌氧氧化菌群驯化及其群落特征%Acclimatization and Characteristics of Microbial Community in Sulphate-Dependent Anaerobic Methane Oxidation

    Institute of Scientific and Technical Information of China (English)

    席婧茹; 刘素琴; 李琳; 刘俊新

    2014-01-01

    The greenhouse effect of methane is 26 times worse than that of carbon dioxide, and wastewater containing high concentrations of sulfate is harmful to water, soil and plants. Therefore, anaerobic oxidation of methane driven by sulfate is one of the effective ways for methane reduction. In this paper, with sulfate as the electron accepter, a microbial consortium capable of oxidating methane under anaerobic condition was cultured. The diversity and characteristics of bacterial and archaeal community were investigated by PCR-DGGE, and phylogenetic analysis of the dominant microorganisms was also carried out. The DGGE fingerprints showed that microbial community structure changed distinctly, and the abundance of methane-oxidizing archea and sulfate-reducing bacteria increased in the acclimatization system added sulfate. After acclimatization, the bacterial diversity increased, while archaea diversity decreased slightly. The representative bands in the DGGE profiles were excised and sequenced. Results indicated that the dominant species in the acclimatization system were Spirochaetes, Desulfuromonadales, Methanosarcinales, Methanosaeta. Methane converted into carbon dioxide while sulfate transformed into hydrogen sulfide and sulfur in the process of anaerobic methane oxidation accompanied by sulphate reduction.%甲烷的温室效应是二氧化碳的26倍,高浓度硫酸盐废水对水体、土壤和植物均有危害。硫酸盐为氧化剂的甲烷厌氧氧化是减少甲烷的主要途径之一。本研究以硫酸盐作为电子受体,驯化培养硫酸盐还原型甲烷厌氧氧化菌群,采用 PCR-DGGE技术分析细菌和古菌菌群多样性和群落结构特征,并对其中的优势菌进行系统发育分析。 DGGE 指纹图谱结果表明,硫酸盐的加入使微生物群落结构和优势种群数量发生了明显的改变,其增强了甲烷氧化古菌和硫酸盐还原细菌的丰度,加入硫酸盐驯化的菌群,其细菌

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

    Science.gov (United States)

    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

  11. Electron transfer in syntrophic communities of anaerobic bacteria and archaea

    NARCIS (Netherlands)

    Stams, A.J.M.; Plugge, C.M.

    2009-01-01

    Interspecies electron transfer is a key process in methanogenic and sulphate-reducing environments. Bacteria and archaea that live in syntrophic communities take advantage of the metabolic abilities of their syntrophic partner to overcome energy barriers and break down compounds that they cannot dig

  12. A mass balance model to estimate the rate of composting, methane oxidation and anaerobic digestion in soil covers and shallow waste layers.

    Science.gov (United States)

    Rafiee, Reza; Obersky, Lizanne; Xie, Sihuang; Clarke, William P

    2017-01-12

    Although CH4 oxidation in landfill soil covers is widely studied, the extent of composting and CH4 oxidation in underlying waste layers has been speculated but not measured. The objective of this study was to develop and validate a mass balance model to estimate the simultaneous rates of anaerobic digestion (rAD), CH4 oxidation (rOX) and composting (rCOM) in environments where O2 penetration is variable and zones of aerobic and anaerobic activity are intermingled. The modelled domain could include, as an example, a soil cover and the underlying shallow waste to a nominated depth. The proposed model was demonstrated on a blend of biogas from three separate known sources of gas representing the three reaction processes: (i) a bottle of laboratory grade 50:50% CH4:CO2 gas representing anaerobic digestion biogas; (ii) an aerated 250mL bottle containing food waste that represented composting activity; and (iii) an aerated 250mL bottle containing non-degradable graphite granules inoculated with methanotrophs and incubated with CH4 and O2 to represent methanotrophic activity. CO2, CH4, O2 and the stable isotope (13)C-CO2 were chosen as the components for the mass balance model. The three reaction rates, r (=rAD, rOX, rCOM) were calculated as fitting parameters to the overdetermined set of 4mass balance equations with the net flux of these components from the bottles q (= [Formula: see text] , [Formula: see text] , [Formula: see text] and [Formula: see text] ) as inputs to the model. The coefficient of determination (r(2)) for observed versus modelled values of r were 1.00, 0.97, 0.98 when the stoichiometry of each reaction was based on gas yields measured in the individual bottles and q was calculated by summing yields from the three bottles. r(2) deteriorated to 0.95, 0.96, 0.87 when using an average stoichiometry from 11 incubations of each of the composting and methane oxidation processes. The significant deterioration in the estimation of rCOM showed that this output

  13. Using 13C isotopes to explore denitrification-dependent anaerobic methane oxidation in a paddy-peatland

    Science.gov (United States)

    Shi, Yao; Wang, Zhongqiang; He, Chunguang; Zhang, Xinyu; Sheng, Lianxi; Ren, Xiaodong

    2017-01-01

    Peatlands are organic-matter-rich but nitrogen-limited natural systems, the carbon/nitrogen (C/N) status of which are subject to increasing exposure from long-term nitrate (NO3−) fertilizer inputs and atmospheric nitrogen (N) deposits. To manage and protect these unique environments, an improved understanding of denitrification-dependent anaerobic oxidation of methane (DAMO) in peatlands is needed. In this study, we used stable isotope measurements and incubation with NO3− additions to facilitate an investigation and comparison of the potential DAMO rates in a paddy-peatland that has been influenced by N fertilizer over 40 years and an undisturbed peatland in northeast China. Monitoring of 13CO2 production confimed DAMO did occur in both the paddy-peatland and the undisturbed peatland, the rates of which increased with NO3− additions, but decreased logarithmically with time. When NO3− was added, there were no significant differences between the CH4 oxidation in the paddy-peatland and peatland samples after 36 hours of incubation (97.08 vs. 143.69 nmol g−1 dry peat) and the potential DAMO rate after incubation for 1 hour (92.53 vs. 69.99 nmol g−1 h−1). These results indicate that the occurrence of DAMO in peatlands might be controlled by the amount of NO3− applied and the depth to which it penetrates into the anoxic layer. PMID:28098207

  14. Using 13C isotopes to explore denitrification-dependent anaerobic methane oxidation in a paddy-peatland

    Science.gov (United States)

    Shi, Yao; Wang, Zhongqiang; He, Chunguang; Zhang, Xinyu; Sheng, Lianxi; Ren, Xiaodong

    2017-01-01

    Peatlands are organic-matter-rich but nitrogen-limited natural systems, the carbon/nitrogen (C/N) status of which are subject to increasing exposure from long-term nitrate (NO3‑) fertilizer inputs and atmospheric nitrogen (N) deposits. To manage and protect these unique environments, an improved understanding of denitrification-dependent anaerobic oxidation of methane (DAMO) in peatlands is needed. In this study, we used stable isotope measurements and incubation with NO3‑ additions to facilitate an investigation and comparison of the potential DAMO rates in a paddy-peatland that has been influenced by N fertilizer over 40 years and an undisturbed peatland in northeast China. Monitoring of 13CO2 production confimed DAMO did occur in both the paddy-peatland and the undisturbed peatland, the rates of which increased with NO3‑ additions, but decreased logarithmically with time. When NO3‑ was added, there were no significant differences between the CH4 oxidation in the paddy-peatland and peatland samples after 36 hours of incubation (97.08 vs. 143.69 nmol g‑1 dry peat) and the potential DAMO rate after incubation for 1 hour (92.53 vs. 69.99 nmol g‑1 h‑1). These results indicate that the occurrence of DAMO in peatlands might be controlled by the amount of NO3‑ applied and the depth to which it penetrates into the anoxic layer.

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

    Science.gov (United States)

    Lawton, Thomas J; Rosenzweig, Amy C

    2016-08-03

    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.

  16. Assessment of active methanogenic archaea in a methanol-fed upflow anaerobic sludge blanket reactor.

    Science.gov (United States)

    Cerrillo, Míriam; Morey, Lluís; Viñas, Marc; Bonmatí, August

    2016-12-01

    Methanogenic archaea enrichment of a granular sludge was undertaken in an upflow anaerobic sludge blanket (UASB) reactor fed with methanol in order to enrich methylotrophic and hydrogenotrophic methanogenic populations. A microbial community assessment, in terms of microbial composition and activity-throughout the different stages of the feeding process with methanol and acetate-was performed using specific methanogenic activity (SMA) assays, quantitative real-time polymerase chain reaction (qPCR), and high-throughput sequencing of 16S ribosomal RNA (rRNA) genes from DNA and complementary DNA (cDNA). Distinct methanogenic enrichment was revealed by qPCR of mcrA gene in the methanol-fed community, being two orders of magnitude higher with respect to the initial inoculum, achieving a final mcrA/16S rRNA ratio of 0.25. High-throughput sequencing analysis revealed that the resulting methanogenic population was mainly composed by methylotrophic archaea (Methanomethylovorans and Methanolobus genus), being also highly active according to the RNA-based assessment. SMA confirmed that the methylotrophic pathway, with a direct conversion of methanol to CH4, was the main step of methanol degradation in the UASB. The biomass from the UASB, enriched in methanogenic archaea, may bear great potential as additional inoculum for bioreactors to carry out biogas production and other related processes.

  17. Genomic expansion of Domain Archaea highlights roles for organisms from new phyla in anaerobic carbon cycling

    Energy Technology Data Exchange (ETDEWEB)

    Castelle, Cindy; Wrighton, Kelly C.; Thomas, Brian C.; Hug, Laura A.; Brown, Christopher T.; Wilkins, Michael J.; Frischkorn, Kyle R.; Tringe, Susannah G.; Singh, Andrea; Markillie, Lye Meng; Taylor, Ronald C.; Williams, Kenneth H.; Banfield, Jillian F.

    2015-03-01

    cultivated representatives, the biogeochemical impacts of this major radiation of archaea are primarily through anaerobic carbon and hydrogen cycling.

  18. Reverse Methanogenesis and Respiration in Methanotrophic Archaea

    Science.gov (United States)

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

    2017-01-01

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

  19. The contribution of fermentative bacteria and methanogenic archaea to azo dye reduction by a thermophilic anaerobic consortium

    NARCIS (Netherlands)

    Santos, dos A.B.; Cervantes, F.J.; Madrid, de M.P.; Bok, de F.A.M.; Stams, A.J.M.; Lier, van J.B.

    2006-01-01

    The contribution of fermentative bacteria and methanogenic archaea to azo dye reduction by a thermophilic anaerobic consortium was studied. Additionally, the effects of different electron-donating substrates and the redox mediator riboflavin on dye reduction were assessed by using either a methanoge

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

    Directory of Open Access Journals (Sweden)

    Victoria J. Orphan

    2011-11-01

    Full Text Available 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

  1. Application of real-time PCR to determination of combined effect of antibiotics on Bacteria, Methanogenic Archaea, Archaea in anaerobic sequencing batch reactors.

    Science.gov (United States)

    Aydin, Sevcan; Ince, Bahar; Ince, Orhan

    2015-06-01

    This study evaluated the long-term effects of erythromycin-tetracycline-sulfamethoxazole (ETS) and sulfamethoxazole-tetracycline (ST) antibiotic combinations on the microbial community and examined the ways in which these antimicrobials impact the performance of anaerobic reactors. Quantitative real-time PCR was used to determine the effect that different antibiotic combinations had on the total and active Bacteria, Archae and Methanogenic Archae. Three primer sets that targeted metabolic genes encoding formylterahydrofolate synthetase, methyl-coenzyme M reductase and acetyl-coA synthetase were also used to determine the inhibition level on the mRNA expression of the homoacetogens, methanogens and specifically acetoclastic methanogens, respectively. These microorganisms play a vital role in the anaerobic degradation of organic waste and targeting these gene expressions offers operators or someone at a treatment plant the potential to control and the improve the anaerobic system. The results of the investigation revealed that acetogens have a competitive advantage over Archaea in the presence of ETS and ST combinations. Although the efficiency with which methane production takes place and the quantification of microbial populations in both the ETS and ST reactors decreased as antibiotic concentrations increased, the ETS batch reactor performed better than the ST batch reactor. According to the expression of genes results, the syntrophic interaction of acetogens and methanogens is critical to the performance of the ETS and ST reactors. Failure to maintain the stability of these microorganisms resulted in a decrease in the performance and stability of the anaerobic reactors.

  2. Precipitation of low-temperature dolomite from an anaerobic microbial consortium: the role of methanogenic Archaea.

    Science.gov (United States)

    Kenward, P A; Goldstein, R H; González, L A; Roberts, J A

    2009-12-01

    Here we report precipitation of dolomite at low temperature (30 degrees C) mediated by a mixed anaerobic microbial consortium composed of dissimilatory iron-reducing bacteria (DIRB), fermenters, and methanogens. Initial solution geochemistry is controlled by DIRB, but after 90 days shifts to a system dominated by methanogens. In live experiments conditions are initially saturated with respect to dolomite (Omega(dol) = 19.40) and increase by two orders of magnitude (Omega(dol) = 2 330.77) only after the onset of methanogenesis, as judged by the increasing [CH(4)] and the detection of methanogenic micro-organisms. We identify ordered dolomite in live microcosms after 90 days via powder X-ray diffraction, while sterile controls precipitate only calcite. Scanning electron microscopy and transmitted electron microscopy demonstrate that the precipitated dolomite is closely associated with cell walls and putative extra-cellular polysaccharides. Headspace gas measurements and denaturing gradient gel electrophoresis confirm the presence of both autotrophic and acetoclastic methanogens and exclude the presence of DIRB and sulfate-reducing bacteria after dolomite begins forming. Furthermore, the absence of dolomite in the controls and prior to methanogenesis confirm that methanogenic Archaea are necessary for the low-temperature precipitation of dolomite under the experimental conditions tested.

  3. Trace methane oxidation studied in several Euryarchaeota under diverse conditions

    Directory of Open Access Journals (Sweden)

    James J. Moran

    2005-01-01

    Full Text Available We used 13C-labeled methane to document the extent of trace methane oxidation by Archaeoglobus fulgidus, Archaeoglobus lithotrophicus, Archaeoglobus profundus, Methanobacterium thermoautotrophicum, Methanosarcina barkeri and Methanosarcina acetivorans. The results indicate trace methane oxidation during growth varied among different species and among methanogen cultures grown on different substrates. The extent of trace methane oxidation by Mb. thermoautotrophicum (0.05 ± 0.04%, ± 2 standard deviations of the methane produced during growth was less than that by M. barkeri (0.15 ± 0.04%, grown under similar conditions with H2 and CO2. Methanosarcina acetivorans oxidized more methane during growth on trimethylamine (0.36 ± 0.05% than during growth on methanol (0.07 ± 0.03%. This may indicate that, in M. acetivorans, either a methyltransferase related to growth on trimethylamine plays a role in methane oxidation, or that methanol is an intermediate of methane oxidation. Addition of possible electron acceptors (O2, NO3–, SO22–, SO32– or H2 to the headspace did not substantially enhance or diminish methane oxidation in M. acetivorans cultures. Separate growth experiments with FAD and NAD+ showed that inclusion of these electron carriers also did not enhance methane oxidation. Our results suggest trace methane oxidized during methanogenesis cannot be coupled to the reduction of these electron acceptors in pure cultures, and that the mechanism by which methane is oxidized in methanogens is independent of H2 concentration. In contrast to the methanogens, species of the sulfate-reducing genus Archaeoglobus did not significantly oxidize methane during growth (oxidizing 0.003 ± 0.01% of the methane provided to A. fulgidus, 0.002 ± 0.009% to A. lithotrophicus and 0.003 ± 0.02% to A. profundus. Lack of observable methane oxidation in the three Archaeoglobus species examined may indicate that methyl-coenzyme M reductase, which is not present in

  4. Methane oxidation needs less stressed plants.

    Science.gov (United States)

    Zhou, Xiaoqi; Smaill, Simeon J; Clinton, Peter W

    2013-12-01

    Methane oxidation rates in soil are liable to be reduced by plant stress responses to climate change. Stressed plants exude ethylene into soil, which inhibits methane oxidation when present in the soil atmosphere. Here we discuss opportunities to use 1-aminocyclopropane-1-carboxylate deaminase to manage methane oxidation by regulating plant stress responses.

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

    Science.gov (United States)

    Hoehler, Tori M.; Alperin, Marc J.; Albert, Daniel B.; Martens, Christopher S.

    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 CO2 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 CO2 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 play a role in the process. We hypothesize that methanogens oxidize methane and produce hydrogen via a reversal of CO2 reduction. The hydrogen is efficiently removed and maintained at low concentrations by sulfate reducers. Pore water H2 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 is consistent not only with the results of this study, but may also be a feasible mechanism for previously documented anaerobic methane oxidation in both freshwater and marine environments.

  6. Decoupling of DAMO archaea from DAMO bacteria in a methane-driven microbial fuel cell.

    Science.gov (United States)

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

    2017-03-01

    Anaerobic oxidation of methane (AOM) contributes significantly to the global methane sink. Previously, studies of anaerobic methanotrophic (ANME) archaea have been limited as they have not been separable from their bacterial partners during the AOM process because of their dependence on the bacteria. A microbial fuel cell (MFC) is a device capable of directly transforming chemical energy to electrical energy via electrochemical reactions involving biochemical pathways. In this study, decoupling of denitrifying anaerobic methane oxidation (DAMO) archaea and DAMO bacteria was investigated in an microbial fuel cell (MFC) using methane as the fuel. The DAMO fuel cell worked successfully but demonstrated weak electrogenic capability with around 25 mV production. After 45 days' enrichment, the sequencing and fluorescence in situ hybridization results showed the DAMO archaea percentage had increased from 26.96% (inoculum) to 65.77% (electrode biofilm), while the DAMO bacteria percentage decreased from 24.39% to 2.07%. Moreover, the amount of ANME-2d had doubled in the electrode biofilm compared with the inoculum. The sequencing results also showed substantial enrichment of the Ignavibacterium and Geobacter genera. The roles of Ignavibacterium and Geobacter in the MFC system need to be further investigated. Nevertheless, these results illustrate that an MFC device may provide a possible approach to separate DAMO archaea from DAMO bacteria.

  7. Archaea in Symbioses

    Directory of Open Access Journals (Sweden)

    Christoph Wrede

    2012-01-01

    Full Text Available During the last few years, the analysis of microbial diversity in various habitats greatly increased our knowledge on the kingdom Archaea. At the same time, we became aware of the multiple ways in which Archaea may interact with each other and with organisms of other kingdoms. The large group of euryarchaeal methanogens and their methane oxidizing relatives, in particular, take part in essential steps of the global methane cycle. Both of these processes, which are in reverse to each other, are partially conducted in a symbiotic interaction with different partners, either ciliates and xylophagous animals or sulfate reducing bacteria. Other symbiotic interactions are mostly of unknown ecological significance but depend on highly specific mechanisms. This paper will give an overview on interactions between Archaea and other organisms and will point out the ecological relevance of these symbiotic processes, as long as these have been already recognized.

  8. Methane oxidation linked to chlorite dismutation

    Science.gov (United States)

    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.

  9. Localization of Methyl-Coenzyme M Reductase as Metabolic Marker for Diverse Methanogenic Archaea

    Directory of Open Access Journals (Sweden)

    Christoph Wrede

    2013-01-01

    Full Text Available Methyl-Coenzyme M reductase (MCR as key enzyme for methanogenesis as well as for anaerobic oxidation of methane represents an important metabolic marker for both processes in microbial biofilms. Here, the potential of MCR-specific polyclonal antibodies as metabolic marker in various methanogenic Archaea is shown. For standard growth conditions in laboratory culture, the cytoplasmic localization of the enzyme in Methanothermobacter marburgensis, Methanothermobacter wolfei, Methanococcus maripaludis, Methanosarcina mazei, and in anaerobically methane-oxidizing biofilms is demonstrated. Under growth limiting conditions on nickel-depleted media, at low linear growth of cultures, a fraction of 50–70% of the enzyme was localized close to the cytoplasmic membrane, which implies “facultative” membrane association of the enzyme. This feature may be also useful for assessment of growth-limiting conditions in microbial biofilms.

  10. Microbial methane oxidation processes and technologies for mitigation of landfill gas emissions

    DEFF Research Database (Denmark)

    Scheutz, Charlotte; Kjeldsen, Peter; Bogner, J.E.;

    2009-01-01

    utilizing oxygen that diffuses into the cover layer from the atmosphere. The methane oxidation process, which is governed by several environmental factors, can be exploited in engineered systems developed for methane emission mitigation. Mathematical models that account for methane oxidation can be used...... to predict methane emissions from landfills. Additional research and technology development is needed before methane mitigation technologies utilizing microbial methane oxidation processes can become commercially viable and widely deployed.......Landfill gas containing methane is produced by anaerobic degradation of organic waste. Methane is a strong greenhouse gas and landfills are one of the major anthropogenic sources of atmospheric methane. Landfill methane may be oxidized by methanotrophic microorganisms in soils or waste materials...

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  13. Enzymes involved in the anaerobic oxidation of n-alkanes: from methane to long-chain paraffins

    OpenAIRE

    Callaghan, Amy V.

    2013-01-01

    Anaerobic microorganisms play key roles in the biogeochemical cycling of methane and non-methane alkanes. To date, there appear to be at least three proposed mechanisms of anaerobic methane oxidation (AOM). The first pathway is mediated by consortia of archaeal anaerobic methane oxidizers and sulfate-reducing bacteria via ‘reverse methanogenesis’ and is catalyzed by a homologue of methyl-coenzyme M reductase. The second pathway is also mediated by anaerobic methane oxidizers and sulfate-red...

  14. Archaea in metazoan diets: implications for food webs and biogeochemical cycling.

    Science.gov (United States)

    Thurber, Andrew R; Levin, Lisa A; Orphan, Victoria J; Marlow, Jeffrey J

    2012-08-01

    Although the importance of trophic linkages, including 'top-down forcing', on energy flow and ecosystem productivity is recognized, the influence of metazoan grazing on Archaea and the biogeochemical processes that they mediate is unknown. Here, we test if: (1) Archaea provide a food source sufficient to allow metazoan fauna to complete their life cycle; (2) neutral lipid biomarkers (including crocetane) can be used to identify Archaea consumers; and (3) archaeal aggregates are a dietary source for methane seep metazoans. In the laboratory, we demonstrated that a dorvilleid polychaete, Ophryotrocha labronica, can complete its life cycle on two strains of Euryarchaeota with the same growth rate as when fed bacterial and eukaryotic food. Archaea were therefore confirmed as a digestible and nutritious food source sufficient to sustain metazoan populations. Both strains of Euryarchaeota used as food sources had unique lipids that were not incorporated into O. labronica tissues. At methane seeps, sulfate-reducing bacteria that form aggregations and live syntrophically with anaerobic-methane oxidizing Archaea contain isotopically and structurally unique fatty acids (FAs). These biomarkers were incorporated into tissues of an endolithofaunal dorvilleid polychaete species from Costa Rica (mean bulk δ(13)C=-92±4‰; polar lipids -116‰) documenting consumption of archaeal-bacterial aggregates. FA composition of additional soft-sediment methane seep species from Oregon and California provided evidence that consumption of archaeal-bacterial aggregates is widespread at methane seeps. This work is the first to show that Archaea are consumed by heterotrophic metazoans, a trophic process we coin as 'archivory'.

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

    Science.gov (United States)

    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.

  16. [Copper in methane oxidation: a review].

    Science.gov (United States)

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

    2014-04-01

    Methane bio-oxidation plays an important role in the global methane balance and warming mitigation, while copper has a crucial function in methane bio-oxidation. On one side, copper is known to be a key factor in regulating the expression of the genes encoding the two forms of methane monooxygenases (MMOs) and is the essential metal element of the particulate methane monooxygenase (pMMO). On the other side, the content and fractionation of copper in the environment have great effects on the distribution of methanotrophs and their metabolic capability of methane and non-methane organic compounds, as well as on the copper-specific uptake systems in methanotrophs. Thus, it is meaningful to know the role of copper in methane bio-oxidation for comprehensive understanding of this process and is valuable for guiding the application of methanotrophs in greenhouse gas removal and pollution remediation. In this paper, the roles of copper in methane oxidation were reviewed, including the effect of copper on methanotrophic community structure and activity, the expression and activity of MMOs as well as the copper uptake systems in methanotrophs. The future studies of copper and methane oxidation were also discussed.

  17. Degradation of Methanethiol by Methylotrophic Methanogenic Archaea in a Lab-Scale Upflow Anaerobic Sludge Blanket Reactor

    NARCIS (Netherlands)

    Bok, de F.A.M.; Leerdam, van R.C.; Lomans, B.P.; Smidt, H.; Lens, P.N.L.; Janssen, A.J.H.; Stams, A.J.M.

    2006-01-01

    In a lab-scale upflow anaerobic sludge blanket reactor inoculated with granular sludge from a full-scale wastewater treatment plant treating paper mill wastewater, methanethiol (MT) was degraded at 30°C to H2S, CO2, and CH4. At a hydraulic retention time of 9 h, a maximum influent concentration of 6

  18. Methane oxidation and degradation of organic compounds in landfill soil covers

    DEFF Research Database (Denmark)

    Scheutz, Charlotte; Kjeldsen, Peter

    2002-01-01

    High rates of methane oxidation and degradation of the lowed halogenated methanes (TCM and DCM) and HCFCs (HCFC-21 and HCFC-22) were found in an investigation of the oxidation of methane and halogenated organic compunds (HOCs) in landfill gas affected soil. The degradation followed zero-order kin......High rates of methane oxidation and degradation of the lowed halogenated methanes (TCM and DCM) and HCFCs (HCFC-21 and HCFC-22) were found in an investigation of the oxidation of methane and halogenated organic compunds (HOCs) in landfill gas affected soil. The degradation followed zero......-order kinetics and occurred in parallel with the oxidation of methane. TeCM, CFC-11, and CFC-12 were not degradable in presence of oxygen and degradation of these compounds in the oxidative zone in landfill top covers is therefore expected to be limited. However these compounds were found degradable...... in the anaerobic zone in the lower part of soil columns permeated with artificial landfill gas. The lesser-chlorinated compounds were degraded in the upper oxic zone with overlapping gradients of methane and oxygen. Methane oxidation and degradation of HOCs in the top-soils may play a very important role...

  19. Anaerobic oxidation of methane by sulfate in hypersaline groundwater of the Dead Sea aquifer.

    Science.gov (United States)

    Avrahamov, N; Antler, G; Yechieli, Y; Gavrieli, I; Joye, S B; Saxton, M; Turchyn, A V; Sivan, O

    2014-11-01

    Geochemical and microbial evidence points to anaerobic oxidation of methane (AOM) likely coupled with bacterial sulfate reduction in the hypersaline groundwater of the Dead Sea (DS) alluvial aquifer. Groundwater was sampled from nine boreholes drilled along the Arugot alluvial fan next to the DS. The groundwater samples were highly saline (up to 6300 mm chlorine), anoxic, and contained methane. A mass balance calculation demonstrates that the very low δ(13) CDIC in this groundwater is due to anaerobic methane oxidation. Sulfate depletion coincident with isotope enrichment of sulfur and oxygen isotopes in the sulfate suggests that sulfate reduction is associated with this AOM. DNA extraction and 16S amplicon sequencing were used to explore the microbial community present and were found to be microbial composition indicative of bacterial sulfate reducers associated with anaerobic methanotrophic archaea (ANME) driving AOM. The net sulfate reduction seems to be primarily controlled by the salinity and the available methane and is substantially lower as salinity increases (2.5 mm sulfate removal at 3000 mm chlorine but only 0.5 mm sulfate removal at 6300 mm chlorine). Low overall sulfur isotope fractionation observed ((34) ε = 17 ± 3.5‰) hints at high rates of sulfate reduction, as has been previously suggested for sulfate reduction coupled with methane oxidation. The new results demonstrate the presence of sulfate-driven AOM in terrestrial hypersaline systems and expand our understanding of how microbial life is sustained under the challenging conditions of an extremely hypersaline environment.

  20. Methyl-coenzyme M reductase from methanogenic archaea: isotope effects on the formation and anaerobic oxidation of methane.

    Science.gov (United States)

    Scheller, Silvan; Goenrich, Meike; Thauer, Rudolf K; Jaun, Bernhard

    2013-10-09

    The nickel enzyme methyl-coenzyme M reductase (MCR) catalyzes two important transformations in the global carbon cycle: methane formation and its reverse, the anaerobic oxidation of methane. MCR uses the methyl thioether methyl-coenzyme M (CH3-S-CH2CH2-SO3(-), Me-S-CoM) and the thiol coenzyme B (CoB-SH) as substrates and converts them reversibly to methane and the corresponding heterodisulfide (CoB-S-S-CoM). The catalytic mechanism is still unknown. Here, we present isotope effects for this reaction in both directions, catalyzed by the enzyme isolated from Methanothermobacter marburgensis . For methane formation, a carbon isotope effect ((12)CH3-S-CoM/(13)CH3-S-CoM) of 1.04 ± 0.01 was measured, showing that breaking of the C-S bond in the substrate Me-S-CoM is the rate-limiting step. A secondary isotope effect of 1.19 ± 0.01 per D in the methyl group of CD3-S-CoM indicates a geometric change of the methyl group from tetrahedral to trigonal planar upon going to the transition state of the rate-limiting step. This finding is consistent with an almost free methyl radical in the highest transition state. Methane activation proceeds with a primary isotope effect of 2.44 ± 0.22 for the C-H vs C-D bond breakage and a secondary isotope effect corresponding to 1.17 ± 0.05 per D. These values are consistent with isotope effects reported for oxidative cleavage/reductive coupling occurring at transition metal centers during C-H activation but are also in the range expected for the radical substitution mechanism proposed by Siegbahn et al. The isotope effects presented here constitute boundary conditions for any suggested or calculated mechanism.

  1. Anaerobic oxidation of methane in grassland soils used for cattle husbandry

    OpenAIRE

    2012-01-01

    While the importance of anaerobic methane oxidation has been reported for marine ecosystems, the role of this process in soils is still questionable. Grasslands used as pastures for cattle-overwintering show an increase in anaerobic soil micro-sites caused by animal treading and excrement deposition. Therefore anaerobic potential methane oxidation activity of severely impacted soil from a cattle winter pasture was investigated in an incubation experiment under anaerobic conditions using

  2. Anaerobic oxidation of methane in grassland soils used for cattle husbandry

    OpenAIRE

    2012-01-01

    While the importance of anaerobic methane oxidation has been reported for marine ecosystems, the role of this process in soils is still questionable. Grasslands used as pastures for cattle overwintering show an increase in anaerobic soil micro-sites caused by animal treading and excrement deposition. Therefore, anaerobic potential methane oxidation activity of severely impacted soil from a cattle winter pasture was investigated in an incubation experiment under anaerobic conditions using <...

  3. Ageing well: methane oxidation and methane oxidizing bacteria along a chronosequence of 2000 years.

    Science.gov (United States)

    Ho, Adrian; Lüke, Claudia; Cao, Zhihong; Frenzel, Peter

    2011-12-01

    Rice is the staple food for more than half of the world's growing population. While the area planted to wetland rice is expected to increase further, virtually nothing is known about the long-term development of the respective microbial communities, and how these might influence biogeochemistry. Focusing on methane oxidizing bacteria, we studied a chronosequence of paddy fields in China aged 50-2000 years. Potential methanotrophic activity increased substantially with age of soil. Community composition was relatively similar in all fields. However, growth and activity of one particular subgroup of methanotrophs correlated to soil age suggesting an intricate abiotic control on methanotrophs evolving with time. Our results demonstrate that continuous rice agriculture does not only shape the microbial community, but also modifies the micro-environment in a way enabling faster growth and higher activity of selected populations.

  4. Kinetics of methane oxidation in selected mineral soils

    Science.gov (United States)

    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.

  5. Trends for Methane Oxidation at Solid Oxide Fuel Cell Conditions

    DEFF Research Database (Denmark)

    Kleis, Jesper; Jones, Glenn; Abild-Pedersen, Frank;

    2009-01-01

    the Ni surfaces to other metals of interest. This allows the reactivity over the different metals to be understood in terms of two reactivity descriptors, namely, the carbon and oxygen adsorption energies. By combining a simple free-energy analysis with microkinetic modeling, activity landscapes of anode......First-principles calculations are used to predict a plausible reaction pathway for the methane oxidation reaction. In turn, this pathway is used to obtain trends in methane oxidation activity at solid oxide fuel cell (SOFC) anode materials. Reaction energetics and barriers for the elementary...

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

    Science.gov (United States)

    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

  7. Effects of trace volatile organic compounds on methane oxidation

    Directory of Open Access Journals (Sweden)

    Wilai Chiemchaisri

    2001-06-01

    Full Text Available The effects of volatile organic compounds (VOCs on methane oxidation in landfill cover soils were examined. The batch experiments were conducted using single and mixed VOCs, such as, dichloromethane (DCM, trichloroethylene (TCE, tetrachloroethylene (PCE, and benzene. The results from all combinations showed a decrease in methane oxidation rate with increase in VOC concentrations. Moreover, inhibition effects of TCE and DCM were found higher than benzene and PCE. The reduction of methane oxidation by benzene and PCE could be attributed to the toxicity effect, whereas TCE and DCM were found to exhibit the competitive-inhibition effect. When the soil was mixed with DCM, no methane oxidation was found. Damage to the cell’s internal membrane was found in a methanotrophic culture exposed to VOC gases which is the attachment site of a key enzyme needed for methane oxidationOs efeitos dos compostos orgânicos voláteis (VOCs na oxidação do metano em camadas superficiais do solo. Os experimentos foram conduzidos usando somente VOCs ou mistura do mesmo, como, diclorometano (DCM, tricloroetileno (TCE, tetracloroetileno (PCE, e benzeno. Os resultados de todas as combinações mostraram uma diminuição na taxa da oxidação do metano com aumento nas concentrações de VOC. Além disso, os efeitos da inibição de TCE e de DCM foram mais elevados do que do benzeno e PCE. A redução da oxidação do metano pelo benzeno e PCE poderia ser atribuída ao efeito da toxicidade, visto que TCE e DCM exibiram o efeito de competição-inibição. Quando o solo foi misturado com o DCM, nenhuma oxidação do metano foi encontrada. Os danos à membrana interna celular foi observada em uma cultura metanotrófica exposta aos gases de VOC que é o local de ligação de uma enzima chave necessário para a oxidação do metano.

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

    Science.gov (United States)

    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...

  9. Different Abilities of Eight Mixed Cultures of Methane-oxidizing Bacteria to Degrade TCE

    DEFF Research Database (Denmark)

    Broholm, Kim; Christensen, Thomas Højlund; Jensen, Bjørn K.

    1993-01-01

    The ability of eight mixed cultures of methane-oxidizing bacteria to degrade trichloroethylene (TCE) was examined in laboratory batch experiments. This is one of the first reported works studying TCE degradation by mixed cultures of methane-oxidizing bacteria at 10°C, a common temperature for soils...

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

    Directory of Open Access Journals (Sweden)

    Christoph Wrede

    2013-01-01

    Full Text Available 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.

  11. Deposition of biogenic iron minerals in a methane oxidizing microbial mat.

    Science.gov (United States)

    Wrede, Christoph; Kokoschka, Sebastian; 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.

  12. Effects of Nitrogen Fertilizer,Soil Moisture and Temperature on Methane Oxidation in Paddy Soil

    Institute of Scientific and Technical Information of China (English)

    YANXIAOYUAN; CAIZUCONG

    1996-01-01

    Effects of nitrogen fertilizer,soil mosture and temperature and temperature on methane oxidation in paddy soil were investigated under laboratory conditions.Addition of 0.05 g N kg-1 soil as NH4Cl strongly inhibited methane oxidation and addition of the same rate of KCl also inhibited the oxidation but with more slight effect,suggesting that the inhibitory effect was partly caused by increase in osmotic potential in microorganism cell,Not only NH4+ but also NO3- greatly affected methane oxidation.Urea did not affect methane oxidation in paddy soil in the first two days of incubation,but strong inhibitory effect was observed afterwards.Methane was oxidized in the treated soil with an optimum moisture of 280 g kg-1 ,and air-drying inhibited methane oxidation entirely.The optimum temperature of methane oxidation was about 30℃ in paddy soil.while no methane oxidation was observed at 5℃or 50℃。

  13. Susceptibility of archaea to antimicrobial agents: applications to clinical microbiology.

    Science.gov (United States)

    Khelaifia, S; Drancourt, M

    2012-09-01

    We herein review the state of knowledge regarding the in vitro and in vivo susceptibility of archaea to antimicrobial agents, including some new molecules. Indeed, some archaea colonizing the human microbiota have been implicated in diseases such as periodontopathy. Archaea are characterized by their broad-spectrum resistance to antimicrobial agents. In particular, their cell wall lacks peptidoglycan, making them resistant to antimicrobial agents interfering with peptidoglycan biosynthesis. Archaea are, however, susceptible to the protein synthesis inhibitor fusidic acid and imidazole derivatives. Also, squalamine, an antimicrobial agent acting on the cell wall, proved effective against human methanogenic archaea. In vitro susceptibility data could be used to design protocols for the decontamination of complex microbiota and the selective isolation of archaea in anaerobic culture.

  14. Inhibition of methane oxidation by nitrogenous fertilizers in a paddy soil

    Directory of Open Access Journals (Sweden)

    M. Saiful Alam

    2012-07-01

    Full Text Available Nitrogenous fertilizers are generally thought to have an important role in regulating methane oxidation. In this study, the effect of ammonium on methane oxidation activity was investigated in a paddy soil using urea at concentrations of 0, 50, 100, 200 and 400 μg N per gram dry weight soil (N/g.d.w.s and ammonium sulfate at concentrations of 0, 50 and 200 μg N/g.d.w.s. The results of this study demonstrate that urea concentrations of 200 μg N/g.d.w.s. and above significantly inhibit methane oxidation activity, whereas no statistically significant difference was observed in methane oxidation activity among soil microcosms with urea concentrations of less than 200 μg N/g.d.w.s after incubation for 27 days. Similar results were obtained in a sense that methane oxidation activity was inhibited only when the ammonium sulfate concentration was 200 μg N/g.d.w.s in soil microcosms in this study. Phylogenetic analysis of pmoA genes showed that nitrogen fertilization resulted in apparent changes in the community composition of methane-oxidizing bacteria (MOB. Type I MOB displayed an increased abundance in soil microcosms amended with nitrogenous fertilizers, whereas type II MOB dominated the native soil. Furthermore, although no statistically significant relationship was observed between pmoA gene and amoA gene abundances, methane oxidation activity was significantly negatively correlated with nitrification activity in the presence of urea or ammonium sulfate. Our results indicate that the methane oxidation activity in paddy soils might be inhibited when the concentration of ammonium fertilizers is high and that the interactions between ammonia and methane oxidizers need to be further investigated.

  15. Environmental control on aerobic methane oxidation in coastal waters

    Science.gov (United States)

    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

  16. Use of stable isotopes to determine methane oxidation in landfill cover soils

    Science.gov (United States)

    Liptay, K.; Chanton, J.; Czepiel, P.; Mosher, B.

    1998-04-01

    The mean isotopic composition of CH4 emitted from six New England (United States) landfills was 13C and D enriched (-48.1 to -50.4‰ and -273 to -281‰) relative to anoxic zone landfill CH4 (mean values of -55.9 to -56.2‰ and -296 to -300‰) owing to the oxidation of methane as it was transported from the landfill to the atmosphere through the soil cap. The fraction of methane oxidized f0 during its passage through the soil cap was calculated from the degree of 13C enrichment in emitted CH4 relative to anoxic zone CH4 in conjunction with values determined for the preference of soil methane oxidizing bacteria for 12CH4 over 13CH4 (α = 1.022 ± 0.008). Mean values for methane oxidation in six landfills were from 24 to 35% of the total flux through the soil during the warm season, depending upon how the data were grouped. Our results bracket recent estimates of methane oxidation of about 30% in the warm summer period produced using a model with the input terms of soil temperature, moisture, depth, and oxygen concentration. Because of variations in the response of methane oxidation to temperature at these New England sites, our study is consistent with the modeling results of Czepiel et al. [1996b] that the best estimate for the annual value for methane oxidation in the landfills considered is about 10%.

  17. Archaea on human skin.

    Directory of Open Access Journals (Sweden)

    Alexander J Probst

    Full Text Available The recent era of exploring the human microbiome has provided valuable information on microbial inhabitants, beneficials and pathogens. Screening efforts based on DNA sequencing identified thousands of bacterial lineages associated with human skin but provided only incomplete and crude information on Archaea. Here, we report for the first time the quantification and visualization of Archaea from human skin. Based on 16 S rRNA gene copies Archaea comprised up to 4.2% of the prokaryotic skin microbiome. Most of the gene signatures analyzed belonged to the Thaumarchaeota, a group of Archaea we also found in hospitals and clean room facilities. The metabolic potential for ammonia oxidation of the skin-associated Archaea was supported by the successful detection of thaumarchaeal amoA genes in human skin samples. However, the activity and possible interaction with human epithelial cells of these associated Archaea remains an open question. Nevertheless, in this study we provide evidence that Archaea are part of the human skin microbiome and discuss their potential for ammonia turnover on human skin.

  18. Anaerobic oxidation of methane in grassland soils used for cattle husbandry

    Directory of Open Access Journals (Sweden)

    A. Bannert

    2012-04-01

    Full Text Available While the importance of anaerobic methane oxidation has been reported for marine ecosystems, the role of this process in soils is still questionable. Grasslands used as pastures for cattle-overwintering show an increase in anaerobic soil micro-sites caused by animal treading and excrement deposition. Therefore anaerobic potential methane oxidation activity of severely impacted soil from a cattle winter pasture was investigated in an incubation experiment under anaerobic conditions using 13C-labeled methane. We were able to detect a high microbial activity utilizing CH4 as nutrient source shown by the respiration of 13CO2. Measurements of possible terminal electron acceptors for anaerobic oxidation of methane were carried out. Soil sulfate concentrations were too low to explain the oxidation of the amount of methane added, but enough nitrate and iron(III were detected. However, only nitrate was consumed during the experiment. 13C-PLFA analyses clearly showed the utilization of CH4 as nutrient source mainly by organisms harbouring 16:1ω7 PLFAs. These lipids were found in Gram-negative microorganisms and anaerobes. The fact that these lipids are also typical for type I methanotrophs, known as aerobic methane oxidizers, might indicate a link between aerobic and anaerobic methane oxidation.

  19. Metabolic capabilities of microorganisms involved in and associated with the anaerobic oxidation of methane

    Directory of Open Access Journals (Sweden)

    Gunter eWegener

    2016-02-01

    Full Text Available In marine sediments the anaerobic oxidation of methane with sulfate as electron acceptor (AOM is responsible for the removal of a major part of the greenhouse gas methane. AOM is performed by consortia of anaerobic methane-oxidizing archaea (ANME and their specific partner bacteria. The physiology of these organisms is poorly understood, which is due to their slow growth with doubling times in the order of months and the phylogenetic diversity in natural and in vitro AOM enrichments. Here we study sediment-free long-term AOM enrichments that were cultivated from seep sediments sampled off the Italian Island Elba (20°C; hereon called E20 and from hot vents of the Guaymas Basin, Gulf of California, cultivated at 37°C (G37 or at 50°C (G50. These enrichments were dominated by consortia of ANME-2 archaea and Seep-SRB2 partner bacteria (E20 or by ANME-1, forming consortia with Seep-SRB2 bacteria (G37 or with bacteria of the HotSeep-1 cluster (G50. We investigate lipid membrane compositions as possible factors for the different temperature affinities of the different ANME clades and show autotrophy as characteristic feature for both ANME clades and their partner bacteria. Although in the absence of additional substrates methane formation was not observed, methanogenesis from methylated substrates (methanol and methylamine could be quickly stimulated in the E20 and the G37 enrichment. Responsible for methanogenesis are archaea from the genus Methanohalophilus and Methanococcoides, which are minor community members during AOM (1 to 7‰ of archaeal 16S rRNA gene amplicons. In the same two cultures also sulfur disproportionation could be quickly stimulated by addition of zero-valent colloidal sulfur. The isolated partner bacteria are likewise minor community members (1 to 9‰ of bacterial 16S rRNA gene amplicons, whereas the dominant partner bacteria (Seep-SRB1a, Seep-SRB2 or HotSeep-1 did not grow on elemental sulfur. Our results support a

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

    Science.gov (United States)

    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.

  1. A Ferredoxin- and F420H2-Dependent, Electron-Bifurcating, Heterodisulfide Reductase with Homologs in the Domains Bacteria and Archaea

    Science.gov (United States)

    Yan, Zhen

    2017-01-01

    ABSTRACT Heterodisulfide reductases (Hdr) of the HdrABC class are ancient enzymes and a component of the anaerobic core belonging to the prokaryotic common ancestor. The ancient origin is consistent with the widespread occurrence of genes encoding putative HdrABC homologs in metabolically diverse prokaryotes predicting diverse physiological functions; however, only one HdrABC has been characterized and that was from a narrow metabolic group of obligate CO2-reducing methanogenic anaerobes (methanogens) from the domain Archaea. Here we report the biochemical characterization of an HdrABC homolog (HdrA2B2C2) from the acetate-utilizing methanogen Methanosarcina acetivorans with unusual properties structurally and functionally distinct from the only other HdrABC characterized. Homologs of the HdrA2B2C2 archetype are present in phylogenetically and metabolically diverse species from the domains Bacteria and Archaea. The expression of the individual HdrA2, HdrB2, and HdrB2C2 enzymes in Escherichia coli, and reconstitution of an active HdrA2B2C2 complex, revealed an intersubunit electron transport pathway dependent on ferredoxin or coenzyme F420 (F420H2) as an electron donor. Remarkably, HdrA2B2C2 couples the previously unknown endergonic oxidation of F420H2 and reduction of ferredoxin with the exergonic oxidation of F420H2 and reduction of the heterodisulfide of coenzyme M and coenzyme B (CoMS-SCoB). The unique electron bifurcation predicts a role for HdrA2B2C2 in Fe(III)-dependent anaerobic methane oxidation (ANME) by M. acetivorans and uncultured species from ANME environments. HdrA2B2C2, ubiquitous in acetotrophic methanogens, was shown to participate in electron transfer during acetotrophic growth of M. acetivorans and proposed to be essential for growth in the environment when acetate is limiting. PMID:28174314

  2. Inhibition of methane oxidation in slurry surface crust by inorganic nitrogen

    DEFF Research Database (Denmark)

    Duan, Yun-Feng; Elsgaard, Lars; Petersen, Søren O

    2013-01-01

    Livestock slurry is an important source of methane (CH4). Depending on dry matter content, a floating crust may form where methane-oxidizing bacteria (MOB) and CH4 oxidation activity have been found, suggesting that surface crusts may reduce CH4 emissions from slurry. However, it is not known how...... MOB in this environment interact with inorganic nitrogen (N). We studied inhibitory effects of ammonium (NH4+), nitrate (NO3–) and nitrite (NO2–) on potential CH4 oxidation in a cattle slurry surface crust. Methane oxidation was assayed at salt concentrations up to 500 mM at 100 and 10,000 ppmv...

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

    Science.gov (United States)

    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

  4. Archaea were widespread in sediments of the Messinian Salinity Crisis

    Science.gov (United States)

    Birgel, Daniel; Peckmann, Jörn

    2015-04-01

    sulfate reduction. One of the important processes fuelling authigenesis was microbial oxidation of methane. Lipid biomarker patterns reveal that a consortium of methanotrophic archaea and sulfate-reducing bacteria consumed methane in anoxic and hypersaline environments. Halophilic archaea other than those archaea involved in methane oxidation have been present in the depositional environment as well. This as to yet still somewhat random selection of examples provides evidence for the great diversity of environmental settings created during the MSC and the abundance of archaea in these environments, calling for more work on the geomicrobiology of the unrivaled archive of dramatic paleooceanographic change during the MSC.

  5. Spatial distribution and inhibition by ammonium of methane oxidation in intertidal freshwater marshes

    NARCIS (Netherlands)

    Van der Nat, F.J.; de Brouwer, J.F.C.; Middelburg, J.J.; Laanbroek, H.J.

    1997-01-01

    In two intertidal marshes, the vertical distribution in the sediment and inhibition by ammonium of methane oxidation were investigated by slurry incubation experiments. The two sites differ in their dominant vegetation type, i.e., reed and bulrush, and in their heights above sea level. The reed site

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

    Science.gov (United States)

    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.

  7. Gene decay in archaea

    Directory of Open Access Journals (Sweden)

    M. W. J. van Passel

    2007-01-01

    Full Text Available The gene-dense chromosomes of archaea and bacteria were long thought to be devoid of pseudogenes, but with the massive increase in available genome sequences, whole genome comparisons between closely related species have identified mutations that have rendered numerous genes inactive. Comparative analyses of sequenced archaeal genomes revealed numerous pseudogenes, which can constitute up to 8.6% of the annotated coding sequences in some genomes. The largest proportion of pseudogenes is created by gene truncations, followed by frameshift mutations. Within archaeal genomes, large numbers of pseudogenes contain more than one inactivating mutation, suggesting that pseudogenes are deleted from the genome more slowly in archaea than in bacteria. Although archaea seem to retain pseudogenes longer than do bacteria, most archaeal genomes have unique repertoires of pseudogenes.

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

    Science.gov (United States)

    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.

  9. Viruses of the Archaea

    DEFF Research Database (Denmark)

    Basta, T.; Garrett, Roger Antony; Prangishvili,, David

    2009-01-01

    Double-stranded deoxyribonucleic acid (DNA) viruses that infect members of the third domain of life, the Archaea, are diverse and exceptional in both their morphotypes and their genomic properties. The majority of characterized species infect hyperthermophilic hosts and carry morphological featur...

  10. Viruses of the Archaea

    DEFF Research Database (Denmark)

    Prangishvili,, David; Basta, Tamara; Garrett, Roger Antony;

    2016-01-01

    Viruses infecting members of Archaea, the third domain of life, constitute an integral, yet unique part of the virosphere. Many of these viruses, specifically the species that infect hyperthermophilic hosts, display morphotypes – for example, bottle shaped, spindle shaped, droplet shaped, coil sh...

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  14. Methane oxidation and formation of EPS in compost: effect of oxygen concentration

    Energy Technology Data Exchange (ETDEWEB)

    Wilshusen, J.H.; Hettiaratchi, J.P.A.; Visscher, A. de; Saint-Fort, R

    2004-05-01

    Oxygen concentration plays an important role in the regulation of methane oxidation and the microbial ecology of methanotrophs. However, this effect is still poorly quantified in soil and compost ecosystems. The effect of oxygen on the formation of exopolymeric substances (EPS) is as yet unknown. We studied the effect of oxygen on the evolution of methanotrophic activity. At both high and low oxygen concentrations, peak activity was observed twice within a period of 6 months. Phospholipid fatty acid analysis showed that there was a shift from type I to type II methanotrophs during this period. At high oxygen concentration, EPS production was about 250% of the amount at low oxygen concentration. It is hypothesized that EPS serves as a carbon cycling mechanism for type I methanotrophs when inorganic nitrogen is limiting. Simultaneously, EPS stimulates nitrogenase activity in type II methanotrophs by creating oxygen-depleted zones. The kinetic results were incorporated in a simulation model for gas transport and methane oxidation in a passively aerated biofilter. Comparison between the model and experimental data showed that, besides acting as a micro-scale diffusion barrier, EPS can act as a barrier to macro-scale diffusion, reducing the performance of such biofilters. - 1.5% oxygen resulted in a slightly higher and more stable methane oxidation activity.

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

    Science.gov (United States)

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

    2016-06-01

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

  16. Enzymes involved in the anaerobic oxidation of n-alkanes: from methane to long-chain paraffins

    Directory of Open Access Journals (Sweden)

    Amy V. Callaghan

    2013-05-01

    Full Text Available Anaerobic microorganisms play key roles in the biogeochemical cycling of methane and non-methane alkanes. To date, there appear to be at least three proposed mechanisms of anaerobic methane oxidation (AOM. The first pathway is mediated by consortia of archaeal anaerobic methane oxidizers and sulfate-reducing bacteria via ‘reverse methanogenesis’ and is catalyzed by a homologue of methyl-coenzyme M reductase. The second pathway is also mediated by anaerobic methane oxidizers and sulfate-reducing bacteria, wherein the archaeal members catalyze both methane oxidation and sulfate reduction and zero-valent sulfur is a key intermediate. The third AOM mechanism is a nitrite-dependent, intra-aerobic pathway described for the denitrifying bacterium, ‘Candidatus Methylomirabilis oxyfera.’ It is hypothesized that AOM proceeds via reduction of nitrite to nitric oxide, followed by the conversion of two nitric oxide molecules to dinitrogen and molecular oxygen. The latter can be used to functionalize the methane via a particulate methane monooxygenase. With respect to non-methane alkanes, there also appears to be novel mechanisms of activation. The most well-described pathway is the addition of non-methane alkanes across the double bond of fumarate to form alkyl-substituted succinates via the putative glycyl radical enzyme, alkylsuccinate synthase (also known as methylalkylsuccinate synthase. Other proposed mechanisms include anaerobic hydroxylation via ethylbenzene dehydrogenase-like enzymes and an ‘intra-aerobic’ denitrification pathway similar to that described for ‘M. oxyfera.’

  17. Molecular isotopic evidence for anaerobic oxidation of methane in deep-sea hydrothermal vent environment in Okinawa Trough

    Science.gov (United States)

    Uchida, M.; Takai, K.; Inagaki, F.

    2003-04-01

    Large amount of methane in anoxic marine sediments as well as cold seeps and hydrothermal vents is recycled through for an anoxic oxidation of methane processes. Now that combined results of field and laboratory studies revealed that microbiological activity associated with syntrophic consortium of archaea performing reversed methanogenesis and sulfate-reducing bacteria is significant roles in methane recycling, anaerobic oxidation of methane (AOM). In this study, we examined the diversity of archaeal and bacterial assemblages of AOM using compound-specific stable carbon isotopic and phylogenetic analyses. "Iheya North" in Okinawa Trough is sediment-rich, back arc type hydrothermal system (27^o47'N, 126^o53'E). Sediment samples were collected from three sites where are "bubbling sites", yellow-colored microbial mats are formed with continuous bubbling from the seafloor bottom, vent mussel's colonies site together with slowly venting and simmering, and control site off 100 m distance from thermal vent. This subsea floor structure has important effect in the microbial ecosystem and interaction between their activity and geochemical processes in the subseafloor habitats. Culture-independent, molecular biological analysis clearly indicated the presence of thermophilic methanogens in deeper area having higher temperatures and potential activity of AMOs consortium in the shallower area. AMO is composed with sulfate-reducing bacterial components (Desulfosarcina spp.) and anoxic methane oxidizing archaea (ANME-2). These results were consistent with the results of compound-specific carbon analysis of archaeal biomarkers. They showed extremely depleted 13C contents (-80 ppm ˜ -100 ppm), which also appeared to be capable of directly oxidizing methane.

  18. Archaea in Yellowstone Lake.

    Science.gov (United States)

    Kan, Jinjun; Clingenpeel, Scott; Macur, Richard E; Inskeep, William P; Lovalvo, Dave; Varley, John; Gorby, Yuri; McDermott, Timothy R; Nealson, Kenneth

    2011-11-01

    The Yellowstone geothermal complex has yielded foundational discoveries that have significantly enhanced our understanding of the Archaea. This study continues on this theme, examining Yellowstone Lake and its lake floor hydrothermal vents. Significant Archaea novelty and diversity were found associated with two near-surface photic zone environments and two vents that varied in their depth, temperature and geochemical profile. Phylogenetic diversity was assessed using 454-FLX sequencing (~51,000 pyrosequencing reads; V1 and V2 regions) and Sanger sequencing of 200 near-full-length polymerase chain reaction (PCR) clones. Automated classifiers (Ribosomal Database Project (RDP) and Greengenes) were problematic for the 454-FLX reads (wrong domain or phylum), although BLAST analysis of the 454-FLX reads against the phylogenetically placed full-length Sanger sequenced PCR clones proved reliable. Most of the archaeal diversity was associated with vents, and as expected there were differences between the vents and the near-surface photic zone samples. Thaumarchaeota dominated all samples: vent-associated organisms corresponded to the largely uncharacterized Marine Group I, and in surface waters, ~69-84% of the 454-FLX reads matched archaeal clones representing organisms that are Nitrosopumilus maritimus-like (96-97% identity). Importance of the lake nitrogen cycling was also suggested by >5% of the alkaline vent phylotypes being closely related to the nitrifier Candidatus Nitrosocaldus yellowstonii. The Euryarchaeota were primarily related to the uncharacterized environmental clones that make up the Deep Sea Euryarchaeal Group or Deep Sea Hydrothermal Vent Group-6. The phylogenetic parallels of Yellowstone Lake archaea to marine microorganisms provide opportunities to examine interesting evolutionary tracks between freshwater and marine lineages.

  19. Improved enrichment culture technique for methane-oxidizing bacteria from marine ecosystems: the effect of adhesion material and gas composition.

    Science.gov (United States)

    Vekeman, Bram; Dumolin, Charles; De Vos, Paul; Heylen, Kim

    2017-02-01

    Cultivation of microbial representatives of specific functional guilds from environmental samples depends largely on the suitability of the applied growth conditions. Especially the cultivation of marine methanotrophs has received little attention, resulting in only a limited number of ex situ cultures available. In this study we investigated the effect of adhesion material and headspace composition on the methane oxidation activity in methanotrophic enrichments obtained from marine sediment. Addition of sterilized natural sediment or alternatively the addition of acid-washed silicon dioxide significantly increased methane oxidation. This positive effect was attributed to bacterial adhesion on the particles via extracellular compounds, with a minimum amount of particles required for effect. As a result, the particles were immobilized, thus creating a stratified environment in which a limited diffusive gas gradients could build up and various microniches were formed. Such diffusive gas gradient might necessitate high headspace concentrations of CH4 and CO2 for sufficient concentrations to reach the methane-oxidizing bacteria in the enrichment culture technique. Therefore, high concentrations of methane and carbon dioxide, in addition to the addition of adhesion material, were tested and indeed further stimulated methane oxidation. Use of adhesion material in combination with high concentrations of methane and carbon dioxide might thus facilitate the cultivation and subsequent enrichment of environmentally important members of this functional guild. The exact mechanism of the observed positive effects on methane oxidation and the differential effect on methanotrophic diversity still needs to be explored.

  20. Evaluation of Methyl Fluoride and Dimethyl Ether as Inhibitors of Aerobic Methane Oxidation

    OpenAIRE

    Oremland, Ronald S.; Culbertson, Charles 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 in...

  1. Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulfidic marine sediments

    Energy Technology Data Exchange (ETDEWEB)

    Glass, DR. Jennifer [California Institute of Technology, Pasadena; Yu, DR. Hang [California Institute of Technology, Pasadena; Steele, Joshua [California Institute of Technology, Pasadena; Dawson, Katherine [California Institute of Technology, Pasadena; Sun, S [University of California, San Diego; Chourey, Karuna [ORNL; Hettich, Robert {Bob} L [ORNL; Orphan, V [California Institute of Technology, Pasadena

    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

  2. Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments

    Energy Technology Data Exchange (ETDEWEB)

    Glass, DR. Jennifer [California Institute of Technology, Pasadena; Yu, DR. Hang [California Institute of Technology, Pasadena; Steele, Joshua [California Institute of Technology, Pasadena; Dawson, Katherine [California Institute of Technology, Pasadena; Sun, S [University of California, San Diego; Chourey, Karuna [ORNL; Pan, Chongle [ORNL; Hettich, Robert {Bob} L [ORNL; Orphan, V [California Institute of Technology, Pasadena

    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.

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Shaun M. Baesman

    2015-06-01

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

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

    Science.gov (United States)

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

    2015-06-23

    The Herman Pit, once a mercury mine, is an impoundment located in an active geothermal area. Its acidic waters are permeated by hundreds of gas seeps. One seep was sampled and found to be composed of mostly CO₂ with some CH₄ present. The δ(13)CH₄ value suggested a complex origin for the methane: i.e., a thermogenic component plus a biological methanogenic portion. The relatively (12)C-enriched CO₂ suggested a reworking of the ebullitive methane by methanotrophic bacteria. Therefore, we tested bottom sediments for their ability to consume methane by conducting aerobic incubations of slurried materials. Methane was removed from the headspace of live slurries, and subsequent additions of methane resulted in faster removal rates. This activity could be transferred to an artificial, acidic medium, indicating the presence of acidophilic or acid-tolerant methanotrophs, the latter reinforced by the observation of maximum activity at pH = 4.5 with incubated slurries. A successful extraction of sterol and hopanoid lipids characteristic of methanotrophs was achieved, and their abundances greatly increased with increased sediment methane consumption. DNA extracted from methane-oxidizing enrichment cultures was amplified and sequenced for pmoA genes that aligned with methanotrophic members of the Gammaproteobacteria. An enrichment culture was established that grew in an acidic (pH 4.5) medium via methane oxidation.

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

    Science.gov (United States)

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

    2016-12-01

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

  7. DNA replication origins in archaea

    OpenAIRE

    Zhenfang eWu; Jingfang eLiu; Haibo eYang; Hua eXiang

    2014-01-01

    DNA replication initiation, which starts at specific chromosomal site (known as replication origins), is the key regulatory stage of chromosome replication. Archaea, the third domain of life, use a single or multiple origin(s) to initiate replication of their circular chromosomes. The basic structure of replication origins is conserved among archaea, typically including an AT-rich unwinding region flanked by several conserved repeats (origin recognition box, ORB) that are located adjacent to ...

  8. Microbial iron reduction and methane oxidation in subsurface sediments of the Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Fernandes, C.E.G.; Judith, M.; Gonsalves, M.J.B.D.; Nazareth, D.R.; Nagarchi, L.; Kamaleson, A.S.

    oxidation. Total bacterial abundance (TC), viable aerobic counts accounting for aerobic and facultative anaerobes (TVCa), viable anaerobic counts (TVCan), methane, sulfate, ferrous [Fe(II], hydroxylamine extractable iron and HCl extractable iron...

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

    Science.gov (United States)

    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

  10. Modelling the growth of methane-oxidizing bacteria in a fixed biofilm

    DEFF Research Database (Denmark)

    Bilbo, Carl Morten; Arvin, Erik; Holst, Helle

    1992-01-01

    Methane-oxidizing bacteria were grown in a fixed biofilm reactor in order to study their ability to degrade chlorinated aliphatic hydrocarbons. Focus is on the growth behaviour of the mixed culture. The growth is described by a model that includes methanotrophic bacteria in the active biomass...... fraction. The inactive biomass fraction consists of exocellular polymers and biodegradable and inert particulate biomass. The model describes the oxygen respiration in detail. Yield coefficients, decay constants and hydrolysis constants are estimated based on the oxygen respiration. An analysis...... of the observability of the system reveals that several of the coefficients cannot be determined explicitly due to the complexity of the model and the limited amount of variables measured. Estimation procedures based on least squares methods are employed and parameter estimates and confidence intervals are computed...

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

    Science.gov (United States)

    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.

  12. Changes in methane oxidation activity and methanotrophic community composition in saline alkaline soils.

    Science.gov (United States)

    Serrano-Silva, Nancy; Valenzuela-Encinas, César; Marsch, Rodolfo; Dendooven, Luc; Alcántara-Hernández, Rocio J

    2014-05-01

    The soil of the former Lake Texcoco is a saline alkaline environment where anthropogenic drainage in some areas has reduced salt content and pH. Potential methane (CH4) consumption rates were measured in three soils of the former Lake Texcoco with different electrolytic conductivity (EC) and pH, i.e. Tex-S1 a >18 years drained soil (EC 0.7 dS m(-1), pH 8.5), Tex-S2 drained for ~10 years (EC 9.0 dS m(-1), pH 10.3) and the undrained Tex-S3 (EC 84.8 dS m(-1), pH 10.3). An arable soil from Alcholoya (EC 0.7 dS m(-1), pH 6.7), located nearby Lake Texcoco was used as control. Methane oxidation in the soil Tex-S1 (lowest EC and pH) was similar to that in the arable soil from Alcholoya (32.5 and 34.7 mg CH4 kg(-1) dry soil day(-1), respectively). Meanwhile, in soils Tex-S2 and Tex-S3, the potential CH4 oxidation rates were only 15.0 and 12.8 mg CH4 kg(-1) dry soil day(-1), respectively. Differences in CH4 oxidation were also related to changes in the methane-oxidizing communities in these soils. Sequence analysis of pmoA gene showed that soils differed in the identity and number of methanotrophic phylotypes. The Alcholoya soil and Tex-S1 contained phylotypes grouped within the upland soil cluster gamma and the Jasper Ridge, California JR-2 clade. In soil Tex-S3, a phylotype related to Methylomicrobium alcaliphilum was detected.

  13. Methane oxidation and abundance of methane oxidizers in tropical agricultural soil (vertisol) in response to CuO and ZnO nanoparticles contamination.

    Science.gov (United States)

    Mohanty, Santosh Ranjan; Rajput, Parul; Kollah, Bharati; Chourasiya, Dipanti; Tiwari, Archana; Singh, Muneshwar; Rao, A Subba

    2014-06-01

    There is worldwide concern over the increase use of nanoparticles (NPs) and their ecotoxicological effect. It is not known if the annual production of tons of industrial nanoparticles (NPs) has the potential to impact terrestrial microbial communities, which are so necessary for ecosystem functioning. Here, we have examined the consequences of adding the NPs particularly the metal oxide (CuO, ZnO) on CH4 oxidation activity in vertisol and the abundance of heterotrophs, methane oxidizers, and ammonium oxidizers. Soil samples collected from the agricultural field located at Madhya Pradesh, India, were incubated with either CuO and ZnO NPs or ionic heavy metals (CuCl2, ZnCl2) separately at 0, 10, and 20 μg g(-1) soil. CH4 oxidation activity in the soil samples was estimated at 60 and 100 % moisture holding capacity (MHC) in order to link soil moisture regime with impact of NPs. NPs amended to soil were highly toxic for the microbial-mediated CH4 oxidation, compared with the ionic form. The trend of inhibition was Zn 20 > Zn 10 > Cu 20 > Cu 10. NPs delayed the lag phase of CH4 oxidation to a maximum of 4-fold and also decreased the apparent rate constant k up to 50 % over control. ANOVA and Pearson correlation analysis (α = 0.01) revealed significant impact of NPs on the CH4 oxidation activity and microbial abundance (p Biplot indicated negative impact of NPs on CH4 oxidation and microbial abundance. Our result also confirmed that higher soil moisture regime alleviates toxicity of NPs and opens new avenues of research to manage ecotoxicity and environmental hazard of NPs.

  14. Eubacteria and Archaea community of simultaneous methanogenesis and denitrification granular sludge

    Institute of Scientific and Technical Information of China (English)

    SUN Yujiao; ZUO Jiane; CHEN Lili; WANG Yong

    2008-01-01

    Based on the successful performance of a lab-scale upflow anaerobic sludge blanket (UASB) reactor with the capacity of simultaneous methanogenesis and denitrification (SMD), the specific phylogenetic groups and community structure of microbes in the SMD granule in the UASB reactor were investigated by the construction of the Eubacteria and Archaea 16S rDNA clone libraries, fragment length polymorphism, and sequence blast. Real time quantitative-polymerase chain reaction (RTQ-PCR) technique was used to quantify the contents of Eubacteria and Archaea in the SMD granule. The contents of some special predominant methanogens were also investigated. The results indicated that the Methanosaeta and Methanobacteria were the predominant methanogens in all Archaea in the SMD granule, with contents of 71. 59% and 22. 73% in all 88 random Archaea clones, respectively. The diversity of Eubacteria was much more complex than that of Archaea. The low GC positive gram bacteria and Б-Protebacteria were the main predominant Eubacteria species in SMD granule, their contents were 49. 62% and 12. 03% in all 133 random Eubacteria clones respectively. The results of RTQ-PCR indicated that the content of Archaea was less than Eubacteria, the Archaea content in total microorganisms in SMD granule was about 27. 6%.

  15. Anaerobic Thermophiles

    Directory of Open Access Journals (Sweden)

    Francesco Canganella

    2014-02-01

    Full Text Available The term “extremophile” was introduced to describe any organism capable of living and growing under extreme conditions. With the further development of studies on microbial ecology and taxonomy, a variety of “extreme” environments have been found and an increasing number of extremophiles are being described. Extremophiles have also been investigated as far as regarding the search for life on other planets and even evaluating the hypothesis that life on Earth originally came from space. The first extreme environments to be largely investigated were those characterized by elevated temperatures. The naturally “hot environments” on Earth range from solar heated surface soils and water with temperatures up to 65 °C, subterranean sites such as oil reserves and terrestrial geothermal with temperatures ranging from slightly above ambient to above 100 °C, to submarine hydrothermal systems with temperatures exceeding 300 °C. There are also human-made environments with elevated temperatures such as compost piles, slag heaps, industrial processes and water heaters. Thermophilic anaerobic microorganisms have been known for a long time, but scientists have often resisted the belief that some organisms do not only survive at high temperatures, but actually thrive under those hot conditions. They are perhaps one of the most interesting varieties of extremophilic organisms. These microorganisms can thrive at temperatures over 50 °C and, based on their optimal temperature, anaerobic thermophiles can be subdivided into three main groups: thermophiles with an optimal temperature between 50 °C and 64 °C and a maximum at 70 °C, extreme thermophiles with an optimal temperature between 65 °C and 80 °C, and finally hyperthermophiles with an optimal temperature above 80 °C and a maximum above 90 °C. The finding of novel extremely thermophilic and hyperthermophilic anaerobic bacteria in recent years, and the fact that a large fraction of them belong

  16. Posttranslational protein modification in Archaea.

    Science.gov (United States)

    Eichler, Jerry; Adams, Michael W W

    2005-09-01

    One of the first hurdles to be negotiated in the postgenomic era involves the description of the entire protein content of the cell, the proteome. Such efforts are presently complicated by the various posttranslational modifications that proteins can experience, including glycosylation, lipid attachment, phosphorylation, methylation, disulfide bond formation, and proteolytic cleavage. Whereas these and other posttranslational protein modifications have been well characterized in Eucarya and Bacteria, posttranslational modification in Archaea has received far less attention. Although archaeal proteins can undergo posttranslational modifications reminiscent of what their eucaryal and bacterial counterparts experience, examination of archaeal posttranslational modification often reveals aspects not previously observed in the other two domains of life. In some cases, posttranslational modification allows a protein to survive the extreme conditions often encountered by Archaea. The various posttranslational modifications experienced by archaeal proteins, the molecular steps leading to these modifications, and the role played by posttranslational modification in Archaea form the focus of this review.

  17. Anaerobic methane oxidation and a deep H2S sink generate isotopically heavy sulfides in Black Sea sediments

    DEFF Research Database (Denmark)

    Jørgensen, BB; Bottcher, ME; Luschen, H.

    2004-01-01

    to isotopically heavy pyrite in a sediment open to diffusion. These results have general implications for the marine sulfur cycle and for the interpretation of sulfur isotopic data in modern sediments and in sedimentary rocks throughout earth's history. Copyright (C) 2004 Elsevier Ltd......The main terminal processes of organic matter mineralization in anoxic Black Sea sediments underlying the sulfidic water column are sulfate reduction in the upper 2-4 m and methanogenesis below the sulfate zone. The modern marine deposits comprise a ca. 1-m-deep layer of coccolith ooze...... and underlying sapropel, below which sea water ions penetrate deep down into the limnic Pleistocene deposits from >9000 years BP. Sulfate reduction rates have a subsurface maximum at the SO42--CH4 transition where H2S reaches 4 maximum concentration. Because of an excess of reactive iron in the deep limnic...

  18. Anaerobic oxidation of methane in grassland soils used for cattle husbandry

    Science.gov (United States)

    Bannert, A.; Bogen, C.; Esperschütz, J.; Koubová, A.; Buegger, F.; Fischer, D.; Radl, V.; Fuß, R.; Chroňáková, A.; Elhottová, D.; Šimek, M.; Schloter, M.

    2012-10-01

    While the importance of anaerobic methane oxidation has been reported for marine ecosystems, the role of this process in soils is still questionable. Grasslands used as pastures for cattle overwintering show an increase in anaerobic soil micro-sites caused by animal treading and excrement deposition. Therefore, anaerobic potential methane oxidation activity of severely impacted soil from a cattle winter pasture was investigated in an incubation experiment under anaerobic conditions using 13C-labelled methane. We were able to detect a high microbial activity utilizing CH4 as nutrient source shown by the respiration of 13CO2. Measurements of possible terminal electron acceptors for anaerobic oxidation of methane were carried out. Soil sulfate concentrations were too low to explain the oxidation of the amount of methane added, but enough nitrate and iron(III) were detected. However, only nitrate was consumed during the experiment. 13C-PLFA analyses clearly showed the utilization of CH4 as nutrient source mainly by organisms harbouring 16:1ω7 PLFAs. These lipids were also found as most 13C-enriched fatty acids by Raghoebarsing et al. (2006) after addition of 13CH4 to an enrichment culture coupling denitrification of nitrate to anaerobic oxidation of methane. This might be an indication for anaerobic oxidation of methane by relatives of "Candidatus Methylomirabilis oxyfera" in the investigated grassland soil under the conditions of the incubation experiment.

  19. Remarkable recovery and colonization behaviour of methane oxidizing bacteria in soil after disturbance is controlled by methane source only.

    Science.gov (United States)

    Pan, Yao; Abell, Guy C J; Bodelier, Paul L E; Meima-Franke, Marion; Sessitsch, Angela; Bodrossy, Levente

    2014-08-01

    Little is understood about the relationship between microbial assemblage history, the composition and function of specific functional guilds and the ecosystem functions they provide. To learn more about this relationship we used methane oxidizing bacteria (MOB) as model organisms and performed soil microcosm experiments comprised of identical soil substrates, hosting distinct overall microbial diversities(i.e., full, reduced and zero total microbial and MOB diversities). After inoculation with undisturbed soil, the recovery of MOB activity, MOB diversity and total bacterial diversity were followed over 3 months by methane oxidation potential measurements and analyses targeting pmoA and 16S rRNA genes. Measurement of methane oxidation potential demonstrated different recovery rates across the different treatments. Despite different starting microbial diversities, the recovery and succession of the MOB communities followed a similar pattern across the different treatment microcosms. In this study we found that edaphic parameters were the dominant factor shaping microbial communities over time and that the starting microbial community played only a minor role in shaping MOB microbial community.

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

    Science.gov (United States)

    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.

  1. Methane oxidation in a landfill cover soil reactor: Changing of kinetic parameters and microorganism community structure.

    Science.gov (United States)

    Xing, Zhi L; Zhao, Tian T; Gao, Yan H; Yang, Xu; Liu, Shuai; Peng, Xu Y

    2017-02-23

    Changing of CH4 oxidation potential and biological characteristics with CH4 concentration was studied in a landfill cover soil reactor (LCSR). The maximum rate of CH4 oxidation reached 32.40 mol d(-1) m(-2) by providing sufficient O2 in the LCSR. The kinetic parameters of methane oxidation in landfill cover soil were obtained by fitting substrate diffusion and consumption model based on the concentration profile of CH4 and O2. The values of [Formula: see text] (0.93-2.29%) and [Formula: see text] (140-524 nmol kgsoil-DW(-1)·s(-1)) increased with CH4 concentration (9.25-20.30%), while the values of [Formula: see text] (312.9-2.6%) and [Formula: see text] (1.3 × 10(-5) to 9.0 × 10(-3) nmol mL(-1) h(-1)) were just the opposite. MiSeq pyrosequencing data revealed that Methylobacter (the relative abundance was decreased with height of LCSR) and Methylococcales_unclassified (the relative abundance was increased expect in H 80) became the key players after incubation with increasing CH4 concentration. These findings provide information for assessing CH4 oxidation potential and changing of biological characteristics in landfill cover soil.

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

    Science.gov (United States)

    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.

  3. “Altiarchaeales”: Uncultivated Archaea from the Subsurface

    Directory of Open Access Journals (Sweden)

    Alexander J. Probst

    2015-05-01

    Full Text Available Due to the limited cultivability of the vast majority of microorganisms, researchers have applied environmental genomics and other state-of-the-art technologies to gain insights into the biology of uncultivated Archaea and bacteria in their natural biotope. In this review, we summarize the scientific findings on a recently proposed order-level lineage of uncultivated Archaea called Altiarchaeales, which includes “Candidatus Altiarchaeum hamiconexum” as the most well-described representative. Ca. A. hamiconexum possesses a complex biology: thriving strictly anaerobically, this microorganism is capable of forming highly-pure biofilms, connecting the cells by extraordinary cell surface appendages (the “hami” and has other highly unusual traits, such as a double-membrane-based cell wall. Indicated by genomic information from different biotopes, the Altiarchaeales seem to proliferate in deep, anoxic groundwater of Earth’s crust bearing a potentially very important function: carbon fixation. Although their net carbon fixation rate has not yet been determined, they appear as highly abundant organisms in their biotopes and may thus represent an important primary producer in the subsurface. In sum, the research over more than a decade on Ca. A. hamiconexum has revealed many interesting features of its lifestyle, its genomic information, metabolism and ultrastructure, making this archaeon one of the best-studied uncultivated Archaea in the literature.

  4. Surface Appendages of Archaea: Structure, Function, Genetics and Assembly

    Directory of Open Access Journals (Sweden)

    Sarah Siu

    2013-01-01

    Full Text Available Organisms representing diverse subgroupings of the Domain Archaea are known to possess unusual surface structures. These can include ones unique to Archaea such as cannulae and hami as well as archaella (archaeal flagella and various types of pili that superficially resemble their namesakes in Bacteria, although with significant differences. Major advances have occurred particularly in the study of archaella and pili using model organisms with recently developed advanced genetic tools. There is common use of a type IV pili-model of assembly for several archaeal surface structures including archaella, certain pili and sugar binding structures termed bindosomes. In addition, there are widespread posttranslational modifications of archaellins and pilins with N-linked glycans, with some containing novel sugars. Archaeal surface structures are involved in such diverse functions as swimming, attachment to surfaces, cell to cell contact resulting in genetic transfer, biofilm formation, and possible intercellular communication. Sometimes functions are co-dependent on other surface structures. These structures and the regulation of their assembly are important features that allow various Archaea, including thermoacidophilic, hyperthermophilic, halophilic, and anaerobic ones, to survive and thrive in the extreme environments that are commonly inhabited by members of this domain.

  5. Anaerobic methanotrophy in tidal wetland: Effects of electron acceptors

    Science.gov (United States)

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

    2016-04-01

    Wetlands have been considered to represent the largest natural source of methane emission, contributing substantially to intensify greenhouse effect. Despite in situ methanogenesis fueled by organic degradation, methanotrophy also plays a vital role in controlling the exact quantity of methane release across the air-sediment interface. As wetlands constantly experience various disturbances of anthropogenic activities, biological burrowing, tidal inundation, and plant development, rapid elemental turnover would enable various electron acceptors available for anaerobic methanotrophy. The effects of electron acceptors on stimulating anaerobic methanotrophy and the population compositions involved in carbon transformation in wetland sediments are poorly explored. In this study, sediments recovered from tidally influenced, mangrove covered wetland in northern Taiwan were incubated under the static conditions to investigate whether anaerobic methanotrophy could be stimulated by the presence of individual electron acceptors. Our results demonstrated that anaerobic methanotrophy was clearly stimulated in incubations amended with no electron acceptor, sulfate, or Fe-oxyhydroxide. No apparent methane consumption was observed in incubations with nitrate, citrate, fumarate or Mn-oxides. Anaerobic methanotrophy in incubations with no exogenous electron acceptor appears to proceed at the greatest rates, being sequentially followed by incubations with sulfate and Fe-oxyhydroxide. The presence of basal salt solution stimulated methane oxidation by a factor of 2 to 3. In addition to the direct impact of electron acceptor and basal salts, incubations with sediments retrieved from low tide period yielded a lower rate of methane oxidation than from high tide period. Overall, this study demonstrates that anaerobic methanotrophy in wetland sediments could proceed under various treatments of electron acceptors. Low sulfate content is not a critical factor in inhibiting methane

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

    Science.gov (United States)

    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

  7. Microbial methane oxidation at the redoxcline of the Gotland Deep (Central Baltic Sea

    Directory of Open Access Journals (Sweden)

    O. Schmale

    2012-07-01

    Full Text Available Methane concentrations in the stratified water column of the Gotland Deep (Central Baltic Sea show a strong gradient from high values in the saline deep water (max. 504nM to low concentrations in the less dense, brackish surface water (about 4 nM. The steepest gradient is present within the redoxcline (between 115 and 135 m water depth that separates the anoxic deep part from the oxygenated surface water, implying a methane consumption rate of 0.28 nM d−1. The process of microbial methane oxidation within the redoxcline is mirrored by a shift of the stable carbon isotope ratio of methane between the bottom water (δ13C CH4 = −82.4‰ and the suboxic depth interval (δ13C CH4 = −38.7‰. A water column sample from 100 m water depth was studied to identify the microorganisms responsible for the methane turnover at the redoxcline. Notably, methane monoxygenase gene expression analyses for the specific water depth demonstrated that accordant methanotrophic activity was due to only one microbial phylotype. An imprint of these organisms on the particular organic matter was revealed by distinctive lipid biomarkers showing bacteriohopanepolyols and lipid fatty acids characteristic for aerobic type I methanotrophic bacteria (e.g. 35-aminobacteriohopane-30,31,32,33,34-pentol. In conjunction with earlier findings, our results support the idea that biogeochemical cycles in Central Baltic Sea redoxclines are mainly driven by only a few microbial key species.

  8. Distribution and activity of methane-oxidizing bacteria in a polluted, stratified lake.

    Science.gov (United States)

    Fisher, M. C.; Udert, K.; Gschwend, P. M.; Cavanaugh, C. M.

    2006-12-01

    Methanotrophs are of global significance in their role as a major biological sink for methane, a greenhouse gas, and are metabolically active where methane and oxygen co-occur. Lake Mishawum in Woburn, MA, is a shallow, permanently stratified lake with a highly saline, anoxic hypolimnion rich in methane and organic pollutants, an oxic epilimnion and an interface between these layers, the metalimnion. This unique stratification is maintained because the bottom water continually receives inputs of salty, polluted groundwater while the upper layer is fed by rainwater runoff and a fast moving brook. Based upon observed decreases in methane and oxygen in metalimnion waters and geochemical modeling of the lake, methanotrophs were hypothesized to play a significant role in methane oxidation at the oxic-anoxic interface of the metalinion and to be found in greatest number at this junction between methane and oxygen. To test this hypothesis, the abundance of methanotrophs in epilimnion, metalimnion and hypolimnion of Lake Mishawum was investigated. Quantitative PCR (QPCR) studies in which the methanol dehydrogenase gene of either Type I or Type II methanotrophs was amplified showed that their populations were in fact similar in number through out the depth of the water column. Fluorescence in situ hybridization (FISH) studies confirmed the presence of methanotrophs in each layer. However, 16S rRNA hybridization studies showed that methanotrophs in the metalimnion and epilimnion have 2-3X greater rRNA content than those in the hypolimnion. These results suggest that methanotrophs are most active in the oxygenate zones of the lake, particulary in the metalimnion where the presence of methane and oxygen allows them to actively metabolize and proliferate. Furthermore, it suggests that the activity of bacteria and not necessarily the number of these populations is the more important variable in assessing the significance of these bacteria in this ecosystem.

  9. Surface composition and catalytic activity of La-Fe mixed oxides for methane oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Fengxiang [School of Chemistry, Beijing Institute of Technology, Liangxiang East Road, Beijing 102488 (China); Li, Zhanping [Analysis Center, Tsinghua University, Beijing 100084 (China); Ma, Hongwei [School of Chemistry, Beijing Institute of Technology, Liangxiang East Road, Beijing 102488 (China); Gao, Zhiming, E-mail: zgao@bit.edu.cn [School of Chemistry, Beijing Institute of Technology, Liangxiang East Road, Beijing 102488 (China)

    2015-10-01

    Graphical abstract: - Highlights: • The sample with La/Fe atomic ratio of 0.94 is single phase perovskite La{sub 0.94}FeO{sub 3−d}. • The excess ironic oxide exists on the surface of the perovskite crystallites. • La{sup 3+} ions are enriched on surface of the oxides even for the La{sub 0.68}Fe sample. - Abstract: Four La-Fe oxide samples with La/Fe atomic ratio y = 1.02 ∼ 0.68 (denoted as LayFe) were prepared by the citrate method. The samples had a decreased specific surface area with the La/Fe atomic ratio decreasing. XRD pattern proved that the sample La{sub 0.94}Fe is single phase perovskite La{sub 0.94}FeO{sub 3−d}. Phase composition of the samples was estimated by the Rietveld refinement method. XPS analyses indicate that La{sup 3+} ions are enriched on surface of crystallites for all the samples, and surface carbonate ions are relatively abundant on the samples La{sub 1.02}Fe and La{sub 0.94}Fe. Catalytic activity for methane oxidation per unit surface area of the samples is in the order of La{sub 0.68}Fe > La{sub 0.76}Fe > La{sub 0.94}Fe > La{sub 1.02}Fe both in the presence and in the absence of gaseous oxygen. A reason for this order would be the higher concentration of Fe{sup 3+} ion on the surface of the samples La{sub 0.68}Fe and La{sub 0.76}Fe.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Islam, Tajul; Jensen, Sigmund; Reigstad, Laila Johanne; Larsen, Oivind; 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 approximately 55 degrees 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.

  14. Niche segregation of ammonia-oxidizing archaea and anammox bacteria in the Arabian Sea oxygen minimum zone

    NARCIS (Netherlands)

    Pitcher, A.; Villanueva, L.; Hopmans, E.C.; Schouten, S.; Reichart, G.J.; Sinninghe Damsté, J.S.

    2011-01-01

    Ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (anammox) bacteria have emerged as significant factors in the marine nitrogen cycle and are responsible for the oxidation of ammonium to nitrite and dinitrogen gas, respectively. Potential for an interaction between these groups exists;

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

    Science.gov (United States)

    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.

  16. Genetic techniques for the archaea.

    Science.gov (United States)

    Farkas, Joel A; Picking, Jonathan W; Santangelo, Thomas J

    2013-01-01

    Genetic techniques for the Archaea have undergone a rapid expansion in complexity, resulting in increased exploration of the role of Archaea in the environment and detailed analyses of the molecular physiology and information-processing systems in the third domain of life. Complementary gains in describing the ever-increasing diversity of archaeal organisms have allowed these techniques to be leveraged in new and imaginative ways to elucidate shared and unique aspects of archaeal diversity and metabolism. In this review, we introduce the four archaeal clades for which advanced genetic techniques are available--the methanogens, halophiles, Sulfolobales, and Thermococcales--with the aim of providing an overall profile of the advantages and disadvantages of working within each clade, as essentially all of the genetically accessible archaeal organisms require unique culturing techniques that present real challenges. We discuss the full repertoire of techniques possible within these clades while highlighting the recent advances that have been made by taking advantage of the most prominent techniques and approaches.

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

    Science.gov (United States)

    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

  18. Effect of nitrogen fertilization on methane oxidation, abundance, community structure, and gene expression of methanotrophs in the rice rhizosphere.

    Science.gov (United States)

    Shrestha, Minita; Shrestha, Pravin Malla; Frenzel, Peter; Conrad, Ralf

    2010-12-01

    Nitrogen, one of the limiting factors for the yield of rice, can also have an important function in methane oxidation, thus affecting its global budget. Rice microcosms, planted in the greenhouse, were treated with the N-fertilizers urea (UPK) and ammonium sulfate (APK) or were only treated with phosphorous and potassium (PK). Methane oxidation rates in PK and UPK treatments were similar during most of the rice-growing season, revealing no effect of urea. However, ammonium sulfate strongly suppressed methanogenesis providing an unfavorable environment for methanotrophs in APK treatment. Roots and rhizospheric soil samples, collected from six different growth stages of the rice plant, were analyzed by terminal restriction fragment length polymorphism (T-RFLP) of the pmoA gene. Assignment of abundant T-RFs to cloned pmoA sequences indicated that the populations on roots were dominated by type-I methanotrophs, whereas the populations in rhizospheric soil were dominated by type-II methanotrophs irrespectively of growth stages and fertilizer treatments. Non-metric multidimensional scaling ordination analysis of T-RFLP profiles revealed that the methanotrophic community was significantly (PAPK treatment.

  19. Use of gas push-pull tests for the measurement of methane oxidation in different landfill cover soils.

    Science.gov (United States)

    Streese-Kleeberg, Jan; Rachor, Ingke; Gebert, Julia; Stegmann, Rainer

    2011-05-01

    In order to optimise methane oxidation in landfill cover soils, it is important to be able to accurately quantify the amount of methane oxidised. This research considers the gas push-pull test (GPPT) as a possible method to quantify oxidation rates in situ. During a GPPT, a gas mixture consisting of one or more reactive gases (e.g., CH(4), O(2)) and one or more conservative tracers (e.g., argon), is injected into the soil. Following this, the mixture of injected gas and soil air is extracted from the same location and periodically sampled. The kinetic parameters for the biological oxidation taking place in the soil can be derived from the differences in the breakthrough curves. The original method of Urmann et al. (2005) was optimised for application in landfill cover soils and modified to reduce the analytical effort required. Optimised parameters included the flow rate during the injection phase and the duration of the experiment. 50 GPPTs have been conducted at different landfills in Germany during different seasons. Generally, methane oxidation rates ranged between 0 and 150 g m(soil air)(-3)h(-1). At one location, rates up to 440 g m(soil air)(-3)h(-1) were measured under particularly favourable conditions. The method is simple in operation and does not require expensive equipment besides standard laboratory gas chromatographs.

  20. Methane seep in shallow-water permeable sediment harbors high diversity of anaerobic methanotrophic communities, Elba, Italy

    Directory of Open Access Journals (Sweden)

    S Emil Ruff

    2016-03-01

    Full Text Available The anaerobic oxidation of methane (AOM is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME and sulfate-reducing bacteria (SRB, and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic-carbon depleted permeable sands off the Island of Elba (Italy. We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g-1 day-1 indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20–50 cm below seafloor as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3 and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise

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

    OpenAIRE

    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 methanot...

  2. Molecular analysis of the biomass of a fluidized bed reactor treating synthetic vinasse at anaerobic and micro-aerobic conditions

    NARCIS (Netherlands)

    Rodriguez, E.; Lopes, A.; Fdz-Polanco, M.; Stams, A.J.M.; Garcia Encina, P.A.

    2012-01-01

    The microbial communities (Bacteria and Archaea) established in an anaerobic fluidized bed reactor used to treat synthetic vinasse (betaine, glucose, acetate, propionate, and butyrate) were characterized by denaturing gradient gel electrophoresis (DGGE) and phylogenetic analysis. This study was focu

  3. Regulated polyploidy in halophilic archaea.

    Directory of Open Access Journals (Sweden)

    Sebastian Breuert

    Full Text Available Polyploidy is common in higher eukaryotes, especially in plants, but it is generally assumed that most prokaryotes contain a single copy of a circular chromosome and are therefore monoploid. We have used two independent methods to determine the genome copy number in halophilic archaea, 1 cell lysis in agarose blocks and Southern blot analysis, and 2 Real-Time quantitative PCR. Fast growing H. salinarum cells contain on average about 25 copies of the chromosome in exponential phase, and their ploidy is downregulated to 15 copies in early stationary phase. The chromosome copy number is identical in cultures with a twofold lower growth rate, in contrast to the results reported for several other prokaryotic species. Of three additional replicons of H. salinarum, two have a low copy number that is not growth-phase regulated, while one replicon even shows a higher degree of growth phase-dependent regulation than the main replicon. The genome copy number of H. volcanii is similarly high during exponential phase (on average 18 copies/cell, and it is also downregulated (to 10 copies as the cells enter stationary phase. The variation of genome copy numbers in the population was addressed by fluorescence microscopy and by FACS analysis. These methods allowed us to verify the growth phase-dependent regulation of ploidy in H. salinarum, and they revealed that there is a wide variation in genome copy numbers in individual cells that is much larger in exponential than in stationary phase. Our results indicate that polyploidy might be more widespread in archaea (or even prokaryotes in general than previously assumed. Moreover, the presence of so many genome copies in a prokaryote raises questions about the evolutionary significance of this strategy.

  4. Dynamics of the Methanogenic Archaea in Tropical Estuarine Sediments

    Science.gov (United States)

    Torres-Alvarado, María del Rocío; Fernández, Francisco José; Ramírez Vives, Florina; Varona-Cordero, Francisco

    2013-01-01

    Methanogenesis may represent a key process in the terminal phases of anaerobic organic matter mineralization in sediments of coastal lagoons. The aim of the present work was to study the temporal and spatial dynamics of methanogenic archaea in sediments of tropical coastal lagoons and their relationship with environmental changes in order to determine how these influence methanogenic community. Sediment samples were collected during the dry (February, May, and early June) and rainy seasons (July, October, and November). Microbiological analysis included the quantification of viable methanogenic archaea (MA) with three substrates and the evaluation of kinetic activity from acetate in the presence and absence of sulfate. The environmental variables assessed were temperature, pH, Eh, salinity, sulfate, solids content, organic carbon, and carbohydrates. MA abundance was significantly higher in the rainy season (106–107 cells/g) compared with the dry season (104–106 cells/g), with methanol as an important substrate. At spatial level, MA were detected in the two layers analyzed, and no important variations were observed either in MA abundance or activity. Salinity, sulfate, solids, organic carbon, and Eh were the environmental variables related to methanogenic community. A conceptual model is proposed to explain the dynamics of the MA. PMID:23401664

  5. Dynamics of the Methanogenic Archaea in Tropical Estuarine Sediments

    Directory of Open Access Journals (Sweden)

    María del Rocío Torres-Alvarado

    2013-01-01

    Full Text Available Methanogenesis may represent a key process in the terminal phases of anaerobic organic matter mineralization in sediments of coastal lagoons. The aim of the present work was to study the temporal and spatial dynamics of methanogenic archaea in sediments of tropical coastal lagoons and their relationship with environmental changes in order to determine how these influence methanogenic community. Sediment samples were collected during the dry (February, May, and early June and rainy seasons (July, October, and November. Microbiological analysis included the quantification of viable methanogenic archaea (MA with three substrates and the evaluation of kinetic activity from acetate in the presence and absence of sulfate. The environmental variables assessed were temperature, pH, Eh, salinity, sulfate, solids content, organic carbon, and carbohydrates. MA abundance was significantly higher in the rainy season (106–107 cells/g compared with the dry season (104–106 cells/g, with methanol as an important substrate. At spatial level, MA were detected in the two layers analyzed, and no important variations were observed either in MA abundance or activity. Salinity, sulfate, solids, organic carbon, and Eh were the environmental variables related to methanogenic community. A conceptual model is proposed to explain the dynamics of the MA.

  6. Novel Cardiolipins from Uncultured Methane-Metabolizing Archaea

    Directory of Open Access Journals (Sweden)

    Marcos Y. Yoshinaga

    2012-01-01

    Full Text Available Novel cardiolipins from Archaea were detected by screening the intact polar lipid (IPL composition of microbial communities associated with methane seepage in deep-sea sediments from the Pakistan margin by high-performance liquid chromatography electrospray ionization mass spectrometry. A series of tentatively identified cardiolipin analogues (dimeric phospholipids or bisphosphatidylglycerol, BPG represented 0.5% to 5% of total archaeal IPLs. These molecules are similar to the recently described cardiolipin analogues with four phytanyl chains from extreme halophilic archaea. It is worth noting that cardiolipin analogues from the seep archaeal communities are composed of four isoprenoidal chains, which may contain differences in chain length (20 and 25 carbon atoms and degrees of unsaturation and the presence of a hydroxyl group. Two novel diether lipids, structurally related to the BPGs, are described and interpreted as degradation products of archaeal cardiolipin analogues. Since archaeal communities in seep sediments are dominated by anaerobic methanotrophs, our observations have implications for characterizing structural components of archaeal membranes, in which BPGs are presumed to contribute to modulation of cell permeability properties. Whether BPGs facilitate interspecies interaction in syntrophic methanotrophic consortia remains to be tested.

  7. Archaea Signal Recognition Particle Shows the Way

    Directory of Open Access Journals (Sweden)

    Christian Zwieb

    2010-01-01

    Full Text Available Archaea SRP is composed of an SRP RNA molecule and two bound proteins named SRP19 and SRP54. Regulated by the binding and hydrolysis of guanosine triphosphates, the RNA-bound SRP54 protein transiently associates not only with the hydrophobic signal sequence as it emerges from the ribosomal exit tunnel, but also interacts with the membrane-associated SRP receptor (FtsY. Comparative analyses of the archaea genomes and their SRP component sequences, combined with structural and biochemical data, support a prominent role of the SRP RNA in the assembly and function of the archaea SRP. The 5e motif, which in eukaryotes binds a 72 kilodalton protein, is preserved in most archaea SRP RNAs despite the lack of an archaea SRP72 homolog. The primary function of the 5e region may be to serve as a hinge, strategically positioned between the small and large SRP domain, allowing the elongated SRP to bind simultaneously to distant ribosomal sites. SRP19, required in eukaryotes for initiating SRP assembly, appears to play a subordinate role in the archaea SRP or may be defunct. The N-terminal A region and a novel C-terminal R region of the archaea SRP receptor (FtsY are strikingly diverse or absent even among the members of a taxonomic subgroup.

  8. Microbiological Hydrogen Production by Anaerobic Fermentation and Photosynthetic Process

    Energy Technology Data Exchange (ETDEWEB)

    Asada, Y.; Ohsawa, M.; Nagai, Y.; Fukatsu, M.; Ishimi, K.; Ichi-ishi, S.

    2009-07-01

    Hydrogen gas is a clean and renewable energy carrier. Microbiological hydrogen production from glucose or starch by combination used of an anaerobic fermenter and a photosynthetic bacterium, Rhodobacter spheroides RV was studied. In 1984, the co-culture of Clostridium butyricum and RV strain to convert glucose to hydrogen was demonstrated by Miyake et al. Recently, we studied anaerobic fermentation of starch by a thermophilic archaea. (Author)

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

    NARCIS (Netherlands)

    Henneberger, R.; Chiri, E.; Bodelier, P.L.E.; Frenzel, P.; Luke, C.; Schroth, M.H.

    2015-01-01

    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

  10. Methane oxidation in pig and cattle slurry storages, and effects of surface crust moisture and methane availability

    DEFF Research Database (Denmark)

    Petersen, S.O.; Ambus, P.

    2006-01-01

    Storages with liquid manure (slurry) may develop a surface crust of particulate organic matter, or an artificial crust can be established. Slurry storages are net sources of atmospheric methane (CH4), but a potential for bacterial oxidation of CH4 in surface crusts was recently suggested in a study......2 during incubation, while intact subsamples were used to characterize CH4 oxidation as a function of CH4 availability and moisture content. Methane oxidation was observed in all materials except for an expanded clay product (Leca) sampled from a pig slurry storage. Despite significant variation...... content, each time followed by determination of CH4 fluxes. Only one surface crust material showed a relationship between CH4 fluxes and moisture content that would implicate gas diffusivity in the regulation of CH4 oxidation. The occurrence of inducible CH4 oxidation activity in slurry storage surface...

  11. Proteomic Properties Reveal Phyloecological Clusters of Archaea

    Science.gov (United States)

    Nikolic, Nela; Smole, Zlatko; Krisko, Anita

    2012-01-01

    In this study, we propose a novel way to describe the variety of environmental adaptations of Archaea. We have clustered 57 Archaea by using a non-redundant set of proteomic features, and verified that the clusters correspond to environmental adaptations to the archaeal habitats. The first cluster consists dominantly of hyperthermophiles and hyperthermoacidophilic aerobes. The second cluster joins together halophilic and extremely halophilic Archaea, while the third cluster contains mesophilic (mostly methanogenic) Archaea together with thermoacidophiles. The non-redundant subset of proteomic features was found to consist of five features: the ratio of charged residues to uncharged, average protein size, normalized frequency of beta-sheet, normalized frequency of extended structure and number of hydrogen bond donors. We propose this clustering to be termed phyloecological clustering. This approach could give additional insights into relationships among archaeal species that may be hidden by sole phylogenetic analysis. PMID:23133575

  12. Proteomic properties reveal phyloecological clusters of Archaea.

    Directory of Open Access Journals (Sweden)

    Nela Nikolic

    Full Text Available In this study, we propose a novel way to describe the variety of environmental adaptations of Archaea. We have clustered 57 Archaea by using a non-redundant set of proteomic features, and verified that the clusters correspond to environmental adaptations to the archaeal habitats. The first cluster consists dominantly of hyperthermophiles and hyperthermoacidophilic aerobes. The second cluster joins together halophilic and extremely halophilic Archaea, while the third cluster contains mesophilic (mostly methanogenic Archaea together with thermoacidophiles. The non-redundant subset of proteomic features was found to consist of five features: the ratio of charged residues to uncharged, average protein size, normalized frequency of beta-sheet, normalized frequency of extended structure and number of hydrogen bond donors. We propose this clustering to be termed phyloecological clustering. This approach could give additional insights into relationships among archaeal species that may be hidden by sole phylogenetic analysis.

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

    Science.gov (United States)

    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.

  14. Diversity and seasonal dynamics of airborne Archaea

    Directory of Open Access Journals (Sweden)

    J. Fröhlich-Nowoisky

    2014-05-01

    Full Text Available Archaea are widespread and abundant in many terrestrial and aquatic environments, accounting for up to ∼10% of the prokaryotes. Compared to Bacteria and other microorganisms, however, very little is known about the abundance, diversity, and dispersal of Archaea in the atmosphere. By DNA analysis targeting the 16S rRNA and amoA genes in samples of air particulate matter collected over one year at a continental sampling site in Germany, we obtained first insights into the seasonal dynamics of airborne Archaea. The detected Archaea were identified as Thaumarchaeota or Euryarchaeota, with soil Thaumarchaeota (group I.1b being present in all samples. The normalized species richness of Thaumarchaeota correlated positively with relative humidity and negatively with temperature. This together with an increase of bare agricultural soil surfaces may explain the diversity peaks observed in fall and winter. The detected Euryarchaeota were mainly methanogens with a low relative frequency of occurrence. A slight increase in their frequency during spring may be linked to fertilization processes in the surrounding agricultural fields. Comparison with samples from the Cape Verde islands and from other coastal and continental sites indicates that the proportions of Euryarchaeota are enhanced in coastal air, which is consistent with their suggested abundance in marine surface waters. We conclude that air transport may play an important role for the dispersal of Archaea, including ammonia-oxidizing Thaumarchaeota and methanogens. Also, anthropogenic activities might influence the atmospheric abundance and diversity of Archaea.

  15. Pathways and bioenergetics of anaerobic carbon monoxide fermentation

    NARCIS (Netherlands)

    Diender, Martijn; Stams, Fons; Machado de Sousa, Diana

    2015-01-01

    Carbon monoxide can act as a substrate for different modes of fermentative anaerobic metabolism. The trait of utilizing CO is spread among a diverse group of microorganisms, including members of bacteria as well as archaea. Over the last decade this metabolism has gained interest due to the poten

  16. Anaerobic oxidation of methane in grassland soils used for cattle husbandry

    Directory of Open Access Journals (Sweden)

    A. Bannert

    2012-10-01

    Full Text Available While the importance of anaerobic methane oxidation has been reported for marine ecosystems, the role of this process in soils is still questionable. Grasslands used as pastures for cattle overwintering show an increase in anaerobic soil micro-sites caused by animal treading and excrement deposition. Therefore, anaerobic potential methane oxidation activity of severely impacted soil from a cattle winter pasture was investigated in an incubation experiment under anaerobic conditions using 13C-labelled methane. We were able to detect a high microbial activity utilizing CH4 as nutrient source shown by the respiration of 13CO2. Measurements of possible terminal electron acceptors for anaerobic oxidation of methane were carried out. Soil sulfate concentrations were too low to explain the oxidation of the amount of methane added, but enough nitrate and iron(III were detected. However, only nitrate was consumed during the experiment. 13C-PLFA analyses clearly showed the utilization of CH4 as nutrient source mainly by organisms harbouring 16:1ω7 PLFAs. These lipids were also found as most 13C-enriched fatty acids by Raghoebarsing et al. (2006 after addition of 13CH4 to an enrichment culture coupling denitrification of nitrate to anaerobic oxidation of methane. This might be an indication for anaerobic oxidation of methane by relatives of "Candidatus Methylomirabilis oxyfera" in the investigated grassland soil under the conditions of the incubation experiment.

  17. Presence of Ammonia-oxidizing Archaea and Their Influence on Nitrogen Cycling in Ilica Bay, Turkey

    Science.gov (United States)

    Gulecal, Y.; Temel, M.

    2011-12-01

    Recenlty, the processes of anaerobic ammonium oxidation (anammox), and ammonia oxidation within the domain Archaea, have been recognized as two new links in the global nitrogen cycle. The distribution and ubiquity of marine Archaea an important role in global carbon and nitrogen cycling (Ingalls et al., 2006; Leininger et al., 2006; Wuchter et al.,2006a). However, our knowledge on archaeal distribution in aquatic ecosystem was largely confined to the extreme environments for a long time until DeLong (1992, 1998) revealed the ubiquity of archaea in common marine environments. Despite the great progress, more efforts need to be given to the study of archaeal diversity in the vast oceans and of the variations in the ecological environment from coastal to oceanic waters (Massana et al.,2000). Our studying area which Ilica Bay in Izmir (Turkey) has a lot of thermal springs. The aim of study was to investigate the presence of ammonia-oxidizing Archaea and their roles of nitrogen cycling in marine enviroments.We have not only used the geochemical analyses but also genetic tools. This study will supply knowledge for marine nitrogen cycling to understanding very well, in addition how Archea genes players in the process of anammox in shallow coastal marine environments.

  18. Diversity and distribution of methane-oxidizing microbial communities associated with different faunal assemblages in a giant pockmark of the Gabon continental margin

    Science.gov (United States)

    Cambon-Bonavita, M. A.; Nadalig, T.; Roussel, E.; Delage, E.; Duperron, S.; Caprais, J. C.; Boetius, A.; Sibuet, M.

    2009-12-01

    A giant 800-m-diameter pockmark named REGAB was discovered on the Gabon continental margin actively emitting methane at a water depth of 3200 m. The microbial diversity in sediments from four different assemblages of chemosynthetic organisms, Mytilidae, Vesicomyidae, Siboglinidae and a bacterial mat, was investigated using comparative 16S rRNA gene sequence analysis. Aggregates of anaerobic methanotrophic archaea (ANME-2) and bacteria of the Desulfosarcina/Desulfococcus cluster were found in all four chemosynthetic habitats. Fluorescence in situ hybridization targeting the ANME-2/ Desulfosarcina/Desulfococcus aggregates showed their presence few centimeters (3-5 cm) below the surface of sediment. 16S rRNA gene sequences from all known marine ANME groups were detected in the pockmark sediments, as well as from both known bacterial partners. The archaeal diversity was limited to the ANME cluster for all investigated samples. The bacterial diversity included members of the Proteobacteria, Bacilliales, Cytophaga/Flavobacteria, Verrucomicrobia, JS1 and Actinobacteria clusters. Bacterial 16S rRNA gene sequences related to those of known sulphide-oxidizing symbionts were recovered from tissues of several invertebrates including vesicomyid clams and siboglinid tubeworms of REGAB.

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

    Science.gov (United States)

    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.

  20. Field-scale treatment of landfill gas with a passive methane oxidizing biofilter

    Energy Technology Data Exchange (ETDEWEB)

    Philopoulos, A. [Alberta Univ., Edmonton, AB (Canada). Dept. of Civil and Environmental Engineering; Felske, C. [Alberta Research Council, Edmonton, AB (Canada); McCartney, D. [Alberta Univ., Edmonton, AB (Canada). Dept. of Civil and Environmental Engineering, Natural Resources Engineering Facility

    2008-09-15

    Municipal solid waste (MSW) landfills produce methane (CH{sub 4}) and carbon dioxide (CO{sub 2}) as a result of the anaerobic biodegradation of organic fractions of waste. This paper provided details of field tests conducted to test 2 approaches that addressed the issue of gases produced at a landfill in Alberta. A CH{sub 4} oxidation layer was applied to replace intermediate and final landfill covers. Landfill gas (LFG) was then trapped using 3 biogenic CH{sub 4} oxidizing biofilters. Mature yard waste was used as a biofilter medium. The LFG was trapped by the liner, accumulated in a collection system, and then passed through the biofilter medium. The study was conducted over a period of 10 months. Results of the study showed that the integration of the biofilter into the landfill cover showed promising results. Low surface emissions were observed in 6 out of 8 monitoring events at 2 of the sites. Low influent LFG fluxes at the third site did not allow for full air sampling analyses to be conducted. 22 refs., 4 tabs., 8 figs.

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

    Science.gov (United States)

    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.

  2. Bioprospecting Archaea: Focus on Extreme Halophiles

    KAUST Repository

    Antunes, André

    2016-12-12

    In 1990, Woese et al. divided the Tree of Life into three separate domains: Eukarya, Bacteria, and Archaea. Archaea were originally perceived as little more than “odd bacteria” restricted to extreme environmental niches, but later discoveries challenged this assumption. Members of this domain populate a variety of unexpected environments (e.g. soils, seawater, and human bodies), and we currently witness ongoing massive expansions of the archaeal branch of the Tree of Life. Archaea are now recognized as major players in the biosphere and constitute a significant fraction of the earth’s biomass, yet they remain underexplored. An ongoing surge in exploration efforts is leading to an increase in the (a) number of isolated strains, (b) associated knowledge, and (c) utilization of Archaea in biotechnology. They are increasingly employed in fields as diverse as biocatalysis, biocomputing, bioplastic production, bioremediation, bioengineering, food, pharmaceuticals, and nutraceuticals. This chapter provides a general overview on bioprospecting Archaea, with a particular focus on extreme halophiles. We explore aspects such as diversity, ecology, screening techniques and biotechnology. Current and future trends in mining for applications are discussed.

  3. Diversity and seasonal dynamics of airborne archaea

    Science.gov (United States)

    Fröhlich-Nowoisky, J.; Ruzene Nespoli, C.; Pickersgill, D. A.; Galand, P. E.; Müller-Germann, I.; Nunes, T.; Gomes Cardoso, J.; Almeida, S. M.; Pio, C.; Andreae, M. O.; Conrad, R.; Pöschl, U.; Després, V. R.

    2014-11-01

    Archaea are widespread and abundant in many terrestrial and aquatic environments, and are thus outside extreme environments, accounting for up to ~10% of the prokaryotes. Compared to bacteria and other microorganisms, however, very little is known about the abundance, diversity, and dispersal of archaea in the atmosphere. By means of DNA analysis and Sanger sequencing targeting the 16S rRNA (435 sequences) and amoA genes in samples of air particulate matter collected over 1 year at a continental sampling site in Germany, we obtained first insights into the seasonal dynamics of airborne archaea. The detected archaea were identified as Thaumarchaeota or Euryarchaeota, with soil Thaumarchaeota (group I.1b) being present in all samples. The normalized species richness of Thaumarchaeota correlated positively with relative humidity and negatively with temperature. This together with an increase in bare agricultural soil surfaces may explain the diversity peaks observed in fall and winter. The detected Euryarchaeota were mainly predicted methanogens with a low relative frequency of occurrence. A slight increase in their frequency during spring may be linked to fertilization processes in the surrounding agricultural fields. Comparison with samples from the Cape Verde islands (72 sequences) and from other coastal and continental sites indicates that the proportions of Euryarchaeota are enhanced in coastal air, which is consistent with their suggested abundance in marine surface waters. We conclude that air transport may play an important role in the dispersal of archaea, including assumed ammonia-oxidizing Thaumarchaeota and methanogens.

  4. 2011 Archaea: Ecology, Metabolism, & Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    Keneth Stedman

    2011-08-05

    Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  5. 2009 Archaea: Ecology, Metabolism & Molecular Biology GRC

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Julie Maupin- Furlow

    2009-07-26

    Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses; and industrial applications. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  6. The use of novel packing material for improving methane oxidation in biofilters.

    Science.gov (United States)

    Brandt, Emanuel Manfred F; Duarte, Felipe V; Vieira, João Paulo R; Melo, Vinícius M; Souza, Cláudio L; Araújo, Juliana C; Chernicharo, Carlos Augusto L

    2016-11-01

    The use of biofilters (working bed volume of 7.85 L) for the oxidation of CH4 at low concentrations (from 0.17%v/v to 3.63%v/v, typically in waste gas from anaerobic sewage treatment) was investigated and four empty bed residence times were tested (in min): 42.8, 29.5, 19.6, and 7.4. Mixtures of organic (composted leaves) and three non-organic materials (sponge-based material - SBM, blast furnace slag - BFS, and expanded vermiculite - ExpV) were used as packing media. Along 188 operational days after the steady state was reached (95 days for start-up), the CH4 mineralization decreased while the inlet loads gradually increased from 3.0 ± 0.8 gCH4 m(-3) h(-1) to 148.8 ± 4.4 gCH4 m(-3) h(-1). The biofilter packed with ExpV showed the best results, since the CH4 conversions decreased from 95.0 ± 5.0% to 12.7 ± 3.7% as a function of inlet concentration, compared to the other two biofilters (SBM and BFS) which showed CH4 conversions decreasing from 56.0 ± 5.4% to 3.5 ± 1.2% as a function of inlet concentration. The methanotrophic activity of biomass taken from ExpV biofilter was three times higher than the activity of biomass from the other two biofilters. Taken together, these results suggested that ExpV provides an attractive environment for microbial growth, besides the mechanical resistance provided to the whole packing media, showing the potential to its use in biofiltration of diffuse CH4 emissions.

  7. 2007 Archaea: Ecology, Metabolism and Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    Imke Schroeder

    2008-09-18

    The Archaea are a fascinating and diverse group of prokaryotic organisms with deep roots overlapping those of eukaryotes. The focus of this GRC conference, 'Archaea: Ecology Metabolism & Molecular Biology', expands on a number of emerging topics highlighting the evolution and composition of microbial communities and novel archaeal species, their impact on the environment, archaeal metabolism, and research that stems from sequence analysis of archaeal genomes. The strength of this conference lies in its ability to couple reputable areas with new scientific topics in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

  8. Extreme sweetness: protein glycosylation in archaea.

    Science.gov (United States)

    Eichler, Jerry

    2013-03-01

    Although N-glycosylation was first reported in archaea almost 40 years ago, detailed insights into this process have become possible only recently, with the availability of complete genome sequences for almost 200 archaeal species and the development of appropriate molecular tools. As a result of these advances, recent efforts have not only succeeded in delineating the pathways involved in archaeal N-glycosylation, but also begun to reveal how such post-translational protein modification helps archaea to survive in some of the harshest environments on the planet.

  9. Functional Encyclopedia of Bacteria and Archaea

    Energy Technology Data Exchange (ETDEWEB)

    Blow, M. J.; Deutschbauer, A. M.; Hoover, C. A.; Lamson, J.; Lamson, J.; Price, M. N.; Waters, J.; Wetmore, K. M.; Bristow, J.; Arkin, A. P.

    2013-03-20

    Bacteria and Archaea exhibit a huge diversity of metabolic capabilities with fundamental importance in the environment, and potential applications in biotechnology. However, the genetic bases of these capabilities remain unclear due largely to an absence of technologies that link DNA sequence to molecular function. To address this challenge, we are developing a pipeline for high throughput annotation of gene function using mutagenesis, growth assays and DNA sequencing. By applying this pipeline to annotate gene function in 50 diverse microbes we hope to discover thousands of new gene functions and produce a proof of principle `Functional Encyclopedia of Bacteria and Archaea?.

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

    Science.gov (United States)

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

    2016-09-29

    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.

  11. Biochemistry and physiology of anaerobic bacteria

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-05-18

    We welcome you to The Power of Anaerobes. This conference serves two purposes. One is to celebrate the life of Harry D. Peck, Jr.,who was born May 18, 1927 and would have celebrated his 73rd birthday at this conference. He died November 20, 1998. The second is to gather investigators to exchange views within the realm of anaerobic microbiology, an area in which tremendous progress has been seen during recent years. It is sufficient to mention discoveries of a new form of life (the archaea), hyper or extreme thermophiles, thermophilic alkaliphiles and anaerobic fungi. With these discoveries has come a new realization about physiological and metabolic properties of microorganisms, and this in turn has demonstrated their importance for the development, maintenance and sustenance of life on Earth.

  12. Anaerobic bacteria

    Science.gov (United States)

    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 ...

  13. A laboratory-scale comparison of compost and sand--compost--perlite as methane-oxidizing biofilter media.

    Science.gov (United States)

    Philopoulos, Andrew; Ruck, Juliane; McCartney, Daryl; Felske, Christian

    2009-03-01

    Municipal solid waste landfills produce methane, a potent greenhouse gas. A treatment approach is to passively vent landfill gas through a methane-oxidizing biofilter medium, a porous substrate that facilitates the growth of methanotrophic bacteria. Two substrates, compost and a sand-compost-perlite (SCP) mixture, were evaluated in a laboratory-scale experiment for their suitability as biofilter media. The SCP mixture was investigated to minimize settlement and was based on a particle size distribution specification used for turf grass. The long-term (218 days) methane removal rates showed that both compost and SCP were capable of removing 100% of the methane influent flux (134 g CH(4) m( -2) day(-1)). The post-experiment analysis showed that compost had compacted more than SCP. This did not affect the results; however, in a field installation, traffic on the biofilter surface (e.g. maintenance) could cause further compaction and negatively affect performance. Exopolymeric substance produced by the methanotrophic bacteria, attributed by others for declining removal rates due to bio-clogging, was not observed to affect the results. The maximum exopolymeric substance values measured were 23.9 and 7.8 mg D-glucose g(-1) (dry basis) for compost and SCP, respectively.

  14. Miniaturized extinction culturing is the preferred strategy for rapid isolation of fast-growing methane-oxidizing bacteria.

    Science.gov (United States)

    Hoefman, Sven; van der Ha, David; De Vos, Paul; Boon, Nico; Heylen, Kim

    2012-05-01

    Methane-oxidizing bacteria (MOB) have a large potential as a microbial sink for the greenhouse gas methane as well as for biotechnological purposes. However, their application in biotechnology has so far been hampered, in part due to the relative slow growth rate of the available strains. To enable the availability of novel strains, this study compares the isolation of MOB by conventional dilution plating with miniaturized extinction culturing, both performed after an initial enrichment step. The extinction approach rendered 22 MOB isolates from four environmental samples, while no MOB could be isolated by plating. In most cases, extinction culturing immediately yielded MOB monocultures making laborious purification redundant. Both type I (Methylomonas spp.) and type II (Methylosinus sp.) MOB were isolated. The isolated methanotrophic diversity represented at least 11 different strains and several novel species based on 16S rRNA gene sequence dissimilarity. These strains possessed the particulate (100%) and soluble (64%) methane monooxygenase gene. Also, 73% of the strains could be linked to a highly active fast-growing mixed MOB community. In conclusion, miniaturized extinction culturing was more efficient in rapidly isolating numerous MOB requiring little effort and fewer materials, compared with the more widely applied plating procedure. This miniaturized approach allowed straightforward isolation and could be very useful for subsequent screening of desired characteristics, in view of their future biotechnological potential.

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

    Science.gov (United States)

    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.

  16. Protein glycosylation in Archaea: sweet and extreme.

    Science.gov (United States)

    Calo, Doron; Kaminski, Lina; Eichler, Jerry

    2010-09-01

    While each of the three domains of life on Earth possesses unique traits and relies on characteristic biological strategies, some processes are common to Eukarya, Bacteria and Archaea. Once believed to be restricted to Eukarya, it is now clear that Bacteria and Archaea are also capable of performing N-glycosylation. However, in contrast to Bacteria, where this posttranslational modification is still considered a rare event, numerous species of Archaea, isolated from a wide range of environments, have been reported to contain proteins bearing Asn-linked glycan moieties. Analysis of the chemical composition of the Asn-linked polysaccharides decorating archaeal proteins has, moreover, revealed the use of a wider variety of sugar subunits than seen in either eukaryal or bacterial glycoproteins. Still, although first reported some 30 years ago, little had been known of the steps or components involved in the archaeal version of this universal posttranslational modification. Now, with the availability of sufficient numbers of genome sequences and the development of appropriate experimental tools, molecular analysis of archaeal N-glycosylation pathways has become possible. Accordingly using halophilic, methanogenic and thermophilic model species, insight into the biosynthesis and attachment of N-linked glycans decorating archaeal glycoproteins is starting to amass. In this review, current understanding of N-glycosylation in Archaea is described.

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

    Science.gov (United States)

    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

  18. A First Analysis of Metallome Biosignatures of Hyperthermophilic Archaea

    Directory of Open Access Journals (Sweden)

    Vyllinniskii Cameron

    2012-01-01

    Full Text Available To date, no experimental data has been reported for the metallome of hyperthermophilic microorganisms although their metal requirements for growth are known to be unique. Here, experiments were conducted to determine (i cellular trace metal concentrations of the hyperthermophilic Archaea Methanococcus jannaschii and Pyrococcus furiosus, and (ii a first estimate of the metallome for these hyperthermophilic species via ICP-MS. The metal contents of these cells were compared to parallel experiments using the mesophilic bacterium Escherichia coli grown under aerobic and anaerobic conditions. Fe and Zn were typically the most abundant metals in cells. Metal concentrations for E. coli grown aerobically decreased in the order Fe > Zn > Cu > Mo > Ni > W > Co. In contrast, M. jannaschii and P. furiosus show almost the reverse pattern with elevated Ni, Co, and W concentrations. Of the three organisms, a biosignature is potentially demonstrated for the methanogen M. jannaschii that may, in part, be related to the metallome requirements of methanogenesis. The bioavailability of trace metals more than likely has varied through time. If hyperthermophiles are very ancient, then the trace metal patterns observed here may begin to provide some insights regarding Earth's earliest cells and in turn, early Earth chemistry.

  19. Spatial and Temporal Variability in Atmospheric-Methane-Oxidizing Bacterial Community Structure and Activity in an Alpine Glacier Forefield

    Science.gov (United States)

    Chiri, E.; Nauer, P. A.; Rainer, E. M.; Zeyer, J. A.; Schroth, M. H.

    2015-12-01

    High-affinity methane-oxidizing bacteria (MOB) play a crucial role in regulating the sink strength for atmospheric methane (CH4) in upland soils. Community structure and activity of MOB have been extensively studied in developed soils. However, little is known about their ecosystem service in young, developing soils. Examples of developing soils are found in Alpine glacier forefields, which progressively expand due to glacial retreat. Glacier forefields exhibit diverse geomorphological landforms, which may differ in biogeochemical properties. Also, glacier forefields are subject to seasonal variability in environmental parameters such as soil temperature and water content, which may affect MOB community structure and activity. We recently showed that glacier-forefield soils are a sink for atmospheric CH4, but a comprehensive understanding of crucial factors affecting MOB community structure and activity is still missing. In this study we assessed soil-atmosphere CH4 flux and MOB community structure in three different glacier-forefield landforms (sandhills, floodplains, terraces) throughout a snow-free sampling season. Specifically, we quantified CH4 flux using the soil-gas-profile method and static flux chambers. The MOB community structure was assessed using next-generation sequencing technology (Illumina-MiSeqTM) targeting the functional gene pmoA. We observed substantial differences in CH4 flux between soils of different landforms, with largest fluxes observed in well-drained sandhills (up to -2.2 mg CH4 m-2 d-1) and considerably smaller fluxes in other landforms. Methane flux showed a prominent seasonal variability, which was attenuated in older forefield soils. High-diversity MOB communities and a remarkable number of landform-specific operational taxonomic units were found in sandhills, whereas a lower diversity was observed in other landforms. Our phylogenetic analysis suggests the presence of a potentially new group of MOB inhabiting glacier-forefield soils.

  20. 甲烷厌氧氧化微生物的研究进展%PROGRESS IN STUDY ON MICROORGANISMS RESPONSIBLE FOR ANAEROBIC OXIDATION OF METHANE

    Institute of Scientific and Technical Information of China (English)

    沈李东; 胡宝兰; 郑平

    2011-01-01

    Methane is a major greenhouse gas, which contributes estimatedly 20% to global warming. Microbially mediated anaerobic oxidation of methane (AOM) is an important way to reduce methane emission in nature. According to different coupling reactions, AOM can be divided into two types, Sulphate-dependent anaerobic methane oxidation( SAMO ) and Denitrification-dependent anaerobic methane oxidation ( DAMO ). S024- and NO2-/NO3- function as their terminal electron acceptors, separately. This review summarizes types of AOM and microorganisms involved, elaborates mechanisms of the AOMs, and discusses orientation of the future research and prospects of the application of AOM.%甲烷是一种重要的温室气体,其对全球气候变暖的贡献率约占20%.微生物进行的甲烷厌氧氧化(Anaerobic oxidation of methane,AOM)是减少自然环境中该温室气体排放的重要生物途径.根据耦联反应的不同,可将AOM分为两类,即硫酸盐还原型甲烷厌氧氧化(Sulphate-dependent anaerobic methane oxidation,SAMO)和反硝化型甲烷厌氧氧化(Denitrification-dependent anaerobic methane oxidation,DAMO),前者以SO2-4作为AOM的最终电子受体,后者以NO2-/NO3-作为AOM的最终电子受体.深入了解这两种类型AOM的发生机理,有助于更好地理解该生物过程的重要性,为AOM工艺的开发提供理论依据.鉴此,本文简要介绍了不同类型的AOM及其参与的微生物,着重阐述了其发生机理,并探讨了AOM未来的研究方向与应用前景.

  1. The Function of Gas Vesicles in Halophilic Archaea and Bacteria: Theories and Experimental Evidence

    Directory of Open Access Journals (Sweden)

    Aharon Oren

    2012-12-01

    Full Text Available A few extremely halophilic Archaea (Halobacterium salinarum, Haloquadratum walsbyi, Haloferax mediterranei, Halorubrum vacuolatum, Halogeometricum borinquense, Haloplanus spp. possess gas vesicles that bestow buoyancy on the cells. Gas vesicles are also produced by the anaerobic endospore-forming halophilic Bacteria Sporohalobacter lortetii and Orenia sivashensis. We have extensive information on the properties of gas vesicles in Hbt. salinarum and Hfx. mediterranei and the regulation of their formation. Different functions were suggested for gas vesicle synthesis: buoying cells towards oxygen-rich surface layers in hypersaline water bodies to prevent oxygen limitation, reaching higher light intensities for the light-driven proton pump bacteriorhodopsin, positioning the cells optimally for light absorption, light shielding, reducing the cytoplasmic volume leading to a higher surface-area-to-volume ratio (for the Archaea and dispersal of endospores (for the anaerobic spore-forming Bacteria. Except for Hqr. walsbyi which abounds in saltern crystallizer brines, gas-vacuolate halophiles are not among the dominant life forms in hypersaline environments. There only has been little research on gas vesicles in natural communities of halophilic microorganisms, and the few existing studies failed to provide clear evidence for their possible function. This paper summarizes the current status of the different theories why gas vesicles may provide a selective advantage to some halophilic microorganisms.

  2. Viruses of the Archaea: a unifying view

    DEFF Research Database (Denmark)

    Prangishvili, David; Forterre, Patrick; Garrett, Roger Antony

    2006-01-01

    DNA viruses of the Archaea have highly diverse and often exceptionally complex morphotypes. Many have been isolated from geothermally heated hot environments, raising intriguing questions about their origins, and contradicting the widespread notion of limited biodiversity in extreme environments........ Here, we provide a unifying view on archaeal viruses, and present them as a particular assemblage that is fundamentally different in morphotype and genome from the DNA viruses of the other two domains of life, the Bacteria and Eukarya.......DNA viruses of the Archaea have highly diverse and often exceptionally complex morphotypes. Many have been isolated from geothermally heated hot environments, raising intriguing questions about their origins, and contradicting the widespread notion of limited biodiversity in extreme environments...

  3. Perspectives on biotechnological applications of archaea

    Directory of Open Access Journals (Sweden)

    Chiara Schiraldi

    2002-01-01

    Full Text Available Many archaea colonize extreme environments. They include hyperthermophiles, sulfur-metabolizing thermophiles, extreme halophiles and methanogens. Because extremophilic microorganisms have unusual properties, they are a potentially valuable resource in the development of novel biotechnological processes. Despite extensive research, however, there are few existing industrial applications of either archaeal biomass or archaeal enzymes. This review summarizes current knowledge about the biotechnological uses of archaea and archaeal enzymes with special attention to potential applications that are the subject of current experimental evaluation. Topics covered include cultivation methods, recent achievements in genomics, which are of key importance for the development of new biotechnological tools, and the application of wild-type biomasses, engineered microorganisms, enzymes and specific metabolites in particular bioprocesses of industrial interest.

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

    Science.gov (United States)

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

    2016-02-01

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

  5. Lipid biomarkers for anaerobic oxidation of methane and sulphate reduction in cold seep sediments of Nyegga pockmarks (Norwegian margin): discrepancies in contents and carbon isotope signatures

    Science.gov (United States)

    Chevalier, Nicolas; Bouloubassi, Ioanna; Stadnitskaia, Alina; Taphanel, Marie-Hélène; Sinninghe Damsté, Jaap S.

    2014-06-01

    Distributions and carbon isotopic compositions of microbial lipid biomarkers were investigated in sediment cores from the G11 and G12 pockmarks in the Nyegga sector of the Storegga Slide on the mid-Norwegian margin to explore differences in depth zonation, type and carbon assimilation mode of anaerobic methane-oxidizing archaea (ANMEs) and associated sulphate-reducing bacteria responsible for anaerobic oxidation of methane (AOM) in these cold seep environments. While the G11 site is characterised by black reduced sediments colonized by gastropods and Siboglinidae tubeworms, the G12 site has black reduced sediments devoid of fauna but surrounded by a peripheral occurrence of gastropods and white filamentous microbial mats. At both sites, bulk sediments contained abundant archaeal and bacterial lipid biomarkers substantially depleted in 13C, consisting mainly of isoprenoidal hydrocarbons and dialkyl glycerol diethers, fatty acids and non-isoprenoidal monoalkylglycerol ethers. At the G11 site, down-core profiles revealed that lipid biomarkers were in maximum abundance from 10 cm depth to the core bottom at 16 cm depth, associated with δ13C values of -57 to -136‰. At the G12 site, by contrast, lipid biomarkers were in high abundance in the upper 5 cm sediment layer, associated with δ13C values of -43 to -133‰. This suggests that, as expected from the benthic fauna characteristics of the sites, AOM takes place mainly at depth in the G11 pockmark but just below the seafloor in the G12 pockmark. These patterns can be explained largely by variable fluid flow rates. Furthermore, at both sites, a dominance of ANME-2 archaea accompanied by their bacterial partners is inferred based on lipid biomarker distributions and carbon isotope signatures, which is in agreement with recently published DNA analyses for the G11 pockmark. However, the present data reveal high discrepancies in the contents and δ13C values for both archaeal and bacterial lipid profiles, implying the

  6. Model-Based Feasibility Assessment of Membrane Biofilm Reactor to Achieve Simultaneous Ammonium, Dissolved Methane, and Sulfide Removal from Anaerobic Digestion Liquor

    Science.gov (United States)

    Chen, Xueming; Liu, Yiwen; Peng, Lai; Yuan, Zhiguo; Ni, Bing-Jie

    2016-04-01

    In this study, the membrane biofilm reactor (MBfR) is proposed to achieve simultaneous removal of ammonium, dissolved methane, and sulfide from main-stream and side-stream anaerobic digestion liquors. To avoid dissolved methane stripping, oxygen is introduced through gas-permeable membranes, which also from the substratum for the growth of a biofilm likely comprising ammonium oxidizing bacteria (AOB), anaerobic ammonium oxidation (Anammox) bacteria, denitrifying anaerobic methane oxidation (DAMO) microorganisms, aerobic methane oxidizing bacteria (MOB), and sulfur oxidizing bacteria (SOB). A mathematical model is developed and applied to assess the feasibility of such a system and the associated microbial community structure under different operational conditions. The simulation studies demonstrate the feasibility of achieving high-level (>97.0%), simultaneous removal of ammonium, dissolved methane, and sulfide in the MBfRs from both main-stream and side-stream anaerobic digestion liquors through adjusting the influent surface loading (or hydraulic retention time (HRT)) and the oxygen surface loading. The optimal HRT was found to be inversely proportional to the corresponding oxygen surface loading. Under the optimal operational conditions, AOB, DAMO bacteria, MOB, and SOB dominate the biofilm of the main-stream MBfR, while AOB, Anammox bacteria, DAMO bacteria, and SOB coexist in the side-stream MBfR to remove ammonium, dissolved methane, and sulfide simultaneously.

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

    Science.gov (United States)

    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

  8. Different methanotrophic potentials in stratified polar fjord waters (Storfjorden, Spitsbergen identified by using a combination of methane oxidation techniques

    Directory of Open Access Journals (Sweden)

    S. Mau

    2013-04-01

    Full Text Available 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 (Spitsbergen by applying a combination of radio-tracer based incubation assays (3H-CH4 and 14H-CH4, stable C-CH4 isotope measurements, and molecular tools (16S rRNA DGGE-fingerprinting, pmoA- and mxaF gene analyses. Strofjorden is stratified in the summertime with melt water (MW in the upper 60 m of the water column, Arctic water (ArW between 60–100 m and brine-enriched shelf water (BSW down to 140 m. CH4 concentrations were supersaturated with respect to the atmospheric equilibrium (∼3 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 −1 at 60 m followed by a decrease in the deeper ArW/BSW. In contrast, rate measurements with 14H-CH4 at elevated CH4 concentrations (incubations were spiked with ∼450 nM of 14H-CH4, providing an estimate of the CH4 oxidation potential showed comparably low turnover rates (−1 at 60 m, but peaked in ArW/BSW at ∼100 m water depth, concomitant with increasing 14C-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. Although, we found pmoA and maxF gene sequences throughout the water column attesting the ubiquitous presence of MOx communities in Storfjorden, deep water amplicons of pmoA and maxF were unusually long

  9. Contribution by the methanogenic endosymbionts of anaerobic ciliates to methane production in Dutch freshwater sediments

    NARCIS (Netherlands)

    Hoek, van A.H.A.M.; Alen, T.A.; Vogels, G.D.; Hackstein, J.H.P.

    2006-01-01

    Biogenic methane contributes substantially to the atmospheric methane concentration and thus to global warming. This trace gas is predominantly produced by strictly anaerobic methanogenic archaea, which thrive in the most divergent ecological niches, e. g. paddy fields, sediments, landfills, and the

  10. Anaerobic biodegradability of macropollutants

    DEFF Research Database (Denmark)

    Angelidaki, Irini

    2002-01-01

    A variety of test procedures for determination of anaerobic biodegradability has been reported. This paper reviews the methods developed for determination of anaerobic biodegradability of macro-pollutants. Anaerobic biodegradability of micro-pollutants is not included. Furthermore, factors import...

  11. Modeling of vapor intrusion from hydrocarbon-contaminated sources accounting for aerobic and anaerobic biodegradation.

    Science.gov (United States)

    Verginelli, Iason; Baciocchi, Renato

    2011-11-01

    A one-dimensional steady state vapor intrusion model including both anaerobic and oxygen-limited aerobic biodegradation was developed. The aerobic and anaerobic layer thickness are calculated by stoichiometrically coupling the reactive transport of vapors with oxygen transport and consumption. The model accounts for the different oxygen demand in the subsurface required to sustain the aerobic biodegradation of the compound(s) of concern and for the baseline soil oxygen respiration. In the case of anaerobic reaction under methanogenic conditions, the model accounts for the generation of methane which leads to a further oxygen demand, due to methane oxidation, in the aerobic zone. The model was solved analytically and applied, using representative parameter ranges and values, to identify under which site conditions the attenuation of hydrocarbons migrating into indoor environments is likely to be significant. Simulations were performed assuming a soil contaminated by toluene only, by a BTEX mixture, by Fresh Gasoline and by Weathered Gasoline. The obtained results have shown that for several site conditions oxygen concentration below the building is sufficient to sustain aerobic biodegradation. For these scenarios the aerobic biodegradation is the primary mechanism of attenuation, i.e. anaerobic contribution is negligible and a model accounting just for aerobic biodegradation can be used. On the contrary, in all cases where oxygen is not sufficient to sustain aerobic biodegradation alone (e.g. highly contaminated sources), anaerobic biodegradation can significantly contribute to the overall attenuation depending on the site specific conditions.

  12. Modeling of vapor intrusion from hydrocarbon-contaminated sources accounting for aerobic and anaerobic biodegradation

    Science.gov (United States)

    Verginelli, Iason; Baciocchi, Renato

    2011-11-01

    A one-dimensional steady state vapor intrusion model including both anaerobic and oxygen-limited aerobic biodegradation was developed. The aerobic and anaerobic layer thickness are calculated by stoichiometrically coupling the reactive transport of vapors with oxygen transport and consumption. The model accounts for the different oxygen demand in the subsurface required to sustain the aerobic biodegradation of the compound(s) of concern and for the baseline soil oxygen respiration. In the case of anaerobic reaction under methanogenic conditions, the model accounts for the generation of methane which leads to a further oxygen demand, due to methane oxidation, in the aerobic zone. The model was solved analytically and applied, using representative parameter ranges and values, to identify under which site conditions the attenuation of hydrocarbons migrating into indoor environments is likely to be significant. Simulations were performed assuming a soil contaminated by toluene only, by a BTEX mixture, by Fresh Gasoline and by Weathered Gasoline. The obtained results have shown that for several site conditions oxygen concentration below the building is sufficient to sustain aerobic biodegradation. For these scenarios the aerobic biodegradation is the primary mechanism of attenuation, i.e. anaerobic contribution is negligible and a model accounting just for aerobic biodegradation can be used. On the contrary, in all cases where oxygen is not sufficient to sustain aerobic biodegradation alone (e.g. highly contaminated sources), anaerobic biodegradation can significantly contribute to the overall attenuation depending on the site specific conditions.

  13. Microbial desulfurization of coal by thermophilic archaea

    Energy Technology Data Exchange (ETDEWEB)

    Olsson, Gunnel

    1994-04-01

    The investigation was focused on the removal of pyrite as well as organic sulfur. One major objective was to identify and outline difficulties associated with microbial desulfurization of coal. The work has particularly been concentrated on the desulfurization environment of the microorganisms, the reprecipitation of dissolved sulfate as jarosite, the effect of microbial treatment on the properties of the coal and the comparison of different thermophilic archaea suggested for coal desulfurization. The investigated microorganisms were the thermophilic archaea Acidianus brierleyi, Sulfolobus acidocaldarius and Sulfolobus solfataricus and for comparison the mesophilic bacterium Thiobacillus ferrooxidans. The major part of the work has been done with Acidianus brierleyi. Compounds leached from coal may seriously affect the growth of microorganisms suggested for coal desulfurization. Degradation of pyritic sulfur with the used strains of S. solfataricus and S. acidocaldarius, was observed to be impossible. However, both the thermophilic archaeon Acidianus brierleyi and the mesophilic bacterium Thiobacillus ferrooxidans, were capable of degrading pure pyrite as well as pyrite from low-sulfur coals. Up to 85% removal of pyritic sulfur was obtained for coals when staring with a pyrite sulfur content of 0.5-0.7%. From kinetic studies, it was shown that A. brierleyi and T. ferrooxidans remove sulfur from coal at roughly the same rate, at least for the coals investigated in this study. However, the rate for microbial oxidation of pure pyrite was seen to be much higher for A. brierleyi than for T. ferroxidans. 62 refs, 16 figs, 5 tabs

  14. Diurnally entrained anticipatory behavior in archaea.

    Directory of Open Access Journals (Sweden)

    Kenia Whitehead

    Full Text Available By sensing changes in one or few environmental factors biological systems can anticipate future changes in multiple factors over a wide range of time scales (daily to seasonal. This anticipatory behavior is important to the fitness of diverse species, and in context of the diurnal cycle it is overall typical of eukaryotes and some photoautotrophic bacteria but is yet to be observed in archaea. Here, we report the first observation of light-dark (LD-entrained diurnal oscillatory transcription in up to 12% of all genes of a halophilic archaeon Halobacterium salinarum NRC-1. Significantly, the diurnally entrained transcription was observed under constant darkness after removal of the LD stimulus (free-running rhythms. The memory of diurnal entrainment was also associated with the synchronization of oxic and anoxic physiologies to the LD cycle. Our results suggest that under nutrient limited conditions halophilic archaea take advantage of the causal influence of sunlight (via temperature on O(2 diffusivity in a closed hypersaline environment to streamline their physiology and operate oxically during nighttime and anoxically during daytime.

  15. Swimming behavior of selected species of Archaea.

    Science.gov (United States)

    Herzog, Bastian; Wirth, Reinhard

    2012-03-01

    The swimming behavior of Bacteria has been studied extensively, at least for some species like Escherichia coli. In contrast, almost no data have been published for Archaea on this topic. In a systematic study we asked how the archaeal model organisms Halobacterium salinarum, Methanococcus voltae, Methanococcus maripaludis, Methanocaldococcus jannaschii, Methanocaldococcus villosus, Pyrococcus furiosus, and Sulfolobus acidocaldarius swim and which swimming behavior they exhibit. The two Euryarchaeota M. jannaschii and M. villosus were found to be, by far, the fastest organisms reported up to now, if speed is measured in bodies per second (bps). Their swimming speeds, at close to 400 and 500 bps, are much higher than the speed of the bacterium E. coli or of a very fast animal, like the cheetah, each with a speed of ca. 20 bps. In addition, we observed that two different swimming modes are used by some Archaea. They either swim very rapidly, in a more or less straight line, or they exhibit a slower kind of zigzag swimming behavior if cells are in close proximity to the surface of the glass capillary used for observation. We argue that such a "relocate-and-seek" behavior enables the organisms to stay in their natural habitat.

  16. Role of Mn2+ and Compatible Solutes in the Radiation Resistance of Thermophilic Bacteria and Archaea

    Directory of Open Access Journals (Sweden)

    Kimberly M. Webb

    2012-01-01

    Full Text Available Radiation-resistant bacteria have garnered a great deal of attention from scientists seeking to expose the mechanisms underlying their incredible survival abilities. Recent analyses showed that the resistance to ionizing radiation (IR in the archaeon Halobacterium salinarum is dependent upon Mn-antioxidant complexes responsible for the scavenging of reactive oxygen species (ROS generated by radiation. Here we examined the role of the compatible solutes trehalose, mannosylglycerate, and di-myo-inositol phosphate in the radiation resistance of aerobic and anaerobic thermophiles. We found that the IR resistance of the thermophilic bacteria Rubrobacter xylanophilus and Rubrobacter radiotolerans was highly correlated to the accumulation of high intracellular concentration of trehalose in association with Mn, supporting the model of Mn2+-dependent ROS scavenging in the aerobes. In contrast, the hyperthermophilic archaea Thermococcus gammatolerans and Pyrococcus furiosus did not contain significant amounts of intracellular Mn, and we found no significant antioxidant activity from mannosylglycerate and di-myo-inositol phosphate in vitro. We therefore propose that the low levels of IR-generated ROS under anaerobic conditions combined with highly constitutively expressed detoxification systems in these anaerobes are key to their radiation resistance and circumvent the need for the accumulation of Mn-antioxidant complexes in the cell.

  17. Isoprenoid biosynthesis in Archaea - Biochemical and evolutionary implications

    NARCIS (Netherlands)

    Matsumi, Rie; Atomi, Haruyuki; Driessen, Arnold J. M.; van der Oost, John

    2011-01-01

    Isoprenoids are indispensable for all types of cellular life in the Archaea, Bacteria, and Eucarya. These membrane-associated molecules are involved in a wide variety of vital biological functions, ranging from compartmentalization and stability, to protection and energy-transduction. In Archaea, is

  18. 生物质炭提高稻田甲烷氧化活性%Biochar improves methane oxidation activity in rice paddy soil

    Institute of Scientific and Technical Information of China (English)

    杨敏; 刘玉学; 孙雪; 董达; 吴伟祥

    2013-01-01

    Paddy fields are regarded as an important anthropogenic source of atmospheric CH4 and play a significant role in global warming. Biochar refers to the highly aromatic substance remaining after thermal decomposition of biomass under complete or partial exclusion of oxygen for the purpose of creating a soil amendment. Its application is widely accepted to be a promising method to decrease CH4 emission from paddy soil. The balance between CH4 production and consumption ultimately determines whether a paddy soil is a net source or a sink of atmospheric CH4. However, there are few studies concerning the effects of biochar amendments on methanogenic and methane oxidation activities in paddy soils. Meanwhile, the feedstock used for biochar production has a substantial impact on the physiochemical characteristics of biochar. These characteristics are then related to the actual environmental function in soil, such as response to methanogenic and methane oxidation activities. In this study, a one-year field experiment was conducted to gain insight into the potential effects of bamboo biochar (BB) and rice straw biochar (SB) amendments at the rate of 22.5 t/hm2 on the methanogenic and methane oxidation activities in rice rhizosphere soil. The SB had more hydrophilic groups such as carboxyl and hydroxyl, higher pH and electrical conductivity (EC) values and lower bulk density than the BB did. Soil water content, pH, and EC values in the SB treatments were greater than those in the BB treatments. Generally, urea application did not have notable impact on soil water content, pH and EC values. Compared with the control treatment, methanogenic activitiy in the rhizosphere soil at the rice seedling stage was significantly increased with the SB amendment. There was no significant difference in the methanogenic activity between the control and the BB treatments during the whole period of rice growth. Differences in the labile components and ash contents between the two biochars may

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

    Science.gov (United States)

    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

  20. Archaea: Evolution, Physiology, and Molecular Biology

    DEFF Research Database (Denmark)

    Introduced by Crafoord Prize winner Carl Woese, this volume combines reviews of the major developments in archaeal research over the past 10-15 years with more specialized articles dealing with important recent breakthroughs. Drawing on major themes presented at the June 2005 meeting held in Muni...... and technological context, and include accounts of cutting-edge research developments. The book spans archaeal evolution, physiology, and molecular and cellular biology and will be an essential reference for both graduate students and researchers....... to honor the archaea pioneers Wolfram Zillig and Karl O. Stetter, the book provides a thorough survey of the field from its controversial beginnings to its ongoing expansion to include aspects of eukaryotic biology. The editors have assembled articles from the premier researchers in this rapidly burgeoning...

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

    Directory of Open Access Journals (Sweden)

    G. Jakobs

    2013-07-01

    Full Text Available 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 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Mayernick, Adam D. [Pennsylvania State Univ., State College, PA (United States); Janik, Michael J. [Pennsylvania State Univ., State College, PA (United States)

    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.

  3. Advances in the research of methane oxidation in forest soils%森林土壤氧化(吸收)甲烷研究进展

    Institute of Scientific and Technical Information of China (English)

    邓湘雯; 杨晶晶; 陈槐; 黄志宏; 项文化; 彭长辉

    2012-01-01

    Methane (CH4) is an important greenhouse gas, which is second only to carbon dioxide and about 25% contribution to global warming. Atmospheric methane can be oxidized by methanotrophic bacteria under aerobic condition. There are numerous reports of atmospheric CH4 oxidation and absorption in forest soils. Methanotrophic bacteria are a group of bacteria physiologically defined by their ability to use methane as sole source of carbon and energy for growth. However, it remains considerable uncertainty about the amounts of CH4 released from forest soils to the atmosphere, which depended on the abundance and relative activity of methanogenus and methanotrophic bacteria in forest ecosystems. Most studies have been focused on the environmental effects on the oxidizability and the biochemical properties of methanotrophic bacteria. The oxidation processes were a kind of high capacity and low affinity oxidation, affected by lots of factors, such as soil temperature, soil aeration, soil pH and nitrogen fertilizer. Generally, soil aeration was influenced by soil texture and soil moisture. And soil bulk density, soil structure and moisture were also influenced by land use types, and thereby affecting soil methane oxidation. Soil methane oxidation capacity also could be influenced by plants through changes in habitat or allelopathy. Few studies on soil animals, only termites in the emissions inventory is included in the global methane accounting. Starting from the classification of the methane-oxidizing bacteria, the methanotrophs on methane oxidation mechanism, the ecological distribution of the bacteria and methane oxidation factors, spatial and temporal heterogeneity, observation methods are reviewed. So, this review could provide a theoretical basis to correctly understand and accurately predict forest soil methane oxidation under the conditions of a certain type of climate and land use intensity.%甲烷是一种重要的温室气体,对全球气

  4. Bacterial community composition and abundance in leachate of semi-aerobic and anaerobic landfills

    Institute of Scientific and Technical Information of China (English)

    Wei Zhang; Bo Yue; Qi Wang; Zechun Huang; Qifei Huang; Zengqiang Zhang

    2011-01-01

    The abundance and phylogenetic composition of bacterial community in leachate of semi-aerobic and anaerobic landfill were compared through real-time polymerase chain reaction and denaturing gradient gel electrophoresis.In semi-aerobic landfill scenario,the bacterial 16S rRNA copy numbers in leachate had no significant reduction from initial stage to stable period.In the scenario of anaerobic landfill,the largest bacterial 16S rRNA gene copy number was found in leachate at initial stage,but it reduced significantly at stable period.Moreover,methane-oxidizing bacteria population in stable period was lower than that in initial period in both two landfill processes.However,semi-aerobic landfill leachate had more methanotrophic bacteria populations than that in the anaerobic one.Furthermore,according to the sequences and phylogenetic analysis,obvious difference could be detected in bacterial community composition in different scenarios.Proteobacteria and bacteroidetes took up a dominantly higher proportion in semi-aerobic landfill leachate.To summarize up,different landfill methods and its landfill ages had crucial impacts on bacterial abundance and composition in leachate of semi-aerobic and anaerobic landfills.

  5. Overview of the genetic tools in the Archaea

    Directory of Open Access Journals (Sweden)

    Haruyuki eAtomi

    2012-10-01

    Full Text Available This section provides an overview of the genetic systems developed in the Archaea. Genetic manipulation is possible in many members of the halophiles, methanogens, Sulfolobus and Thermococcales. We describe the selection/counterselection principles utilized in each of these groups, which consist of antibiotics and their resistance markers, and auxotrophic host strains and complementary markers. The latter strategy utilizes techniques similar to those developed in yeast. However, Archaea are resistant to many of the antibiotics routinely used for selection in the Bacteria, and a number of strategies specific to the Archaea have been developed. In addition, examples utilizing the genetic systems developed for each group will be briefly described.

  6. Arsenic, Anaerobes, and Astrobiology

    Science.gov (United States)

    Stolz, J. F.; Oremland, R. S.; Switzer Blum, J.; Hoeft, S. E.; Baesman, S. M.; Bennett, S.; Miller, L. G.; Kulp, T. R.; Saltikov, C.

    2013-12-01

    Arsenic is an element best known for its highly poisonous nature, so it is not something one would associate with being a well-spring for life. Yet discoveries made over the past two decades have delineated that not only are some microbes resistant to arsenic, but that this element's primary redox states can be exploited to conserve energy and support prokaryotic growth ('arsenotrophy') in the absence of oxygen. Hence, arsenite [As(III)] can serve as an electron donor for chemo- or photo-autotrophy while arsenate [As(V)] will serve as an electron acceptor for chemo-heterotrophs and chemo-autotrophs. The phylogenetic diversity of these microbes is broad, encompassing many individual species from diverse taxonomic groups in the Domain Bacteria, with fewer representatives in the Domain Archaea. Speculation with regard to the evolutionary origins of the key functional genes in anaerobic arsenic transformations (arrA and arxA) and aerobic oxidation (aioB) has led to a disputation as to which gene and function is the most ancient and whether arsenic metabolism extended back into the Archaean. Regardless of its origin, robust arsenic metabolism has been documented in extreme environments that are rich in their arsenic content, such as hot springs and especially hypersaline soda lakes associated with volcanic regions. Searles Lake, CA is an extreme, salt-saturated end member where vigorous arsenic metabolism occurs, but there is no detectable sulfate-reduction or methanogenesis. The latter processes are too weak bio-energetically to survive as compared with arsenotrophy, and are also highly sensitive to the abundance of borate ions present in these locales. These observations have implications with respect to the search for microbial life elsewhere in the Solar System where volcanic-like processes have been operative. Hence, because of the likelihood of encountering dense brines in the regolith of Mars (formed by evapo-concentration) or beneath the ice layers of Europa

  7. Experimental fossilisation of viruses from extremophilic Archaea

    Directory of Open Access Journals (Sweden)

    F. Orange

    2011-06-01

    Full Text Available The role of viruses at different stages of the origin of life has recently been reconsidered. It appears that viruses may have accompanied the earliest forms of life, allowing the transition from an RNA to a DNA world and possibly being involved in the shaping of tree of life in the three domains that we know presently. In addition, a large variety of viruses has been recently identified in extreme environments, hosted by extremophilic microorganisms, in ecosystems considered as analogues to those of the early Earth. Traces of life on the early Earth were preserved by the precipitation of silica on the organic structures. We present the results of the first experimental fossilisation by silica of viruses from extremophilic Archaea (SIRV2 – Sulfolobus islandicus rod-shaped virus 2, TPV1 – Thermococcus prieurii virus 1, and PAV1 – Pyrococcus abyssi virus 1. Our results confirm that viruses can be fossilised, with silica precipitating on the different viral structures (proteins, envelope over several months in a manner similar to that of other experimentally and naturally fossilised microorganisms. This study thus suggests that viral remains or traces could be preserved in the rock record although their identification may be challenging due to the small size of the viral particles.

  8. 2003 Archaea: Ecology, Metabolism and Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    Richard F. Shand

    2004-09-21

    The Gordon Research Conference (GRC) on 2003 Archaea: Ecology, Metabolism and Molecular Biology was held at Proctor Academy, Andover, NH from August 3-8, 2003. The Conference was well-attended with 150 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. In designing the formal speakers program, emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate lively discussion about the key issues in the field today. Time for formal presentations was limited in the interest of group discussions. In order that more scientists could communicate their most recent results, poster presentation time was scheduled. Attached is a copy of the formal schedule and speaker program and the poster program. In addition to these formal interactions, ''free time'' was scheduled to allow informal discussions. Such discussions are fostering new collaborations and joint efforts in the field. I want to personally thank you for your support of this Conference. As you know, in the interest of promoting the presentation of unpublished and frontier-breaking research, Gordon Research Conferences does not permit publication of meeting proceedings. If you wish any further details, please feel free to contact me. Thank you, Dr. Richard F. Shand, 2003 Conference Chair.

  9. Molecular characterization of hydrolytic enzymes from hyperthermophilic archaea.

    OpenAIRE

    Voorhorst, W.G.B.

    1998-01-01

    Hyperthermophiles are recently discovered microorganisms which are able to grow optimally above 85 °C. Most hyperthermophiles belong to the Archaea, the third domain of life. One of the main interests in hyperthermophiles to deepen the insight in the way their proteins are stabilized and how to apply this knowledge to improve the stability of biotechnologically relevant enzymes. In this thesis attention has been focused on hydrolytic enzymes from hyperthermophilic archaea to provide insight i...

  10. Towards Glycoengineering in Archaea: Replacement of Haloferax volcanii AglD with Homologous Glycosyltransferases from Other Halophilic Archaea

    OpenAIRE

    Calo, Doron; Eilam, Yael; Lichtenstein, Rachel G.; Eichler, Jerry

    2010-01-01

    Like eukarya and bacteria, archaea also perform N-glycosylation. However, the N-linked glycans of archaeal glycoproteins present a variety not seen elsewhere. Archaea accordingly rely on N-glycosylation pathways likely involving a broad range of species-specific enzymes. To harness the enormous applied potential of such diversity for the generation of glycoproteins bearing tailored N-linked glycans, the development of an appropriate archaeal glycoengineering platform is required. With a seque...

  11. Anaerobic Digestion: Process

    DEFF Research Database (Denmark)

    Angelidaki, Irini; Batstone, Damien J.

    2011-01-01

    with very little dry matter may also be called a digest. The digest should not be termed compost unless it specifically has been composted in an aerated step. This chapter describes the basic processes of anaerobic digestion. Chapter 9.5 describes the anaerobic treatment technologies, and Chapter 9.......6 addresses the mass balances and environmental aspects of anaerobic digestion....

  12. A bioreactor approach to investigate the linkage between methane oxidation and nitrate/nitrite reduction in the pelagic oxic-anoxic transition zone of the central Baltic Sea

    Directory of Open Access Journals (Sweden)

    Gunnar Jakobs

    2016-08-01

    Full Text Available Evidence of aerobic methane oxidation coupled to denitrification has been provided for different freshwater environments, whereas the significance of this process for the marine realm has not been adequately investigated. The goal of this study was to investigate the methane-related reduction of nitrate/nitrite in a marine environment (salinity 8.5. A water sample was collected from the oxic-anoxic transition zone of the Gotland Deep (central Baltic Sea and the microorganisms contained therein were cultivated in a bioreactor under hypoxic conditions (0.5 µM O2. To enrich the microorganisms involved in the coupled process the bioreactor was continuously sparged with methane as the sole energy and carbon source and simultaneously supplied with a nutrient solution rich in nitrate and nitrite. The bioreactor experiment showed a relationship between the turnover of methane and the concomitant concentration decrease of nitrite and nitrate at the early stage of the experiment. This relationship indicates the role of methanotrophs, which may support heterotrophic denitrifiers by the release of organic compounds as an energy source. Besides, a mixture of uncultured microorganisms, aerobic methanotrophic and heterotrophic denitrifying bacteria were identified in the enrichment culture. Microbial incorporation of nitrite and methane was proven on the cellular and gene levels via 15NO2- / 13CH4 incubation experiments and subsequent analyses with nano secondary ion mass spectrometry (NanoSIMS and stable isotope probing (SIP. The NanoSIMS showed the incorporation of 15N in almost all the bacteria and in 9% of those there was a concomitant enrichment in 13C. The relatively low abundance of methane-consuming bacteria in the bioreactor was further reflected in specific fatty acids indicative for type I methanotrophic bacteria. Based on pmoA gene analyses, this bacterium is different from the one that was identified as the only key player of methane oxidation in

  13. Pathways and Bioenergetics of Anaerobic Carbon Monoxide Fermentation.

    Science.gov (United States)

    Diender, Martijn; Stams, Alfons J M; Sousa, Diana Z

    2015-01-01

    Carbon monoxide can act as a substrate for different modes of fermentative anaerobic metabolism. The trait of utilizing CO is spread among a diverse group of microorganisms, including members of bacteria as well as archaea. Over the last decade this metabolism has gained interest due to the potential of converting CO-rich gas, such as synthesis gas, into bio-based products. Three main types of fermentative CO metabolism can be distinguished: hydrogenogenesis, methanogenesis, and acetogenesis, generating hydrogen, methane and acetate, respectively. Here, we review the current knowledge on these three variants of microbial CO metabolism with an emphasis on the potential enzymatic routes and bio-energetics involved.

  14. Pathways and bioenergetics of anaerobic carbon monoxide fermentation.

    Directory of Open Access Journals (Sweden)

    Martijn eDiender

    2015-11-01

    Full Text Available Carbon monoxide can act as a substrate for different modes of fermentative anaerobic metabolism. The trait of utilizing CO is spread among a diverse group of microorganisms, including members of bacteria as well as archaea. Over the last decade this metabolism has gained interest due to the potential of converting CO rich gas, such as synthesis gas, into bio-based products. Three main types of fermentative CO metabolism can be distinguished: hydrogenogenesis, methanogenesis and acetogenesis, generating hydrogen, methane and acetate, respectively. Here, we review the current knowledge on these three variants of microbial CO metabolism with an emphasis on the potential enzymatic routes and bio-energetics involved.

  15. Survival or revival: long-term preservation induces a reversible viable but non-culturable state in methane-oxidizing bacteria.

    Directory of Open Access Journals (Sweden)

    Sven Hoefman

    Full Text Available Knowledge on long-term preservation of micro-organisms is limited and research in the field is scarce despite its importance for microbial biodiversity and biotechnological innovation. Preservation of fastidious organisms such as methane-oxidizing bacteria (MOB has proven difficult. Most MOB do not survive lyophilization and only some can be cryopreserved successfully for short periods. A large-scale study was designed for a diverse set of MOB applying fifteen cryopreservation or lyophilization conditions. After three, six and twelve months of preservation, the viability (via live-dead flow cytometry and culturability (via most-probable number analysis and plating of the cells were assessed. All strains could be cryopreserved without a significant loss in culturability using 1% trehalose in 10-fold diluted TSB (TT as preservation medium and 5% DMSO as cryoprotectant. Several other cryopreservation and lyophilization conditions, all of which involved the use of TT medium, also allowed successful preservation but showed a considerable loss in culturability. We demonstrate here that most of these non-culturables survived preservation according to viability assessment indicating that preservation induces a viable but non-culturable (VBNC state in a significant fraction of cells. Since this state is reversible, these findings have major implications shifting the emphasis from survival to revival of cells in a preservation protocol. We showed that MOB cells could be significantly resuscitated from the VBNC state using the TT preservation medium.

  16. Methane oxidation at redox stable fuel cell electrode La0.75Sr0.25Cr0.5Mn0.5O(3-delta).

    Science.gov (United States)

    Tao, Shanwen; Irvine, John T S; Plint, Steven M

    2006-11-02

    Because of its widespread availability, natural gas is the most important fuel for early application of stationary fuel cells, and furthermore, methane containing biogases are one of the most promising renewable energy alternatives; thus, it is very important to be able to efficiently utilize methane in fuel cells. Typically, external steam reforming is applied to allow methane utilization in high temperature fuel cells; however, direct oxidation will provide a much better solution. Recently, we reported good electrochemical performance for an oxide anode La0.75Sr0.25Cr0.5Mn0.5O3 (LSCM) in low moisture (3% H2O) H2 and CH4 fuels without significant coking in CH4. Here, we investigate the catalytic activity of this oxide with respect to its ability to utilize methane. This oxide is found to exhibit fairly low reforming activity for both H2O and CO2 reforming but is active for methane oxidation. LSCM is found to be a full oxidation catalyst rather than a partial oxidation catalyst as CO2 production dominates CO production even in CH4-rich CH4/O2 mixtures. X-ray adsorption spectroscopy was utilized to confirm that Mn was the redox active species, clearly demonstrating that this material has the oxidation catalytic behavior that might be expected from a Mn perovskite and that the Cr ion is only present to ensure stability under fuel atmospheres.

  17. Anaerobic oxidation of methane above gas hydrates at Hydrate Ridge, NE Pacific Ocean

    DEFF Research Database (Denmark)

    Treude, T.; Boetius, A.; Knittel, K.;

    2003-01-01

    At Hydrate Ridge (HR), Cascadia convergent margin, surface sediments contain massive gas hydrates formed from methane that ascends together with fluids along faults from deeper reservoirs. Anaerobic oxidation of methane (AOM), mediated by a microbial consortium of archaea and sulfate-reducing...... bacteria, generates high concentrations of hydrogen sulfide in the surface sediments. The production of sulfide supports chemosynthetic communities that gain energy from sulfide oxidation. Depending on fluid flow, the surface communities are dominated either by the filamentous sulfur bacteria Beggiatoa...

  18. Methane oxidation kinetics of bio-cover sewage sludge modified by coal ash for landfill%垃圾填埋场覆盖材料改性污泥的甲烷氧化动力学

    Institute of Scientific and Technical Information of China (English)

    王丹; 赵玲; 尹平河; 肖娟宜; 黄思明

    2012-01-01

    在实验室模拟条件下,以粉煤灰改性污泥为垃圾填埋场生物覆盖材料,分析了初始甲烷浓度、初始氧气浓度对甲烷氧化效率的影响,并测定了甲烷氧化动力学方程及动力学参数,旨在为材料实际工程应用提供理论依据.结果表明:初始CH4、O2浓度制约生物覆盖材料的甲烷氧化效率,初始CH4、O2浓度越高,材料甲烷氧化能力越强;甲烷氧化过程符合2级动力学方程-dV(CH4)/dt=kV(CH4)V(O2);利用Michaelis-Menten模型得出覆盖层材料的最大氧化速率Vmax为2.54 μmol g-1h-1,半速常数Km为0.49 μmol.%In this study, laboratory-scale experiments were carried out to examine the effects of initial methane and oxygen contents on methane oxidation efficiency in landfill bio-cover sewage sludge, and the kinetic equation and corresponding parameters were also determined, aiming to provide scientific basis for the practical engineering application. The results showed that the methane and oxygen contents strongly affected the methane oxidation efficiency. The higher methane and oxygen contents resulted in stronger methane oxidation efficiency. The kinetics of methane oxidation was - dV( CH4)/di = kV{ CH4 ) V( 02) , which fit the second-order reaction. As calculated from Michaelis-Menten equation, the largest methane oxidation rate ( Kmax ) was 2. 54 μmol g ‐ 1h‐ 1, and the half saturation constant ( Km ) was found at 0. 49 μmol.

  19. Diversity of Cultured Thermophilic Anaerobes in Hot Springs of Yunnan Province, China

    Science.gov (United States)

    Lin, L.; Lu, Y.; Dong, X.; Liu, X.; Wei, Y.; Ji, X.; Zhang, C.

    2010-12-01

    Thermophilic anaerobes including Archaea and Bacteria refer to those growing optimally at temperatures above 50°C and do not use oxygen as the terminal electron acceptor for growth. Study on thermophilic anaerobes will help to understand how life thrives under extreme conditions. Meanwhile thermophilic anaerobes are of importance in potential application and development of thermophilic biotechnology. We have surveyed culturable thermophilic anaerobes in hot springs (pH6.5-7.5; 70 - 94°C) in Rehai of Tengchong, Bangnazhang of Longlin, Eryuan of Dali,Yunnan, China. 50 strains in total were cultured from the hot springs water using Hungate anaerobic technique, and 30 strains were selected based on phenotypic diversity for analysis of 16S rDNA sequences. Phylogenetic analysis showed that 28 strains belonged to the members of five genera: Caldanaerobacter, Calaramator, Thermoanaerobacter, Dictyoglomus and Fervidobacterium, which formed five branches on the phylogenetic tree. Besides, 2 strains of methanogenic archaea were obtained. The majority of the isolates were the known species, however, seven strains were identified as novel species affiliated to the five genera based on the lower 16S rDNA sequence similarities (less than 93 - 97%) with the described species. This work would provide the future study on their diversity, distribution among different regions and the potential application of thermophilic enzyme. Supported by State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences(SKLMR-080605)and the Foundation of State Natural Science (30660009, 30960022, 31081220175).

  20. Effects of ferric iron on the anaerobic treatment and microbial biodiversity in a coupled microbial electrolysis cell (MEC)--anaerobic reactor.

    Science.gov (United States)

    Zhang, Jingxin; Zhang, Yaobin; Quan, Xie; Chen, Shuo

    2013-10-01

    Adding Fe(III) into a MEC - anaerobic reactor enhanced the degradation of organic matters. To clarify the respective effects of combining Fe(III) dosage and a MEC and Fe(III) dosage only on strengthening anaerobic digestion, three anaerobic reactors were operated in parallel: a MEC - anaerobic reactor with dosing Fe(OH)3 (R1), an anaerobic reactor with dosing Fe(OH)3 (R2) and a common anaerobic reactor (R3). With increasing influent COD from 1500 to 4000 mg/L, the COD removal in R1 was maintained at 88.3% under a voltage of 0.8 V, which was higher than that in reactor R2 and R3. When the power was cut off, the COD removal in R1 decreased by 5.9%. The addition of Fe(OH)3 enhanced both anaerobic digestion and anodic oxidation, resulting in the effective mineralization of volatile fatty acids (VFAs). The reduced Fe(II) combined with electric field resulted more extracellular polymeric substances (EPS) production. Quantitative real - time PCR showed a higher abundance of bacteria in the anodic biofilm and R1. Pyrosequencing and denaturing gradient gel electrophoresis (DGGE) analysis revealed that the dominant bacteria and archaea communities were richer and more abundant in the anode biofilm and R1.

  1. Mimicking the oxygen minimum zones: stimulating interaction of aerobic archaeal and anaerobic bacterial ammonia oxidizers in a laboratory-scale model system

    NARCIS (Netherlands)

    Yan, J.; Haaijer, S.C.M.; Op den Camp, H.J.M.; van Niftrik, L.; Stahl, D.A.; Könneke, M.; Rush, D.; Sinninghe Damsté, J.S.; Hu, Y.Y.; Jetten, M.S.M.

    2012-01-01

    In marine oxygen minimum zones (OMZs), ammonia-oxidizing archaea (AOA) rather than marine ammonia-oxidizing bacteria (AOB) may provide nitrite to anaerobic ammonium-oxidizing (anammox) bacteria. Here we demonstrate the cooperation between marine anammox bacteria and nitrifiers in a laboratory-scale

  2. Microbial ecology of the stratified water column of the Black Sea as revealed by a comprehensive biomarker study

    DEFF Research Database (Denmark)

    Wakeham, Stuart G.; Amann, Rudi; Freemann, Katherine H.;

    2007-01-01

    ) and sulfate reducing bacteria. We also measured a wide range of bacterial and archaeal lipid biomarkers. Depth distributions of diagnostic biomarkers are matched with zonation of microbial processes, including aerobic bacterial oxidation of methane, oxidation of ammonium by bacteria and archaea, metal...... reduction, and sulfide oxidation at the chemocline, and bacterial sulfate reduction and anaerobic oxidation of methane by archaea in the anoxic zone. Cell densities for archaea and sulfate reducing bacteria are estimated based on water column biomarker concentrations and compared with CARD-FISH results....

  3. Hydrogen production by hyperthermophilic and extremely thermophilic bacteria and archaea: mechanisms for reductant disposal

    NARCIS (Netherlands)

    Verhaart, M.R.A.; Bielen, A.A.M.; Oost, van der J.; Stams, A.J.M.; Kengen, S.W.M.

    2010-01-01

    Hydrogen produced from biomass by bacteria and archaea is an attractive renewable energy source. However, to make its application more feasible, microorganisms are needed with high hydrogen productivities. For several reasons, hyperthermophilic and extremely thermophilic bacteria and archaea are pro

  4. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

    Directory of Open Access Journals (Sweden)

    Wolf Yuri I

    2012-12-01

    Full Text Available Abstract Background Collections of Clusters of Orthologous Genes (COGs provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs. Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. Results The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major ‘highways’ of horizontal gene transfer. Conclusions The updated collection

  5. In-Vitro Archaeacidal Activity of Biocides against Human-Associated Archaea

    OpenAIRE

    2013-01-01

    BACKGROUND: Several methanogenic archaea have been detected in the human intestinal microbiota. These intestinal archaea may contaminate medical devices such as colonoscopes. However, no biocide activity has been reported among these human-associated archaea. METHODOLOGY: The minimal archaeacidal concentration (MAC) of peracetic acid, chlorhexidine, squalamine and twelve parent synthetic derivatives reported in this study was determined against five human-associated methanogenic archaea inclu...

  6. On the Response of Halophilic Archaea to Space Conditions

    Directory of Open Access Journals (Sweden)

    Stefan Leuko

    2014-02-01

    Full Text Available Microorganisms are ubiquitous and can be found in almost every habitat and ecological niche on Earth. They thrive and survive in a broad spectrum of environments and adapt to rapidly changing external conditions. It is of great interest to investigate how microbes adapt to different extreme environments and with modern human space travel, we added a new extreme environment: outer space. Within the last 50 years, technology has provided tools for transporting microbial life beyond Earth’s protective shield in order to study in situ responses to selected conditions of space. This review will focus on halophilic archaea, as, due to their ability to survive in extremes, they are often considered a model group of organisms to study responses to the harsh conditions associated with space. We discuss ground-based simulations, as well as space experiments, utilizing archaea, examining responses and/or resistance to the effects of microgravity and UV in particular. Several halophilic archaea (e.g., Halorubrum chaoviator have been exposed to simulated and actual space conditions and their survival has been determined as well as the protective effects of halite shown. Finally, the intriguing potential of archaea to survive on other planets or embedded in a meteorite is postulated.

  7. Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea

    DEFF Research Database (Denmark)

    Frigaard, Niels-Ulrik; Martinez, Asuncion; Mincer, Tracy J;

    2006-01-01

    Planktonic Bacteria, Archaea and Eukarya reside and compete in the ocean's photic zone under the pervasive influence of light. Bacteria in this environment were recently shown to contain photoproteins called proteorhodopsins, thought to contribute to cellular energy metabolism by catalysing light...

  8. Molecular characterization of hydrolytic enzymes from hyperthermophilic archaea.

    NARCIS (Netherlands)

    Voorhorst, W.G.B.

    1998-01-01

    Hyperthermophiles are recently discovered microorganisms which are able to grow optimally above 85 °C. Most hyperthermophiles belong to the Archaea, the third domain of life. One of the main interests in hyperthermophiles to deepen the insight in the way their proteins are stabilized and how to appl

  9. Sweet to the extreme: protein glycosylation in Archaea.

    Science.gov (United States)

    Yurist-Doutsch, Sophie; Chaban, Bonnie; VanDyke, David J; Jarrell, Ken F; Eichler, Jerry

    2008-06-01

    Post-translational modifications account for much of the biological diversity generated at the proteome level. Of these, glycosylation is the most prevalent. Long thought to be unique to Eukarya, it is now clear that both Bacteria and Archaea are also capable of N-glycosylation, namely the covalent linkage of oligosaccharides to select target asparagine residues. However, while the eukaryal and bacterial N-glycosylation pathways are relatively well defined, little is known of the parallel process in Archaea. Of late, however, major advances have been made in describing the process of archaeal N-glycosylation. Such efforts have shown, as is often the case in archaeal biology, that protein N-glycosylation in Archaea combines particular aspects of the eukaryal and bacterial pathways along with traits unique to this life form. For instance, while the oligosaccharides of archaeal glycoproteins include nucleotide-activated sugars formed by bacterial pathways, the lipid carrier on which such oligosaccharides are assembled is the same as used in eukaryal N-glycosylation. By contrast, transfer of assembled oligosaccharides to their protein targets shows Archaea-specific properties. Finally, addressing N-glycosylation from an archaeal perspective is providing new general insight into this event, as exemplified by the solution of the first crystal structure of an oligosaccharide transferase from an archaeal source.

  10. Anaerobic Digestion and its Applications

    Science.gov (United States)

    Anaerobic digestion is a natural biological process. The initials "AD" may refer to the process of anaerobic digestion, or the built systems of anaerobic digesters. While there are many kinds of digesters, the biology is basically the same for all. Anaerobic digesters are built...

  11. Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea

    OpenAIRE

    Hatzenpichler, Roland

    2012-01-01

    Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, has been suggested to have been a central part of the global biogeochemical nitrogen cycle since the oxygenation of Earth. The cultivation of several ammonia-oxidizing archaea (AOA) as well as the discovery that archaeal ammonia monooxygenase (amo)-like gene sequences are nearly ubiquitously distributed in the environment and outnumber their bacterial counterparts in many habitats fundamentally revised our understanding o...

  12. Classification of Bacteria and Archaea: past, present and future.

    Science.gov (United States)

    Schleifer, Karl Heinz

    2009-12-01

    The late 19th century was the beginning of bacterial taxonomy and bacteria were classified on the basis of phenotypic markers. The distinction of prokaryotes and eukaryotes was introduced in the 1960s. Numerical taxonomy improved phenotypic identification but provided little information on the phylogenetic relationships of prokaryotes. Later on, chemotaxonomic and genotypic methods were widely used for a more satisfactory classification. Archaea were first classified as a separate group of prokaryotes in 1977. The current classification of Bacteria and Archaea is based on an operational-based model, the so-called polyphasic approach, comprised of phenotypic, chemotaxonomic and genotypic data, as well as phylogenetic information. The provisional status Candidatus has been established for describing uncultured prokaryotic cells for which their phylogenetic relationship has been determined and their authenticity revealed by in situ probing. The ultimate goal is to achieve a theory-based classification system based on a phylogenetic/evolutionary concept. However, there are currently two contradictory opinions about the future classification of Bacteria and Archaea. A group of mostly molecular biologists posits that the yet-unclear effect of gene flow, in particular lateral gene transfer, makes the line of descent difficult, if not impossible, to describe. However, even in the face of genomic fluidity it seems that the typical geno- and phenotypic characteristics of a taxon are still maintained, and are sufficient for reliable classification and identification of Bacteria and Archaea. There are many well-defined genotypic clusters that are congruent with known species delineated by polyphasic approaches. Comparative sequence analysis of certain core genes, including rRNA genes, may be useful for the characterization of higher taxa, whereas various character genes may be suitable as phylogenetic markers for the delineation of lower taxa. Nevertheless, there may still be

  13. Asgard archaea illuminate the origin of eukaryotic cellular complexity.

    Science.gov (United States)

    Zaremba-Niedzwiedzka, Katarzyna; Caceres, Eva F; Saw, Jimmy H; Bäckström, Disa; Juzokaite, Lina; Vancaester, Emmelien; Seitz, Kiley W; Anantharaman, Karthik; Starnawski, Piotr; Kjeldsen, Kasper U; Stott, Matthew B; Nunoura, Takuro; Banfield, Jillian F; Schramm, Andreas; Baker, Brett J; Spang, Anja; Ettema, Thijs J G

    2017-01-19

    The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the 'Asgard' superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota. Asgard archaea affiliate with eukaryotes in phylogenomic analyses, and their genomes are enriched for proteins formerly considered specific to eukaryotes. Notably, thorarchaeal genomes encode several homologues of eukaryotic membrane-trafficking machinery components, including Sec23/24 and TRAPP domains. Furthermore, we identify thorarchaeal proteins with similar features to eukaryotic coat proteins involved in vesicle biogenesis. Our results expand the known repertoire of 'eukaryote-specific' proteins in Archaea, indicating that the archaeal host cell already contained many key components that govern eukaryotic cellular complexity.

  14. Molecular Tools for the Detection of Nitrogen Cycling Archaea

    Directory of Open Access Journals (Sweden)

    Antje Rusch

    2013-01-01

    Full Text Available Archaea are widespread in extreme and temperate environments, and cultured representatives cover a broad spectrum of metabolic capacities, which sets them up for potentially major roles in the biogeochemistry of their ecosystems. The detection, characterization, and quantification of archaeal functions in mixed communities require Archaea-specific primers or probes for the corresponding metabolic genes. Five pairs of degenerate primers were designed to target archaeal genes encoding key enzymes of nitrogen cycling: nitrite reductases NirA and NirB, nitrous oxide reductase (NosZ, nitrogenase reductase (NifH, and nitrate reductases NapA/NarG. Sensitivity towards their archaeal target gene, phylogenetic specificity, and gene specificity were evaluated in silico and in vitro. Owing to their moderate sensitivity/coverage, the novel nirB-targeted primers are suitable for pure culture studies only. The nirA-targeted primers showed sufficient sensitivity and phylogenetic specificity, but poor gene specificity. The primers designed for amplification of archaeal nosZ performed well in all 3 criteria; their discrimination against bacterial homologs appears to be weakened when Archaea are strongly outnumbered by bacteria in a mixed community. The novel nifH-targeted primers showed high sensitivity and gene specificity, but failed to discriminate against bacterial homologs. Despite limitations, 4 of the new primer pairs are suitable tools in several molecular methods applied in archaeal ecology.

  15. Carotenoid Production by Halophilic Archaea Under Different Culture Conditions.

    Science.gov (United States)

    Calegari-Santos, Rossana; Diogo, Ricardo Alexandre; Fontana, José Domingos; Bonfim, Tania Maria Bordin

    2016-05-01

    Carotenoids are pigments that may be used as colorants and antioxidants in food, pharmaceutical, and cosmetic industries. Since they also benefit human health, great efforts have been undertaken to search for natural sources of carotenoids, including microbial ones. The optimization of culture conditions to increase carotenoid yield is one of the strategies used to minimize the high cost of carotenoid production by microorganisms. Halophilic archaea are capable of producing carotenoids according to culture conditions. Their main carotenoid is bacterioruberin with 50 carbon atoms. In fact, the carotenoid has important biological functions since it acts as cell membrane reinforcement and it protects the microorganism against DNA damaging agents. Moreover, carotenoid extracts from halophilic archaea have shown high antioxidant capacity. Therefore, current review summarizes the effect of different culture conditions such as salt and carbon source concentrations in the medium, light incidence, and oxygen tension on carotenoid production by halophilic archaea and the strategies such as optimization methodology and two-stage cultivation already used to increase the carotenoid yield of these microorganisms.

  16. Evolution of DNA replication protein complexes in eukaryotes and Archaea.

    Directory of Open Access Journals (Sweden)

    Nicholas Chia

    Full Text Available BACKGROUND: The replication of DNA in Archaea and eukaryotes requires several ancillary complexes, including proliferating cell nuclear antigen (PCNA, replication factor C (RFC, and the minichromosome maintenance (MCM complex. Bacterial DNA replication utilizes comparable proteins, but these are distantly related phylogenetically to their archaeal and eukaryotic counterparts at best. METHODOLOGY/PRINCIPAL FINDINGS: While the structures of each of the complexes do not differ significantly between the archaeal and eukaryotic versions thereof, the evolutionary dynamic in the two cases does. The number of subunits in each complex is constant across all taxa. However, they vary subtly with regard to composition. In some taxa the subunits are all identical in sequence, while in others some are homologous rather than identical. In the case of eukaryotes, there is no phylogenetic variation in the makeup of each complex-all appear to derive from a common eukaryotic ancestor. This is not the case in Archaea, where the relationship between the subunits within each complex varies taxon-to-taxon. We have performed a detailed phylogenetic analysis of these relationships in order to better understand the gene duplications and divergences that gave rise to the homologous subunits in Archaea. CONCLUSION/SIGNIFICANCE: This domain level difference in evolution suggests that different forces have driven the evolution of DNA replication proteins in each of these two domains. In addition, the phylogenies of all three gene families support the distinctiveness of the proposed archaeal phylum Thaumarchaeota.

  17. Anaerobic Digestion Foaming Causes

    OpenAIRE

    Ganidi, Nafsika

    2008-01-01

    Anaerobic digestion foaming has been encountered in several sewage treatment plants in the UK. Foaming has raised major concerns for the water utilities due to significant impacts on process efficiency and operational costs. Several foaming causes have been suggested over the past few years by researchers. However, the supporting experimental information is limited and in some cases site specific. The present report aimed to provide a better understanding of the anaerobic di...

  18. Simulation model for oxygen consumption flux and prediction of methane oxidation in landfill cover soil%覆盖层氧气消耗通量模型及甲烷氧化能力预测

    Institute of Scientific and Technical Information of China (English)

    邢志林; 赵天涛; 陈新安; 车轮; 张丽杰; 全学军

    2015-01-01

    填埋场覆盖层生物气扩散规律和甲烷氧化能力的评估是甲烷减排研究的重要组成部分。以数值模拟方法分析了氧气在覆盖层中的扩散规律,得到了指数方程形式的氧气扩散模型(R2范围0.8941~0.9975);通过检测有机碳和甲烷浓度变化进一步考察了模拟覆盖层不同深度的甲烷氧化能力,证实了在0.05~0.25 m范围内甲烷氧化活性最高;以Fick定律和轴向扩散模型推导了模拟覆盖层中氧气消耗通量模型,该模型计算得到的氧气消耗通量与覆盖层中微生物甲烷氧化经验方程相比无显著差异;结合以上模型推演出覆盖层甲烷消耗通量模型,与实际检测值相比,预测结果理想(R2=0.9983)。该成果可为揭示填埋场覆盖层生物气扩散规律、强化甲烷氧化能力以及预测甲烷排放提供新的思路和理论依据。%Diffusion process of biogas and evaluation of methane oxidation in landfill cover soil are important parts of research on methane emission. Diffusion process of oxygen in landfill cover soil was analyzed by simulation, and an oxygen diffusion model fitted by exponential equation (0.8941methane oxidation in different landfill cover depths was also investigated by analyzing organic carbon and monitoring methane concentration. The most intensive methane oxidation occurred at the layer of 0.05—0.25 m. An oxygen consumption flux model in landfill cover was derived on the basis of Fick’s law and axial dispersion model. There was no significant difference between fitted values by oxygen consumption flux model and derived values by empirical equation of biological methane oxidation. Based on the above model, a methane consumption flux model was derived finally, and the prediction was consistent with detection. These results provided new ideas and theoretical basis for revealing biogas diffusion process in landfill cover soil

  19. Evidence for horizontal gene transfer of anaerobic carbon monoxide dehydrogenases

    Directory of Open Access Journals (Sweden)

    Stephen eTechtmann

    2012-04-01

    Full Text Available Carbon monoxide (CO is commonly known as a toxic gas, yet it is used by both aerobic and anaerobic bacteria and many archaea. In this study, we determined the prevalence of anaerobic carbon monoxide dehydrogenases (anaerobic CODHs, or [Ni,Fe]-CODHs in currently available genomic sequence databases. More than 6% (185 genomes out of 2887 bacterial and archaeal genome sequences in the IMG database possess at least one gene encoding [Ni,Fe]-CODH, the key enzyme for anaerobic CO utilization. The phylogenetic study of this extended protein family revealed nine distinct clades of [Ni,Fe]-CODHs. These clades consisted of [Ni,Fe]-CODHs that, while apparently monophyletic within the clades, were encoded by microorganisms of disparate phylogeny, based on 16S rRNA sequences, and widely ranging physiology. Following this discovery, it was therefore of interest to examine the extent and possible routes of horizontal gene transfer (HGT affecting [Ni,Fe]-CODH genes and gene clusters that include [Ni,Fe]-CODHs.The genome sequence of the extreme thermophile Thermosinus carboxydivorans was used as a case study for HGT. The [Ni,Fe]-CODH operon of T. carboxydivorans differs from its whole genome in its G+C content by 8.2 mol%. Here, we apply statistical methods to establish acquisition by T. carboxydivorans of the gene cluster including [Ni,Fe]-CODH via HGT. Analysis of tetranucleotide frequency and codon usage with application of the Kullback-Leibler divergence metric showed that the [Ni,Fe]-CODH-1 operon of T. carboxidyvorans is quite dissimilar to the whole genome. Using the same metrics, the T. carboxydivorans [Ni,Fe]-CODH-1 operon is highly similar to the genome of the phylogenetically distant anaerobic carboxydotroph Carboxydothermus hydrogenoformans. These results allow to assume recent HTG of the gene cluster from a relative of C. hydrogenoformans to T. carboxydivorans or a more ancient transfer from a C. hydrogenoformans ancestor to a T. carboxydivorans

  20. Anaerobic Fungi: A Potential Source of Biological H2 in the Oceanic Crust

    Science.gov (United States)

    Ivarsson, Magnus; Schnürer, Anna; Bengtson, Stefan; Neubeck, Anna

    2016-01-01

    The recent recognition of fungi in the oceanic igneous crust challenges the understanding of this environment as being exclusively prokaryotic and forces reconsiderations of the ecology of the deep biosphere. Anoxic provinces in the igneous crust are abundant and increase with age and depth of the crust. The presence of anaerobic fungi in deep-sea sediments and on the seafloor introduces a type of organism with attributes of geobiological significance not previously accounted for. Anaerobic fungi are best known from the rumen of herbivores where they produce molecular hydrogen, which in turn stimulates the growth of methanogens. The symbiotic cooperation between anaerobic fungi and methanogens in the rumen enhance the metabolic rate and growth of both. Methanogens and other hydrogen-consuming anaerobic archaea are known from subseafloor basalt; however, the abiotic production of hydrogen is questioned to be sufficient to support such communities. Alternatively, biologically produced hydrogen could serve as a continuous source. Here, we propose anaerobic fungi as a source of bioavailable hydrogen in the oceanic crust, and a close interplay between anaerobic fungi and hydrogen-driven prokaryotes. PMID:27433154

  1. Anaerobic Biodegradation of Detergent Surfactants

    Directory of Open Access Journals (Sweden)

    Erich Jelen

    2009-03-01

    Full Text Available Detergent surfactantscan be found in wastewater in relevant concentrations. Most of them are known as ready degradable under aerobic conditions, as required by European legislation. Far fewer surfactants have been tested so far for biodegradability under anaerobic conditions. The natural environment is predominantly aerobic, but there are some environmental compartments such as river sediments, sub-surface soil layer and anaerobic sludge digesters of wastewater treatment plants which have strictly anaerobic conditions. This review gives an overview on anaerobic biodegradation processes, the methods for testing anaerobic biodegradability, and the anaerobic biodegradability of different detergent surfactant types (anionic, nonionic, cationic, amphoteric surfactants.

  2. Influence of co-substrates in the anaerobic degradation of an anionic surfactant

    Directory of Open Access Journals (Sweden)

    D. Y. Okada

    2013-09-01

    Full Text Available The removal of linear alkylbenzene sulfonate (LAS was evaluated in a UASB reactor using short-chain alcohols (ethanol and methanol and complex co-substrate (yeast extract. Using only methanol and ethanol as co-substrates resulted in removal of LAS between 30 and 41%. At the end, addition of a complex substrate (yeast extract increased the removal of LAS to 50%. During the assay, water supply aeration increased the volatile fatty acid of the effluent (70 mg HAc.L-1 and decreased the removal of LAS (from 40 to 30%. According to the fluorescence in situ hybridization (FISH results, the amount of Archaea decreased due to water supply aeration (from 64 to 48%. Furthermore, addition of complex co-substrate increased the total anaerobic bacteria and methanogenic archaea content (three and four log units, respectively, which were estimated using the most probable number technique.

  3. Archaea: From Genomics to Physiology and the Origin of Life

    Science.gov (United States)

    Vothknecht, Ute C.; Tumbula, Debra L.

    1999-01-01

    This document represents a report on a meeting about Archaea. The meeting had an unusually diversified mix of topics all related to Archaea highlighting their differences and similarities with other kingdoms of life. Thus, a large number of scientists from others areas of biology participated in this conference. One-third of the speakers (11 of 33) represented laboratories whose main interests have not been archaea and who have not previously participated in similar symposia or workshops. Thus, this symposium provided a unique opportunity for archaeal researchers to interact in a wider forum. Because of the broad range of topics covered, the conference also introduced many of the participants to new areas of archaeal research. The discussions of genomics, molecular mechanisms of transcription, metabolic pathways and evolution were at a very high level. Talks and posters provided detailed discussions of the state of the current knowledge in RNA processing, transcriptional initiation, chromatin structure, aminoacyl-tRNA synthetases, autotrophic CO2 fixation, Upid biosynthesis and a wide range of other topics. In addition to providing overviews, major areas of scientific argument were clearly delineated, particularly in the discussions of genomics and evolution. Some of the questions raised included: how representative are individual gene trees of organismal evolution, how prevalent is horizontal evolution, how reliable are functional assignments in genomics? On these topics, the different points of view were well represented. The future of any field depends on the enthusiasm and intellectual engagement of young scientists working in the area. Therefore, the participation of 29 graduate and postdoctoral students (out of about 135 participants) was a highlight of the meeting. This was the consequence of funding contributions by NSF and NASA.

  4. A bioenergetic basis for membrane divergence in archaea and bacteria.

    Science.gov (United States)

    Sojo, Víctor; Pomiankowski, Andrew; Lane, Nick

    2014-08-01

    Membrane bioenergetics are universal, yet the phospholipid membranes of archaea and bacteria-the deepest branches in the tree of life-are fundamentally different. This deep divergence in membrane chemistry is reflected in other stark differences between the two domains, including ion pumping and DNA replication. We resolve this paradox by considering the energy requirements of the last universal common ancestor (LUCA). We develop a mathematical model based on the premise that LUCA depended on natural proton gradients. Our analysis shows that such gradients can power carbon and energy metabolism, but only in leaky cells with a proton permeability equivalent to fatty acid vesicles. Membranes with lower permeability (equivalent to modern phospholipids) collapse free-energy availability, precluding exploitation of natural gradients. Pumping protons across leaky membranes offers no advantage, even when permeability is decreased 1,000-fold. We hypothesize that a sodium-proton antiporter (SPAP) provided the first step towards modern membranes. SPAP increases the free energy available from natural proton gradients by ∼60%, enabling survival in 50-fold lower gradients, thereby facilitating ecological spread and divergence. Critically, SPAP also provides a steadily amplifying advantage to proton pumping as membrane permeability falls, for the first time favoring the evolution of ion-tight phospholipid membranes. The phospholipids of archaea and bacteria incorporate different stereoisomers of glycerol phosphate. We conclude that the enzymes involved took these alternatives by chance in independent populations that had already evolved distinct ion pumps. Our model offers a quantitatively robust explanation for why membrane bioenergetics are universal, yet ion pumps and phospholipid membranes arose later and independently in separate populations. Our findings elucidate the paradox that archaea and bacteria share DNA transcription, ribosomal translation, and ATP synthase, yet

  5. Purine biosynthesis in archaea: variations on a theme

    Directory of Open Access Journals (Sweden)

    Brown Anne M

    2011-12-01

    Full Text Available Abstract Background The ability to perform de novo biosynthesis of purines is present in organisms in all three domains of life, reflecting the essentiality of these molecules to life. Although the pathway is quite similar in eukaryotes and bacteria, the archaeal pathway is more variable. A careful manual curation of genes in this pathway demonstrates the value of manual curation in archaea, even in pathways that have been well-studied in other domains. Results We searched the Integrated Microbial Genome system (IMG for the 17 distinct genes involved in the 11 steps of de novo purine biosynthesis in 65 sequenced archaea, finding 738 predicted proteins with sequence similarity to known purine biosynthesis enzymes. Each sequence was manually inspected for the presence of active site residues and other residues known or suspected to be required for function. Many apparently purine-biosynthesizing archaea lack evidence for a single enzyme, either glycinamide ribonucleotide formyltransferase or inosine monophosphate cyclohydrolase, suggesting that there are at least two more gene variants in the purine biosynthetic pathway to discover. Variations in domain arrangement of formylglycinamidine ribonucleotide synthetase and substantial problems in aminoimidazole carboxamide ribonucleotide formyltransferase and inosine monophosphate cyclohydrolase assignments were also identified. Manual curation revealed some overly specific annotations in the IMG gene product name, with predicted proteins without essential active site residues assigned product names implying enzymatic activity (21 proteins, 2.8% of proteins inspected or Enzyme Commission (E. C. numbers (57 proteins, 7.7%. There were also 57 proteins (7.7% assigned overly generic names and 78 proteins (10.6% without E.C. numbers as part of the assigned name when a specific enzyme name and E. C. number were well-justified. Conclusions The patchy distribution of purine biosynthetic genes in archaea is

  6. Characterization of Methane Degradation and Methane-Degrading Microbes in Alaska Coastal Water

    Energy Technology Data Exchange (ETDEWEB)

    Kirchman, David L. [Univ. of Delaware, Lewes, DE (United States)

    2012-03-29

    The net flux of methane from methane hydrates and other sources to the atmosphere depends on methane degradation as well as methane production and release from geological sources. The goal of this project was to examine methane-degrading archaea and organic carbon oxidizing bacteria in methane-rich and methane-poor sediments of the Beaufort Sea, Alaska. The Beaufort Sea system was sampled as part of a multi-disciplinary expedition (Methane in the Arctic Shelf or MIDAS) in September 2009. Microbial communities were examined by quantitative PCR analyses of 16S rRNA genes and key methane degradation genes (pmoA and mcrA involved in aerobic and anaerobic methane degradation, respectively), tag pyrosequencing of 16S rRNA genes to determine the taxonomic make up of microbes in these sediments, and sequencing of all microbial genes (metagenomes ). The taxonomic and functional make-up of the microbial communities varied with methane concentrations, with some data suggesting higher abundances of potential methane-oxidizing archaea in methane-rich sediments. Sequence analysis of PCR amplicons revealed that most of the mcrA genes were from the ANME-2 group of methane oxidizers. According to metagenomic data, genes involved in methane degradation and other degradation pathways changed with sediment depth along with sulfate and methane concentrations. Most importantly, sulfate reduction genes decreased with depth while the anaerobic methane degradation gene (mcrA) increased along with methane concentrations. The number of potential methane degradation genes (mcrA) was low and inconsistent with other data indicating the large impact of methane on these sediments. The data can be reconciled if a small number of potential methane-oxidizing archaea mediates a large flux of carbon in these sediments. Our study is the first to report metagenomic data from sediments dominated by ANME-2 archaea and is one of the few to examine the entire microbial assemblage potentially involved in

  7. Methane oxidation with in situ enhanced facultative bacteria from aged-refuse%矿化垃圾中兼性营养菌原位强化甲烷氧化

    Institute of Scientific and Technical Information of China (English)

    赵天涛; 张云茹; 张丽杰; 全学军; 彭绪亚

    2012-01-01

    引言好氧甲烷氧化菌在新陈代谢上具有独一无二的特性:它们能够利用甲烷和其他一碳化合物作为唯一碳源和能源.这类微生物最典型的特点是利用甲烷单加氧酶( MMO,methane monooxygenase)催化甲烷氧化为甲醇[1].长时间来,所有的甲烷氧化菌都被认为是专一营养的,即它们无法利用含有碳碳键的化合物生长.%Facultative methanotrophs can utilize methane as well as multi-carbon compounds, including organic acids and carbohydrates. Facultative methanotrophs from aged-refuse were enhanced in situ to overcome the limitations of methane oxidation by existing landfill covers. Methanotrophs from oligotrophic aged-refuse had a better environmental tolerance by analysis of scanning electron microscope (SEM). These bacteria could enrich quickly in the presence of carbon source. However, the methane-oxidation capability could not be improved if only adding carbohydrates or nitrate mineral salts (NMS) medium alone. Compound acclimation of facultative methanotrophs were carried out by NMS medium and glucose/ starch. After a delay period of 7-9 d, methane consumption came into a logarithmic growth period, which indicated that facultative methanotrophs had strong biological activity and high substrate competitive advantage. Metabolic pathways of facultative methanotrophs were modified by adding NMS medium, and methane could be utilized despite the presence of other carbon sources. The activity of facultative methanotrophs was enhanced by low concentration of chloroform. Oxidation rate of methane reached 0. 114 ml·d-1·g-1 as the concentration of chloroform was 50 mg·L-1. The problems about the engineering application of obligate methanotrophs were overcome due to the discovery of the new method, and the results would have important implication for understanding the methane-oxidizing bacteria and the factors controlling methane fluxes in the environment.

  8. Seasonal Variation on Microbial Community and Methane Production during Anaerobic Digestion of Cattle Manure in Brazil.

    Science.gov (United States)

    Resende, Juliana Alves; Godon, Jean-Jacques; Bonnafous, Anaïs; Arcuri, Pedro Braga; Silva, Vânia Lúcia; Otenio, Marcelo Henrique; Diniz, Cláudio Galuppo

    2016-04-01

    Anaerobic digestion is an alternative method for the treatment of animal manure and wastewater. The anaerobic bioconversion of biomass requires a multi-step biological process, including microorganisms with distinct roles. The diversity and composition of microbial structure in pilot-scale anaerobic digestion operating at ambient temperature in Brazil were studied. Influence of the seasonal and temporal patterns on bacterial and archaeal communities were assessed by studying the variations in density, dynamic and diversity and structure. The average daily biogas produced in the summer and winter months was 18.7 and 16 L day(-1), respectively, and there was no difference in the average methane yield. Quantitative PCR analysis revealed that no differences in abundances and dynamics were found for bacterial communities and the total number of Archaea in different seasons. Analysis of bacterial clone libraries revealed a predominance of Firmicutes (54.5 %/summer and 46.7 %/winter) and Bacteroidetes (31.4 %/summer and 44.4 %/winter). Within the Archaea, the phylum Euryarchaeota was predominant in both digesters. Phylogenetic distribution showed changes in percentage between the phyla identified, but no alterations were recorded in the quality and amount of produced methane or community dynamics. The results may suggest that redundancy of microbial groups may have occurred, pointing to a more complex microbial community in the ecosystem related to this ambient temperature system.

  9. Anaerobic bacteria in otitis media.

    Science.gov (United States)

    Fulghum, R S; Daniel, H J; Yarborough, J G

    1977-01-01

    Anaerobic bacteria, Peptostrepotococcus intermedius and Propionibacterium acnes, were found in mixed culture specimens from four to ten tested cases of chronic secretory otitis media. These anaerobic bacteria were in a mixed infection flora with aerobic bacteria most often Staphylococcus epidermidis and Cornybacterium sp. which do not fit any established species. The findings of anaerobic bacteria in otitis media is consistent with the sporadic report of the involvement of anaerobic bacteria in otitis media in the literature since 1898.

  10. Complex community of nitrite-dependent anaerobic methane oxidation bacteria in coastal sediments of the Mai Po wetland by PCR amplification of both 16S rRNA and pmoA genes.

    Science.gov (United States)

    Chen, Jing; Zhou, Zhichao; Gu, Ji-Dong

    2015-02-01

    In the present work, both 16S rRNA and pmoA gene-based PCR primers were employed successfully to study the diversity and distribution of n-damo bacteria in the surface and lower layer sediments at the coastal Mai Po wetland. The occurrence of n-damo bacteria in both the surface and subsurface sediments with high diversity was confirmed in this study. Unlike the two other known n-damo communities from coastal areas, the pmoA gene-amplified sequences in the present work clustered not only with some freshwater subclusters but also within three newly erected marine subclusters mostly, indicating the unique niche specificity of n-damo bacteria in this wetland. Results suggested vegetation affected the distribution and community structures of n-damo bacteria in the sediments and n-damo could coexist with sulfate-reducing methanotrophs in the coastal ecosystem. Community structures of the Mai Po n-damo bacteria based on 16S rRNA gene were different from those of either the freshwater or the marine. In contrast, structures of the Mai Po n-damo communities based on pmoA gene grouped with the marine ones and were clearly distinguished from the freshwater ones. The abundance of n-damo bacteria at this wetland was quantified using 16S rRNA gene PCR primers to be 2.65-6.71 × 10(5) copies/g dry sediment. Ammonium and nitrite strongly affected the community structures and distribution of n-damo bacteria in the coastal Mai Po wetland sediments.

  11. A comparative genomic analysis of energy metabolism in sulfate reducing bacteria and archaea

    Directory of Open Access Journals (Sweden)

    Inês A. C. ePereira

    2011-04-01

    Full Text Available The number of sequenced genomes of sulfate-reducing organisms (SRO has increased significantly in the recent years, providing an opportunity for a broader perspective into the energy metabolism of such organisms. In this work we carried out a comparative survey of energy metabolism genes found in twenty-five available genomes of SRO. This analysis revealed a higher diversity of possible energy conserving pathways than classically considered to be present in these organisms, and permitted the identification of new proteins not known to be present in this group. The Deltaproteobacteria (and Thermodesulfovibrio yellowstonii are characterized by a large number of cytochromes c and cytochrome c-associated membrane redox complexes, indicating that periplasmic electron transfer pathways are important in these bacteria. The Archaea and Clostridia groups contain practically no cytochromes c or associated membrane complexes. However, despite the absence of a periplasmic space, a few extracytoplasmic membrane redox proteins were detected in the Gram-positive bacteria. Several ion-translocating complexes were detected in SRO including H+-pyrophosphatases, complex I homologues, Rnf and Ech/Coo hydrogenases. Furthermore, we found evidence that cytoplasmic electron bifurcating mechanisms, recently described for other anaerobes, are also likely to play an important role in energy metabolism of SRO. A number of cytoplasmic [NiFe] and [FeFe] hydrogenases, formate dehydrogenases and heterodisulfide reductase-related proteins are likely candidates to be involved in energy coupling through electron bifurcation, from diverse electron donors such as H2, formate, pyruvate, NAD(PH, β-oxidation and others. In conclusion, this analysis indicates that energy metabolism of SRO is far more versatile than previously considered, and that both chemiosmotic and flavin-based electron bifurcating mechanisms provide alternative strategies for energy conservation.

  12. A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea.

    Science.gov (United States)

    Rodionova, Irina A; Vetting, Matthew W; Li, Xiaoqing; Almo, Steven C; Osterman, Andrei L; Rodionov, Dmitry A

    2017-01-09

    Riboflavin (vitamin B2) is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide, which are essential coenzymes in all free-living organisms. Riboflavin biosynthesis in many Bacteria but not in Archaea is controlled by FMN-responsive riboswitches. We identified a novel bifunctional riboflavin kinase/regulator (RbkR), which controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain. Using comparative genomics, we predicted RbkR operator sites and reconstructed RbkR regulons in 94 archaeal genomes. While the identified RbkR operators showed significant variability between archaeal lineages, the conserved core of RbkR regulons includes riboflavin biosynthesis genes, known/predicted vitamin uptake transporters and the rbkR gene. The DNA motifs and CTP-dependent riboflavin kinase activity of two RbkR proteins were experimentally validated in vitro The DNA binding activity of RbkR was stimulated by CTP and suppressed by FMN, a product of riboflavin kinase. The crystallographic structure of RbkR from Thermoplasma acidophilum was determined in complex with CTP and its DNA operator revealing key residues for operator and ligand recognition. Overall, this study contributes to our understanding of metabolic and regulatory networks for vitamin homeostasis in Archaea.

  13. Thermoacidophilic archaea for pyrite oxidation in coal desulphurization

    Energy Technology Data Exchange (ETDEWEB)

    Larsson, Liselotte

    1995-10-01

    The desulfurization of low-sulfur coals has been demonstrated with the thermoacidophilic archaeon Acidianus brierleyi. A. brierleyi facilitates the removal of inorganic sulfur from coal and oxidizes mineral pyrite. The results imply that the mechanism behind microbial coal desulfurization and pyrite oxidation is a combination of biotic and abiotic leaching of pyrite. The extent of sulfur removal is dependent on the type of coal and is closely related to he amount of pyritic sulfur in the coal. Studies have shown that neither ash content nor heating value were dramatically affected by the microbial treatment. The use of the archaea Sulfolobus acidocaldarius and Sulfolobus solfataricus, as well as the mesophilic bacteria Thiobacillus ferrooxidans and several Pseudomonas species, has also been studied for coal desulfurization and mineral pyrite oxidation. The archaea and Pseudomonas species did not grow autotrophically on mineral pyrite neither did they oxidize pyrite in coal. The oxidation rate was, however, 5-10 times less than with A. brierleyi on mineral pyrite. The rate of sulfur removal from coal was in the same range as for A. brierleyi which indicates that different reactions are rate limiting in coal depyritization than in mineral pyrite oxidation. 133 refs, 18 figs, 3 tabs

  14. Tropical Aquatic Archaea Show Environment-Specific Community Composition

    Science.gov (United States)

    Silveira, Cynthia B.; Cardoso, Alexander M.; Coutinho, Felipe H.; Lima, Joyce L.; Pinto, Leonardo H.; Albano, Rodolpho M.; Clementino, Maysa M.; Martins, Orlando B.; Vieira, Ricardo P.

    2013-01-01

    The Archaea domain is ubiquitously distributed and extremely diverse, however, environmental factors that shape archaeal community structure are not well known. Aquatic environments, including the water column and sediments harbor many new uncultured archaeal species from which metabolic and ecological roles remain elusive. Some environments are especially neglected in terms of archaeal diversity, as is the case of pristine tropical areas. Here we investigate the archaeal composition in marine and freshwater systems from Ilha Grande, a South Atlantic tropical environment. All sampled habitats showed high archaeal diversity. No OTUs were shared between freshwater, marine and mangrove sediment samples, yet these environments are interconnected and geographically close, indicating environment-specific community structuring. Group II Euryarchaeota was the main clade in marine samples, while the new putative phylum Thaumarchaeota and LDS/RCV Euryarchaeota dominated freshwaters. Group III Euryarchaeota, a rare clade, was also retrieved in reasonable abundance in marine samples. The archaeal community from mangrove sediments was composed mainly by members of mesophilic Crenarchaeota and by a distinct clade forming a sister-group to Crenarchaeota and Thaumarchaeota. Our results show strong environment-specific community structuring in tropical aquatic Archaea, as previously seen for Bacteria. PMID:24086729

  15. CRISPR loci reveal networks of gene exchange in archaea

    Directory of Open Access Journals (Sweden)

    Brodt Avital

    2011-12-01

    Full Text Available Abstract Background CRISPR (Clustered, Regularly, Interspaced, Short, Palindromic Repeats loci provide prokaryotes with an adaptive immunity against viruses and other mobile genetic elements. CRISPR arrays can be transcribed and processed into small crRNA molecules, which are then used by the cell to target the foreign nucleic acid. Since spacers are accumulated by active CRISPR/Cas systems, the sequences of these spacers provide a record of the past "infection history" of the organism. Results Here we analyzed all currently known spacers present in archaeal genomes and identified their source by DNA similarity. While nearly 50% of archaeal spacers matched mobile genetic elements, such as plasmids or viruses, several others matched chromosomal genes of other organisms, primarily other archaea. Thus, networks of gene exchange between archaeal species were revealed by the spacer analysis, including many cases of inter-genus and inter-species gene transfer events. Spacers that recognize viral sequences tend to be located further away from the leader sequence, implying that there exists a selective pressure for their retention. Conclusions CRISPR spacers provide direct evidence for extensive gene exchange in archaea, especially within genera, and support the current dogma where the primary role of the CRISPR/Cas system is anti-viral and anti-plasmid defense. Open peer review This article was reviewed by: Profs. W. Ford Doolittle, John van der Oost, Christa Schleper (nominated by board member Prof. J Peter Gogarten

  16. The anaerobic digestion process

    Energy Technology Data Exchange (ETDEWEB)

    Rivard, C.J. [National Renewable Energy Lab., Golden, CO (United States); Boone, D.R. [Oregon Graduate Inst., Portland, OR (United States)

    1996-01-01

    The microbial process of converting organic matter into methane and carbon dioxide is so complex that anaerobic digesters have long been treated as {open_quotes}black boxes.{close_quotes} Research into this process during the past few decades has gradually unraveled this complexity, but many questions remain. The major biochemical reactions for forming methane by methanogens are largely understood, and evolutionary studies indicate that these microbes are as different from bacteria as they are from plants and animals. In anaerobic digesters, methanogens are at the terminus of a metabolic web, in which the reactions of myriads of other microbes produce a very limited range of compounds - mainly acetate, hydrogen, and formate - on which the methanogens grow and from which they form methane. {open_quotes}Interspecies hydrogen-transfer{close_quotes} and {open_quotes}interspecies formate-transfer{close_quotes} are major mechanisms by which methanogens obtain their substrates and by which volatile fatty acids are degraded. Present understanding of these reactions and other complex interactions among the bacteria involved in anaerobic digestion is only now to the point where anaerobic digesters need no longer be treated as black boxes.

  17. Anaerobic digestion without biogas?

    NARCIS (Netherlands)

    Kleerebezem, R.; Joosse, B.; Rozendaal, R.; Van Loosdrecht, M.C.M.

    2015-01-01

    Anaerobic digestion for the production of methane containing biogas is the classic example of a resource recovery process that combines stabilization of particulate organic matter or wastewater treatment with the production of a valuable end-product. Attractive features of the process include the pr

  18. One millimetre makes the difference: high-resolution analysis of methane-oxidizing bacteria and their specific activity at the oxic-anoxic interface in a flooded paddy soil.

    Science.gov (United States)

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

    2012-11-01

    Aerobic methane-oxidizing bacteria (MOB) use a restricted substrate range, yet >30 species-equivalent operational taxonomical units (OTUs) are found in one paddy soil. How these OTUs physically share their microhabitat is unknown. Here we highly resolved the vertical distribution of MOB and their activity. Using microcosms and cryosectioning, we sub-sampled the top 3-mm of a water-saturated soil at near in situ conditions in 100-μm steps. We assessed the community structure and activity using the particulate methane monooxygenase gene pmoA as a functional and phylogenetic marker by terminal restriction fragment length polymorphism (t-RFLP), a pmoA-specific diagnostic microarray, and cloning and sequencing. pmoA genes and transcripts were quantified using competitive reverse transcriptase PCR combined with t-RFLP. Only a subset of the methanotroph community was active. Oxygen microprofiles showed that 89% of total respiration was confined to a 0.67-mm-thick zone immediately above the oxic-anoxic interface, most probably driven by methane oxidation. In this zone, a Methylobacter-affiliated OTU was highly active with up to 18 pmoA transcripts per cell and seemed to be adapted to oxygen and methane concentrations in the micromolar range. Analysis of transcripts with a pmoA-specific microarray found a Methylosarcina-affiliated OTU associated with the surface zone. High oxygen but only nanomolar methane concentrations at the surface suggested an adaptation of this OTU to oligotrophic conditions. No transcripts of type II methanotrophs (Methylosinus, Methylocystis) were found, which indicated that this group was represented by resting stages only. Hence, different OTUs within a single guild shared the same microenvironment and exploited different niches.

  19. Life at extreme limits: the anaerobic halophilic alkalithermophiles.

    Science.gov (United States)

    Mesbah, Noha M; Wiegel, Juergen

    2008-03-01

    The ability of anaerobic microorganisms to proliferate under extreme conditions is of widespread importance for microbial physiology, remediation, industry, and evolution. The halophilic alkalithermophiles are a novel group of polyextremophiles. Tolerance to alkaline pH, elevated NaCl concentrations, and high temperatures necessitates mechanisms for cytoplasmic pH acidification; permeability control of the cell membrane; and stability of proteins, the cell wall, and other cellular constituents to multiple extreme conditions. Although it is generally assumed that extremophiles growing at more than one extreme combine adaptive mechanisms for each individual extreme, adaptations for individual extremes often counteract each other. However, in alkaline, hypersaline niches heated via intense solar irradiation, culture-independent analyses have revealed the presence of an extensive diversity of aerobic and anaerobic microorganisms belonging to Bacteria and Archaea that survive and grow under multiple harsh conditions. Thus, polyextremophiles must have developed novel adaptive strategies enabling them to grow and proliferate under multiple extreme conditions. The recent isolation of two novel anaerobic, halophilic alkalithermophiles, Natranaerobius thermophilus and Halonatronum saccharophilum, will provide a platform for detailed biochemical, genomic, and proteomic experiments, allowing a greater understanding of the novel adaptive mechanisms undoubtedly employed by polyextremophiles. In this review, we highlight growth characteristics, ecology, and phylogeny of the anaerobic halophilic alkalithermophiles isolated. We also describe the bioenergetic and physiological problems posed by growth at the multiple extreme conditions of alkaline pH, high NaCl concentration, and elevated temperature under anoxic conditions and highlight recent findings and unresolved problems regarding adaptation to multiple extreme conditions.

  20. Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes

    DEFF Research Database (Denmark)

    Degli Esposti, Mauro; Cortez, Diego; Lozano, Luis

    2016-01-01

    . The consensus is based upon genetic and metabolic similarities between mitochondria and aerobic α proteobacteria but fails to explain the origin of several enzymes found in the mitochondria-derived organelles of anaerobic eukaryotes such as Trichomonas and Entamoeba. These enzymes are thought to derive from......Eukaryogenesis, a major transition in evolution of life, originated from the symbiogenic fusion of an archaea with a metabolically versatile bacterium. By general consensus, the latter organism belonged to a proteobacteria, subsequently evolving into the mitochondrial organelle of our cells...

  1. Enhancing anaerobic digestion of waste activated sludge by pretreatment: effect of volatile to total solids.

    Science.gov (United States)

    Wang, Xiao; Duan, Xu; Chen, Jianguang; Fang, Kuo; Feng, Leiyu; Yan, Yuanyuan; Zhou, Qi

    2016-01-01

    In this study the effect of volatile to total solids (VS/TS) on anaerobic digestion of waste activated sludge (WAS) pretreated by alkaline, thermal and thermal-alkaline strategies was studied. Experimental results showed that the production of methane from sludge was increased with VS/TS. When anaerobic digesters were fed with sludge pretreated by the thermal-alkaline method, the average methane yield was improved from 2.8 L/d at VS/TS 0.35 to 4.7 L/d at VS/TS 0.56. Also, the efficiency of VS reduction during sludge anaerobic digestion varied between 18.9% and 45.6%, and increased gradually with VS/TS. Mechanism investigation of VS/TS on WAS anaerobic digestion suggested that the general activities of anaerobic microorganisms, activities of key enzymes related to sludge hydrolysis, acidification and methanogenesis, and the ratio of Archaea to Bacteria were all increased with VS/TS, showing good agreement with methane production.

  2. Evaluation of the impact of organic material on the anaerobic methane and ammonium removal in a membrane aerated biofilm reactor (MABR) based on the multispecies biofilm modeling.

    Science.gov (United States)

    Wu, Jun; Zhang, Yue

    2017-01-01

    The simultaneous nitrogen and methane removal by the combined nitritation, anaerobic ammonium oxidation (anammox), and nitrite dependent anaerobic methane oxidation (n-damo) processes in the membrane aerated biofilm reactor (MABR) offers clear advantages in term of energy saving and greenhouse gas emission mitigation. The rejected water from sludge digestion usually contained high ammonium, COD, and dissolved methane. The impact of influent COD on the anaerobic methane and ammonium removal in an MABR was evaluated in the model based study. The results indicated that the influent COD did not reduce the methane and ammonium removal efficiency at C/N ratio (influent COD/NH4(+)-N) less than 0.1. At high C/N ratio, the oxygen transfer coefficient needed to be increased to achieve high methane and nitrogen removal. Substrate flux analysis indicated that heterotrophic denitrification in the outside layer of biofilm reduced the impact of influent COD. Heterotrophic growth needed to be limited at the outside layer by using NO3(-) as electron acceptor; otherwise, the heterotrophic bacteria would compete NO2(-) and space with anammox and n-damo bacteria in the inner layers and reduce the nitrogen and methane removal efficiency.

  3. Production of oceanic nitrous oxide by ammonia-oxidizing archaea

    Directory of Open Access Journals (Sweden)

    C. R. Löscher

    2012-07-01

    Full Text Available The recent finding that microbial ammonia oxidation in the ocean is performed by archaea to a greater extent than by bacteria has drastically changed the view on oceanic nitrification. The numerical dominance of archaeal ammonia-oxidizers (AOA over their bacterial counterparts (AOB in large parts of the ocean leads to the hypothesis that AOA rather than AOB could be the key organisms for the oceanic production of the strong greenhouse gas nitrous oxide (N2O that occurs as a by-product of nitrification. Very recently, enrichment cultures of marine ammonia-oxidizing archaea have been reported to produce N2O.

    Here, we demonstrate that archaeal ammonia monooxygenase genes (amoA were detectable throughout the water column of the eastern tropical North Atlantic (ETNA and eastern tropical South Pacific (ETSP Oceans. Particularly in the ETNA, comparable patterns of abundance and expression of archaeal amoA genes and N2O co-occurred in the oxygen minimum, whereas the abundances of bacterial amoA genes were negligible. Moreover, selective inhibition of archaea in seawater incubations from the ETNA decreased the N2O production significantly. In studies with the only cultivated marine archaeal ammonia-oxidizer Nitrosopumilus maritimus SCM1, we provide the first direct evidence for N2O production in a pure culture of AOA, excluding the involvement of other microorganisms as possibly present in enrichments. N. maritimus showed high N2O production rates under low oxygen concentrations comparable to concentrations existing in the oxycline of the ETNA, whereas the N2O production from two AOB cultures was comparably low under similar conditions. Based on our findings, we hypothesize that the production of N2O in tropical ocean areas results mainly from archaeal nitrification and will be affected by the predicted decrease in dissolved

  4. Production of oceanic nitrous oxide by ammonia-oxidizing archaea

    Directory of Open Access Journals (Sweden)

    C. R. Loescher

    2012-02-01

    Full Text Available The recent finding that microbial ammonia oxidation in the ocean is performed by archaea to a greater extent than by bacteria has drastically changed the view on oceanic nitrification. The numerical dominance of archaeal ammonia-oxidizers (AOA over their bacterial counterparts (AOB in large parts of the ocean leads to the hypothesis that AOA rather than AOB could be the key organisms for the oceanic production of the strong greenhouse gas nitrous oxide (N2O which occurs as a by-product of nitrification. Very recently, enrichment cultures of marine ammonia-oxidizing archaea have been described to produce N2O. Here, we demonstrate that archaeal ammonia monooxygenase genes (amoA were detectable throughout the water column of the Eastern Tropical North Atlantic (ETNA and Eastern Tropical South Pacific Oceans (ETSP. Particularly in the ETNA, maxima in abundance and expression of archaeal amoA genes correlated with the N2O maximum and the oxygen minimum, whereas the abundances of bacterial amoA genes were negligible. Moreover, selective inhibition of archaea in seawater incubations from the ETNA decreased the N2O production significantly. In studies with the only cultivated marine archaeal ammonia-oxidizer Nitrosopumilus maritimus SCM1, we provide the first direct evidence for N2O production in a pure culture of AOA, excluding the involvement of other microorganisms as possibly present in enrichments. N. maritimus showed high N2O production rates under low oxygen concentrations comparable to concentrations existing in the oxycline of the ETNA, whereas the N2O production from two AOB cultures was comparably low under similar conditions. Based on our findings, we hypothesize that the production of N2O in tropical ocean areas results mainly from archaeal nitrification and will be affected by the predicted decrease in dissolved oxygen

  5. Microbial desulfurization of coal by Thiobacillus ferrooxidans and thermophilic archaea

    Energy Technology Data Exchange (ETDEWEB)

    Olsson, G.; Pott, B.-M.; Larsson, L.; Holst, O.; Karlsson, H.T. (Univ. of Lund, Lund (Sweden). Dept. of Chemical Engineering II, Chemical Center)

    1994-11-01

    Several different microorganisms have been suggested for desulfurization. In the present investigation, the thermophilic archaea [ital Acidianus brierleyi] (DSM 1651), [ital Sulfolobus acidocaldarius] (DSM 639) and [ital Sulfolobus solfataricus] (DSM 1616) were compared with the mesophyilic bacterium [ital Thiobacillus ferrooxidans] (DSM 583) concerning their capability of removing sulfur from coal. The desulfurization rate as well as the amount of sulfur removed by the microorganisms was studied. Two of the investigated microorganisms [ital Thiobacillus ferrooxidans] and [ital Acidianus brierleyi], were capable of oxidizing pure pyrite as well as oxidizing sulfur in coal. A kinetic analysis was performed assuming first order reactions. The rate constant for oxidation of pure pyrite by [ital A. brierleyi] was observed to be higher than for [ital T. ferrooxidans]. The values of the rate constants for sulfur removal from coal were comparable for the two microorganisms, but were higher than for oxidation of pure pyrite. 18 refs., 2 figs., 1 tab.

  6. Influence of Martian regolith analogs on the activity and growth of methanogenic archaea, with special regard to long-term desiccation

    Directory of Open Access Journals (Sweden)

    Janosch eSchirmack

    2015-03-01

    Full Text Available Methanogenic archaea have been studied as model organisms for possible life on Mars for several reasons: they can grow lithoautotrophically by using hydrogen and carbon dioxide as energy and carbon sources, respectively; they are anaerobes; and they evolved at a time when conditions on early Earth are believed to have looked similar to those of early Mars. As Mars is currently dry and cold and as water might be available only at certain time intervals, any organism living on this planet would need to cope with desiccation. On Earth there are several regions with low water availability as well, e.g. permafrost environments, desert soils and salt pans. Here, we present the results of a set of experiments investigating the influence of different Martian regolith analogs on the metabolic activity and growth of three methanogenic strains exposed to culture conditions as well as long-term desiccation. In most cases, concentrations below 1 %wt of regolith in the media resulted in an increase of methane production rates, whereas higher concentrations decreased the rates, thus prolonging the lag phase. Further experiments showed that methanogenic archaea are capable of producing methane when incubated on a water-saturated sedimentary matrix of regolith lacking nutrients. Survival of methanogens under these conditions was analyzed with a 400 day desiccation experiment in the presence of regolith analogs. All tested strains of methanogens survived the desiccation period as it was determined through reincubation on fresh medium and via qPCR following propidium monoazide treatment to identify viable cells. The survival of long-term desiccation and the ability of active metabolism on water-saturated MRAs strengthens the possibility of methanogenic archaea or physiologically similar organisms to exist in environmental niches on Mars. The best results were achieved in presence of a phyllosilicate, which provides insights of possible positive effects in habitats

  7. Halophilic Archaea determined from geothermal steam vent aerosols.

    Science.gov (United States)

    Ellis, Dean G; Bizzoco, Richard W; Kelley, Scott T

    2008-06-01

    Hydrothermal vents, known as 'fumaroles', are ubiquitous features of geothermal areas. Although their geology has been extensively characterized, little is known about the subsurface microbial ecology of fumaroles largely because of the difficulty in collecting sufficient numbers of cells from boiling steam water for DNA extraction and culture isolation. Here we describe the first collection, molecular analysis and isolation of microbes from fumarole steam waters in Russia (Kamchatka) and the USA (Hawaii, New Mexico, California and Wyoming). Surprisingly, the steam vent waters from all the fumaroles contained halophilic Archaea closely related to the Haloarcula spp. found in non-geothermal salt mats, saline soils, brine pools and salt lakes around the world. Microscopic cell counting estimated the cell dispersal rate at approximately 1.6 x 10(9) cells year(-1) from a single fumarole. We also managed to enrich microbes in high-salt media from every vent sample, and to isolate Haloarcula from a Yellowstone vent in a 20% salt medium after a month-long incubation, demonstrating both salt tolerance and viability of cells collected from high-temperature steam. Laboratory tests determined that microbes enriched in salt media survived temperatures greater than 75 degrees C for between 5 and 30 min during the collection process. Hawaiian fumaroles proved to contain the greatest diversity of halophilic Archaea with four new lineages that may belong to uncultured haloarchaeal genera. This high diversity may have resulted from the leaching of salts and minerals through the highly porous volcanic rock, creating a chemically complex saline subsurface.

  8. An intertwined evolutionary history of methanogenic archaea and sulfate reduction.

    Directory of Open Access Journals (Sweden)

    Dwi Susanti

    Full Text Available Hydrogenotrophic methanogenesis and dissimilatory sulfate reduction, two of the oldest energy conserving respiratory systems on Earth, apparently could not have evolved in the same host, as sulfite, an intermediate of sulfate reduction, inhibits methanogenesis. However, certain methanogenic archaea metabolize sulfite employing a deazaflavin cofactor (F(420-dependent sulfite reductase (Fsr where N- and C-terminal halves (Fsr-N and Fsr-C are homologs of F(420H(2 dehydrogenase and dissimilatory sulfite reductase (Dsr, respectively. From genome analysis we found that Fsr was likely assembled from freestanding Fsr-N homologs and Dsr-like proteins (Dsr-LP, both being abundant in methanogens. Dsr-LPs fell into two groups defined by following sequence features: Group I (simplest, carrying a coupled siroheme-[Fe(4-S(4] cluster and sulfite-binding Arg/Lys residues; Group III (most complex, with group I features, a Dsr-type peripheral [Fe(4-S(4] cluster and an additional [Fe(4-S(4] cluster. Group II Dsr-LPs with group I features and a Dsr-type peripheral [Fe(4-S(4] cluster were proposed as evolutionary intermediates. Group III is the precursor of Fsr-C. The freestanding Fsr-N homologs serve as F(420H(2 dehydrogenase unit of a putative novel glutamate synthase, previously described membrane-bound electron transport system in methanogens and of assimilatory type sulfite reductases in certain haloarchaea. Among archaea, only methanogens carried Dsr-LPs. They also possessed homologs of sulfate activation and reduction enzymes. This suggested a shared evolutionary history for methanogenesis and sulfate reduction, and Dsr-LPs could have been the source of the oldest (3.47-Gyr ago biologically produced sulfide deposit.

  9. Comprehensive microbial analysis of combined mesophilic anaerobic-thermophilic aerobic process treating high-strength food wastewater.

    Science.gov (United States)

    Jang, Hyun Min; Ha, Jeong Hyub; Park, Jong Moon; Kim, Mi-Sun; Sommer, Sven G

    2015-04-15

    A combined mesophilic anaerobic-thermophilic aerobic process was used to treat high-strength food wastewater in this study. During the experimental period, most of solid residue from the mesophilic anaerobic reactor (R1) was separated by centrifugation and introduced into the thermophilic aerobic reactor (R2) for further digestion. Then, thermophilic aerobically-digested sludge was reintroduced into R1 to enhance reactor performance. The combined process was operated with two different Runs: Run I with hydraulic retention time (HRT) = 40 d (corresponding OLR = 3.5 kg COD/m(3) d) and Run II with HRT = 20 d (corresponding OLR = 7 kg COD/m(3)). For a comparison, a single-stage mesophilic anaerobic reactor (R3) was operated concurrently with same OLRs and HRTs as the combined process. During the overall digestion, all reactors showed high stability without pH control. The combined process demonstrated significantly higher organic matter removal efficiencies (over 90%) of TS, VS and COD and methane production than did R3. Quantitative real-time PCR (qPCR) results indicated that higher populations of both bacteria and archaea were maintained in R1 than in R3. Pyrosequencing analysis revealed relatively high abundance of phylum Actinobacteria in both R1 and R2, and a predominance of phyla Synergistetes and Firmicutes in R3 during Run II. Furthermore, R1 and R2 shared genera (Prevotella, Aminobacterium, Geobacillus and Unclassified Actinobacteria), which suggests synergy between mesophilic anaerobic digestion and thermophilic aerobic digestion. For archaea, in R1 methanogenic archaea shifted from genus Methanosaeta to Methanosarcina, whereas genera Methanosaeta, Methanobacterium and Methanoculleus were predominant in R3. The results demonstrated dynamics of key microbial populations that were highly consistent with an enhanced reactor performance of the combined process.

  10. The key microorganisms for anaerobic degradation of pentachlorophenol in paddy soil as revealed by stable isotope probing

    Energy Technology Data Exchange (ETDEWEB)

    Tong, Hui [Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650 (China); Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Liu, Chengshuai [State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550009 (China); Li, Fangbai, E-mail: cefbli@soil.gd.cn [Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650 (China); Luo, Chunling [Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Chen, Manjia; Hu, Min [Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650 (China)

    2015-11-15

    Highlights: • SIP suggested that Dechloromonas can mineralize PCP in soil. • Methanosaeta and Methanocella acquired PCP-derived carbon. • Lactate enhanced microbial degradation of PCP in soil. - Abstract: Pentachlorophenol (PCP) is a common residual persistent pesticide in paddy soil and has resulted in harmful effect on soil ecosystem. The anaerobic microbial transformation of PCP, therefore, has been received much attentions, especially the functional microbial communities for the reductive transformation. However, the key functional microorganisms for PCP mineralization in the paddy soil still remain unknown. In this work, DNA-based stable isotope probing (SIP) was applied to explore the key microorganisms responsible for PCP mineralization in paddy soil. The SIP results indicated that the dominant bacteria responsible for PCP biodegradation belonged to the genus Dechloromonas of the class β-Proteobacteria. In addition, the increased production of {sup 13}CH{sub 4} and {sup 13}CO{sub 2} indicated that the addition of lactate enhanced the rate of biodegradation and mineralization of PCP. Two archaea classified as the genera of Methanosaeta and Methanocella of class Methanobacteria were enriched in the heavy fraction when with lactate, whereas no archaea was detected in the absence of lactate. These findings provide direct evidence for the species of bacteria and archaea responsible for anaerobic PCP or its breakdown products mineralization and reveal a new insight into the microorganisms linked with PCP degradation in paddy soil.

  11. Towards glycoengineering in archaea: replacement of Haloferax volcanii AglD with homologous glycosyltransferases from other halophilic archaea.

    Science.gov (United States)

    Calo, Doron; Eilam, Yael; Lichtenstein, Rachel G; Eichler, Jerry

    2010-09-01

    Like eukarya and bacteria, archaea also perform N-glycosylation. However, the N-linked glycans of archaeal glycoproteins present a variety not seen elsewhere. Archaea accordingly rely on N-glycosylation pathways likely involving a broad range of species-specific enzymes. To harness the enormous applied potential of such diversity for the generation of glycoproteins bearing tailored N-linked glycans, the development of an appropriate archaeal glycoengineering platform is required. With a sequenced genome, a relatively well-defined N-glycosylation pathway, and molecular tools for gene manipulation, the haloarchaeon Haloferax volcanii (Hfx. volcanii) represents a promising candidate. Accordingly, cells lacking AglD, a glycosyltransferase involved in adding the final hexose of a pentasaccharide N-linked to the surface (S)-layer glycoprotein, were transformed to express AglD homologues from other haloarchaea. The introduction of nonnative versions of AglD led to the appearance of an S-layer glycoprotein similar to the protein from the native strain. Indeed, mass spectrometry confirmed that AglD and its homologues introduce the final hexose to the N-linked S-layer glycoprotein pentasaccharide. Heterologously expressed haloarchaeal AglD homologues contributed to N-glycosylation in Hfx. volcanii despite an apparent lack of AglD function in those haloarchaea from where the introduced homologues came. For example, although functional in Hfx. volcanii, no transcription of the Halobacterium salinarum aglD homologue, OE1482, was detected in cells of the native host grown under various conditions. Thus, at least one AglD homologue works more readily in Hfx. volcanii than in the native host. These results warrant the continued assessment of Hfx. volcanii as a glycosylation "workshop."

  12. The impacts of triclosan on anaerobic community structures, function, and antimicrobial resistance.

    Science.gov (United States)

    McNamara, Patrick J; LaPara, Timothy M; Novak, Paige J

    2014-07-01

    Triclosan is a widespread antimicrobial agent that accumulates in anaerobic digesters used to treat the residual solids generated at municipal wastewater treatment plants; there is very little information, however, about how triclosan impacts microbial communities in anaerobic digesters. We investigated how triclosan impacts the community structure, function and antimicrobial resistance genes in lab-scale anaerobic digesters. Previously exposed (to triclosan) communities were amended with 5, 50, and 500 mg/kg of triclosan, corresponding to the median, 95th percentile, and 4-fold higher than maximum triclosan concentration that has been detected in U.S. biosolids. Triclosan amendment caused all of the Bacteria and Archaea communities to structurally diverge from that of the control cultures (based on ARISA). At the end of the experiment, all triclosan-amended Archaea communities had diverged from the control communities, regardless of the triclosan concentration added. In contrast, over time the Bacteria communities that were amended with lower concentrations of triclosan (5 mg/kg and 50 mg/kg) initially diverged and then reconverged with the control community structure. Methane production at 500 mg/kg was nearly half the methane production in control cultures. At 50 mg/kg, a large variability in methane production was observed, suggesting that 50 mg/kg may be a tipping point where function begins to fail in some communities. When previously unexposed communities were exposed to 500 mg triclosan/kg, function was maintained, but the abundance of a gene encoding for triclosan resistance (mexB) increased. This research suggests that triclosan could inhibit methane production in anaerobic digesters if concentrations were to increase and may also select for resistant Bacteria. In both cases, microbial community composition and exposure history alter the influence of triclosan.

  13. Effect of domestication on microorganism diversity and anaerobic digestion of food waste.

    Science.gov (United States)

    Bi, S J; Hong, X J; Wang, G X; Li, Y; Gao, Y M; Yan, L; Wang, Y J; Wang, W D

    2016-08-19

    To accomplish the rapid start-up and stable operation of biogas digesters, an efficient inoculum is required. To obtain such an inoculum for food waste anaerobic digestion, we domesticated dairy manure anaerobic digestion residue by adding food waste every day. After 36 days, the pH and biogas yield stabilized signifying the completion of domestication. During domestication, the microbial communities in the inocula were investigated by constructing 16S rDNA clone libraries. We evaluated the effect of the domesticated inoculum by testing batch food waste anaerobic digestion with a non-domesticated inoculum as a control. The pH and methane yield of the digestion systems were determined as measurement indices. Domestication changed the composition and proportion of bacteria and archaea in the inocula. Of the bacteria, Clostridia (49.3%), Bacteroidales (19.5%), and Anaerolinaceae (8.1%) species were dominant in the seed sludge; Anaerolinaceae (49.0%), Clostridia (28.4%), and Bacteroidales (9.1%), in domestication sludge. Methanosaeta was the dominant genus in both of the seed (94.3%) and domestication (74.3%) sludge. However, the diversity of methanogenic archaea was higher in the domestication than in seed sludge. Methanoculleus, which was absent from the seed sludge, appeared in the domestication sludge (21.7%). When the domesticated inoculum was used, the digestion system worked stably (organic loading rate: 20 gVS/L; methane yield: 292.2 ± 9.8 mL/gVS; VS = volatile solids), whereas the digestion system inoculated with seed sludge failed to generate biogas. The results indicate that inoculum domestication ensures efficient and stable anaerobic digestion by enriching the methanogenic strains.

  14. Impact of sulfate pollution on anaerobic biogeochemical cycles in a wetland sediment.

    Science.gov (United States)

    Baldwin, Darren S; Mitchell, Alison

    2012-03-15

    The impact of sulfate pollution is increasingly being seen as an issue in the management of inland aquatic ecosystems. In this study we use sediment slurry experiments to explore the addition of sulfate, with or without added carbon, on the anaerobic biogeochemical cycles in a wetland sediment that previously had not been exposed to high levels of sulfate. Specifically we looked at the cycling of S (sulfate, dissolved and particulate sulfide--the latter measured as acid volatile sulfide; AVS), C (carbon dioxide, bicarbonate, methane and the short chain volatile fatty acids formate, acetate, butyrate and propionate), N (dinitrogen, ammonium, nitrate and nitrite) and redox active metals (Fe(II) and Mn(II)). Sulfate had the largest effects on the cycling of S and C. All the added S at lower loadings were converted to AVS over the course of the experiment (30 days). At the highest loading (8 mmol) less than 50% of consumed S was converted to AVS, however this is believed to be a kinetic effect. Although sulfate reduction was occurring in sediments with added sulfate, dissolved sulfide concentrations remained low throughout the study. Sulfate addition affected methanogenesis. In the absence of added carbon, addition of sulfate, even at a loading of 1 mmol, resulted in a halving of methane formation. The initial rate of formation of methane was not affected by sulfate if additional carbon was added to the sediment. However, there was evidence for anaerobic methane oxidation in those sediments with added sulfate and carbon, but not in those sediments treated only with carbon. Surprisingly, sulfate addition had little apparent impact on N dynamics; previous studies have shown that sulfide can inhibit denitrification and stimulate dissimilatory nitrate reduction to ammonia. We propose that because most of the reduced sulfur was in particulate form, levels of dissolved sulfide were too low to interfere with the N cycle.

  15. New perspectives in anaerobic digestion

    DEFF Research Database (Denmark)

    van Lier, J.B.; Tilche, A.; Ahring, Birgitte Kiær;

    2001-01-01

    The IWA specialised group on anaerobic digestion (AD) is one of the oldest working groups of the former IAWQ organisation. Despite the fact that anaerobic technology dates back more than 100 years, the technology is still under development, adapting novel treatment systems to the modern...... requirements. In fact, most advances were achieved during the last three decades, when high-rate reactor systems were developed and a profound insight was obtained in the microbiology of the anaerobic communities. This insight led to a better understanding of anaerobic treatment and, subsequently, to a broader...

  16. Microbial community structure and performance of an anaerobic reactor digesting cassava pulp and pig manure.

    Science.gov (United States)

    Panichnumsin, P; Ahring, B; Nopharatana, A; Chaiprasert, P

    2012-01-01

    Microbial community dynamics in response to changes in substrate types (i.e. pig manure (PM), cassava pulp (CP) and mixtures of PM and CP) were investigated in an anaerobic continuously stirred tank reactor (CSTR). Molecular identification of bacterial and archaeal domains were performed, using a 16S rDNA clone library with polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) screening and phylogenetic analysis. Analysis of bacterial clone libraries revealed that the differences in the community structure corresponded to the substrate types. However, the Bacteroidetes were the most abundant group in all substrates, followed by the Clostridia. With pure PM, the dominant bacterial groups were Bacteroidales, Clostridia and Paludibacter. With a co-substrate, at CP to PM (CP:PM) ratio of 50:50, the sequences analysis revealed the greatest diversity of bacterial communities at class level, and the sequences affiliated with Cytophaga sp. became an exclusive predominant. With CP alone, Bacteroides sp. was the dominant species and this reactor had the lowest diversity of bacteria. Archaea observed in the CSTR fed with all substrate types were Methanosaeta sp., Methanosaeta concilii and Methanospirillum hungatei. Among the Archaea, Methanosaeta sp. was the exclusive predominant. The relative distribution of Archaea also changed regarding to the substrate types.

  17. Biochemistry of methyl-coenzyme M reductase: the nickel metalloenzyme that catalyzes the final step in synthesis and the first step in anaerobic oxidation of the greenhouse gas methane.

    Science.gov (United States)

    Ragsdale, Stephen W

    2014-01-01

    Methane, the major component of natural gas, has been in use in human civilization since ancient times as a source of fuel and light. Methanogens are responsible for synthesis of most of the methane found on Earth. The enzyme responsible for catalyzing the chemical step of methanogenesis is methyl-coenzyme M reductase (MCR), a nickel enzyme that contains a tetrapyrrole cofactor called coenzyme F430, which can traverse the Ni(I), (II), and (III) oxidation states. MCR and methanogens are also involved in anaerobic methane oxidation. This review describes structural, kinetic, and computational studies aimed at elucidating the mechanism of MCR. Such studies are expected to impact the many ramifications of methane in our society and environment, including energy production and greenhouse gas warming.

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

    KAUST Repository

    Meulepas, Roel J W

    2010-05-06

    Anaerobic oxidation of methane (AOM) coupled to sulfate reduction (SR) is assumed to be a syntrophic process, in which methanotrophic archaea produce an interspecies electron carrier (IEC), which is subsequently utilized by sulfate-reducing bacteria. In this paper, six methanogenic substrates are tested as candidate-IECs by assessing their effect on AOM and SR by an anaerobic methanotrophic enrichment. The presence of acetate, formate or hydrogen enhanced SR, but did not inhibit AOM, nor did these substrates trigger methanogenesis. Carbon monoxide also enhanced SR but slightly inhibited AOM. Methanol did not enhance SR nor did it inhibit AOM, and methanethiol inhibited both SR and AOM completely. Subsequently, it was calculated at which candidate-IEC concentrations no more Gibbs free energy can be conserved from their production from methane at the applied conditions. These concentrations were at least 1,000 times lower can the final candidate-IEC concentration in the bulk liquid. Therefore, the tested candidate-IECs could not have been produced from methane during the incubations. Hence, acetate, formate, methanol, carbon monoxide, and hydrogen can be excluded as sole IEC in AOM coupled to SR. Methanethiol did inhibit AOM and can therefore not be excluded as IEC by this study.

  19. Distribution and Abundance of Archaea in South China Sea Sponge Holoxea sp. and the Presence of Ammonia-Oxidizing Archaea in Sponge Cells

    Directory of Open Access Journals (Sweden)

    Fang Liu

    2011-01-01

    Full Text Available Compared with bacterial symbionts, little is known about archaea in sponges especially about their spatial distribution and abundance. Understanding the distribution and abundance of ammonia-oxidizing archaea will help greatly in elucidating the potential function of symbionts in nitrogen cycling in sponges. In this study, gene libraries of 16S rRNA gene and ammonia monooxygenase subunit A (amoA genes and quantitative real-time PCR were used to study the spatial distribution and abundance of archaea in the South China Sea sponge Holoxea sp. As a result, Holoxea sp. specific AOA, mainly group C1a (marine group I: Crenarchaeota were identified. The presence of ammonia-oxidizing crenarchaea was observed for the first time within sponge cells. This study suggested a close relationship between sponge host and its archaeal symbionts as well as the archaeal potential contribution to sponge host in the ammonia-oxidizing process of nitrification.

  20. Identification of a glycolytic regulon in the Archaea Pyrococcus and Thermococcus

    NARCIS (Netherlands)

    Werken, van de H.J.G.; Verhees, C.H.; Akerboom, A.P.; Vos, de W.M.; Oost, van der J.

    2006-01-01

    The glycolytic pathway of the hyperthermophilic archaea that belong to the order Thermococcales (Pyrococcus, Thermococcus and Palaeococcus) differs significantly from the canonical Embden-Meyerhof pathway in bacteria and eukarya. This archaeal glycolysis variant consists of several novel enzymes, so

  1. Anaerobic digestion of aircraft deicing fluid wastes: interactions and toxicity of corrosion inhibitors and surfactants.

    Science.gov (United States)

    Gruden, Cyndee L; Hernandez, Mark

    2002-01-01

    Corrosion inhibitors and surfactants are present in aircraft deicing fluids (ADFs) at significant concentrations (> 1% w/w). The purpose of this research was to study the interactions of a common nonionic surfactant with the commercially significant corrosion inhibitors used in modern ADF (4- and 5-methylbenzotriazole [MeBT]), and to determine the effects of their mixture on the conventional anaerobic digestion process. In mesophilic anaerobic microcosms codigesting wastewater solids, propylene glycol, and MeBT, increasing surfactant levels resulted in enhanced MeBT sorption on digester solids. As judged by anaerobic toxicity assays, responses from digesters containing surfactant concentrations below their critical micelle concentration (CMC) suggested that low nonionic surfactant concentrations could facilitate a reduction in the apparent toxicity of MeBT. In microcosms exposed to surfactant concentrations above their CMC, no increase in MeBT solubility was observed, and the anaerobic toxicity response corresponded to control systems not containing surfactant. Direct microscopic measurements of digesting biomass using fluorescent phylogenetic probes (fluorescent in situ hybridization) revealed that members of the domain Bacteria were more sensitive to MeBT in the presence of surfactant than were members of the domain Archaea.

  2. Anaerobic Digestion of Piggery Waste

    NARCIS (Netherlands)

    Velsen, van A.F.M.

    1981-01-01

    Anaerobic digestion is a biological process by which organic matter is converted to methane and carbon dioxide by microbes in the absence of air (oxygen). In nature, anaerobic conversions occur at all places where organic material accumulates and the supply of oxygen is deficient, e.g. in marshes an

  3. Economic viability of anaerobic digestion

    Energy Technology Data Exchange (ETDEWEB)

    Wellinger, A. [INFOENERGIE, Ettenhausen (Switzerland)

    1996-01-01

    The industrial application of anaerobic digestion is a relatively new, yet proven waste treatment technology. Anaerobic digestion reduces and upgrades organic waste, and is a good way to control air pollution as it reduces methane and nitrous gas emissions. For environmental and energy considerations, anaerobic digestion is a nearly perfect waste treatment process. However, its economic viability is still in question. A number of parameters - type of waste (solid or liquid), digester system, facility size, product quality and end use, environmental requirements, cost of alternative treatments (including labor), and interest rates - define the investment and operating costs of an anaerobic digestion facility. Therefore, identical facilities that treat the same amount and type of waste may, depending on location, legislation, and end product characteristics, reveal radically different costs. A good approach for evaluating the economics of anaerobic digestion is to compare it to treatment techniques such as aeration or conventional sewage treatment (for industrial wastewater), or composting and incineration (for solid organic waste). For example, the cost (per ton of waste) of in-vessel composting with biofilters is somewhat higher than that of anaerobic digestion, but the investment costs 1 1/2 to 2 times more than either composting or anaerobic digestion. Two distinct advantages of anaerobic digestion are: (1) it requires less land than either composting or incinerating, which translates into lower costs and milder environmental and community impacts (especially in densely populated areas); and (2) it produces net energy, which can be used to operate the facility or sold to nearby industries.

  4. Anaerobic digestion of solid material

    DEFF Research Database (Denmark)

    Vavilin, V.A.; Lokshina, L.Y.; Flotats, X.

    2007-01-01

    A new multidimensional (3 and 2D) anaerobic digestion model for cylindrical reactor with non-uniform influent concentration distributions was developed to study the way in which mixing intensity affects the efficiency of continuous-flow anaerobic digestion. Batch experiments reported and simulate...

  5. Chaperonin Polymers in Archaea: The Cytoskeleton of Prokaryotes?

    Science.gov (United States)

    Trent, J. D.; Kagawa, H. K.; Zaluzec, N. J.

    1997-07-01

    Chaperonins are protein complexes that play a critical role in folding nascent polypeptides under normal conditions and refolding damaged proteins under stress conditions. In all organisms these complexes are composed of evolutionarily conserved 60-kDa proteins arranged in double-ring structures with between 7 and 9 protein subunits per ring. These double ring structures are assumed to be the functional units in vivo, although they have never been observed inside cells. Here the authors show that the purified chaperonin from the hyperthermophilic archaeon Sulfolobus shibatae, which is closely related to chaperonins in eukaryotes, has a double ring structure at low concentrations (0.1 mg/ml), but at more physiological concentrations, the rings stack end to end to form polymers. The polymers are stable at physiological temperatures (75 C) and closely resemble structures observed inside unfixed S. shibatae cells. The authors suggest that in vivo chaperonin activity may be regulated by polymerization and that chaperonin polymers may act as a cytoskeleton-like structure in archaea and bacteria.

  6. Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea

    Directory of Open Access Journals (Sweden)

    Xu Ying

    2008-01-01

    Full Text Available Abstract Background Mobile genetic elements (MGEs play an essential role in genome rearrangement and evolution, and are widely used as an important genetic tool. Results In this article, we present genetic maps of recently active Insertion Sequence (IS elements, the simplest form of MGEs, for all sequenced cyanobacteria and archaea, predicted based on the previously identified ~1,500 IS elements. Our predicted IS maps are consistent with the NCBI annotations of the IS elements. By linking the predicted IS elements to various characteristics of the organisms under study and the organism's living conditions, we found that (a the activities of IS elements heavily depend on the environments where the host organisms live; (b the number of recently active IS elements in a genome tends to increase with the genome size; (c the flanking regions of the recently active IS elements are significantly enriched with genes encoding DNA binding factors, transporters and enzymes; and (d IS movements show no tendency to disrupt operonic structures. Conclusion This is the first genome-scale maps of IS elements with detailed structural information on the sequence level. These genetic maps of recently active IS elements and the several interesting observations would help to improve our understanding of how IS elements proliferate and how they are involved in the evolution of the host genomes.

  7. Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea.

    Science.gov (United States)

    Hatzenpichler, Roland

    2012-11-01

    Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, has been suggested to have been a central part of the global biogeochemical nitrogen cycle since the oxygenation of Earth. The cultivation of several ammonia-oxidizing archaea (AOA) as well as the discovery that archaeal ammonia monooxygenase (amo)-like gene sequences are nearly ubiquitously distributed in the environment and outnumber their bacterial counterparts in many habitats fundamentally revised our understanding of nitrification. Surprising insights into the physiological distinctiveness of AOA are mirrored by the recognition of the phylogenetic uniqueness of these microbes, which fall within a novel archaeal phylum now known as Thaumarchaeota. The relative importance of AOA in nitrification, compared to ammonia-oxidizing bacteria (AOB), is still under debate. This minireview provides a synopsis of our current knowledge of the diversity and physiology of AOA, the factors controlling their ecology, and their role in carbon cycling as well as their potential involvement in the production of the greenhouse gas nitrous oxide. It emphasizes the importance of activity-based analyses in AOA studies and formulates priorities for future research.

  8. Picoheterotroph (Bacteria and Archaea biomass distribution in the global ocean

    Directory of Open Access Journals (Sweden)

    M. R. Landry

    2012-09-01

    Full Text Available We compiled a database of 39 766 data points consisting of flow cytometric and microscopical measurements of picoheterotroph abundance, including both Bacteria and Archaea. After gridding with 1° spacing, the database covers 1.3% of the ocean surface. There are data covering all ocean basins and depths except the Southern Hemisphere below 350 m or from April until June. The average picoheterotroph biomass is 3.9 ± 3.6 μg C l−1 with a 20-fold decrease between the surface and the deep sea. We estimate a total ocean inventory of about 1.3 × 1029 picoheterotroph cells. Surprisingly, the abundance in the coastal regions is the same as at the same depths in the open ocean. Using an average of published open ocean measurements for the conversion from abundance to carbon biomass of 9.1 fg cell−1, we calculate a picoheterotroph carbon inventory of about 1.2 Pg C. The main source of uncertainty in this inventory is the conversion factor from abundance to biomass. Picoheterotroph biomass is ~2 times higher in the tropics than in the polar oceans. doi:10.1594/PANGAEA.779142

  9. Intercontinental dispersal of bacteria and archaea by transpacific winds

    Science.gov (United States)

    D. Smith,; H. Timonen,; D. Jaffe,; Griffin, Dale W.; M. Birmele,; Perry, K.D.; Ward, P.D.; M. Roberts,

    2013-01-01

    Microorganisms are abundant in the upper atmosphere, particularly downwind of arid regions, where winds can mobilize large amounts of topsoil and dust. However, the challenge of collecting samples from the upper atmosphere and reliance upon culture-based characterization methods have prevented a comprehensive understanding of globally dispersed airborne microbes. In spring 2011 at the Mt. Bachelor Observatory in North America (2.8 km above sea level), we captured enough microbial biomass in two transpacific air plumes to permit a microarray analysis using 16S rRNA genes. Thousands of distinct bacterial taxa spanning a wide range of phyla and surface environments were detected before, during, and after each Asian long-range transport event. Interestingly, the transpacific plumes delivered higher concentrations of taxa already in the background air (particularly Proteobacteria, Actinobacteria, and Firmicutes). While some bacterial families and a few marine archaea appeared for the first and only time during the plumes, the microbial community compositions were similar, despite the unique transport histories of the air masses. It seems plausible, when coupled with atmospheric modeling and chemical analysis, that microbial biogeography can be used to pinpoint the source of intercontinental dust plumes. Given the degree of richness measured in our study, the overall contribution of Asian aerosols to microbial species in North American air warrants additional investigation.

  10. Involvement of thermophilic archaea in the biocorrosion of oil pipelines.

    Science.gov (United States)

    Davidova, Irene A; Duncan, Kathleen E; Perez-Ibarra, B Monica; Suflita, Joseph M

    2012-07-01

    Two thermophilic archaea, strain PK and strain MG, were isolated from a culture enriched at 80°C from the inner surface material of a hot oil pipeline. Strain PK could ferment complex organic nitrogen sources (e.g. yeast extract, peptone, tryptone) and was able to reduce elemental sulfur (S°), Fe(3+) and Mn(4+) . Phylogenetic analysis revealed that the organism belonged to the order Thermococcales. Incubations of this strain with elemental iron (Fe°) resulted in the abiotic formation of ferrous iron and the accumulation of volatile fatty acids during yeast extract fermentation. The other isolate, strain MG, was a H(2) :CO(2) -utilizing methanogen, phylogenetically affiliated with the genus Methanothermobacter family. Co-cultures of the strains grew as aggregates that produced CH(4) without exogenous H(2) amendment. The co-culture produced the same suite but greater concentrations of fatty acids from yeast extract than did strain PK alone. Thus, the physiological characteristics of organisms both alone and in combination could conceivably contribute to pipeline corrosion. The Thermococcus strain PK could reduce elemental sulfur to sulfide, produce fatty acids and reduce ferric iron. The hydrogenotrophic methanogen strain MG enhanced fatty acid production by fermentative organisms but could not couple the dissolution Fe° with the consumption of water-derived H(2) like other methanogens.

  11. Bridging domains : a comparison between information processing in Archaea and Eukarya

    OpenAIRE

    de Koning

    2015-01-01

    Bridging Domains A Comparison between Information Processing in Archaea and Eukarya Studying Information Processing Living cells evolved complex systems to handle the flow of information both accurately and efficiently. These systems are highly comparable between the three domains of life: eukaryotes, bacteria and archaea. The central components of replication, transcription, aminoacylation, and translation are found in every living cell known today, with only relatively small deviations, des...

  12. Large Tailed Spindle Viruses of Archaea: a New Way of Doing Viral Business.

    Science.gov (United States)

    Hochstein, Rebecca; Bollschweiler, Daniel; Engelhardt, Harald; Lawrence, C Martin; Young, Mark

    2015-09-01

    Viruses of Archaea continue to surprise us. Archaeal viruses have revealed new morphologies, protein folds, and gene content. This is especially true for large spindle viruses, which infect only Archaea. We present a comparison of particle morphologies, major coat protein structures, and gene content among the five characterized large spindle viruses to elucidate defining characteristics. Structural similarities and a core set of genes support the grouping of the large spindle viruses into a new superfamily.

  13. Genome sequencing of methanogenic Archaea Methanosarcina mazei TUC01 strain isolated from an Amazonian Flooded Area

    Science.gov (United States)

    Baraúna, R. A.; Graças, D. A.; Ramos, R. T.; Carneiro, A. R.; Lopes, T. S.; Lima, A. R.; Zahlouth, R. L.; Pellizari, V. H.; Silva, A.

    2013-05-01

    Methanosarcina mazei is a strictly anaerobic methanogen from the Methanosarcinales order. This species is known for its broad catabolic range among methanogens and is widespread throughout diverse environments. The draft genome of a strain cultivated from the sediment of the Tucuruí hydroelectric power station, the fourth largest hydroelectric dam in the world, is described here. Approximately 80% of methane is produced by biogenic sources, such as methanogenic archaea from M. mazei species. Although the methanogenesis pathway is well known, some aspects of the core genome, genome evolution and shared genes are still unclear. A sediment sample from the Tucuruí hydropower station reservoir was inoculated in mineral media supplemented with acetate and methanol. This media was maintained in an H2:CO2 (80:20) atmosphere to enrich and cultivate M. mazei. The enrichment was conducted at 30°C under standard anaerobic conditions. After several molecular and cellular analyses, total DNA was extracted from a non-pure culture of M. mazei, amplified using phi29 DNA polymerase (BioLabs) and finally used as a source template for genome sequencing. The draft genome was obtained after two rounds of sequencing. First, the genome was sequenced using a SOLiD System V3 with a mate-paired library, which yielded 24,405,103 and 24,399,268 reads (50 bp) for the R3 and F3 tags, respectively. The second round of sequencing was performed using the SOLiD 5500 XL platform with a mate-paired library, resulting in a total of 113,588,848 reads (60 bp) for each tag (F3 and R3). All reads obtained by this procedure were filtered using Quality Assessment software, whereby reads with an average quality score below Phred 20 were removed. Velvet and Edena were used to assemble the reads, and Simplifier was used to remove the redundant sequences. After this, a total of 16,811 contigs were obtained. M. mazei GO1 (AE008384) genome was used to map the contigs and generate the scaffolds. We used the

  14. The implementation of artificial neural networks to model methane oxidation in landfill soil covers[Includes the CSCE forum on professional practice and career development : 1. international engineering mechanics and materials specialty conference : 1. international/3. coastal, estuarine and offshore engineering specialty conference : 2. international/8. construction specialty conference

    Energy Technology Data Exchange (ETDEWEB)

    Szeto, A.; Albanna, M.; Warith, M. [Ottawa Univ., ON (Canada). Faculty of Civil and Environmental Engineering

    2009-07-01

    The disposal of solid waste significantly contributes to the total anthropogenic emissions of methane (CH{sub 4}), a greenhouse gas that negatively affects climate change. The oxidation of methane in landfill bio-covers takes place through the use of methanotrophic bacteria which provides a sink for methane. The rate at which methane is biologically oxidized depends on several parameters. This study provided a better understanding of the oxidation of methane in landfill soil covers through modeling methane oxidation with artificial neural networks (ANNs). An ANN was trained and tested to model methane oxidation in various batch scale systems for 3 types of soils. Input data consisted of temperature, moisture content, soil composition and the nutrient content added to the system. Model results were in good agreement with experimental results reported by other researchers. It was concluded that the use of ANNs to model methane oxidation in batch scale bio-covers can address the large number of complicated physical and biochemical processes that occur within the landfill bio-cover. 10 refs., 7 tabs., 5 figs.

  15. Distance-decay and taxa-area relationships for bacteria, archaea and methanogenic archaea in a tropical lake sediment.

    Directory of Open Access Journals (Sweden)

    Davi Pedroni Barreto

    Full Text Available The study of of the distribution of microorganisms through space (and time allows evaluation of biogeographic patterns, like the species-area index (z. Due to their high dispersal ability, high reproduction rates and low rates of extinction microorganisms tend to be widely distributed, and they are thought to be virtually cosmopolitan and selected primarily by environmental factors. Recent studies have shown that, despite these characteristics, microorganisms may behave like larger organisms and exhibit geographical distribution. In this study, we searched patterns of spatial diversity distribution of bacteria and archaea in a contiguous environment. We collected 26 samples of a lake sediment, distributed in a nested grid, with distances between samples ranging from 0.01 m to 1000 m. The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism targeting mcrA (coding for a subunit of methyl-coenzyme M reductase and the genes of Archaeal and Bacterial 16S rRNA. From the qualitative and quantitative results (relative abundance of operational taxonomic units we calculated the similarity index for each pair to evaluate the taxa-area and distance decay relationship slopes by linear regression. All results were significant, with mcrA genes showing the highest slope, followed by Archaeal and Bacterial 16S rRNA genes. We showed that the microorganisms of a methanogenic community, that is active in a contiguous environment, display spatial distribution and a taxa-area relationship.

  16. Diversity of Ammonia Oxidizing Archaea in Tropical Compost Systems

    Directory of Open Access Journals (Sweden)

    Vidya eDe Gannes

    2012-07-01

    Full Text Available Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from combinations of plant waste materials common in tropical agriculture (rice straw, sugar cane bagasse, coffee hulls, which were mixed with either cow- or sheep-manure. The objective was to determine how AOA abundance and diversity varied as a function of compost system and time, the latter being a contrast between the start of the compost process (mesophilic phase and the finished product (mature phase. The results showed that AOA were relatively abundant in composts of tropical agricultural wastes, and significantly more so than were the ammonia-oxidizing bacteria. Furthermore, while the AOA communities in the composts were predominatly group I.1b, the communities were diverse and exhibited structures that diverged between compost types and phases. These patterns could be taken as indicators of the ecophysiological diversity in the soil AOA (groub I.1b, in that significantly different AOA communties developed when exposed to varying physico-chemical environments. Nitrification patterns and levels differed in the composts which, for the mature material, could have signifcant effects on its performanc as a plant growth medium. Thus, it will also be important to determine the association of AOA (and diversity in their communities with nitrification in these systems.

  17. Isolation and Cultivation of Anaerobes

    DEFF Research Database (Denmark)

    Aragao Börner, Rosa

    2016-01-01

    Anaerobic microorganisms play important roles in different biotechnological processes. Their complex metabolism and special cultivation requirements have led to less isolated representatives in comparison to their aerobic counterparts.In view of that, the isolation and cultivation of anaerobic...... microorganisms is still a promising venture, and conventional methodologies as well as considerations and modifications are presented here. An insight into new methodologies and devices as well as a discussion on future perspectives for the cultivation of anaerobes may open the prospects of the exploitation...

  18. In-vitro archaeacidal activity of biocides against human-associated archaea.

    Directory of Open Access Journals (Sweden)

    Saber Khelaifia

    Full Text Available BACKGROUND: Several methanogenic archaea have been detected in the human intestinal microbiota. These intestinal archaea may contaminate medical devices such as colonoscopes. However, no biocide activity has been reported among these human-associated archaea. METHODOLOGY: The minimal archaeacidal concentration (MAC of peracetic acid, chlorhexidine, squalamine and twelve parent synthetic derivatives reported in this study was determined against five human-associated methanogenic archaea including Methanobrevibacter smithii, Methanobrevibacter oralis, Methanobrevibacter arboriphilicus, Methanosphaera stadtmanae, Methanomassiliicoccus luminyensis and two environmental methanogens Methanobacterium beijingense and Methanosaeta concilii by using a serial dilution technique in Hungates tubes. PRINCIPAL FINDINGS: MAC of squalamine derivative S1 was 0.05 mg/L against M. smithii strains, M. oralis, M. arboriphilicus, M. concilii and M. beijingense whereas MAC of squalamine and derivatives S2-S12 varied from 0.5 to 5 mg/L. For M. stadtmanae and M. luminyensis, MAC of derivative S1 was 0.1 mg/L and varied from 1 to ≥ 10 mg/L for squalamine and its parent derivatives S2-S12. Under the same experimental conditions, chlorhexidine and peracetic acid lead to a MAC of 0.2 and 1.5 mg/L, respectively against all tested archaea. CONCLUSIONS/SIGNIFICANCE: Squalamine derivative S1 exhibited a 10-200 higher archaeacidal activity than other tested squalamine derivatives, on the majority of human-associated archaea. As previously reported and due to their week corrosivity and their wide spectrum of antibacterial and antifungal properties, squalamine and more precisely derivative S1 appear as promising compounds to be further tested for the decontamination of medical devices contaminated by human-associated archaea.

  19. Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis

    Directory of Open Access Journals (Sweden)

    Gupta Radhey S

    2007-03-01

    Full Text Available Abstract Background The Archaea are highly diverse in terms of their physiology, metabolism and ecology. Presently, very few molecular characteristics are known that are uniquely shared by either all archaea or the different main groups within archaea. The evolutionary relationships among different groups within the Euryarchaeota branch are also not clearly understood. Results We have carried out comprehensive analyses on each open reading frame (ORFs in the genomes of 11 archaea (3 Crenarchaeota – Aeropyrum pernix, Pyrobaculum aerophilum and Sulfolobus acidocaldarius; 8 Euryarchaeota – Pyrococcus abyssi, Methanococcus maripaludis, Methanopyrus kandleri, Methanococcoides burtonii, Halobacterium sp. NCR-1, Haloquadratum walsbyi, Thermoplasma acidophilum and Picrophilus torridus to search for proteins that are unique to either all Archaea or for its main subgroups. These studies have identified 1448 proteins or ORFs that are distinctive characteristics of Archaea and its various subgroups and whose homologues are not found in other organisms. Six of these proteins are unique to all Archaea, 10 others are only missing in Nanoarchaeum equitans and a large number of other proteins are specific for various main groups within the Archaea (e.g. Crenarchaeota, Euryarchaeota, Sulfolobales and Desulfurococcales, Halobacteriales, Thermococci, Thermoplasmata, all methanogenic archaea or particular groups of methanogens. Of particular importance is the observation that 31 proteins are uniquely present in virtually all methanogens (including M. kandleri and 10 additional proteins are only found in different methanogens as well as A. fulgidus. In contrast, no protein was exclusively shared by various methanogen and any of the Halobacteriales or Thermoplasmatales. These results strongly indicate that all methanogenic archaea form a monophyletic group exclusive of other archaea and that this lineage likely evolved from Archaeoglobus. In addition, 15 proteins

  20. Anaerobic Biodegradation of Detergent Surfactants

    OpenAIRE

    Erich Jelen; Ute Merrettig-Bruns

    2009-01-01

    Detergent surfactantscan be found in wastewater in relevant concentrations. Most of them are known as ready degradable under aerobic conditions, as required by European legislation. Far fewer surfactants have been tested so far for biodegradability under anaerobic conditions. The natural environment is predominantly aerobic, but there are some environmental compartments such as river sediments, sub-surface soil layer and anaerobic sludge digesters of wastewater treatment plants which have str...

  1. Presence of Archaea in the Indoor Environment and Their Relationships with Housing Characteristics.

    Science.gov (United States)

    Pakpour, Sepideh; Scott, James A; Turvey, Stuart E; Brook, Jeffrey R; Takaro, Timothy K; Sears, Malcolm R; Klironomos, John

    2016-08-01

    Archaea are widespread and abundant in soils, oceans, or human and animal gastrointestinal (GI) tracts. However, very little is known about the presence of Archaea in indoor environments and factors that can regulate their abundances. Using a quantitative PCR approach, and targeting the archaeal and bacterial 16S rRNA genes in floor dust samples, we found that Archaea are a common part of the indoor microbiota, 5.01 ± 0.14 (log 16S rRNA gene copies/g dust, mean ± SE) in bedrooms and 5.58 ± 0.13 in common rooms, such as living rooms. Their abundance, however, was lower than bacteria: 9.20 ± 0.32 and 9.17 ± 0.32 in bedrooms and common rooms, respectively. In addition, by measuring a broad array of environmental factors, we obtained preliminary insights into how the abundance of total archaeal 16S rRNA gene copies in indoor environment would be associated with building characteristics and occupants' activities. Based on the results, Archaea are not equally distributed within houses, and the areas with greater input of outdoor microbiome and higher traffic and material heterogeneity tend to have a higher abundance of Archaea. Nevertheless, more research is needed to better understand causes and consequences of this microbial group in indoor environments.

  2. Exploring the diversity of extremely halophilic archaea in food-grade salts.

    Science.gov (United States)

    Henriet, Olivier; Fourmentin, Jeanne; Delincé, Bruno; Mahillon, Jacques

    2014-11-17

    Salting is one of the oldest means of food preservation: adding salt decreases water activity and inhibits microbial development. However, salt is also a source of living bacteria and archaea. The occurrence and diversity of viable archaea in this extreme environment were assessed in 26 food-grade salts from worldwide origin by cultivation on four culture media. Additionally, metagenomic analysis of 16S rRNA gene was performed on nine salts. Viable archaea were observed in 14 salts and colony counts reached more than 10(5)CFU per gram in three salts. All archaeal isolates identified by 16S rRNA gene sequencing belonged to the Halobacteriaceae family and were related to 17 distinct genera among which Haloarcula, Halobacterium and Halorubrum were the most represented. High-throughput sequencing generated extremely different profiles for each salt. Four of them contained a single major genus (Halorubrum, Halonotius or Haloarcula) while the others had three or more genera of similar occurrence. The number of distinct genera per salt ranged from 21 to 27. Halorubrum had a significant contribution to the archaeal diversity in seven salts; this correlates with its frequent occurrence in crystallization ponds. On the contrary, Haloquadratum walsbyi, the halophilic archaea most commonly found in solar salterns, was a minor actor of the food-grade salt diversity. Our results indicate that the occurrence and diversity of viable halophilic archaea in salt can be important, while their fate in the gastrointestinal tract after ingestion remains largely unknown.

  3. 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)

    Science.gov (United States)

    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.

  4. Succession of microbial community and enhanced mechanism of a ZVI-based anaerobic granular sludge process treating chloronitrobenzenes wastewater

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Liang, E-mail: felix79cn@hotmail.com [Department of Environmental Engineering, Zhejiang University, Hangzhou 310058 (China); Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058 (China); Jin, Jie [Department of Environmental Engineering, Zhejiang University, Hangzhou 310058 (China); Lin, Haizhuan [Department of Environmental Engineering, Zhejiang University, Hangzhou 310058 (China); Wenzhou Environmental Protection Design Scientific Institute, Wenzhou 325000 (China); Gao, Kaituo [Department of Environmental Engineering, Zhejiang University, Hangzhou 310058 (China); Xu, Xiangyang, E-mail: xuxy@zju.edu.cn [Department of Environmental Engineering, Zhejiang University, Hangzhou 310058 (China); Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058 (China)

    2015-03-21

    Highlights: • The combined ZVI–UASB process was established for the degradation of chloronitrobenzenes. • There were the better shock resistance and buffering capacity for anaerobic acidification in the combined process. • Novel ZVI-based anaerobic granular sludge (ZVI–AGS) was successfully developed. • Adaptive shift of microbial community was significant in ZVI-based anaerobic granular sludge system. - Abstract: The combined zero-valent iron (ZVI) and upflow anaerobic sludge blanket (UASB) process is established for the treatment of chloronitrobenzenes (ClNBs) wastewater, and the succession of microbial community and its enhanced mechanism are investigated in the study. Results showed that compared with the control UASB (R1), the stable COD removal, ClNBs transformation, and dechlorination occurred in the combined system (R2) when operated at influent COD and 3,4-Dichloronitrobenzene (3,4-DClNB) loading rates of 4200–7700 g m{sup −3} d{sup −1} and 6.0–70.0 g m{sup −3} d{sup −1}, and R2 had the better shock resistance and buffering capacity for the anaerobic acidification. The dechlorination for the intermediate products of p-chloroanaline (p-ClAn) to analine (AN) occurred in R2 reactor after 45 days, whereas it did not occur in R1 after a long-term operation. The novel ZVI-based anaerobic granular sludge (ZVI–AGS) was successfully developed in the combined system, and higher microbial activities including ClNB transformation and H{sub 2}/CH{sub 4} production were achieved simultaneously. The dominant bacteria were closely related to the groups of Megasphaera, Chloroflexi, and Clostridium, and the majority of archaea were correlated with the groups of Methanosarcinalesarchaeon, Methanosaetaconcilii, and Methanothrixsoehngenii, which are capable of reductively dechlorinating PCB, HCB, and TCE in anaerobic niche and EPS secretion.

  5. 杜儿坪矿中部风井风排瓦斯氧化处理项目设计%The Design of Ventilation Air Methane Oxidation Treatment Project of

    Institute of Scientific and Technical Information of China (English)

    罗申国

    2013-01-01

    我国煤矿风排瓦斯量巨大,直接排放造成环境污染和能源浪费,利用乏风氧化机组将其销毁,同时产生热能,不仅改善大气环境,还为矿井风排瓦斯处理开辟了一条新途径。以杜儿坪矿中部风井风排瓦斯氧化处理项目设计为例,介绍了工程概况、机组选型、装机规模及工艺系统设计方案,并论述了避免对矿井通风安全造成影响的措施。%There is a huge number of coal mine ventilation air methane in China,emptying directly lead to envi-ronmental pollution and energy waste,using oxidation unit will be destroyed,and generate heat,not only improve the atmospheric environment,also for mine ventilation air methane treatment has opened up a new way.Takes the ventila-tion air methane oxidation treatment project design in Du'erping coal mine central ventilation shaft as an example,in-troduces the engineering general situation,the unit type selection,installed capacity and design scheme of process system,and discusses the measures to avoid affecting the safety of mine ventilation.

  6. The TrmB family: a versatile group of transcriptional regulators in Archaea.

    Science.gov (United States)

    Gindner, Antonia; Hausner, Winfried; Thomm, Michael

    2014-09-01

    Microbes are organisms which are well adapted to their habitat. Their survival depends on the regulation of gene expression levels in response to environmental signals. The most important step in regulation of gene expression takes place at the transcriptional level. This regulation is intriguing in Archaea because the eu-karyotic-like transcription apparatus is modulated by bacterial-like transcription regulators. The transcriptional regulator of mal operon (TrmB) family is well known as a very large group of regulators in Archaea with more than 250 members to date. One special feature of these regulators is that some of them can act as repressor, some as activator and others as both repressor and activator. This review gives a short updated overview of the TrmB family and their regulatory patterns in different Archaea as a lot of new data have been published on this topic since the last review from 2008.

  7. Untapped Resources: Biotechnological Potential of Peptides and Secondary Metabolites in Archaea

    Science.gov (United States)

    Charlesworth, James C.; Burns, Brendan P.

    2015-01-01

    Archaea are an understudied domain of life often found in “extreme” environments in terms of temperature, salinity, and a range of other factors. Archaeal proteins, such as a wide range of enzymes, have adapted to function under these extreme conditions, providing biotechnology with interesting activities to exploit. In addition to producing structural and enzymatic proteins, archaea also produce a range of small peptide molecules (such as archaeocins) and other novel secondary metabolites such as those putatively involved in cell communication (acyl homoserine lactones), which can be exploited for biotechnological purposes. Due to the wide array of metabolites produced there is a great deal of biotechnological potential from antimicrobials such as diketopiperazines and archaeocins, as well as roles in the cosmetics and food industry. In this review we will discuss the diversity of small molecules, both peptide and nonpeptide, produced by archaea and their potential biotechnological applications. PMID:26504428

  8. A unique isotopic fingerprint during sulfate-driven anaerobic oxidation of methane

    Science.gov (United States)

    Antler, G.; Turchyn, A. V.; Herut, B.; Sivan, O.

    2014-12-01

    Bacterial sulfate reduction is responsible for the majority of anaerobic methane oxidation in modern marine sediments. This sulfate-driven AOM can often metabolize all the methane produced within marine sediments, preventing any from reaching the overlying ocean. In certain areas, however, methane concentrations are high enough to form bubbles, which can reach the seafloor, only partially metabolized through sulfate-driven AOM; these areas where methane bubbles into the ocean are called cold seeps, or methane seeps. We use the sulfur and oxygen isotopes of sulfate (d34SSO4 and d18OSO4) in locations where sulfate-driven AOM is occurring both in methane seeps as well as lower flux methane transition zones to show that in methane seeps, the d34SSO4 and d18OSO4 data during the coupled sulfate reduction fall into a very narrow range and with a close to linear relationship (slope 0.37± 0.01 (R^2= 0.98, n=52, 95% confidence interval). In the studied environments, considerably different physical properties exist, excluding the possibility that this linear relationship can be attributed to physical processes such as diffusion, advection or mixing of two end-members. This unique isotopic signature emerges during bacterial sulfate reduction by methane in 'cold' seeps and differs when sulfate is reduced by either organic matter oxidation or by a slower, diffusive flux of methane within marine sediments. We show also that this unique isotope fingerprint is preserved in the rock record in authigenic build-ups of carbonates and barite associated with methane seeps, and may serve as a powerful tool for identifying catastrophic methane release in the geological record.

  9. Interrogation of Chesapeake Bay sediment microbial communities for intrinsic alkane-utilizing potential under anaerobic conditions.

    Science.gov (United States)

    Johnson, Jamie M; Wawrik, Boris; Isom, Catherine; Boling, Wilford B; Callaghan, Amy V

    2015-02-01

    Based on the transient exposure of Chesapeake Bay sediments to hydrocarbons and the metabolic versatility of known anaerobic alkane-degrading microorganisms, it was hypothesized that distinct Bay sediment communities, governed by geochemical gradients, would have intrinsic alkane-utilizing potential under sulfate-reducing and/or methanogenic conditions. Sediment cores were collected along a transect of the Bay. Community DNA was interrogated via pyrosequencing of 16S rRNA genes, PCR of anaerobic hydrocarbon activation genes, and qPCR of 16S rRNA genes and genes involved in sulfate reduction/methanogenesis. Site sediments were used to establish microcosms amended with n-hexadecane under sulfate-reducing and methanogenic conditions. Sequencing of 16S rRNA genes indicated that sediments associated with hypoxic water columns contained significantly greater proportions of Bacteria and Archaea consistent with syntrophic degradation of organic matter and methanogenesis compared to less reduced sediments. Microbial taxa frequently associated with hydrocarbon-degrading communities were found throughout the Bay, and the genetic potential for hydrocarbon metabolism was demonstrated via the detection of benzyl-(bssA) and alkylsuccinate synthase (assA) genes. Although microcosm studies did not indicate sulfidogenic alkane degradation, the data suggested that methanogenic conversion of alkanes was occurring. These findings highlight the potential role that anaerobic microorganisms could play in the bioremediation of hydrocarbons in the Bay.

  10. Microbial community structure and dynamics during anaerobic digestion of various agricultural waste materials.

    Science.gov (United States)

    Ziganshin, Ayrat M; Liebetrau, Jan; Pröter, Jürgen; Kleinsteuber, Sabine

    2013-06-01

    The influence of the feedstock type on the microbial communities involved in anaerobic digestion was investigated in laboratory-scale biogas reactors fed with different agricultural waste materials. Community composition and dynamics over 2 months of reactors' operation were investigated by amplicon sequencing and profiling terminal restriction fragment length polymorphisms of 16S rRNA genes. Major bacterial taxa belonged to the Clostridia and Bacteroidetes, whereas the archaeal community was dominated by methanogenic archaea of the orders Methanomicrobiales and Methanosarcinales. Correlation analysis revealed that the community composition was mainly influenced by the feedstock type with the exception of a temperature shift from 38 to 55 °C which caused the most pronounced community shifts. Bacterial communities involved in the anaerobic digestion of conventional substrates such as maize silage combined with cattle manure were relatively stable and similar to each other. In contrast, special waste materials such as chicken manure or Jatropha press cake were digested by very distinct and less diverse communities, indicating partial ammonia inhibition or the influence of other inhibiting factors. Anaerobic digestion of chicken manure relied on syntrophic acetate oxidation as the dominant acetate-consuming process due to the inhibition of aceticlastic methanogenesis. Jatropha as substrate led to the enrichment of fiber-degrading specialists belonging to the genera Actinomyces and Fibrobacter.

  11. Biodegradation of linear alkylbenzene sulfonate in commercial laundry wastewater by an anaerobic fluidized bed reactor.

    Science.gov (United States)

    Braga, Juliana K; Motteran, Fabrício; Macedo, Thaís Z; Sakamoto, Isabel K; Delforno, Tiago P; Okada, Dagoberto Y; Silva, Edson L; Varesche, Maria Bernadete A

    2015-01-01

    The biodegradation of linear alkylbenzene sulfonate (LAS) from commercial laundry wastewater was evaluated in an anaerobic fluidized bed reactor (FBR) fed with synthetic substrate (598 mg L(-1) to 723 mg L(-1) of organic matter) supplemented with 9.5±3.1 mg L(-1) to 27.9±9.6 mg L(-1) of LAS. The average chemical oxygen demand (COD) removal efficiency was 89% and the biodegradation of LAS was 57% during the 489 days of anaerobic FBR. Higher levels of volatile fatty acids (VFA) were observed in the effluent at the stage with the best LAS removal performance. Increasing the surfactant concentration did not increase the VFA production in the effluent. The predominant VFAs after the addition of LAS were as follows: isovaleric acid and valeric acid, followed by propionic acid, caproic acid and formic acid. The similarities of 64% and 45% to Archaea and Bacteria domains were observed in the samples taken in the operating period of anaerobic FBR fed with 23.6±10 mg L(-1) and 27.9±10 mg L(-1) of LAS. During the operation stages in the reactor, Gemmatimonas, Desulfobulbus and Zoogloea were determined as the most abundant genera related to surfactant degradation using 454-Pyrosequencing.

  12. Gene Expression in Archaea: Studies of Transcriptional Promoters, Messenger RNA Processing, and Five Prime Untranslated Regions in "Methanocaldococcus Jannashchii"

    Science.gov (United States)

    Zhang, Jian

    2009-01-01

    Gene expression in Archaea is less understood than those in Bacteria and Eucarya. In general, three steps are involved in gene expression--transcription, RNA processing, and translation. To expand our knowledge of these processes in Archaea, I have studied transcriptional promoters, messenger RNA processing, and 5'-untranslated regions in…

  13. Massive Expansion of Marine Archaea During The Early Albian Oceanic Anoxic Event 1B

    Science.gov (United States)

    Kuypers, M. M.; Kuypers, M. M.; Blokker, P.; Erbacher, J.; Kinkel, H.; Pancost, R. D.; Pancost, R. D.; Schouten, S.; Sinninghe Damsté, J. S.

    2001-12-01

    Oceanic anoxic events (OAEs), periods of globally enhanced burial of organic matter (OM) in the marine realm, played an important role in the mid-Cretaceous `greenhouse climate' by effectively reducing atmospheric carbon dioxide concentrations. It is generally believed that these OAEs were caused either by decreased remineralisation or increased production of phytoplanktonic OM. Here we show that enhanced organic carbon (OC) burial during the early Albian OAE1b (~112 My) was caused by a different process. Combined biogeochemical and stable carbon isotopic analyses indicate that black shales from this period contain up to 80% of OC derived from archaea. Archaea-derived isoprenoidal tetraether membrane lipids and free and macromolecularly bound isoprenoid alkanes are abundantly present in these black shales. More specifically the presence of certain ether lipids (cyclic biphytane tetraethers) indicates representatives of the pelagic archaea. To the best of our knowledge this is the earliest fossil evidence for marine planktonic archaea, extending their geological record by more than 60 million years. The diversity of archaeal lipids recovered from the OAE1b black shales suggests that they derive from a multitude of archaeal species. However, the specific 13C enrichment of all such lipids indicates a common `heavy' (13C-rich) carbon source for the archaea and/or a common pathway of carbon-fixation with a reduced 13C fractionation effect compared to the Calvin cycle used by algae, cyanobacteria and higher plants. The large differences (up to 12%) in 13C/12C ratios between the algal biomarkers and the much more abundant archaeal molecular fossils suggest that the latter were not living heterotrophically on photoautotrophic biomass. It seems likely that the archaea present during OAE1b used a chemical energy source (possibly ammonium) for carbon fixation since photoautotrophy within the domain of the Archaea is restricted to only a few species from hypersaline

  14. Potential for anaerobic conversion of xenobiotics

    DEFF Research Database (Denmark)

    Mogensen, Anders Skibsted; Dolfing, J.; Haagensen, Frank;

    2003-01-01

    This review covers the latest research on the anaerobic biodegradation of aromatic xenobiotic compounds, with emphasis on surfactants, polycyclic aromatic hydrocarbons, phthalate esters, polychlorinated biphenyls, halogenated phenols, and pesticides. The versatility of anaerobic reactor systems...

  15. RISK FACTORS IN NEONATAL ANAEROBIC INFECTIONS

    Directory of Open Access Journals (Sweden)

    M. S. Tabib

    2008-06-01

    Full Text Available Anaerobic bacteria are well known causes of sepsis in adults but there are few studies regarding their role in neonatal sepsis. In an attempt to define the incidence of neonatal anaerobic infections a prospective study was performed during one year period. A total number of 400 neonates under sepsis study were entered this investigation. Anaerobic as well as aerobic cultures were sent. The patients were subjected to comparison in two groups: anaerobic culture positive and anaerobic culture negative and this comparison were analyzed statistically. There were 7 neonates with positive anaerobic culture and 35 neonates with positive aerobic culture. A significant statistical relationship was found between anaerobic infections and abdominal distention and pneumonia. It is recommended for those neonates with abdominal distention and pneumonia refractory to antibiotic treatment to be started on antibiotics with anaerobic coverage.

  16. A time-course analysis of four full-scale anaerobic digesters in relation to the dynamics of change of their microbial communities.

    Science.gov (United States)

    Pycke, B F G; Etchebehere, C; Van de Caveye, P; Negroni, A; Verstraete, W; Boon, N

    2011-01-01

    This study describes the microbial community richness, -dynamics, and -organization of four full-scale anaerobic digesters during a time-course study of 45 days. The microbial community was analyzed using a Bacteria- and Archaea-targeting 16S rRNA gene-based Terminal-Restriction Fragment Length Polymorphism approach. Clustering analysis separated meso- and thermophilic reactors for both archaeal and bacterial communities. Regardless of the operating temperature, each installation possessed a distinct community profile. For both microbial domains, about 8 dominant terminal-restriction fragments could be observed, with a minimum of 4 and a maximum of 14. The bacterial community organization (a coefficient which describes the specific degree of evenness) showed a factor 2 more variation in the mesophilic reactors, compared with the thermophilic ones. The archaeal community structure of the mesophilic UASB reactor was found to be more stable. The community composition was highly dynamic for Bacteria and Archaea, with a rate of change between 20-50% per 15 days. This study illustrated that microbial communities in full-scale anaerobic digesters are unique to the installation and that community properties are dynamic. Converging complex microbial processes such as anaerobic digestion which rely on a multitude of microbial teams apparently can be highly dynamic.

  17. Effects of phosphate addition on methane fermentation in the batch and upflow anaerobic sludge blanket (UASB) reactors.

    Science.gov (United States)

    Suzuki, Sho; Shintani, Masaki; Sanchez, Zoe Kuizon; Kimura, Kohei; Numata, Mitsuru; Yamazoe, Atsushi; Kimbara, Kazuhide

    2015-12-01

    Ammonia inhibition of methane fermentation is one of the leading causes of failure of anaerobic digestion reactors. In a batch anaerobic digestion reactor with 429 mM NH3-N/L of ammonia, the addition of 25 mM phosphate resulted in an increase in methane production rate. Similar results were obtained with the addition of disodium phosphate in continuous anaerobic digestion using an upflow anaerobic sludge blanket (UASB) reactor. While methane content and production rate decreased in the presence of more than 143 mM NH3-N/L of ammonium chloride in UASB, the addition of 5 mM disodium phosphate suppressed ammonia inhibition at 214 mM NH3-N/L of ammonium chloride. The addition prevented acetate/propionate accumulation, which might be one of the effects of the phosphate on the ammonia inhibition. The effects on the microbial community in the UASB reactor was also assessed, which was composed of Bacteria involved in hydrolysis, acidogenesis, acetogenesis, and dehydrogenation, as well as Archaea carrying out methanogenesis. The change in the microbial community was observed by ammonia inhibition and the addition of phosphate. The change indicates that the suppression of ammonia inhibition by disodium phosphate addition could stimulate the activity of methanogens, reduce shift in bacterial community, and enhance hydrogen-producing bacteria. The addition of phosphate will be an important treatment for future studies of methane fermentation.

  18. Effects of Metal Nanoparticles on Methane Production from Waste-Activated Sludge and Microorganism Community Shift in Anaerobic Granular Sludge

    Science.gov (United States)

    Wang, Tao; Zhang, Dong; Dai, Lingling; Chen, Yinguang; Dai, Xiaohu

    2016-05-01

    Extensive use of nanoparticles (NPs) in consumer and industrial products has led to concerns about their potential environmental impacts; however, the influences of different NPs (e.g., nZVI (nano zero-valent iron), Ag NPs, Fe2O3 NPs and MgO NPs) on the anaerobic digestion of sludge have not yet been studied in depth. Additionally, a new guideline or the use of different NPs in the anaerobic digestion of sludge should be established to improve the anaerobic digestion of sludge and avoid inhibitory effects. This study investigated the effects of four representative NPs (i.e., nZVI, Ag NPs, Fe2O3 NPs and MgO NPs) on methane production during the anaerobic digestion of waste activated sludge (WAS). The presence of 10 mg/g total suspended solids (TSS) nZVI and 100 mg/g TSS Fe2O3 NPs increased methane production to 120% and 117% of the control, respectively, whereas 500 mg/g TSS Ag NPs and 500 mg/g TSS MgO NPs generated lower levels of methane production (73.52% and 1.08% that of the control, respectively). These results showed that low concentrations of nZVI and Fe2O3 NPs promoted the amount of microbes (Bacteria and Archaea) and activities of key enzymes but that higher concentrations of Ag NPs and MgO NPs inhibited them.

  19. Molecular analysis of the human faecal archaea in a southern Indian population

    Indian Academy of Sciences (India)

    SANDYA B RANI; RAMADASS BALAMURUGAN; BALAKRISHNAN S RAMAKRISHNA

    2017-03-01

    Archaea are an important constituent of the human gut microbiota, but there is no information on human gut archaea inan Indian population. In this study, faecal samples were obtained from different age groups (neonatal babies, preschoolchildren, school-going children, adolescents, adults and elderly) of a southern Indian population, and from atribal population also resident in southern India). 16S rRNA gene sequences specific to Archaea were amplified frompooled faecal DNA in each group, sequenced, and aligned against the NCBI database. Of the 806 adequate sequencesin the study, most aligned with 22 known sequences. There were 9 novel sequences in the present study. All sequenceswere deposited in the GenBank nucleotide sequence database with the following accession numbers: KF607113 -KF607918. Methanobrevibacter was the most prevalent genus among all the age groups accounting for 98% inneonates, 96% in post-weaning, and 100% each in preschool, school and adult population. In the elderly, Methanobrevibacteraccounted for 96% and in tribal adults, 99% of the clones belonged to Methanobrevibacter genus. Othergenera detected included Caldisphaera, Halobaculum, Methanosphaeraand Thermogymnomonas. Methanobrevibactersmithii predominated in all age groups, accounting for 749 (92.9%) of the 806 sequences. Archaea can befound in the faeces of southern Indian residents immediately after birth. Methanobrevibacter smithii was the dominantfaecal archeon in all age groups, with other genera being found at the extremes of age.

  20. Massive expansion of marine archaea during a mid-Cretaceous oceanic anoxic event

    DEFF Research Database (Denmark)

    Kuypers, M.M.M.; Blokker, P.; Erbacher, J.;

    2001-01-01

    Biogeochemical and stable carbon isotopic analysis of black-shale sequences deposited during an Albian oceanic anoxic event (∼112 million years ago) indicate that up to 80 weight percent of sedimentary organic carbon is derived from marine, nonthermophilic archaea. The carbon-13 content of archae...

  1. Murein and pseudomurein cell wall binding domains of bacteria and archaea-a comparative view

    NARCIS (Netherlands)

    Visweswaran, Ganesh Ram R.; Dijkstra, Bauke W.; Kok, Jan

    2011-01-01

    The cell wall, a major barrier protecting cells from their environment, is an essential compartment of both bacteria and archaea. It protects the organism from internal turgor pressure and gives a defined shape to the cell. The cell wall serves also as an anchoring surface for various proteins and a

  2. UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili

    NARCIS (Netherlands)

    Ajon, Malgorzata; Froels, Sabrina; van Wolferen, Marleen; Stoecker, Kilian; Teichmann, Daniela; Driessen, Arnold J. M.; Grogan, Dennis W.; Albers, Sonja-Verena; Schleper, Christa; Ajon, Małgorzata

    2011-01-01

    Archaea, like bacteria and eukaryotes, contain proteins involved in various mechanisms of DNA repair, highlighting the importance of these processes for all forms of life. Species of the order Sulfolobales of hyperthermophilic crenarchaeota are equipped with a strongly UV-inducible type IV pilus sys

  3. Analysis of putative nonulosonic acid biosynthesis pathways in Archaea reveals a complex evolutionary history.

    Science.gov (United States)

    Kandiba, Lina; Eichler, Jerry

    2013-08-01

    Sialic acids and the other nonulosonic acid sugars, legionaminic acid and pseudaminic acid, are nine carbon-containing sugars that can be detected as components of the glycans decorating proteins and other molecules in Eukarya and Bacteria. Yet, despite the prevalence of N-glycosylation in Archaea and the variety of sugars recruited for the archaeal version of this post-translational modification, only a single report of a nonulosonic acid sugar in an archaeal N-linked glycan has appeared. Hence, to obtain a clearer picture of nonulosonic acid sugar biosynthesis capability in Archaea, 122 sequenced genomes were scanned for the presence of genes involved in the biogenesis of these sugars. The results reveal that while Archaea and Bacteria share a common route of sialic acid biosynthesis, numerous archaeal nonulosonic acid sugar biosynthesis pathway components were acquired from elsewhere via various routes. Still, the limited number of Archaea encoding components involved in the synthesis of nonulosonic acid sugars implies that such saccharides are not major components of glycans in this domain.

  4. Role of multiprotein bridging factor 1 in archaea: bridging the domains?

    NARCIS (Netherlands)

    Koning, de B.; Blombach, F.; Wu Hao,; Brouns, S.J.J.; Oost, van der J.

    2009-01-01

    MBF1 (multiprotein bridging factor 1) is a highly conserved protein in archaea and eukaryotes. It was originally identified as a mediator of the eukaryotic transcription regulator BmFTZ-F1 (Bombyx mori regulator of fushi tarazu). MBF1 was demonstrated to enhance transcription by forming a bridge bet

  5. Bridging domains : a comparison between information processing in Archaea and Eukarya

    NARCIS (Netherlands)

    Koning, de B.

    2015-01-01

    Bridging Domains A Comparison between Information Processing in Archaea and Eukarya

    Studying Information Processing Living cells evolved complex systems to handle the flow of information both accurately and efficiently.

  6. A virus of hyperthermophilic archaea with a unique architecture among DNA viruses

    NARCIS (Netherlands)

    Rensen, E.I.; Mochizuki, T,; Quemin, E.R. J.; Schouten, S.; Krupovica, M.; Prangishvili, D.

    2016-01-01

    Viruses package their genetic material in diverse ways. Most known strategies include encapsulation of nucleic acids into spherical or filamentous virions with icosahedral or helical symmetry, respectively. Filamentous viruses with dsDNA genomes are currently associated exclusively with Archaea. Her

  7. Unique clusters of Archaea in Salar de Huasco, an athalassohaline evaporitic basin of the Chilean Altiplano.

    Science.gov (United States)

    Dorador, Cristina; Vila, Irma; Remonsellez, Francisco; Imhoff, Johannes F; Witzel, Karl-Paul

    2010-08-01

    Analyses of clone libraries from water and sediments of different sites from Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano, revealed the presence of five unique clusters of uncultured Archaea that have not been previously reported or specifically assigned. These sequences were distantly related (83-96% sequence identity) to a limited number of other clone sequences and revealed no identity to cultured Archaea. The abundance of Archaea and Bacteria was estimated using qPCR and community composition was examined through the construction of clone libraries of archaeal 16S rRNA gene. Archaea were found to be dominant over Bacteria in sediments from two saline sites (sites H4: 6.31 x 10(4) and site H6: 1.37 x 10(4) microS cm(-1)) and in one of the water samples (freshwater from site H0: 607 muS cm(-1)). Euryarchaeotal sequences were more abundant than crenarchaeotal sequences. Many of the clone sequences (52%) were similar to uncultured archaeal groups found in marine ecosystems having identity values between 99% and 97%. A major fraction of the sequences (40%) were members of Methanobacteria, while others were included in the Marine Benthic Groups B and D, the Miscellaneous Crenarchaeotic Group, the Terrestrial Miscellaneous Euryarchaeotal Group, Marine Group I and Halobacteria. The presence of uncultured archaeal groups in Salar de Huasco extends their known distribution in inland waters, providing new clues about their possible function in the environment.

  8. Diversity of membrane transport proteins for vitamins in bacteria and archaea

    NARCIS (Netherlands)

    Jähme, Michael; Slotboom, Dirk Jan

    2014-01-01

    BACKGROUND: All organisms use cofactors to extend the catalytic capacities of proteins. Many bacteria and archaea can synthesize cofactors from primary metabolites, but there are also prokaryotes that do not have the complete biosynthetic pathways for all essential cofactors. These organisms are dep

  9. A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea

    Science.gov (United States)

    Kono, Takunari; Mehrotra, Sandhya; Endo, Chikako; Kizu, Natsuko; Matusda, Mami; Kimura, Hiroyuki; Mizohata, Eiichi; Inoue, Tsuyoshi; Hasunuma, Tomohisa; Yokota, Akiho; Matsumura, Hiroyoshi; Ashida, Hiroki

    2017-01-01

    Two enzymes are considered to be unique to the photosynthetic Calvin–Benson cycle: ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for CO2 fixation, and phosphoribulokinase (PRK). Some archaea possess bona fide RuBisCOs, despite not being photosynthetic organisms, but are thought to lack PRK. Here we demonstrate the existence in methanogenic archaea of a carbon metabolic pathway involving RuBisCO and PRK, which we term ‘reductive hexulose-phosphate' (RHP) pathway. These archaea possess both RuBisCO and a catalytically active PRK whose crystal structure resembles that of photosynthetic bacterial PRK. Capillary electrophoresis-mass spectrometric analysis of metabolites reveals that the RHP pathway, which differs from the Calvin–Benson cycle only in a few steps, is active in vivo. Our work highlights evolutionary and functional links between RuBisCO-mediated carbon metabolic pathways in methanogenic archaea and photosynthetic organisms. Whether the RHP pathway allows for autotrophy (that is, growth exclusively with CO2 as carbon source) remains unknown. PMID:28082747

  10. Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea

    NARCIS (Netherlands)

    Kim, Jong-Geol; Park, Soo-Je; Sinninghe Damsté, Jaap S.; Schouten, Stefan; Rijpstra, W. Irene C.; Jung, Man-Young; Kim, So-Jeong; Gwak, Joo-Han; Hong, Heeji; Si, Ok-Ja; Lee, Sanghoon; Madsen, Eugene L.; Rhee, Sung-Keun

    2016-01-01

    Ammonia-oxidizing archaea (AOA), that is, members of the Thaumarchaeota phylum, occur ubiquitously in the environment and are of major significance for global nitrogen cycling. However, controls on cell growth and organic carbon assimilation by AOA are poorly understood. We isolated an ammonia-oxidi

  11. Evidence for a Xer/dif system for chromosome resolution in archaea.

    Directory of Open Access Journals (Sweden)

    Diego Cortez

    2010-10-01

    Full Text Available Homologous recombination events between circular chromosomes, occurring during or after replication, can generate dimers that need to be converted to monomers prior to their segregation at cell division. In Escherichia coli, chromosome dimers are converted to monomers by two paralogous site-specific tyrosine recombinases of the Xer family (XerC/D. The Xer recombinases act at a specific dif site located in the replication termination region, assisted by the cell division protein FtsK. This chromosome resolution system has been predicted in most Bacteria and further characterized for some species. Archaea have circular chromosomes and an active homologous recombination system and should therefore resolve chromosome dimers. Most archaea harbour a single homologue of bacterial XerC/D proteins (XerA, but not of FtsK. Therefore, the role of XerA in chromosome resolution was unclear. Here, we have identified dif-like sites in archaeal genomes by using a combination of modeling and comparative genomics approaches. These sites are systematically located in replication termination regions. We validated our in silico prediction by showing that the XerA protein of Pyrococcus abyssi specifically recombines plasmids containing the predicted dif site in vitro. In contrast to the bacterial system, XerA can recombine dif sites in the absence of protein partners. Whereas Archaea and Bacteria use a completely different set of proteins for chromosome replication, our data strongly suggest that XerA is most likely used for chromosome resolution in Archaea.

  12. 21 CFR 866.2120 - Anaerobic chamber.

    Science.gov (United States)

    2010-04-01

    ... and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2120 Anaerobic chamber. (a) Identification. An anaerobic chamber is a device intended for medical purposes to maintain an anaerobic...

  13. The phenomenon of granulation of anaerobic sludge.

    NARCIS (Netherlands)

    Hulshoff Pol, L.W.

    1989-01-01

    Successful high-rate anaerobic wastewater treatment can only be accomplished when the slowgrowing anaerobic biomass is efficiently held back in the anaerobic treatment system. This biomass retention can be achieved in various ways including immobilization of the organisms on fixed materials and immo

  14. Comparative Analysis of Methanogenic Communities in Different Laboratory-Scale Anaerobic Digesters

    Directory of Open Access Journals (Sweden)

    Ayrat M. Ziganshin

    2016-01-01

    Full Text Available Comparative analysis of methanogenic archaea compositions and dynamics in 11 laboratory-scale continuous stirred tank reactors fed with different agricultural materials (chicken manure, cattle manure, maize straw, maize silage, distillers grains, and Jatropha press cake was carried out by analysis of the methyl coenzyme-M reductase α-subunit (mcrA gene. Various taxa within Methanomicrobiales, Methanobacteriaceae, Methanosarcinaceae, Methanosaetaceae, and Methanomassiliicoccales were detected in the biogas reactors but in different proportions depending on the substrate type utilized as well as various process parameters. Improved coverage and higher taxonomic resolution of methanogens were obtained compared to a previous 16S rRNA gene based study of the same reactors. Some members of the genus Methanoculleus positively correlated with the relative methane content, whereas opposite correlations were found for Methanobacterium. Specific biogas production was found to be significantly correlating with Methanosarcinaceae. Statistical analysis also disclosed that some members of the genus Methanoculleus positively correlated with the ammonia level, whereas the prevalence of Methanocorpusculum, Methanobacterium, and Methanosaeta was negatively correlated with this parameter. These results suggest that the application of methanogenic archaea adapted to specific feedstock might enhance the anaerobic digestion of such waste materials in full-scale biogas reactors.

  15. Comparative Analysis of Methanogenic Communities in Different Laboratory-Scale Anaerobic Digesters

    Science.gov (United States)

    Ziganshin, Ayrat M.; Ziganshina, Elvira E.

    2016-01-01

    Comparative analysis of methanogenic archaea compositions and dynamics in 11 laboratory-scale continuous stirred tank reactors fed with different agricultural materials (chicken manure, cattle manure, maize straw, maize silage, distillers grains, and Jatropha press cake) was carried out by analysis of the methyl coenzyme-M reductase α-subunit (mcrA) gene. Various taxa within Methanomicrobiales, Methanobacteriaceae, Methanosarcinaceae, Methanosaetaceae, and Methanomassiliicoccales were detected in the biogas reactors but in different proportions depending on the substrate type utilized as well as various process parameters. Improved coverage and higher taxonomic resolution of methanogens were obtained compared to a previous 16S rRNA gene based study of the same reactors. Some members of the genus Methanoculleus positively correlated with the relative methane content, whereas opposite correlations were found for Methanobacterium. Specific biogas production was found to be significantly correlating with Methanosarcinaceae. Statistical analysis also disclosed that some members of the genus Methanoculleus positively correlated with the ammonia level, whereas the prevalence of Methanocorpusculum, Methanobacterium, and Methanosaeta was negatively correlated with this parameter. These results suggest that the application of methanogenic archaea adapted to specific feedstock might enhance the anaerobic digestion of such waste materials in full-scale biogas reactors. PMID:28074084

  16. Grappling archaea: ultrastructural analyses of an uncultivated, cold-loving archaeon and its biofilm

    Directory of Open Access Journals (Sweden)

    Alexandra ePerras

    2014-08-01

    Full Text Available Similarly to Bacteria, Archaea are microorganisms that interact with their surrounding environment in a versatile manner. To date, interactions based on cellular structure and surface appendages have mainly been documented using model systems of cultivable archaea under laboratory conditions. Here, we report on the microbial interactions and ultrastructural features of the uncultivated SM1 Euryarchaeon, which is highly dominant in its biotope. Therefore, biofilm samples taken from the Sippenauer Moor, Germany, were investigated via transmission electron microscopy (TEM; negative staining, thin-sectioning and scanning electron microscopy (SEM in order to elucidate the fine structures of the microbial cells and the biofilm itself. The biofilm consisted of small archaeal cocci (0.6 µm diameter, arranged in a regular pattern (1.2-2.0 µm distance from cell to cell, whereas each archaeon was connected to 6 other archaea on average. Extracellular polymeric substances (EPS were limited to the close vicinity of the archaeal cells, and specific cell surface appendages (hami, Moissl et al., 2005 protruded beyond the EPS matrix enabling microbial interaction by cell-cell contacts among the archaea and between archaea and bacteria. All analyzed hami revealed their previously described architecture of nano-grappling hooks and barb-wire basal structures. Considering the archaeal cell walls, the SM1 Euryarchaea exhibited a double-membrane, which has rarely been reported for members of this phylogenetic domain. Based on these findings, the current generalized picture on archaeal cell walls needs to be revisited, as archaeal cell structures are more complex and sophisticated than previously assumed, particularly when looking into the uncultivated majority.

  17. Community analysis of a full-scale anaerobic bioreactor treating paper mill wastewater.

    Science.gov (United States)

    Roest, Kees; Heilig, Hans G H J; Smidt, Hauke; de Vos, Willem M; Stams, Alfons J M; Akkermans, Antoon D L

    2005-03-01

    To get insight into the microbial community of an Upflow Anaerobic Sludge Blanket reactor treating paper mill wastewater, conventional microbiological methods were combined with 16S rRNA gene analyses. Particular attention was paid to microorganisms able to degrade propionate or butyrate in the presence or absence of sulphate. Serial enrichment dilutions allowed estimating the number of microorganisms per ml sludge that could use butyrate with or without sulphate (10(5)), propionate without sulphate (10(6)), or propionate and sulphate (10(8)). Quantitative RNA dot-blot hybridisation indicated that Archaea were two-times more abundant in the microbial community of anaerobic sludge than Bacteria. The microbial community composition was further characterised by 16S rRNA-gene-targeted Denaturing Gradient Gel Electrophoresis (DGGE) fingerprinting, and via cloning and sequencing of dominant amplicons from the bacterial and archaeal patterns. Most of the nearly full length (approximately 1.45 kb) bacterial 16S rRNA gene sequences showed less than 97% similarity to sequences present in public databases, in contrast to the archaeal clones (approximately. 1.3 kb) that were highly similar to known sequences. While Methanosaeta was found as the most abundant genus, also Crenarchaeote-relatives were identified. The microbial community was relatively stable over a period of 3 years (samples taken in July 1999, May 2001, March 2002 and June 2002) as indicated by the high similarity index calculated from DGGE profiles (81.9+/-2.7% for Bacteria and 75.1+/-3.1% for Archaea). 16S rRNA gene sequence analysis indicated the presence of unknown and yet uncultured microorganisms, but also showed that known sulphate-reducing bacteria and syntrophic fatty acid-oxidising microorganisms dominated the enrichments.

  18. Perspectives of Anaerobic Soil Disinfestation

    NARCIS (Netherlands)

    Lamers, J.G.; Runia, W.T.; Molendijk, L.P.G.; Bleeker, P.O.

    2010-01-01

    Biological soil disinfestation is an environmentally friendly method to disinfest soil. From now on we refer to it as anaerobic soil disinfestation (ASD). With ASD a green manure crop (40 t/ha) is homogeneously incorporated into the topsoil (0-30 cm) after which the field is lightly compacted and ir

  19. Methane oxidation in contrasting soil types

    DEFF Research Database (Denmark)

    D'Imperio, Ludovica; Nielsen, Cecilie Skov; Westergaard-Nielsen, Andreas

    2017-01-01

    Arctic ecosystems are characterized by a wide range of soil moisture conditions and thermal regimes and contribute differently to the net methane (CH4) budget. Yet, it is unclear how climate change will affect the capacity of those systems to act as a net source or sink of CH4. Here, we present...... subsequently scaled to the entire study area of 0.15 km2, a landscape also consisting of wetlands with a seasonally integrated methane release of 0.10 ± 0.01 g CH4-C m−2 (3.7 ± 1.2 g CO2-eq m−2). The result was a net landscape sink of 12.71 kg CH4-C (0.48 tonne CO2-eq) during the growing season...

  20. 'Methane oxidation on supported gold catalysts'

    DEFF Research Database (Denmark)

    Walther, Guido

    2008-01-01

    Methane (CH4), a major compound of natural gas, has been suggested as a future energy carrier. However, it is also known to be a strong greenhouse gas. The use of CH4 obtained from crude oil as an associated gas is often uneconomical, and it is thus burned off. Avoiding flaring and making...

  1. A new diet for methane oxidizers

    DEFF Research Database (Denmark)

    Rotaru, Amelia-Elena; Thamdrup, Bo

    2016-01-01

    Background Cancers of the liver, bile duct, gall bladder and pancreas (HPB-c) are a heterogeneous group, united almost exclusively by a poor prognosis. As the number of elderly in the Western world continues to rise and HPB-c are associated with age, we wanted to examine changes in incidence.......Conclusion As the number of persons aged 80 years or more will increase dramatically in the following years, and our results show a gap in relative survival, it is important to continue to study this population in order to improve management and outcome....

  2. Anaerobic granular sludge and biofilm reactors

    DEFF Research Database (Denmark)

    Skiadas, Ioannis V.; Gavala, Hariklia N.; Schmidt, Jens Ejbye

    2003-01-01

    by the immobilization of the biomass, which forms static biofilms, particle-supported biofilms, or granules depending on the reactor's operational conditions. The advantages of the high-rate anaerobic digestion over the conventional aerobic wastewater treatment methods has created a clear trend for the change......-rate anaerobic treatment systems based on anaerobic granular sludge and biofilm are described in this chapter. Emphasis is given to a) the Up-flow Anaerobic Sludge Blanket (UASB) systems, b) the main characteristics of the anaerobic granular sludge, and c) the factors that control the granulation process...

  3. The Sulfate-Rich and Extreme Saline Sediment of the Ephemeral Tirez Lagoon: A Biotope for Acetoclastic Sulfate-Reducing Bacteria and Hydrogenotrophic Methanogenic Archaea

    Directory of Open Access Journals (Sweden)

    Lilia Montoya

    2011-01-01

    Full Text Available Our goal was to examine the composition of methanogenic archaea (MA and sulfate-reducing (SRP and sulfur-oxidizing (SOP prokaryotes in the extreme athalassohaline and particularly sulfate-rich sediment of Tirez Lagoon (Spain. Thus, adenosine-5′-phosphosulfate (APS reductase α (aprA and methyl coenzyme M reductase α (mcrA gene markers were amplified given that both enzymes are specific for SRP, SOP, and MA, respectively. Anaerobic populations sampled at different depths in flooded and dry seasons from the anoxic sediment were compared qualitatively via denaturing gradient gel electrophoresis (DGGE fingerprint analysis. Phylogenetic analyses allowed the detection of SRP belonging to Desulfobacteraceae, Desulfohalobiaceae, and Peptococcaceae in ∂-proteobacteria and Firmicutes and SOP belonging to Chromatiales/Thiotrichales clade and Ectothiorhodospiraceae in γ-proteobacteria as well as MA belonging to methylotrophic species in Methanosarcinaceae and one hydrogenotrophic species in Methanomicrobiaceae. We also estimated amino acid composition, GC content, and preferential codon usage for the AprA and McrA sequences from halophiles, nonhalophiles, and Tirez phylotypes. Even though our results cannot be currently conclusive regarding the halotolerant strategies carried out by Tirez phylotypes, we discuss the possibility of a plausible “salt-in” signal in SRP and SOP as well as of a speculative complementary haloadaptation between salt-in and salt-out strategies in MA.

  4. Microbiological investigation of methane- and hydrocarbon-discharging mud volcanoes in the Carpathian Mountains, Romania.

    Science.gov (United States)

    Alain, Karine; Holler, Thomas; Musat, Florin; Elvert, Marcus; Treude, Tina; Krüger, Martin

    2006-04-01

    Paclele Mici is a terrestrial mud volcano field located in the Carpathian Mountains (Romania), where thermal alteration of sedimentary organic compounds leads to methane, higher hydrocarbons and other petroleum compounds that are continuously released into the environment. The hydrocarbons represent potential substrates for microorganisms. We studied lipid biomarkers, stable isotope ratios, the effect of substrate (methane, other organic compounds) addition and 16S rRNA genes to gain insights into the hitherto unknown microbial community at this site. Quantitative real-time polymerase chain reaction analysis demonstrated that bacteria were much more abundant than archaea. Phylogenetic analyses of 16S rDNA clone sequences indicated the presence of bacterial and archaeal lineages generally associated with the methane cycle (methanogens, aerobic and anaerobic methanotrophs), the sulfur cycle (sulfate reducers), and groups linked to the anaerobic degradation of alkanes or aromatic hydrocarbons. The presence of sulfate reducers, methanogens and methanotrophs in this habitat was also confirmed by concurrent surveys of lipid biomarkers and their isotopic signatures. Incubation experiments with several common and complex substrates revealed the potential of the indigenous microbial community for sulfate reduction, methanogenesis and aerobic methanotrophy. Additionally, consistently to the detection of methane-oxidizing archaea (ANME) and 13C-depleted archaeal lipids, a weak but significant activity of anaerobic methane oxidation was measured by radiotracer techniques and in vitro. This survey is the first to report the presence and activity of ANME in a terrestrial environment.

  5. A comprehensive study into the molecular methodology and molecular biology of methanogenic Archaea

    DEFF Research Database (Denmark)

    Lange, M.; Ahring, Birgitte Kiær

    2001-01-01

    Methanogens belong to the kingdom of Euryarchaeota in the domain of Archaea. The Archaea differ from Bacteria in many aspects important to molecular work. Among these are cell wall composition, their sensitivity to antibiotics, their translation and transcription machinery, and their very strict...... procedures. Efficient genetic manipulation systems, including shuttle and integration vector systems, have appeared for mesophilic, but not for thermophilic species within the last few years and will have a major impact on future investigations of methanogenic molecular biology....... complete methanogenic genomes have been sequenced and published and more are underway. Besides, sequences are known from a multitude of individual genes from methanogens. Standard methods for simple DNA and RNA work can normally be employed, but permeabilization of the cell wall may demand special...

  6. Lipid sugar carriers at the extremes: The phosphodolichols Archaea use in N-glycosylation.

    Science.gov (United States)

    Eichler, Jerry; Guan, Ziqiang

    2017-03-19

    N-glycosylation, a post-translational modification whereby glycans are covalently linked to select Asn residues of target proteins, occurs in all three domains of life. Across evolution, the N-linked glycans are initially assembled on phosphorylated cytoplasmically-oriented polyisoprenoids, with polyprenol (mainly C55 undecaprenol) fulfilling this role in Bacteria and dolichol assuming this function in Eukarya and Archaea. The eukaryal and archaeal versions of dolichol can, however, be distinguished on the basis of their length, degree of saturation and by other traits. As is true for many facets of their biology, Archaea, best known in their capacity as extremophiles, present unique approaches for synthesizing phosphodolichols. At the same time, general insight into the assembly and processing of glycan-bearing phosphodolichols has come from studies of the archaeal enzymes responsible. In this review, these and other aspects of archaeal phosphodolichol biology are addressed.

  7. Methanogenic Archaea and oral infections – ways to unravel the black box

    Directory of Open Access Journals (Sweden)

    Hans-Peter Horz

    2011-02-01

    Full Text Available Archaea, organisms that make up the third domain of cellular life are members of the human oral microflora. They are strikingly less diverse than oral bacteria and appear to be relatively rare with respect to their numerical abundance. Since they have been exclusively found in association with oral infections such as periodontitis and apical periodontitis and given their unique physiology and energy metabolism, it is highly plausible that they are more than just secondary colonizers of infected areas, but instead are actively involved in the overall poly-microbial infection process. Conversely, it is a highly challenging task to clearly demonstrate their possible active participation – mostly due to the difficulty to grow them in routine microbiology laboratories. This current review points out the importance for understanding the medical impact of methanogens and aims at devising strategies for elucidating the true function of archaea in the oral ecosystem.

  8. Glycosyltransferases and oligosaccharyltransferases in Archaea: putative components of the N-glycosylation pathway in the third domain of life.

    Science.gov (United States)

    Magidovich, Hilla; Eichler, Jerry

    2009-11-01

    The ability of Eukarya, Bacteria and Archaea to perform N-glycosylation underlies the importance and possible antiquity of this post-translational protein modification. However, in contrast to the relatively well-studied eukaryal and bacterial pathways, the archaeal N-glycosylation process is less understood. To remedy this disparity, the following study has examined 56 available archaeal genomes with the aim of identifying glycosyltransferases and oligosaccharyltransferases, including those putatively catalyzing this post-translational processing event. This analysis reveals that while oligosaccharyltransferases, central components of the N-glycosylation pathway, are found across the range of archaeal phenotypes, the N-glycosylation machinery of hyperthermophilic Archaea may well rely on fewer components than do the parallel systems of nonhyperthermophilic Archaea. Moreover, genes encoding predicted glycosyltransferases of hyperthermophilic Archaea tend to be far more scattered within the genome than is the case with nonhyperthermophilic species, where putative glycosyltransferase genes are often clustered around identified oligosaccharyltransferase-encoding sequences.

  9. Ammonia-oxidizing Bacteria and Archaea in the Rhizosphere of Freshwater Macrophytes

    DEFF Research Database (Denmark)

    Herrmann, Martina; Schramm, Andreas

    2007-01-01

    AMMONIA-OXIDIZING ARCHAEA AND BACTERIA IN THE RHIZOSPHERE OF FRESHWATER MACROPHYTES Martina Herrmann and Andreas Schramm Department of Biological Sciences, Microbiology, University of Aarhus, Denmark Aquatic macrophytes such as Littorella uniflora and Lobelia dortmanna release oxygen from...... their roots and thereby stimulate nitrification and coupled nitrification-denitrification in their rhizosphere. However, oxygen release and inorganic nitrogen concentrations differ markedly between macrophyte species. We therefore propose (i) that the rhizosphere of freshwater macrophytes harbours a species...

  10. Accurate Prediction of the Statistics of Repetitions in Random Sequences: A Case Study in Archaea Genomes.

    Science.gov (United States)

    Régnier, Mireille; Chassignet, Philippe

    2016-01-01

    Repetitive patterns in genomic sequences have a great biological significance and also algorithmic implications. Analytic combinatorics allow to derive formula for the expected length of repetitions in a random sequence. Asymptotic results, which generalize previous works on a binary alphabet, are easily computable. Simulations on random sequences show their accuracy. As an application, the sample case of Archaea genomes illustrates how biological sequences may differ from random sequences.

  11. A review of ammonia-oxidizing bacteria and archaea in Chinese soils

    OpenAIRE

    Ji-Zheng eHe; Ju-Pei eShen; Li-Mei eZhang; Hong J eDi

    2012-01-01

    Ammonia (NH3) oxidation, the first and rate-limiting step of nitrification, is a key step in the global Nitrogen (N) cycle. Major advances have been made in recent years in our knowledge and understanding of the microbial communities involved in ammonia oxidation in a wide range of habitats, including Chinese agricultural soils. In this mini-review, we focus our attention on the distribution and community diversity of ammonia-oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) in Chi...

  12. Post-translational Modification of Extremophilic Proteins: N-glycosylation in Archaea

    Science.gov (United States)

    2014-12-02

    Conference, Lucca, Italy 2013-Proteins: From birth to death. Jerusalem, Israel 2014-Meeting of the Korean Society for Microbiology and Biotechnology ...it all, trends in microbiology , (11 2012): 512. doi: 10.1016/j.tim.2012.08.007 J. Eichler, K. Jarrell, S. Albers. A proposal for the naming of N...Jerry Eichler. Extreme sweetness: protein glycosylation in archaea, Nature Reviews Microbiology , (01 2013): 151. doi: 10.1038/nrmicro2957 Lina

  13. Simple and convenient method for culturing anaerobic bacteria.

    OpenAIRE

    Behbehani, M J; Jordan, H. V.; Santoro, D L

    1982-01-01

    A simple and convenient method for culturing anaerobic bacteria is described. Cultures can be grown in commercially available flasks normally used for preparation of sterile external solutions. A special disposable rubber flask closure maintains anaerobic conditions in the flask after autoclaving. Growth of a variety of anaerobic oral bacteria was comparable to that obtained after anaerobic incubation of broth cultures in Brewer Anaerobic Jars.

  14. Phylogenetic diversity of Archaea in the intestinal tract of termites from different lineages.

    Science.gov (United States)

    Shi, Yu; Huang, Zhou; Han, Shuai; Fan, Shuo; Yang, Hong

    2015-08-01

    Termites are among the few arthropods that emit methane to the atmosphere, which is a significant source of global greenhouse gas due to their huge biomass on earth. In this study, phylogenetic diversity of Archaea of five termite species from different lineages were analyzed based on 16S rRNA genes. Archaea associated with wood-feeding lower termite, R. chinensis were exclusively Methanobrevibacter in the order Methanobacteriales. This type of methanogens was also found in Nasutitermes sp. and Microcerotermes sp. but not in the fungus-cultivating termites, Odontotermes formosanus and Macrotermes barneyi, which harbor Archaea of the order Methanoplasmatales and Methanosarcinales in their guts. Archaeal diversity of wood-feeding higher termites was higher than wood-feeding lower termites. The highest archaeal diversity was found in Nasutitermes sp. In addition to methanogens affiliated with the orders Methanobacteriales, Methanomicrobiales, and Methanoplasmatales, 37% of archaeal clones were affiliated with non-methanogenic Thaumarchaeota. The results of this study will be significant for further understanding of symbiotic relationship between intestinal microbiota and termites.

  15. Archaea-based microbial fuel cell operating at high ionic strength conditions.

    Science.gov (United States)

    Abrevaya, Ximena C; Sacco, Natalia; Mauas, Pablo J D; Cortón, Eduardo

    2011-11-01

    In this work, two archaea microorganisms (Haloferax volcanii and Natrialba magadii) used as biocatalyst at a microbial fuel cell (MFC) anode were evaluated. Both archaea are able to grow at high salt concentrations. By increasing the media conductivity, the internal resistance was diminished, improving the MFC's performance. Without any added redox mediator, maximum power (P (max)) and current at P (max) were 11.87/4.57/0.12 μW cm(-2) and 49.67/22.03/0.59 μA cm(-2) for H. volcanii, N. magadii and E. coli, respectively. When neutral red was used as the redox mediator, P (max) was 50.98 and 5.39 μW cm(-2) for H. volcanii and N. magadii, respectively. In this paper, an archaea MFC is described and compared with other MFC systems; the high salt concentration assayed here, comparable with that used in Pt-catalyzed alkaline hydrogen fuel cells, will open new options when MFC scaling up is the objective necessary for practical applications.

  16. Methane production and methanogenic Archaea in the digestive tracts of millipedes (Diplopoda.

    Directory of Open Access Journals (Sweden)

    Vladimír Šustr

    Full Text Available Methane production by intestinal methanogenic Archaea and their community structure were compared among phylogenetic lineages of millipedes. Tropical and temperate millipedes of 35 species and 17 families were investigated. Species that emitted methane were mostly in the juliform orders Julida, Spirobolida, and Spirostreptida. The irregular phylogenetic distribution of methane production correlated with the presence of the methanogen-specific mcrA gene. The study brings the first detailed survey of methanogens' diversity in the digestive tract of millipedes. Sequences related to Methanosarcinales, Methanobacteriales, Methanomicrobiales and some unclassified Archaea were detected using molecular profiling (DGGE. The differences in substrate preferences of the main lineages of methanogenic Archaea found in different millipede orders indicate that the composition of methanogen communities may reflect the differences in available substrates for methanogenesis or the presence of symbiotic protozoa in the digestive tract. We conclude that differences in methane production in the millipede gut reflect differences in the activity and proliferation of intestinal methanogens rather than an absolute inability of some millipede taxa to host methanogens. This inference was supported by the general presence of methanogenic activity in millipede faecal pellets and the presence of the 16S rRNA gene of methanogens in all tested taxa in the two main groups of millipedes, the Helminthophora and the Pentazonia.

  17. Methane production and methanogenic Archaea in the digestive tracts of millipedes (Diplopoda).

    Science.gov (United States)

    Šustr, Vladimír; Chroňáková, Alica; Semanová, Stanislava; Tajovský, Karel; Šimek, Miloslav

    2014-01-01

    Methane production by intestinal methanogenic Archaea and their community structure were compared among phylogenetic lineages of millipedes. Tropical and temperate millipedes of 35 species and 17 families were investigated. Species that emitted methane were mostly in the juliform orders Julida, Spirobolida, and Spirostreptida. The irregular phylogenetic distribution of methane production correlated with the presence of the methanogen-specific mcrA gene. The study brings the first detailed survey of methanogens' diversity in the digestive tract of millipedes. Sequences related to Methanosarcinales, Methanobacteriales, Methanomicrobiales and some unclassified Archaea were detected using molecular profiling (DGGE). The differences in substrate preferences of the main lineages of methanogenic Archaea found in different millipede orders indicate that the composition of methanogen communities may reflect the differences in available substrates for methanogenesis or the presence of symbiotic protozoa in the digestive tract. We conclude that differences in methane production in the millipede gut reflect differences in the activity and proliferation of intestinal methanogens rather than an absolute inability of some millipede taxa to host methanogens. This inference was supported by the general presence of methanogenic activity in millipede faecal pellets and the presence of the 16S rRNA gene of methanogens in all tested taxa in the two main groups of millipedes, the Helminthophora and the Pentazonia.

  18. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents.

    Directory of Open Access Journals (Sweden)

    Christian Hoffmann

    Full Text Available Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. Here we investigate associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool. For fungi, we found 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota. For archaea, Methanobrevibacter was the most prevalent genus, present in 30% of samples. Several other archaeal genera were detected in lower abundance and frequency. Myriad associations were detected for fungi and archaea with diet, with each other, and with bacterial lineages. Methanobrevibacter and Candida were positively associated with diets high in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids. A previous study emphasized that bacterial population structure was associated primarily with long-term diet, but high Candida abundance was most strongly associated with the recent consumption of carbohydrates. Methobrevibacter abundance was associated with both long term and recent consumption of carbohydrates. These results confirm earlier targeted studies and provide a host of new associations to consider in modeling the effects of diet on the gut microbiome and human health.

  19. Distribution of glutathione transferases in Gram-positive bacteria and Archaea.

    Science.gov (United States)

    Allocati, Nerino; Federici, Luca; Masulli, Michele; Di Ilio, Carmine

    2012-03-01

    Glutathione transferases (GSTs) have been widely studied in Gram-negative bacteria and the structure and function of several representatives have been elucidated. Conversely, limited information is available about the occurrence, classification and functional features of GSTs both in Gram-positive bacteria and in Archaea. An analysis of 305 fully-sequenced Gram-positive genomes highlights the presence of 49 putative GST genes in the genera of both Firmicutes and Actinobacteria phyla. We also performed an analysis on 81 complete genomes of the Archaea domain. Eleven hits were found in the Halobacteriaceae family of the Euryarchaeota phylum and only one in the Crenarchaeota phylum. A comparison of the identified sequences with well-characterized GSTs belonging to both Gram-negative and eukaryotic GSTs sheds light on their putative function and the evolutionary relationships within the large GST superfamily. This analysis suggests that the identified sequences mainly cluster in the new Xi class, while Beta class GSTs, widely distributed in Gram-negative bacteria, are under-represented in Gram-positive bacteria and absent in Archaea.

  20. A review of acquired thermotolerance, heat shock proteins, and molecular chaperones in archaea

    Energy Technology Data Exchange (ETDEWEB)

    Trent, J.D.

    1996-05-01

    Acquired thermotolerance, the associated synthesis of heat-shock proteins (HSPs) under stress conditions, and the role of HSPs as molecular chaperones under normal growth conditions have been studied extensively in eukaryotes and bacteria, whereas research in these areas in archaea is only beginning. All organisms have evolved a variety of strategies for coping with high-temperature stress, and among these strategies is the increased synthesis of HSPs. The facts that both high temperatures and chemical stresses induce the HSPs and that some of the HSPs recognize and bind to unfolded proteins in vitro have led to the theory that the function of HSPs is to prevent protein aggregation in vivo. The facts that some HSPs are abundant under normal growth conditions and that they assist in protein folding in vitro have led to the theory that they assist protein folding in vivo; in this role, they are referred to as molecular chaperones. The limited research on acquired thermotolerance, HSPs, and molecular chaperones in archaea, particularly the hyperthermophilic archaea, suggests that these extremophiles provide a new perspective in these areas of research, both because they are members of a separate phylogenetic domain and because they have evolved to live under extreme conditions.

  1. Anaerobic Growth of Haloarchaeon Haloferax volcanii by Denitrification Is Controlled by the Transcription Regulator NarO

    Science.gov (United States)

    Hattori, Tatsuya; Shiba, Hiromichi; Ashiki, Ken-ichi; Araki, Takuma; Nagashima, Yoh-kow; Yoshimatsu, Katsuhiko

    2016-01-01

    ABSTRACT The extremely halophilic archaeon Haloferax volcanii grows anaerobically by denitrification. A putative DNA-binding protein, NarO, is encoded upstream of the respiratory nitrate reductase gene of H. volcanii. Disruption of the narO gene resulted in a loss of denitrifying growth of H. volcanii, and the expression of the recombinant NarO recovered the denitrification capacity. A novel CXnCXCX7C motif showing no remarkable similarities with known sequences was conserved in the N terminus of the NarO homologous proteins found in the haloarchaea. Restoration of the denitrifying growth was not achieved by expression of any mutant NarO in which any one of the four conserved cysteines was individually replaced by serine. A promoter assay experiment indicated that the narO gene was usually transcribed, regardless of whether it was cultivated under aerobic or anaerobic conditions. Transcription of the genes encoding the denitrifying enzymes nitrate reductase and nitrite reductase was activated under anaerobic conditions. A putative cis element was identified in the promoter sequence of haloarchaeal denitrifying genes. These results demonstrated a significant effect of NarO, probably due to its oxygen-sensing function, on the transcriptional activation of haloarchaeal denitrifying genes. IMPORTANCE H. volcanii is an extremely halophilic archaeon capable of anaerobic growth by denitrification. The regulatory mechanism of denitrification has been well understood in bacteria but remains unknown in archaea. In this work, we show that the helix-turn-helix (HTH)-type regulator NarO activates transcription of the denitrifying genes of H. volcanii under anaerobic conditions. A novel cysteine-rich motif, which is critical for transcriptional regulation, is present in NarO. A putative cis element was also identified in the promoter sequence of the haloarchaeal denitrifying genes. PMID:26787768

  2. The key nickel enzyme of methanogenesis catalyses the anaerobic oxidation of methane.

    Science.gov (United States)

    Scheller, Silvan; Goenrich, Meike; Boecher, Reinhard; Thauer, Rudolf K; Jaun, Bernhard

    2010-06-03

    Large amounts (estimates range from 70 Tg per year to 300 Tg per year) of the potent greenhouse gas methane are oxidized to carbon dioxide in marine sediments by communities of methanotrophic archaea and sulphate-reducing bacteria, and thus are prevented from escaping into the atmosphere. Indirect evidence indicates that the anaerobic oxidation of methane might proceed as the reverse of archaeal methanogenesis from carbon dioxide with the nickel-containing methyl-coenzyme M reductase (MCR) as the methane-activating enzyme. However, experiments showing that MCR can catalyse the endergonic back reaction have been lacking. Here we report that purified MCR from Methanothermobacter marburgensis converts methane into methyl-coenzyme M under equilibrium conditions with apparent V(max) (maximum rate) and K(m) (Michaelis constant) values consistent with the observed in vivo kinetics of the anaerobic oxidation of methane with sulphate. This result supports the hypothesis of 'reverse methanogenesis' and is paramount to understanding the still-unknown mechanism of the last step of methanogenesis. The ability of MCR to cleave the particularly strong C-H bond of methane without the involvement of highly reactive oxygen-derived intermediates is directly relevant to catalytic C-H activation, currently an area of great interest in chemistry.

  3. Kinetic modelling and microbial community assessment of anaerobic biphasic fixed film bioreactor treating distillery spent wash.

    Science.gov (United States)

    Acharya, Bhavik K; Pathak, Hilor; Mohana, Sarayu; Shouche, Yogesh; Singh, Vasdev; Madamwar, Datta

    2011-08-01

    Anaerobic digestion, microbial community structure and kinetics were studied in a biphasic continuously fed, upflow anaerobic fixed film reactor treating high strength distillery wastewater. Treatment efficiency of the bioreactor was investigated at different hydraulic retention times (HRT) and organic loading rates (OLR 5-20 kg COD m⁻³ d⁻¹). Applying the modified Stover-Kincannon model to the reactor, the maximum removal rate constant (U(max)) and saturation value constant (K(B)) were found to be 2 kg m⁻³ d⁻¹ and 1.69 kg m⁻³ d⁻¹ respectively. Bacterial community structures of acidogenic and methanogenic reactors were assessed using culture-independent analyses. Sequencing of 16S rRNA genes exhibited a total of 123 distinct operational taxonomic units (OTUs) comprising 49 from acidogenic reactor and 74 (28 of eubacteria and 46 of archaea) from methanogenic reactor. The findings reveal the role of Lactobacillus sp. (Firmicutes) as dominant acid producing organisms in acidogenic reactor and Methanoculleus sp. (Euryarchaeotes) as foremost methanogens in methanogenic reactor.

  4. Influence of transitional states on the microbial ecology of anaerobic digesters treating solid wastes.

    Science.gov (United States)

    Regueiro, Leticia; Veiga, Patricia; Figueroa, Mónica; Lema, Juan M; Carballa, Marta

    2014-03-01

    A better understanding of the microbial ecology of anaerobic processes during transitional states is important to achieve a long-term efficient reactor operation. Five wastes (pig manure, biodiesel residues, ethanol stillage, molasses residues, and fish canning waste) were treated in five anaerobic reactors under the same operational conditions. The influence of the type of substrate and the effect of modifying feeding composition on the microbial community structure was evaluated. The highest biomethanation efficiency was observed in reactors fed with fish canning waste, which also presented the highest active archaeal population and the most diverse microbial communities. Only two Bacteria populations could be directly related to a particular substrate: Ilyobacter with biodiesel residues and Trichococcus with molasses residues. Results showed that the time to achieve steady-state performance after these transitional states was not dependent on the substrate treated. But reactors needed more time to handle the stress conditions derived from the start-up compared to the adaptation to a new feeding. Cluster analyses showed that the type of substrate had a clear influence on the microbiology of the reactors, and that segregation was related to the reactors performance. Finally, we conclude that the previous inoculum history treating solid waste and higher values of active Archaea population are important factors to face a successful change in substrate not entailing stability failure.

  5. Modelling Methane Production and Sulfate Reduction in Anaerobic Granular Sludge Reactor with Ethanol as Electron Donor

    Science.gov (United States)

    Sun, Jing; Dai, Xiaohu; Wang, Qilin; Pan, Yuting; Ni, Bing-Jie

    2016-10-01

    In this work, a mathematical model based on growth kinetics of microorganisms and substrates transportation through biofilms was developed to describe methane production and sulfate reduction with ethanol being a key electron donor. The model was calibrated and validated using experimental data from two case studies conducted in granule-based Upflow Anaerobic Sludge Blanket reactors. The results suggest that the developed model could satisfactorily describe methane and sulfide productions as well as ethanol and sulfate removals in both systems. The modeling results reveal a stratified distribution of methanogenic archaea, sulfate-reducing bacteria and fermentative bacteria in the anaerobic granular sludge and the relative abundances of these microorganisms vary with substrate concentrations. It also indicates sulfate-reducing bacteria can successfully outcompete fermentative bacteria for ethanol utilization when COD/SO42‑ ratio reaches 0.5. Model simulation suggests that an optimal granule diameter for the maximum methane production efficiency can be achieved while the sulfate reduction efficiency is not significantly affected by variation in granule size. It also indicates that the methane production and sulfate reduction can be affected by ethanol and sulfate loading rates, and the microbial community development stage in the reactor, which provided comprehensive insights into the system for its practical operation.

  6. Molecular ecology of anaerobic reactor systems

    DEFF Research Database (Denmark)

    Hofman-Bang, H. Jacob Peider; Zheng, D.; Westermann, Peter;

    2003-01-01

    Anaerobic reactor systems are essential for the treatment of solid and liquid wastes and constitute a core facility in many waste treatment plants. Although much is known about the basic metabolism in different types of anaerobic reactors, little is known about the microbes responsible...... to the abundance of each microbe in anaerobic reactor systems by rRNA probing. This chapter focuses on various molecular techniques employed and problems encountered when elucidating the microbial ecology of anaerobic reactor systems. Methods such as quantitative dot blot/fluorescence in-situ probing using various...

  7. Evaluation of a prereduced anaerobically sterilized medium (PRAS II) system for identification anaerobic microorganisms.

    Science.gov (United States)

    Beaucage, C M; Onderdonk, A B

    1982-09-01

    A prereduced, anaerobically sterilized system of tubed media (PRAS II; Scott Laboratories, Fiskeville, R.I.) was evaluated for accuracy in the identification of anerobic microorganisms. PRAS II was found to be a rapid and accurate identification system for obligate anaerobes which does not require the use of gas cannula inoculation or incubation in a special anaerobic environment.

  8. Evaluation of a prereduced anaerobically sterilized medium (PRAS II) system for identification anaerobic microorganisms.

    OpenAIRE

    Beaucage, C M; Onderdonk, A B

    1982-01-01

    A prereduced, anaerobically sterilized system of tubed media (PRAS II; Scott Laboratories, Fiskeville, R.I.) was evaluated for accuracy in the identification of anerobic microorganisms. PRAS II was found to be a rapid and accurate identification system for obligate anaerobes which does not require the use of gas cannula inoculation or incubation in a special anaerobic environment.

  9. Effects of Cd(II) and Cu(II) on microbial characteristics in 2-chlorophenol-degradation anaerobic bioreactors

    Institute of Scientific and Technical Information of China (English)

    HUANG Aiqun; CHEN Hao; CHEN Ling; DAI Yalei; ZHAO Jianfu

    2008-01-01

    The effects of Cd2+ and CU2+ at 300 mg/L on anaerobic microbial communities that degrade 2.cholorophenol(2-CP) were examined. Based on the polymerase chain reaction (PCR) of 16S rDNA, bacterial community diversity and archaeal community structure were analyzed with denaturing gradient gel electrophoresis (DGGE) and cloning,respectively.Degradation capabilities of the anaerobic microbial community were drastically abated and the degradation efficiency of 2-CP was reduced to 60%after shock by Cu2+ and Cd2+, respectively.The bacterial community structure was disturbed and the biodiversity Was reduced after shock by Cu2+ and Cdz+ for 3 d.Some new metal-resistant microbes which could cope with the new condition appeared.The sequence analysis showed that there existed common Archaea species in control sludge and systems when treated with Cu2+ and Cd2+, such as Methanothrix soehngenii,Methanosaeta concilii,uncultured euryarchaeote, and so on.Both the abundance and diversity of archaeal species were altered with addition of Cd2+ and Cu2+ at high concentration.AIthough the abundance of the predominant archaeal species decreased wim Cd2+ and Cu2+ addition for 3 d.tIley recovered to some extent after 10 d.The diversity of archaeal species Was remarkably reduced after recovery for 10 d and the shift in archaeal composition seemed to be irreversible.The 2-CP-degradation anaerobic system was more sensitive to Cu2+ than Cd2+.

  10. Geochemistry and Mixing Drive the Spatial Distribution of Free-living Archaea and Bacteria in Yellowstone Lake

    Directory of Open Access Journals (Sweden)

    Jinjun eKan

    2016-02-01

    Full Text Available Yellowstone Lake, the largest subalpine lake in the United States, harbors great novelty and diversity of Bacteria and Archaea. Size-fractionated water samples (0.1-0.8 µm, 0.8-3.0 µm, and 3.0-20 µm were collected from surface photic zone, deep mixing zone, and vent fluids at different locations in the lake by using a remotely operated vehicle (ROV. Quantification with real-time PCR indicated that Bacteria dominated free-living microorganisms with Bacteria/Archaea ratios ranging from 4037:1 (surface water to 25:1 (vent water. Microbial population structures (both Bacteria and Archaea were assessed using 454-FLX sequencing with a total of 662,302 pyrosequencing reads for V1 & V2 regions of 16S rRNA genes. Nonmetric multidimensional scaling (NMDS analyses indicated that strong spatial distribution patterns existed from surface to deep vents for free-living Archaea and Bacteria in the Lake. Along with pH, major vent-associated geochemical constituents including CH4, CO2, H2, DIC (dissolved inorganic carbon, DOC (dissolved organic carbon, SO42-, O2 and metals were likely the major drivers for microbial population structures, however mixing events occurring in the lake also impacted the distribution patterns. Distinct Bacteria and Archaea were present among size fractions, and bigger size fractions included particle-associated microbes (>3 µm and contained higher predicted OTU richness and microbial diversities (genus level than free-living ones (< 0.8 µm. Our study represents the first attempt at addressing the spatial distribution of Bacteria and Archaea in Yellowstone Lake, and our results highlight the variable contribution of Archaea and Bacteria to the hydrogeochemical-relevant metabolism of hydrogen, carbon, nitrogen, and sulfur.

  11. Effects of titanium dioxide and zinc oxide nanoparticles on methane production from anaerobic co-digestion of primary and excess sludge.

    Science.gov (United States)

    Zheng, Xiong; Wu, Lijuan; Chen, Yinguang; Su, Yinglong; Wan, Rui; Liu, Kun; Huang, Haining

    2015-01-01

    Anaerobic co-digestion of primary and excess sludge is regarded as an efficient way to reuse sludge organic matter to produce methane. In this study, short-term and long-term exposure experiments were conducted to investigate the possible effects of titanium dioxide (TiO2) and zinc oxide (ZnO) nanoparticles (NPs) on methane production from anaerobic co-digestion of primary and excess sludge. The data showed that TiO2 NPs had no measurable impact on methane production, even at a high concentration (150 mg/g total suspended solids (TSS)). However, short-term (8 days) exposure to 30 or 150 mg/g-TSS of ZnO NPs significantly decreased methane production. More importantly, these negative effects of ZnO NPs on anaerobic sludge co-digestion were not alleviated by increasing the adaptation time to 105 days. Further studies indicated that the presence of ZnO NPs substantially decreased the abundance of methanogenic archaea, which reduced methane production. Meanwhile, the activities of some key enzymes involved in methane production, such as protease, acetate kinase, and coenzyme F420, were remarkably inhibited by the presence of ZnO NPs, which was also an important reason for the decreased methane production. These results provide a better understanding of the potential risks of TiO2 and ZnO NPs to methane production from anaerobic sludge co-digestion.

  12. Carbon monoxide conversion by anaerobic bioreactor sludges

    NARCIS (Netherlands)

    Sipma, J.; Stams, A.J.M.; Lens, P.N.L.; Lettinga, G.

    2003-01-01

    Seven different anaerobic sludges from wastewater treatment reactors were screened for their ability to convert carbon monoxide (CO) at 30 and 55degreesC
    Seven different anaerobic sludges from wastewater treatment reactors were screened for their ability to convert carbon monoxide (CO) at 30 and

  13. Anaerobic critical velocity in four swimming techniques.

    Science.gov (United States)

    Neiva, H P; Fernandes, R J; Vilas-Boas, J P

    2011-03-01

    The aim of this study was to assess critical velocity in order to control and evaluate anaerobic swimming training. 51 highly trained male swimmers performed maximal 15, 25, 37.5 and 50 m in the 4 swimming techniques to determine critical velocity from the distance-time relationship. Anaerobic critical velocity was compared with 100 m swimming performance and corresponding partials. Complementarily, 9 swimmers performed a 6×50 m (4 min interval) training series at front crawl individual anaerobic critical velocity, capillary blood lactate concentrations being assessed after each repetition. The mean±SD values of anaerobic critical velocity and its relationship with the 100 m event were: 1.61±0.07 (r=0.60, p=0.037), 1.53±0.05 (r=0.81, p=0.015), 1.33±0.05 (r=0.83, p=0.002), and 1.75±0.05 (r=0.74, p=0.001), for butterfly, backstroke, breaststroke and front crawl, respectively. However, differences between anaerobic critical velocity and performance were observed (with exception of the second half of the 100 m swimming events in breaststroke and butterfly). Lactate concentration values at the end of the series were 14.52±1.06 mmol.l (-1), which suggests that it was indeed an anaerobic training set. In this sense, anaerobic critical velocity can be used to prescribe anaerobic training intensities.

  14. Integrated anaerobic and aerobic treatment of sewage.

    NARCIS (Netherlands)

    Kaijun Wang,

    1994-01-01

    This thesis describes results of investigations dealing with sequential concept of anaerobic-aerobic treatment of municipal wastewater. The main purposes of the study were 1) to develop a proper anaerobic hydrolytic pretreatment unit, consisting of a Hydrolysis Upflow Sludge Bed (HUSB-) reactor and

  15. Anaerobic degradation of linear alkylbenzene sulfonate

    DEFF Research Database (Denmark)

    Mogensen, Anders Skibsted; Haagensen, Frank; Ahring, Birgitte Kiær

    2003-01-01

    increases during anaerobic stabilization due to transformation of easily degradable organic matter. Hence, LAS is regarded as resistant to biodegradation under anaerobic conditions. We present data from a lab-scale semi-continuously stirred tank reactor (CSTR) spiked with linear dodecylbenzene sulfonate (C...

  16. Prospects of Anaerobic Digestion Technology in China

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    As the world's largest developing country, China must face the problem of managing municipal solid waste, and the challenge of organic waste disposal is even more serious. Considering the characteristics of traditional waste disposal technologies and the subsequent secondary pollution, anaerobic digestion has various advantages such as reduction in the land needed for disposal and preservation of environmental quality. In light of the energy crisis, this paper focuses on the potential production of biogas from biowaste through anaerobic digestion processes, the problems incurred by the waste collection system, and the efficiency of the anaerobic digestion process. Use of biogas in a combined heat and power cogeneration system is also discussed. Finally, the advantages of anaerobic digestion technology for the Chinese market are summarized. The anaerobic digestion is suggested to be a promising treating technology for the organic wastes in China.

  17. Toxicants inhibiting anaerobic digestion: a review.

    Science.gov (United States)

    Chen, Jian Lin; Ortiz, Raphael; Steele, Terry W J; Stuckey, David C

    2014-12-01

    Anaerobic digestion is increasingly being used to treat wastes from many sources because of its manifold advantages over aerobic treatment, e.g. low sludge production and low energy requirements. However, anaerobic digestion is sensitive to toxicants, and a wide range of compounds can inhibit the process and cause upset or failure. Substantial research has been carried out over the years to identify specific inhibitors/toxicants, and their mechanism of toxicity in anaerobic digestion. In this review we present a detailed and critical summary of research on the inhibition of anaerobic processes by specific organic toxicants (e.g., chlorophenols, halogenated aliphatics and long chain fatty acids), inorganic toxicants (e.g., ammonia, sulfide and heavy metals) and in particular, nanomaterials, focusing on the mechanism of their inhibition/toxicity. A better understanding of the fundamental mechanisms behind inhibition/toxicity will enhance the wider application of anaerobic digestion.

  18. Public aquaria as long-term enrichments for investigating planktonic Archaea

    Science.gov (United States)

    Goldenstein, Nadine I.; Warren, Courtney E.; Lipp, Julius S.; Pagani, Mark; Hinrichs, Kai-Uwe

    2016-04-01

    The most abundant group of planktonic Archaea , the so-called Thaumarchaeota, represents 20% of all marine planktonic microorganisms (Karner et al., 2001) and their energy efficient performance of nitrification makes them key players in the global nitrogen- and carbon-cycle (Könneke et al., 2014). Furthermore, planktonic Archaea are considered to be the major producers of specific microbial membrane lipids that are extensively used as paleoproxies in marine climate research (Schouten et al., 2002). Therefore, assessing the parameters controlling the distribution of Archaea in the marine water column is crucial for studies of modern and past marine environments. Although diverse studies utilizing DNA- and biomarker-based approaches have constrained the turnover and distribution of marine Archaea, the environmental factors affecting their abundance and activity (e.g., Wuchter et al., 2006; Bale et al., 2013) are still poorly understood. Further, previous surveys, using enrichment cultivation and pure culture experiments, provided valuable information on adaptation of planktonic Archaea to changes of parameters affecting growth conditions, such as temperature, salinity and growth stage (Elling et al., 2014, 2015). Hence, we know that planktonic Archaea directly adapt their membranes to changing growth conditions, but also that environmental selection for individual phylogenetic groups of these organisms is also reflected in the membrane lipid pool. Extending these studies, this project further aims at constraining the environmental parameters controlling archaeal abundance in the marine environment. Public aquaria, which are comparable to perfectly monitored long-term enrichment cultures, are optimal sampling sites for this task. A comprehensive set of 120 water and substrate samples from fresh, marine and brackish systems exhibiting diverse conditions was selected from 15 public aquaria at the east and west coast of the USA. These samples were examined for their

  19. Rooting the domain archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota.

    Science.gov (United States)

    Petitjean, Céline; Deschamps, Philippe; López-García, Purificación; Moreira, David

    2014-12-19

    The first 16S rRNA-based phylogenies of the Archaea showed a deep division between two groups, the kingdoms Euryarchaeota and Crenarchaeota. This bipartite classification has been challenged by the recent discovery of new deeply branching lineages (e.g., Thaumarchaeota, Aigarchaeota, Nanoarchaeota, Korarchaeota, Parvarchaeota, Aenigmarchaeota, Diapherotrites, and Nanohaloarchaeota) which have also been given the same taxonomic status of kingdoms. However, the phylogenetic position of some of these lineages is controversial. In addition, phylogenetic analyses of the Archaea have often been carried out without outgroup sequences, making it difficult to determine if these taxa actually define lineages at the same level as the Euryarchaeota and Crenarchaeota. We have addressed the question of the position of the root of the Archaea by reconstructing rooted archaeal phylogenetic trees using bacterial sequences as outgroup. These trees were based on commonly used conserved protein markers (32 ribosomal proteins) as well as on 38 new markers identified through phylogenomic analysis. We thus gathered a total of 70 conserved markers that we analyzed as a concatenated data set. In contrast with previous analyses, our trees consistently placed the root of the archaeal tree between the Euryarchaeota (including the Nanoarchaeota and other fast-evolving lineages) and the rest of archaeal species, which we propose to class within the new kingdom Proteoarchaeota. This implies the relegation of several groups previously classified as kingdoms (e.g., Crenarchaeota, Thaumarchaeota, Aigarchaeota, and Korarchaeota) to a lower taxonomic rank. In addition to taxonomic implications, this profound reorganization of the archaeal phylogeny has also consequences on our appraisal of the nature of the last archaeal ancestor, which most likely was a complex organism with a gene-rich genome.

  20. Chromosome segregation in Archaea mediated by a hybrid DNA partition machine.

    Science.gov (United States)

    Kalliomaa-Sanford, Anne K; Rodriguez-Castañeda, Fernando A; McLeod, Brett N; Latorre-Roselló, Victor; Smith, Jasmine H; Reimann, Julia; Albers, Sonja V; Barillà, Daniela

    2012-03-06

    Eukarya and, more recently, some bacteria have been shown to rely on a cytoskeleton-based apparatus to drive chromosome segregation. In contrast, the factors and mechanisms underpinning this fundamental process are underexplored in archaea, the third domain of life. Here we establish that the archaeon Sulfolobus solfataricus harbors a hybrid segrosome consisting of two interacting proteins, SegA and SegB, that play a key role in genome segregation in this organism. SegA is an ortholog of bacterial, Walker-type ParA proteins, whereas SegB is an archaea-specific factor lacking sequence identity to either eukaryotic or bacterial proteins, but sharing homology with a cluster of uncharacterized factors conserved in both crenarchaea and euryarchaea, the two major archaeal sub-phyla. We show that SegA is an ATPase that polymerizes in vitro and that SegB is a site-specific DNA-binding protein contacting palindromic sequences located upstream of the segAB cassette. SegB interacts with SegA in the presence of nucleotides and dramatically affects its polymerization dynamics. Our data demonstrate that SegB strongly stimulates SegA polymerization, possibly by promoting SegA nucleation and accelerating polymer growth. Increased expression levels of segAB resulted in severe growth and chromosome segregation defects, including formation of anucleate cells, compact nucleoids confined to one half of the cell compartment and fragmented nucleoids. The overall picture emerging from our findings indicates that the SegAB complex fulfills a crucial function in chromosome segregation and is the prototype of a DNA partition machine widespread across archaea.

  1. Possible energetic linkage between primary production and deep-sea benthic archaea: insight from biogeochemical lipidomics

    Science.gov (United States)

    Takano, Yoshinori; Ohkouchi, Naohiko

    2013-04-01

    Marine archaea have been recognized as a cosmopolitan player for global carbon and nitrogen cycles in the water column and sub-seafloor environments. Recent molecular evidence based on lipids and DNA suggests that uncultured benthic archaea dominate biomass in marine sediment, implying past primary production is a crucial factor for their presently ongoing heterotrophy (e.g., 1-4). Focusing on benthic archaeal heterotrophic processes in deep-sea sediment, we preliminarily traced 13C-signature in archaeal lipids to determine de novo and salvage pathway by in situ 13C-experiment. On the basis of the differential 13C-uptake, we suggest that benthic archaea recycles sedimentary relic membrane lipids to minimize the energy expenditure during 405 days (5). The 16S rRNA and quantitative PCR analysis indicated a community shift in the composition of the benthic archaeal community (e.g., Marine Group I, Marine Benthic Group, Miscellaneous Crenarchaeotic Group). In bacteria and eukarya, it is commonly recognized that free fatty acids are incorporated into cells and converted to acyl-CoA, which are eventually incorporated into membrane lipids as a salvage pathway (cf. 6). Considering the suggestion of salvage pathway in archaeal membrane synthesis (7,8), we discuss archaeal heterotrophic processes in terms of possible biogeochemical lipidomics. Reference [1] Biddle et al., (2006) PNAS, 103, 3846-3851. [2] Lipp et al., (2008) Nature, 454, 991-994. [3] Kallmeyer et al., (2012) PNAS, doi: 10.1073/pnas.1203849109 [4] Hinrichs and Inagaki, (2012) Science, 338, 204-205. [5] Takano et al., (2010) Nature Geosci., 3, 858-861. [6] Silbert et al., (1968) J Bacteriol., 95, 1658-1665. [7] Poulter et al., (1988) JACS, 110, 2620-2624. [8] Ohnuma et al., (1996) J Biochem., 119, 541-547.

  2. Higher-level classification of the Archaea: evolution of methanogenesis and methanogens

    Directory of Open Access Journals (Sweden)

    Éric Bapteste

    2005-01-01

    Full Text Available We used a phylogenetic approach to analyze the evolution of methanogenesis and methanogens. We show that 23 vertically transmitted ribosomal proteins do not support the monophyly of methanogens, and propose instead that there are two distantly related groups of extant archaea that produce methane, which we have named Class I and Class II. Based on this finding, we subsequently investigated the uniqueness of the origin of methanogenesis by studying both the enzymes of methanogenesis and the proteins that synthesize its specific coenzymes. We conclude that hydrogenotrophic methanogenesis appeared only once during evolution. Genes involved in the seven central steps of the methanogenic reduction of carbon dioxide (CO2 are ubiquitous in methanogens and share a common history. This suggests that, although extant methanogens produce methane from various substrates (CO2, formate, acetate, methylated C-1 compounds, these archaea have a core of conserved enzymes that have undergone little evolutionary change. Furthermore, this core of methanogenesis enzymes seems to originate (as a whole from the last ancestor of all methanogens and does not appear to have been horizontally transmitted to other organisms or between members of Class I and Class II. The observation of a unique and ancestral form of methanogenesis suggests that it was preserved in two independent lineages, with some instances of specialization or added metabolic flexibility. It was likely lost in the Halobacteriales, Thermoplasmatales and Archaeoglobales. Given that fossil evidence for methanogenesis dates back 2.8 billion years, a unique origin of this process makes the methanogenic archaea a very ancient taxon.

  3. Overcoming organic and nitrogen overload in thermophilic anaerobic digestion of pig slurry by coupling a microbial electrolysis cell.

    Science.gov (United States)

    Cerrillo, Míriam; Viñas, Marc; Bonmatí, August

    2016-09-01

    The combination of the anaerobic digestion (AD) process with a microbial electrolysis cell (MEC) coupled to an ammonia stripping unit as a post-treatment was assessed both in series operation, to improve the quality of the effluent, and in loop configuration recirculating the effluent, to increase the AD robustness. The MEC allowed maintaining the chemical oxygen demand removal of the whole system of 46±5% despite the AD destabilization after doubling the organic and nitrogen loads, while recovering 40±3% of ammonia. The AD-MEC system, in loop configuration, helped to recover the AD (55% increase in methane productivity) and attained a more stable and robust operation. The microbial population assessment revealed an enhancement of AD methanogenic archaea numbers and a shift in eubacterial population. The AD-MEC combined system is a promising strategy for stabilizing AD against organic and nitrogen overloads, while improving the quality of the effluent and recovering nutrients for their reutilization.

  4. Complete genome sequence of the bile-resistant pigment- producing anaerobe Alistipes finegoldii type strain (AHN2437T)

    Energy Technology Data Exchange (ETDEWEB)

    Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Stackebrandt, Erko [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Munk, Christine [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Gronow, Sabine [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute

    2013-01-01

    Alistipes finegoldii Rautio et al. 2003 is one of five species of Alistipes with a validly pub- lished name: family Rikenellaceae, order Bacteroidetes, class Bacteroidia, phylum Bacteroidetes. This rod-shaped and strictly anaerobic organism has been isolated mostly from human tissues. Here we describe the features of the type strain of this species, together with the complete genome sequence, and annotation. A. finegoldii is the first member of the genus Alistipes for which the complete genome sequence of its type strain is now available. The 3,734,239 bp long single replicon genome with its 3,302 protein-coding and 68 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  5. Relation between methanogenic archaea and methane production potential in selected natural wetland ecosystems across China

    Science.gov (United States)

    Liu, D. Y.; Ding, W. X.; Jia, Z. J.; Cai, Z. C.

    2011-02-01

    Methane (CH4) emissions from natural wetland ecosystems exhibit large spatial variability at regional, national, and global levels related to temperature, water table, plant type and methanogenic archaea etc. To understand the underlying factors that induce spatial differences in CH4 emissions, and the relationship between the population of methanogenic archaea and CH4 production potential in natural wetlands around China, we measured the CH4 production potential and the abundance of methanogenic archaea in vertical soil profiles sampled from the Poyang wetland in the subtropical zone, the Hongze wetland in the warm temperate zone, the Sanjiang marsh in the cold temperate zone, and the Ruoergai peatland in the Qinghai-Tibetan Plateau in the alpine climate zone. The top soil layer had the highest population of methanogens (1.07-8.29 × 109 cells g-1 soil) in all wetlands except the Ruoergai peatland and exhibited the maximum CH4 production potential measured at the mean in situ summer temperature. There is a significant logarithmic correlation between the abundance of methanogenic archaea and the soil organic carbon (R2 = 0.72, P nitrogen concentrations (R2 = 0.76, P affect the population of methanogens in wetland ecosystems. While the CH4 production potential is not significantly related to methanogen population (R2 = 0.01, P > 0.05, n = 13), it is related to the dissolved organic carbon concentration (R2 = 0.31, P = 0.05, n = 13). This suggests that the methanogen population might be not an effective index for predicting the CH4 production in wetland ecosystems. The CH4 production rate of the top soil layer increases with increasing latitude, from 273.64 μg CH4 kg-1 soil d-1 in the Poyang wetland to 664.59 μg CH4 kg-1 soil d-1 in the Carex lasiocarpa marsh of the Sanjiang Plain. We conclude that CH4 production potential in the freshwater wetlands of Eastern China is mainly affected by the supply of methanogenic substrates rather than temperature; in contrast

  6. Identification of Archaea-specific chemotaxis proteins which interact with the flagellar apparatus

    Directory of Open Access Journals (Sweden)

    Müller Judith

    2009-03-01

    Full Text Available Abstract Background Archaea share with bacteria the ability to bias their movement towards more favorable locations, a process known as taxis. Two molecular systems drive this process: the motility apparatus and the chemotaxis signal transduction system. The first consists of the flagellum, the flagellar motor, and its switch, which allows cells to reverse the rotation of flagella. The second targets the flagellar motor switch in order to modulate the switching frequency in response to external stimuli. While the signal transduction system is conserved throughout archaea and bacteria, the archaeal flagellar apparatus is different from the bacterial one. The proteins constituting the flagellar motor and its switch in archaea have not yet been identified, and the connection between the bacterial-like chemotaxis signal transduction system and the archaeal motility apparatus is unknown. Results Using protein-protein interaction analysis, we have identified three proteins in Halobacterium salinarum that interact with the chemotaxis (Che proteins CheY, CheD, and CheC2, as well as the flagella accessory (Fla proteins FlaCE and FlaD. Two of the proteins belong to the protein family DUF439, the third is a HEAT_PBS family protein. In-frame deletion strains for all three proteins were generated and analyzed as follows: a photophobic responses were measured by a computer-based cell tracking system b flagellar rotational bias was determined by dark-field microscopy, and c chemotactic behavior was analyzed by a swarm plate assay. Strains deleted for the HEAT_PBS protein or one of the DUF439 proteins proved unable to switch the direction of flagellar rotation. In these mutants, flagella rotate only clockwise, resulting in exclusively forward swimming cells that are unable to respond to tactic signals. Deletion of the second DUF439 protein had only minimal effects. HEAT_PBS proteins could be identified in the chemotaxis gene regions of all motile haloarchaea

  7. Diversity of bacteria and archaea from a landfill in Chandigarh, India as revealed by culture-dependent and culture-independent molecular approaches.

    Science.gov (United States)

    Krishnamurthi, S; Chakrabarti, T

    2013-02-01

    The bacterial community structure of a municipal landfill in Chandigarh, India was analysed by culture-dependent as well as culture-independent molecular approaches, and archaeal structure by the latter method. Samples were collected in two phases from the surface and a depth of 0.91 m in June, 2004 and from 0.91 m, 1.52 m and 1.68 m in May, 2005. After serial dilutions, samples were plated onto tryptic soy agar (TSA), plate count agar (PCA), tryptic soy broth agar (TSBA) and TSBA100 (TSBA diluted 100 times and solidified with agarose), and incubated aerobically at 30°C. The number of bacteria (CFU) on different media ranged between 9.4×10⁵g⁻¹ (on PCA) and 1.9×10⁷g⁻¹ (on TSA) (wet weight). The numbers of bacteria enumerated from plates incubated anaerobically (anaerobic agar and reinforced clostridial agar) were 2.1×10⁷and 1.7×10⁶g⁻¹, respectively. Of the 468 isolated and purified bacteria (183 in the first phase and 285 in the second phase), 135 were characterised using phenotypic characteristics as well as 16S rRNA gene sequence analysis. It was found that members of the phylum Firmicutes were overwhelmingly predominant (86.6%) in the landfill, followed by Actinobacteria (9.6%) and Proteobacteria (3.7%). Among the Firmicutes, at least 17 species from the single genus Bacillus were the most abundant inhabitants of the landfill. Detailed polyphasic characterisation of many of these isolates led to the discovery of a novel genus Paenisporosarcina (and the species P. quisquiliarum), a novel species of Microbacterium, M. immunditiarum, and reclassification of Sporosarcina macmurdoensis, Pelagibacillus goriensis, Bacillus silvestris, Bacillus insolitus, Bacillus psychrotolerans and Bacillus psychrodurans. Culture-independent analysis of two 16S rRNA gene libraries also revealed that the phylum Firmicutes was the predominant group in this community. The diversity of Archaea was found to be limited mainly to members of two orders: Methanosarcinales

  8. Quantification of ammonia oxidation rates and the distribution of ammonia-oxidizing Archaea and Bacteria in marine sediment depth profiles from Catalina Island, California

    Directory of Open Access Journals (Sweden)

    J. Michael eBeman

    2012-07-01

    Full Text Available Microbial communities present in marine sediments play a central role in nitrogen biogeochemistry at local to global scales. Along the oxidation-reduction gradients present in sediment profiles, multiple nitrogen cycling processes (such as nitrification, denitrification, nitrogen fixation, and anaerobic ammonium oxidation are active and actively coupled to one another—yet the microbial communities responsible for these transformations and the rates at which they occur are still poorly understood. We report pore water geochemical (O2, NH4+, NO3- profiles, quantitative profiles of archaeal and bacterial amoA genes, and ammonia oxidation rate measurements, from bioturbated marine sediments of Catalina Island, California. Across triplicate sediment cores collected offshore at Bird Rock and within Catalina Harbor, oxygen penetration (0.24-0.5 cm depth and the abundance of amoA genes (up to 9.30 x 107 genes g-1 varied with depth and between cores. Bacterial amoA genes were consistently present at depths of up to 10 cm, and archaeal amoA was readily detected in Bird Rock cores, and Catalina Harbor cores from 2008, but not 2007. Although detection of DNA is not necessarily indicative of active growth and metabolism, ammonia oxidation rate measurements made in 2008 (using isotope tracer demonstrated the production of oxidized nitrogen at depths where amoA was present. Rates varied with depth and between cores, but indicate that active ammonia oxidation occurs at up to 10 cm depth in bioturbated Catalina Harbor sediments, where it may be carried out by either or both ammonia-oxidizing Archaea and Bacteria.

  9. Quantification of ammonia oxidation rates and the distribution of ammonia-oxidizing Archaea and Bacteria in marine sediment depth profiles from Catalina Island, California.

    Science.gov (United States)

    Beman, J M; Bertics, Victoria J; Braunschweiler, Thomas; Wilson, Jesse M

    2012-01-01

    Microbial communities present in marine sediments play a central role in nitrogen biogeochemistry at local to global scales. Along the oxidation-reduction gradients present in sediment profiles, multiple nitrogen cycling processes (such as nitrification, denitrification, nitrogen fixation, and anaerobic ammonium oxidation) are active and actively coupled to one another - yet the microbial communities responsible for these transformations and the rates at which they occur are still poorly understood. We report pore water geochemical (O(2), [Formula: see text], and [Formula: see text]) profiles, quantitative profiles of archaeal and bacterial amoA genes, and ammonia oxidation rate measurements, from bioturbated marine sediments of Catalina Island, California. Across triplicate sediment cores collected offshore at Bird Rock (BR) and within Catalina Harbor (CH), oxygen penetration (0.24-0.5 cm depth) and the abundance of amoA genes (up to 9.30 × 10(7) genes g(-) (1)) varied with depth and between cores. Bacterial amoA genes were consistently present at depths of up to 10 cm, and archaeal amoA was readily detected in BR cores, and CH cores from 2008, but not 2007. Although detection of DNA is not necessarily indicative of active growth and metabolism, ammonia oxidation rate measurements made in 2008 (using isotope tracer) demonstrated the production of oxidized nitrogen at depths where amoA was present. Rates varied with depth and between cores, but indicate that active ammonia oxidation occurs at up to 10 cm depth in bioturbated CH sediments, where it may be carried out by either or both ammonia-oxidizing archaea and bacteria.

  10. Macroscopic biofilms in fracture-dominated sediment that anaerobically oxidize methane

    Science.gov (United States)

    Briggs, B.R.; Pohlman, J.W.; Torres, M.; Riedel, M.; Brodie, E.L.; Colwell, F.S.

    2011-01-01

    Methane release from seafloor sediments is moderated, in part, by the anaerobic oxidation of methane (AOM) performed by consortia of archaea and bacteria. These consortia occur as isolated cells and aggregates within the sulfate-methane transition (SMT) of diffusion and seep-dominant environments. Here we report on a new SMT setting where the AOM consortium occurs as macroscopic pink to orange biofilms within subseafloor fractures. Biofilm samples recovered from the Indian and northeast Pacific Oceans had a cellular abundance of 10 7 to 10 8 cells cm -3. This cell density is 2 to 3 orders of magnitude greater than that in the surrounding sediments. Sequencing of bacterial 16S rRNA genes indicated that the bacterial component is dominated by Deltaproteobacteria, candidate division WS3, and Chloroflexi, representing 46%, 15%, and 10% of clones, respectively. In addition, major archaeal taxa found in the biofilm were related to the ANME-1 clade, Thermoplasmatales, and Desulfurococcales, representing 73%, 11%, and 10% of archaeal clones, respectively. The sequences of all major taxa were similar to sequences previously reported from cold seep environments. PhyloChip microarray analysis detected all bacterial phyla identified by the clone library plus an additional 44 phyla. However, sequencing detected more archaea than the PhyloChip within the phyla of Methanosarcinales and Desulfurococcales. The stable carbon isotope composition of the biofilm from the SMT (-35 to-43%) suggests that the production of the biofilm is associated with AOM. These biofilms are a novel, but apparently widespread, aggregation of cells represented by the ANME-1 clade that occur in methane-rich marine sediments. ?? 2011, American Society for Microbiology.

  11. The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes.

    Science.gov (United States)

    Luijsterburg, Martijn S; White, Malcolm F; van Driel, Roel; Dame, Remus Th

    2008-01-01

    The genomic DNA of all organisms across the three kingdoms of life needs to be compacted and functionally organized. Key players in these processes are DNA supercoiling, macromolecular crowding and architectural proteins that shape DNA by binding to it. The architectural proteins in bacteria, archaea and eukaryotes generally do not exhibit sequence or structural conservation especially across kingdoms. Instead, we propose that they are functionally conserved. Most of these proteins can be classified according to their architectural mode of action: bending, wrapping or bridging DNA. In order for DNA transactions to occur within a compact chromatin context, genome organization cannot be static. Indeed chromosomes are subject to a whole range of remodeling mechanisms. In this review, we discuss the role of (i) DNA supercoiling, (ii) macromolecular crowding and (iii) architectural proteins in genome organization, as well as (iv) mechanisms used to remodel chromosome structure and to modulate genomic activity. We conclude that the underlying mechanisms that shape and remodel genomes are remarkably similar among bacteria, archaea and eukaryotes.

  12. Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function

    Science.gov (United States)

    2017-01-01

    Decades of biochemical, bioinformatic, and sequencing data are currently being systematically compiled into genome-scale metabolic reconstructions (GEMs). Such reconstructions are knowledge-bases useful for engineering, modeling, and comparative analysis. Here we review the fifteen GEMs of archaeal species that have been constructed to date. They represent primarily members of the Euryarchaeota with three-quarters comprising representative of methanogens. Unlike other reviews on GEMs, we specially focus on archaea. We briefly review the GEM construction process and the genealogy of the archaeal models. The major insights gained during the construction of these models are then reviewed with specific focus on novel metabolic pathway predictions and growth characteristics. Metabolic pathway usage is discussed in the context of the composition of each organism's biomass and their specific energy and growth requirements. We show how the metabolic models can be used to study the evolution of metabolism in archaea. Conservation of particular metabolic pathways can be studied by comparing reactions using the genes associated with their enzymes. This demonstrates the utility of GEMs to evolutionary studies, far beyond their original purpose of metabolic modeling; however, much needs to be done before archaeal models are as extensively complete as those for bacteria. PMID:28133437

  13. Lipid-Based Immuno-Magnetic Separation of Archaea from a Mixed Community

    Science.gov (United States)

    Frickle, C. M.; Bailey, J.; Lloyd, K. G.; Shumaker, A.; Flood, B.

    2014-12-01

    Despite advancing techniques in microbiology, an estimated 98% of all microbial species on Earth have yet to be isolated in pure culture. Natural samples, once transferred to the lab, are commonly overgrown by "weed" species whose metabolic advantages enable them to monopolize available resources. Developing new methods for the isolation of thus-far uncultivable microorganisms would allow us to better understand their ecology, physiology and genetic potential. Physically separating target organisms from a mixed community is one approach that may allow enrichment and growth of the desired strain. Here we report on a novel method that uses known physiological variations between taxa, in this case membrane lipids, to segregate the desired organisms while keeping them alive and viable for reproduction. Magnetic antibodies bound to the molecule squalene, which is found in the cell membranes of certain archaea, but not bacteria, enable separation of archaea from bacteria in mixed samples. Viability of cells was tested by growing the separated fractions in batch culture. Efficacy and optimization of the antibody separation technique are being evaluated using qPCR and cell counts. Future work will apply this new separation technique to natural samples.

  14. N-linked glycosylation in Archaea: a structural, functional, and genetic analysis.

    Science.gov (United States)

    Jarrell, Ken F; Ding, Yan; Meyer, Benjamin H; Albers, Sonja-Verena; Kaminski, Lina; Eichler, Jerry

    2014-06-01

    N-glycosylation of proteins is one of the most prevalent posttranslational modifications in nature. Accordingly, a pathway with shared commonalities is found in all three domains of life. While excellent model systems have been developed for studying N-glycosylation in both Eukarya and Bacteria, an understanding of this process in Archaea was hampered until recently by a lack of effective molecular tools. However, within the last decade, impressive advances in the study of the archaeal version of this important pathway have been made for halophiles, methanogens, and thermoacidophiles, combining glycan structural information obtained by mass spectrometry with bioinformatic, genetic, biochemical, and enzymatic data. These studies reveal both features shared with the eukaryal and bacterial domains and novel archaeon-specific aspects. Unique features of N-glycosylation in Archaea include the presence of unusual dolichol lipid carriers, the use of a variety of linking sugars that connect the glycan to proteins, the presence of novel sugars as glycan constituents, the presence of two very different N-linked glycans attached to the same protein, and the ability to vary the N-glycan composition under different growth conditions. These advances are the focus of this review, with an emphasis on N-glycosylation pathways in Haloferax, Methanococcus, and Sulfolobus.

  15. Solid-state fermentation as a potential technique for esterase/lipase production by halophilic archaea.

    Science.gov (United States)

    Martin del Campo, Martha; Camacho, Rosa M; Mateos-Díaz, Juan C; Müller-Santos, Marcelo; Córdova, Jesus; Rodríguez, Jorge A

    2015-11-01

    Halophilic archaea are extremophiles, adapted to high-salt environments, showing a big biotechnological potential as enzyme, lipids and pigments producers. Four inert supports (perlite, vermiculite, polyurethane foam and glass fiber) were employed for solid-state fermentation (SSF) of the halophilic archaeon Natronococcus sp. TC6 to investigate biomass and esterase production. A very low esterase activity and high water activity were observed when perlite, vermiculite and polyurethane were used as supports. When glass fiber was employed, an important moisture loss was observed (8.6%). Moreover, moisture retention was improved by mixing polyurethane and glass fiber, resulting in maximal biomass and esterase production. Three halophilic archaea: Natronococcus sp. TC6, Halobacterium sp. NRC-1 and Haloarcula marismortui were cultured by submerged fermentation (SmF) and by SSF; an improvement of 1.3- to 6.2-fold was observed in the biomass and esterase production when SSF was used. Growth was not homogeneous in the mixture, but was predominant in the glass fiber thus was probably because the glass fiber provides a holder to the cells, while the polyurethane acts as an impregnation medium reservoir. To the best of our knowledge, this work is the first report on haloarchaea cultivation by SSF aiming biomass and esterase/lipase activity production.

  16. Impact of cystic fibrosis disease on archaea and bacteria composition of gut microbiota.

    Science.gov (United States)

    Miragoli, Francesco; Federici, Sara; Ferrari, Susanna; Minuti, Andrea; Rebecchi, Annalisa; Bruzzese, Eugenia; Buccigrossi, Vittoria; Guarino, Alfredo; Callegari, Maria Luisa

    2017-02-01

    Cystic fibrosis is often associated with intestinal inflammation due to several factors, including altered gut microbiota composition. In this study, we analyzed the fecal microbiota among patients with cystic fibrosis of 10-22 years of age, and compared the findings with age-matched healthy subjects. The participating patients included 14 homozygotes and 14 heterozygotes with the delF508 mutation, and 2 heterozygotes presenting non-delF508 mutations. We used PCR-DGGE and qPCR to analyze the presence of bacteria, archaea and sulfate-reducing bacteria. Overall, our findings confirmed disruption of the cystic fibrosis gut microbiota. Principal component analysis of the qPCR data revealed no differences between homozygotes and heterozygotes, while both groups were distinct from healthy subjects who showed higher biodiversity. Archaea were under the detection limit in all homozygotes subjects, whereas methanogens were detected in 62% of both cystic fibrosis heterozygotes and healthy subjects. Our qPCR results revealed a low frequency of sulfate-reducing bacteria in the homozygote (13%) and heterozygote (13%) patients with cystic fibrosis compared with healthy subjects (87.5%). This is a pioneer study showing that patients with cystic fibrosis exhibit significant reduction of H2-consuming microorganisms, which could increase hydrogen accumulation in the colon and the expulsion of this gas through non-microbial routes.

  17. RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes

    Directory of Open Access Journals (Sweden)

    Decatur Wayne A

    2008-10-01

    Full Text Available Abstract Background Naturally occurring RNAs contain numerous enzymatically altered nucleosides. Differences in RNA populations (RNomics and pattern of RNA modifications (Modomics depends on the organism analyzed and are two of the criteria that distinguish the three kingdoms of life. If the genomic sequences of the RNA molecules can be derived from whole genome sequence information, the modification profile cannot and requires or direct sequencing of the RNAs or predictive methods base on the presence or absence of the modifications genes. Results By employing a comparative genomics approach, we predicted almost all of the genes coding for the t+rRNA modification enzymes in the mesophilic moderate halophile Haloferax volcanii. These encode both guide RNAs and enzymes. Some are orthologous to previously identified genes in Archaea, Bacteria or in Saccharomyces cerevisiae, but several are original predictions. Conclusion The number of modifications in t+rRNAs in the halophilic archaeon is surprisingly low when compared with other Archaea or Bacteria, particularly the hyperthermophilic organisms. This may result from the specific lifestyle of halophiles that require high intracellular salt concentration for survival. This salt content could allow RNA to maintain its functional structural integrity with fewer modifications. We predict that the few modifications present must be particularly important for decoding, accuracy of translation or are modifications that cannot be functionally replaced by the electrostatic interactions provided by the surrounding salt-ions. This analysis also guides future experimental validation work aiming to complete the understanding of the function of RNA modifications in Archaeal translation.

  18. Genomic Analysis of Deeply-Branching Bacteria and Archaea from IODP Leg 347: Baltic Sea Paleoenvironment

    Science.gov (United States)

    Bird, J. T.; Lloyd, K. G.

    2014-12-01

    Among the diverse inhabitants of the marine subsurface are "deeply-branching" bacteria and archaea, whose recent evolutionary ancestors have eluded isolation and characterization by traditional culture-based methods. By using single-cell genomics, we were able to target members of common deeply-branching mircorganisms found in a sediment core acquired during IODP Leg 347. Cells were separated from sediment layers (37 and 84 meters below the seafloor) deposited at site 60, hole B, near Anholt Island tens to hundreds of thousands of years ago. Ten single amplified genomes from 4 bacterial and 1 archaeal lineages were chosen from the 60 successfully sorted cells. The lineages include: Desulfobacterium sp., OPB41, OP8, NT-B2, Marine Group II archaea. Two lineages have not been genomically sampled before, while all 5 are frequently found in a variety of marine sediment habitats. The genome assemblies range in completeness from 45 - 85% and contain a number of phylogenetically relevant genes that has helped to anchor their position in the tree of life. The metabolic strategies, including putative sulfate reduction and carbon degradation pathways, employed by these cells have allowed them to survive in an environment with diminishing sources of labile carbon substrates.

  19. Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales.

    Science.gov (United States)

    Leigh, John A; Albers, Sonja-Verena; Atomi, Haruyuki; Allers, Thorsten

    2011-07-01

    The tree of life is split into three main branches: eukaryotes, bacteria, and archaea. Our knowledge of eukaryotic and bacteria cell biology has been built on a foundation of studies in model organisms, using the complementary approaches of genetics and biochemistry. Archaea have led to some exciting discoveries in the field of biochemistry, but archaeal genetics has been slow to get off the ground, not least because these organisms inhabit some of the more inhospitable places on earth and are therefore believed to be difficult to culture. In fact, many species can be cultivated with relative ease and there has been tremendous progress in the development of genetic tools for both major archaeal phyla, the Euryarchaeota and the Crenarchaeota. There are several model organisms available for methanogens, halophiles, and thermophiles; in the latter group, there are genetic systems for Sulfolobales and Thermococcales. In this review, we present the advantages and disadvantages of working with each archaeal group, give an overview of their different genetic systems, and direct the neophyte archaeologist to the most appropriate model organism.

  20. Halophilic archaea cultivated from surface sterilized middle-late eocene rock salt are polyploid.

    Directory of Open Access Journals (Sweden)

    Salla T Jaakkola

    Full Text Available Live bacteria and archaea have been isolated from several rock salt deposits of up to hundreds of millions of years of age from all around the world. A key factor affecting their longevity is the ability to keep their genomic DNA intact, for which efficient repair mechanisms are needed. Polyploid microbes are known to have an increased resistance towards mutations and DNA damage, and it has been suggested that microbes from deeply buried rock salt would carry several copies of their genomes. Here, cultivable halophilic microbes were isolated from a surface sterilized middle-late Eocene (38-41 million years ago rock salt sample, drilled from the depth of 800 m at Yunying salt mine, China. Eight unique isolates were obtained, which represented two haloarchaeal genera, Halobacterium and Halolamina. We used real-time PCR to show that our isolates are polyploid, with genome copy numbers of 11-14 genomes per cell in exponential growth phase. The ploidy level was slightly downregulated in stationary growth phase, but the cells still had an average genome copy number of 6-8. The polyploidy of halophilic archaea living in ancient rock salt might be a factor explaining how these organisms are able to overcome the challenge of prolonged survival during their entombment.

  1. Structure determination of archaea-specific ribosomal protein L46a reveals a novel protein fold

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Yingang, E-mail: fengyg@qibebt.ac.cn [Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101 (China); Song, Xiaxia [Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing 100083 (China); Lin, Jinzhong [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Xuan, Jinsong [Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing 100083 (China); Cui, Qiu [Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101 (China); Wang, Jinfeng [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)

    2014-07-18

    Highlights: • The archaea-specific ribosomal protein L46a has no homology to known proteins. • Three dimensional structure and backbone dynamics of L46a were determined by NMR. • The structure of L46a represents a novel protein fold. • A potential rRNA-binding surface on L46a was identified. • The potential position of L46a on the ribosome was proposed. - Abstract: Three archaea-specific ribosomal proteins recently identified show no sequence homology with other known proteins. Here we determined the structure of L46a, the most conserved one among the three proteins, from Sulfolobus solfataricus P2 using NMR spectroscopy. The structure presents a twisted β-sheet formed by the N-terminal part and two helices at the C-terminus. The L46a structure has a positively charged surface which is conserved in the L46a protein family and is the potential rRNA-binding site. Searching homologous structures in Protein Data Bank revealed that the structure of L46a represents a novel protein fold. The backbone dynamics identified by NMR relaxation experiments reveal significant flexibility at the rRNA binding surface. The potential position of L46a on the ribosome was proposed by fitting the structure into a previous electron microscopy map of the ribosomal 50S subunit, which indicated that L46a contacts to domain I of 23S rRNA near a multifunctional ribosomal protein L7ae.

  2. Identification of a glycolytic regulon in the archaea Pyrococcus and Thermococcus.

    Science.gov (United States)

    van de Werken, Harmen J G; Verhees, Corné H; Akerboom, Jasper; de Vos, Willem M; van der Oost, John

    2006-07-01

    The glycolytic pathway of the hyperthermophilic archaea that belong to the order Thermococcales (Pyrococcus, Thermococcus and Palaeococcus) differs significantly from the canonical Embden-Meyerhof pathway in bacteria and eukarya. This archaeal glycolysis variant consists of several novel enzymes, some of which catalyze unique conversions. Moreover, the enzymes appear not to be regulated allosterically, but rather at transcriptional level. To elucidate details of the gene expression control, the transcription initiation sites of the glycolytic genes in Pyrococcus furiosus have been mapped by primer extension analysis and the obtained promoter sequences have been compared with upstream regions of non-glycolytic genes. Apart from consensus sequences for the general transcription factors (TATA-box and BRE) this analysis revealed the presence of a potential transcription factor binding site (TATCAC-N(5)-GTGATA) in glycolytic and starch utilizing promoters of P. furiosus and several thermococcal species. The absence of this inverted repeat in Pyrococcus abyssi and Pyrococcus horikoshii probably reflects that their reduced catabolic capacity does not require this regulatory system. Moreover, this phyletic pattern revealed a TrmB-like regulator (PF0124 and TK1769) which may be involved in recognizing the repeat. This Thermococcales glycolytic regulon, with more than 20 genes, is the largest regulon that has yet been described for Archaea.

  3. Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene.

    Science.gov (United States)

    Offre, Pierre; Prosser, James I; Nicol, Graeme W

    2009-10-01

    Autotrophic ammonia-oxidizing bacteria were considered to be responsible for the majority of ammonia oxidation in soil until the recent discovery of the autotrophic ammonia-oxidizing archaea. To assess the relative contributions of bacterial and archaeal ammonia oxidizers to soil ammonia oxidation, their growth was analysed during active nitrification in soil microcosms incubated for 30 days at 30 degrees C, and the effect of an inhibitor of ammonia oxidation (acetylene) on their growth and soil nitrification kinetics was determined. Denaturing gradient gel electrophoresis (DGGE) analysis of bacterial ammonia oxidizer 16S rRNA genes did not detect any change in their community composition during incubation, and quantitative PCR (qPCR) analysis of bacterial amoA genes indicated a small decrease in abundance in control and acetylene-containing microcosms. DGGE fingerprints of archaeal amoA and 16S rRNA genes demonstrated changes in the relative abundance of specific crenarchaeal phylotypes during active nitrification. Growth was also indicated by increases in crenarchaeal amoA gene copy number, determined by qPCR. In microcosms containing acetylene, nitrification and growth of the crenarchaeal phylotypes were suppressed, suggesting that these crenarchaea are ammonia oxidizers. Growth of only archaeal but not bacterial ammonia oxidizers occurred in microcosms with active nitrification, indicating that ammonia oxidation was mostly due to archaea in the conditions of the present study.

  4. Intraspecific variation in aerobic and anaerobic locomotion

    DEFF Research Database (Denmark)

    Svendsen, Jon Christian; Tirsgård, Bjørn; Cordero, Gerardo A.;

    2015-01-01

    Intraspecific variation and trade-off in aerobic and anaerobic traits remain poorly understood in aquatic locomotion. Using gilthead sea bream (Sparus aurata) and Trinidadian guppy (Poecilia reticulata), both axial swimmers, this study tested four hypotheses: (1) gait transition from steady...... to unsteady (i.e., burst-assisted) swimming is associated with anaerobic metabolism evidenced as excess post exercise oxygen consumption (EPOC); (2) variation in swimming performance (critical swimming speed; U crit) correlates with metabolic scope (MS) or anaerobic capacity (i.e., maximum EPOC); (3...

  5. Energy from anaerobic methane production. [Sweden

    Energy Technology Data Exchange (ETDEWEB)

    1982-02-01

    Since 1970 Swedish researchers have been testing the ANAMET (anaerobic-aerobic-methane) process, which involves converting industrial wastewaters via an initial anaerobic microbiological step followed by an aerobic one. Recycling the biomass material in each step allows shorter hydraulic retention times without decreasing stability or solids reduction. Since the first ANAMET plants began operating at a Swedish sugar factory in 1972, 17 more plants have started up or are under construction. Moreover, the ANAMET process has engendered to offshoot BIOMET (biomass-methane) process, a thermophilic anaerobic scheme that can handle sugar-beet pulp as well as grass and other soft, fast-growing biomasses.

  6. Relation between methanogenic archaea and methane production potential in selected natural wetland ecosystems across China

    Directory of Open Access Journals (Sweden)

    D. Y. Liu

    2011-02-01

    Full Text Available Methane (CH4 emissions from natural wetland ecosystems exhibit large spatial variability at regional, national, and global levels related to temperature, water table, plant type and methanogenic archaea etc. To understand the underlying factors that induce spatial differences in CH4 emissions, and the relationship between the population of methanogenic archaea and CH4 production potential in natural wetlands around China, we measured the CH4 production potential and the abundance of methanogenic archaea in vertical soil profiles sampled from the Poyang wetland in the subtropical zone, the Hongze wetland in the warm temperate zone, the Sanjiang marsh in the cold temperate zone, and the Ruoergai peatland in the Qinghai-Tibetan Plateau in the alpine climate zone. The top soil layer had the highest population of methanogens (1.07–8.29 × 109 cells g−1 soil in all wetlands except the Ruoergai peatland and exhibited the maximum CH4 production potential measured at the mean in situ summer temperature. There is a significant logarithmic correlation between the abundance of methanogenic archaea and the soil organic carbon (R2 = 0.72, P < 0.001, n = 13 and between the abundance of methanogenic archaea and the total nitrogen concentrations (R2 = 0.76, P < 0.001, n = 13 in wetland soils. This indicates that the amount of soil organic carbon may affect the population of methanogens in wetland ecosystems. While the CH4 production potential is not significantly related to methanogen population (R2 = 0.01, P > 0.05, n = 13, it is related to the dissolved organic carbon concentration (R2 = 0.31, P = 0.05, n = 13. This suggests that the methanogen population might be not an effective index for predicting the CH4 production in wetland

  7. Anaerobic degradation and toxicity of commercial cationic surfactants in anaerobic screening tests.

    Science.gov (United States)

    García, M T; Campos, E; Sánchez-Leal, J; Ribosa, I

    2000-09-01

    Anaerobic biodegradability and toxicity on anaerobic bacteria of di(hydrogenated tallow) dimethyl ammonium chloride (DHTDMAC) and two esterquats have been investigated. A batch test system containing municipal digester solids as a source of anaerobic bacteria, based on the method proposed by the ECETOC, has been applied. To evaluate the potential toxicity of such surfactants on anaerobic sludge, a co-substrate, an easily biodegradable compound in anaerobic conditions, has been added to the samples to test and the effects on biogas production have been determined. For the esterquats studied high biodegradation levels were obtained and no toxic effects on anaerobic bacteria were observed even at the highest concentrations tested, 100 and 200 mg C/l, respectively. On the contrary, DHTDMAC was not degradated at the same test conditions. However, no inhibitory effects on the biogas production were detected for this surfactant at concentrations <100 mg C/l.

  8. Antimicrobial resistance and susceptibility testing of anaerobic bacteria.

    Science.gov (United States)

    Schuetz, Audrey N

    2014-09-01

    Infections due to anaerobic bacteria can be severe and life-threatening. Susceptibility testing of anaerobes is not frequently performed in laboratories, but such testing is important to direct appropriate therapy. Anaerobic resistance is increasing globally, and resistance trends vary by geographic region. An overview of a variety of susceptibility testing methods for anaerobes is provided, and the advantages and disadvantages of each method are reviewed. Specific clinical situations warranting anaerobic susceptibility testing are discussed.

  9. Anaerobe Tolerance to Oxygen and the Potentials of Anaerobic and Aerobic Cocultures for Wastewater Treatment

    Directory of Open Access Journals (Sweden)

    M.T. Kato

    1997-12-01

    Full Text Available The anaerobic treatment processes are considered to be well-established methods for the elimination of easily biodegradable organic matter from wastewaters. Some difficulties concerning certain wastewaters are related to the possible presence of dissolved oxygen. The common belief is that anaerobes are oxygen intolerant. Therefore, the common practice is to use sequencing anaerobic and aerobic steps in separate tanks. Enhanced treatment by polishing off the residual biodegradable oxygen demand from effluents of anaerobic reactors, or the biodegradation of recalcitrant wastewater pollutants, usually requires sequenced anaerobic and aerobic bacteria activities. However, the combined activity of both bacteria can also be obtained in a single reactor. Previous experiments with either pure or mixed cultures showed that anaerobes can tolerate oxygen to a certain extent. The oxygen toxicity to methanogens in anaerobic sludges was quantified in batch experiments, as well as in anaerobic reactors. The results showed that methanogens have a high tolerance to oxygen. In practice, it was confirmed that dissolved oxygen does not constitute any detrimental effect on reactor treatment performance. This means that the coexistence of anaerobic and aerobic bacteria in one single reactor is feasible and increases the potentials of new applications in wastewater treatment

  10. Exocellular electron transfer in anaerobic microbial communities

    NARCIS (Netherlands)

    Stams, A.J.M.; Bok, de F.A.M.; Plugge, C.M.; Eekert, van M.H.A.; Dolfing, J.; Schraa, G.

    2006-01-01

    Exocellular electron transfer plays an important role in anaerobic microbial communities that degrade organic matter. Interspecies hydrogen transfer between microorganisms is the driving force for complete biodegradation in methanogenic environments. Many organic compounds are degraded by obligatory

  11. An anaerobic mitochondrion that produces hydrogen

    NARCIS (Netherlands)

    Boxma, Brigitte; Graaf, Rob M. de; Staay, Georg W.M. van der; Alen, Theo A. van; Ricard, Guenola; Gabaldón, Toni; Hoek, Angela H.A.M. van; Moon-van der Staay, Seung Yeo; Koopman, Werner J.H.; Hellemond, Jaap J. van; Tielens, Aloysius G.M.; Friedrich, Thorsten; Veenhuis, Marten; Huynen, Martijn A.; Hackstein, Johannes H.P.

    2005-01-01

    Hydrogenosomes are organelles that produce ATP and hydrogen, and are found in various unrelated eukaryotes, such as anaerobic flagellates, chytridiomycete fungi and ciliates. Although all of these organelles generate hydrogen, the hydrogenosomes from these organisms are structurally and metabolicall

  12. Anaerobic Toxicity of Cationic Silver Nanoparticles

    Data.gov (United States)

    U.S. Environmental Protection Agency — Toxicity data for the impact of nano-silver on anaerobic degradation. This dataset is associated with the following publication: Gitipour, A., S. Thiel, K. Scheckel,...

  13. Anaerobic membrane bioreactor under extreme conditions (poster)

    NARCIS (Netherlands)

    Munoz Sierra, J.D.; De Kreuk, M.K.; Spanjers, H.; Van Lier, J.B.

    2013-01-01

    Membrane bioreactors ensure biomass retention by the application of micro or ultrafiltration processes. This allows operation at high sludge concentrations. Previous studies have shown that anaerobic membrane bioreactors is an efficient way to retain specialist microorganisms for treating wastewater

  14. EFFECT OF MUSIC ON ANAEROBIC EXERCISE PERFORMANCE

    OpenAIRE

    Atan, T.

    2013-01-01

    For years, mostly the effects of music on cardiorespiratory exercise performance have been studied, but a few studies have examined the effect of music on anaerobic exercise. The purpose of this study was to assess the effect of listening to music and its rhythm on anaerobic exercise: on power output, heart rate and the concentration of blood lactate. 28 male subjects were required to visit the laboratory on 6 occasions, each separated by 48 hours. Firstly, each subject performed the Running-...

  15. Anaerobic digester for treatment of organic waste

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, V. K. [Indian Insitute of Technology, Delhi (India)]|[ENEA, Centro Ricerche Trisaia, Matera (Italy); Fortuna, F.; Canditelli, M.; Cornacchia, G. [ENEA, Centro Ricerche Trisaia, Matera (Italy). Dipt. Ambiente; Farina, R. [ENEA, centro Ricerche ``Ezio Clementel``, Bologna (Italy). Dipt. Ambiente

    1997-09-01

    The essential features of both new and more efficient reactor systems and their appropriate applications for various organic waste management situations, description of several working plants are discussed in the present communication. It is hoped that significant development reported here would be useful in opening a new vista to the application of anaerobic biotechnology for the waste treatment of both low/high organic strength and specialized treatment for toxic substances, using appropriate anaerobic methods.

  16. Anaerobic digestion foaming causes – A review

    OpenAIRE

    Ganidi, Nafsika; Tyrrel, Sean F.; Cartmell, Elise

    2009-01-01

    Anaerobic digestion foaming has been encountered in several sewage treatment plants in the UK. Foaming has raised major concerns for the water companies due to significant impacts on process efficiency and operational costs. Several foaming causes have been identified over the past few years by researchers. However, the supporting experimental information is limited and in some cases absent. The present report aims to provide a detailed review of the current anaerobic digestion foaming proble...

  17. SLEEP DEPRIVATION INDUCED ANXIETY AND ANAEROBIC PERFORMANCE

    Directory of Open Access Journals (Sweden)

    Selma Arzu Vardar

    2007-12-01

    Full Text Available The aim of this study was to investigate the effects of sleep deprivation induced anxiety on anaerobic performance. Thirteen volunteer male physical education students completed the Turkish version of State Anxiety Inventory and performed Wingate anaerobic test for three times: (1 following a full-night of habitual sleep (baseline measurements, (2 following 30 hours of sleep deprivation, and (3 following partial-night sleep deprivation. Baseline measurements were performed the day before total sleep deprivation. Measurements following partial sleep deprivation were made 2 weeks later than total sleep deprivation measurements. State anxiety was measured prior to each Wingate test. The mean state anxiety following total sleep deprivation was higher than the baseline measurement (44.9 ± 12.9 vs. 27.6 ± 4.2, respectively, p = 0.02 whereas anaerobic performance parameters remained unchanged. Neither anaerobic parameters nor state anxiety levels were affected by one night partial sleep deprivation. Our results suggest that 30 hours continuous wakefulness may increase anxiety level without impairing anaerobic performance, whereas one night of partial sleep deprivation was ineffective on both state anxiety and anaerobic performance

  18. The role of tetraether lipid composition in the adaptation of thermophilic archaea to acidity.

    Science.gov (United States)

    Boyd, Eric S; Hamilton, Trinity L; Wang, Jinxiang; He, Liu; Zhang, Chuanlun L

    2013-01-01

    Diether and tetraether lipids are fundamental components of the archaeal cell membrane. Archaea adjust the degree of tetraether lipid cyclization in order to maintain functional membranes and cellular homeostasis when confronted with pH and/or thermal stress. Thus, the ability to adjust tetraether lipid composition likely represents a critical phenotypic trait that enabled archaeal diversification into environments characterized by extremes in pH and/or temperature. Here we assess the relationship between geochemical variation, core- and polar-isoprenoid glycerol dibiphytanyl glycerol tetraether (C-iGDGT and P-iGDGT, respectively) lipid composition, and archaeal 16S rRNA gene diversity and abundance in 27 geothermal springs in Yellowstone National Park, Wyoming. The composition and abundance of C-iGDGT and P-iGDGT lipids recovered from geothermal ecosystems were distinct from surrounding soils, indicating that they are synthesized endogenously. With the exception of GDGT-0 (no cyclopentyl rings), the abundances of individual C-iGDGT and P-iGDGT lipids were significantly correlated. The abundance of a number of individual tetraether lipids varied positively with the relative abundance of individual 16S rRNA gene sequences, most notably crenarchaeol in both the core and polar GDGT fraction and sequences closely affiliated with Candidatus Nitrosocaldus yellowstonii. This finding supports the proposal that crenarchaeol is a biomarker for nitrifying archaea. Variation in the degree of cyclization of C- and P-iGDGT lipids recovered from geothermal mats and sediments could best be explained by variation in spring pH, with lipids from acidic environments tending to have, on average, more internal cyclic rings than those from higher pH ecosystems. Likewise, variation in the phylogenetic composition of archaeal 16S rRNA genes could best be explained by spring pH. In turn, the phylogenetic similarity of archaeal 16S rRNA genes was significantly correlated with the similarity

  19. Diversity and Abundance of Ammonia-Oxidizing Archaea in Hydrothermal Vent Chimneys of the Juan de Fuca Ridge▿ †

    Science.gov (United States)

    Wang, Shufang; Xiao, Xiang; Jiang, Lijing; Peng, Xiaotong; Zhou, Huaiyang; Meng, Jun; Wang, Fengping

    2009-01-01

    The abundance and diversity of archaeal ammonia monooxygenase subunit A (amoA) genes from hydrothermal vent chimneys at the Juan de Fuca Ridge were investigated. The majority of the retrieved archaeal amoA sequences exhibited identities of less than 95% to those in the GenBank database. Novel ammonia-oxidizing archaea may exist in the hydrothermal vent environments. PMID:19395559

  20. Anaerobic Nitrogen Fixers on Mars

    Science.gov (United States)

    Lewis, B. G.

    2000-07-01

    The conversion of atmospheric nitrogen gas to the protein of living systems is an amazing process of nature. The first step in the process is biological nitrogen fixation, the transformation of N2 to NH3. The phenomenon is crucial for feeding the billions of our species on Earth. On Mars, the same process may allow us to discover how life can adapt to a hostile environment, and render it habitable. Hostile environments also exist on Earth. For example, nothing grows in coal refuse piles due to the oxidation of pyrite and marcasite to sulfuric acid. Yet, when the acidity is neutralized, alfalfa and soybean plants develop root nodules typical of symbiotic nitrogen fixation with Rhizobium species possibly living in the pyritic material. When split open, these nodules exhibited the pinkish color of leghemoglobin, a protein in the nodule protecting the active nitrogen-fixing enzyme nitrogenase against the toxic effects of oxygen. Although we have not yet obtained direct evidence of nitrogenase activity in these nodules (reduction of acetylene to ethylene, for example), these findings suggested the possibility that nitrogen fixation was taking place in this hostile, non-soil material. This immediately raises the possibility that freeliving anaerobic bacteria which fix atmospheric nitrogen on Earth, could do the same on Mars.

  1. Characterising the CRISPR immune system in Archaea using genome sequence analysis

    DEFF Research Database (Denmark)

    Shah, Shiraz Ali

    Archaea, a group of microorganisms distinct from bacteria and eukaryotes, are equipped with an adaptive immune system called the CRISPR system, which relies on an RNA interference mechanism to combat invading viruses and plasmids. Using a genome sequence analysis approach, the four components...... of archaeal genomic CRISPR loci were analysed, namely, repeats, spacers, leaders and cas genes. Based on analysis of spacer sequences it was predicted that the immune system combats viruses and plasmids by targeting their DNA. Furthermore, analysis of repeats, leaders and cas genes revealed that CRISPR...... systems exist as distinct families which have key differences between themselves. Closely related organisms were seen harbouring different CRISPR systems, while some distantly related species carried similar systems, indicating frequent horizontal exchange. Moreover, it was found that cas genes of Type I...

  2. The discovery of archaea origin phosphomannomutase in algae based on the algal transcriptome

    Institute of Scientific and Technical Information of China (English)

    FENG Yanjing; CHI Shan; LIU Cui; CHEN Shengping; YU Jun; WANG Xumin; LIU Tao

    2014-01-01

    Phosphomannomutase (PMM;EC 5.4.2.8) is an enzyme that catalyzes the interconversion reaction between mannose-6-phosphate and mannose-1-phosphate. However, its systematic molecular and functional in-vestigations in algae have not hitherto been reported. In this work, with the accomplishment of the 1 000 Plant Project (OneKP) in which more than 218 species of Chromista, including 19 marine phaeophytes, 22 marine rhodophytes, 171 chlorophytes, 5 cryptophytes, 4 haptophytes, and 5 glaucophytes were sequenced, we used a gene analysis method to analyze the PMM gene sequences in algae and confirm the existence of the PMM gene in the transcriptomic sequencing data of Rhodophyta and Ochrophyta. Our results showed that only one type of PMM with four conserved motifs exists in Chromista which is similar to human PMM. Moreover, the phylogenetic tree revealed that algae PMM possibly originated from archaea.

  3. Not just for Eukarya anymore: protein glycosylation in Bacteria and Archaea.

    Science.gov (United States)

    Abu-Qarn, Mehtap; Eichler, Jerry; Sharon, Nathan

    2008-10-01

    Of the many post-translational modifications proteins can undergo, glycosylation is the most prevalent and the most diverse. Today, it is clear that both N-glycosylation and O-glycosylation, once believed to be restricted to eukaryotes, also transpire in Bacteria and Archaea. Indeed, prokaryotic glycoproteins rely on a wider variety of monosaccharide constituents than do those of eukaryotes. In recent years, substantial progress in describing the enzymes involved in bacterial and archaeal glycosylation pathways has been made. It is becoming clear that enhanced knowledge of bacterial glycosylation enzymes may be of therapeutic value, while the demonstrated ability to introduce bacterial glycosylation genes into Escherichia coli represents a major step forward in glyco-engineering. A better understanding of archaeal protein glycosylation provides insight into this post-translational modification across evolution as well as protein processing under extreme conditions. Here, we discuss new structural and biosynthetic findings related to prokaryotic protein glycosylation, until recently a neglected topic.

  4. Genetic analysis of the br gene in halophilic archaea isolated from Xinjiang region, China

    Institute of Scientific and Technical Information of China (English)

    Xiaohong XU; Min WU; Huibin ZHANG; Zhihu LIU

    2008-01-01

    Some novel members of extremely halophilic archaea, strains AJ 11, AJ 12 and AJ 13, were isolated from the Aularz Lake located in the Altun Mountain National Nature Reserve of Xinjiang, Uygur Autonomous Region in China. Partial DNA fragments encoding a bacteriorho-dopsin (BR), as well as for 16S rRNA of isolated strains, were amplified by PCR and their DNA sequences were determined subsequently. On the basis of homology and phylogenetic analysis of the 16S rDNA, we thought that the isolated strains forming a microbiological population are the members of the genus Natrinema. The results of genetic analysis, such as GC content, transition/transver-sion (Ti/Tv) rate ratios and synonymous substitution rates (Ks) indicate that the br fragments, with a high level of genetic divergence, are faced with both purifying selection and bias mutation pressure. The study provides the basis for use of species and BR proteins resources.

  5. 2001 Gordon Research Conference on Archaea: Ecology [sic], Metabolism. Final progress report [agenda and attendee list

    Energy Technology Data Exchange (ETDEWEB)

    Daniels, Charles

    2001-08-10

    The Gordon Research Conference on Archaea: Ecology, Metabolism [and Molecular Biology] was held at Proctor Academy, Andover, New Hampshire, August 5-10, 2001. The conference was attended by 135 participants. The attendees represented the spectrum of endeavor in this field, coming from academia, industry, and government laboratories, and included US and foreign scientists, senior researchers, young investigators, and students. Emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate discussion about the key issues in the field today. Session topics included the following: Ecology and genetic elements; Genomics and evolution; Ecology, genomes and gene regulation; Replication and recombination; Chromatin and transcription; Gene regulation; Post-transcription processing; Biochemistry and metabolism; Proteomics and protein structure; Metabolism and physiology. The featured speaker addressed the topic: ''Archaeal viruses, witnesses of prebiotic evolution?''

  6. Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops.

    Directory of Open Access Journals (Sweden)

    Yuejian Mao

    Full Text Available Widespread adaptation of biomass production for bioenergy may influence important biogeochemical functions in the landscape, which are mainly carried out by soil microbes. Here we explore the impact of four potential bioenergy feedstock crops (maize, switchgrass, Miscanthus X giganteus, and mixed tallgrass prairie on nitrogen cycling microorganisms in the soil by monitoring the changes in the quantity (real-time PCR and diversity (barcoded pyrosequencing of key functional genes (nifH, bacterial/archaeal amoA and nosZ and 16S rRNA genes over two years after bioenergy crop establishment. The quantities of these N-cycling genes were relatively stable in all four crops, except maize (the only fertilized crop, in which the population size of AOB doubled in less than 3 months. The nitrification rate was significantly correlated with the quantity of ammonia-oxidizing archaea (AOA not bacteria (AOB, indicating that archaea were the major ammonia oxidizers. Deep sequencing revealed high diversity of nifH, archaeal amoA, bacterial amoA, nosZ and 16S rRNA genes, with 229, 309, 330, 331 and 8989 OTUs observed, respectively. Rarefaction analysis revealed the diversity of archaeal amoA in maize markedly decreased in the second year. Ordination analysis of T-RFLP and pyrosequencing results showed that the N-transforming microbial community structures in the soil under these crops gradually differentiated. Thus far, our two-year study has shown that specific N-transforming microbial communities develop in the soil in response to planting different bioenergy crops, and each functional group responded in a different way. Our results also suggest that cultivation of maize with N-fertilization increases the abundance of AOB and denitrifiers, reduces the diversity of AOA, and results in significant changes in the structure of denitrification community.

  7. Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops.

    Science.gov (United States)

    Mao, Yuejian; Yannarell, Anthony C; Mackie, Roderick I

    2011-01-01

    Widespread adaptation of biomass production for bioenergy may influence important biogeochemical functions in the landscape, which are mainly carried out by soil microbes. Here we explore the impact of four potential bioenergy feedstock crops (maize, switchgrass, Miscanthus X giganteus, and mixed tallgrass prairie) on nitrogen cycling microorganisms in the soil by monitoring the changes in the quantity (real-time PCR) and diversity (barcoded pyrosequencing) of key functional genes (nifH, bacterial/archaeal amoA and nosZ) and 16S rRNA genes over two years after bioenergy crop establishment. The quantities of these N-cycling genes were relatively stable in all four crops, except maize (the only fertilized crop), in which the population size of AOB doubled in less than 3 months. The nitrification rate was significantly correlated with the quantity of ammonia-oxidizing archaea (AOA) not bacteria (AOB), indicating that archaea were the major ammonia oxidizers. Deep sequencing revealed high diversity of nifH, archaeal amoA, bacterial amoA, nosZ and 16S rRNA genes, with 229, 309, 330, 331 and 8989 OTUs observed, respectively. Rarefaction analysis revealed the diversity of archaeal amoA in maize markedly decreased in the second year. Ordination analysis of T-RFLP and pyrosequencing results showed that the N-transforming microbial community structures in the soil under these crops gradually differentiated. Thus far, our two-year study has shown that specific N-transforming microbial communities develop in the soil in response to planting different bioenergy crops, and each functional group responded in a different way. Our results also suggest that cultivation of maize with N-fertilization increases the abundance of AOB and denitrifiers, reduces the diversity of AOA, and results in significant changes in the structure of denitrification community.

  8. Ammonia-oxidizing Archaea in the Arctic Ocean and Antarctic coastal waters.

    Science.gov (United States)

    Kalanetra, Karen M; Bano, Nasreen; Hollibaugh, James T

    2009-09-01

    We compared abundance, distributions and phylogenetic composition of Crenarchaeota and ammonia-oxidizing Archaea (AOA) in samples collected from coastal waters west of the Antarctic Peninsula during the summers of 2005 and 2006, with samples from the central Arctic Ocean collected during the summer of 1997. Ammonia-oxidizing Archaea and Crenarchaeota abundances were estimated from quantitative PCR measurements of amoA and 16S rRNA gene abundances. Crenarchaeota and AOA were approximately fivefold more abundant at comparable depths in the Antarctic versus the Arctic Ocean. Crenarchaeota and AOA were essentially absent from the Antarctic Summer Surface Water (SSW) water mass (0-45 m depth). The ratio of Crenarchaeota 16S rRNA to archaeal amoA gene abundance in the Winter Water (WW) water mass (45-105 m depth) of the Southern Ocean was much lower (0.15) than expected and in sharp contrast to the ratio (2.0) in the Circumpolar Deep Water (CDW) water mass (105-3500 m depth) immediately below it. We did not observe comparable segregation of this ratio by depth or water mass in Arctic Ocean samples. A ubiquitous, abundant and polar-specific crenarchaeote was the dominant ribotype in the WW and important in the upper halocline of the Arctic Ocean. Our data suggest that this organism does not contain an ammonia monooxygenase gene. In contrast to other studies where Crenarchaeota populations apparently lacking amoA genes are found in bathypelagic waters, this organism appears to dominate in well-defined, ammonium-rich, near-surface water masses in polar oceans.

  9. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea.

    Science.gov (United States)

    Chun, Jongsik; Rainey, Fred A

    2014-02-01

    The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA-DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12,000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11,000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

  10. The Role of Tetraether Lipid Composition in the Adaptation of Thermophilic Archaea to Acidity

    Directory of Open Access Journals (Sweden)

    Eric eBoyd

    2013-04-01

    Full Text Available Diether and tetraether lipids are fundamental components of the archaeal cell membrane. Archaea adjust the degree of tetraether lipid cyclization in order to maintain functional membranes and cellular homeostasis when confronted with pH and/or thermal stress. Thus, the ability to adjust tetraether lipid composition likely represents a critical phenotypic trait that enabled archaeal diversification into environments characterized by extremes in pH and/or temperature. Here we assess the relationship between geochemical variation, core- and polar-isoprenoid glycerol dibiphytanyl glycerol tetraether (C-iGDGT and P-iGDGT, respectively lipid composition, and archaeal 16S rRNA gene diversity and abundance in 27 geothermal springs in Yellowstone National Park (YNP, Wyoming. The composition and abundance of C-iGDGT and P-iGDGT lipids recovered from geothermal ecosystems were distinct from surrounding soils, indicating that they are synthesized endogenously. With the exception of GDGT-0 (no cyclopentyl rings, the abundances of individual C-iGDGT and P-iGDGT lipids were significantly correlated. The abundance of a number of individual tetraether lipids varied positively with the relative abundance of individual 16S rRNA gene sequences, most notably crenarchaeol in both the core and polar GDGT fraction and sequences closely affiliated with Candidatus Nitrosocaldus yellowstonii. This finding supports the proposal that crenarchaeol is a biomarker for nitrifying archaea. Variation in the degree of cyclization of C- and P-iGDGT lipids recovered from geothermal mats and sediments could best be explained by variation in spring pH, with lipids from acidic environments tending to have, on average, more internal cyclic rings than those from higher pH ecosystems. Likewise, variation in the phylogenetic composition of archaeal 16S rRNA genes could best be explained by spring pH. In turn, the phylogenetic similarity of archaeal 16S rRNA genes was significantly

  11. Application of dynamic membranes in anaerobic membranes in anaerobic membrane bioreactor systems

    NARCIS (Netherlands)

    Erşahin, M.E.

    2015-01-01

    Anaerobic membrane bioreactors (AnMBRs) physically ensure biomass retention by the application of a membrane filtration process. With growing application experiences from aerobic membrane bioreactors (MBRs), the combination of membrane and anaerobic processes has received much attention and become m

  12. Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Xueju [Georgia Inst. of Technology, Atlanta, GA (United States); Handley, Kim M. [Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States); Gilbert, Jack A. [Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States); Marine Biological Lab., Woods Hole, MA (United States); Zhejiang Univ., Hangzhou (China); Kostka, Joel E. [Georgia Inst. of Technology, Atlanta, GA (United States)

    2015-05-22

    To probe the metabolic potential of abundant Archaea in boreal peats, we reconstructed two near-complete archaeal genomes, affiliated with Thaumarchaeota group 1.1c (bin Fn1, 8% abundance), which was a genomically unrepresented group, and Thermoplasmata (bin Bg1, 26% abundance), from metagenomic data acquired from deep anoxic peat layers. Each of the near-complete genomes encodes the potential to degrade long-chain fatty acids (LCFA) via β-oxidation. Fn1 has the potential to oxidize LCFA either by syntrophic interaction with methanogens or by coupling oxidation with anaerobic respiration using fumarate as a terminal electron acceptor (TEA). Fn1 is the first Thaumarchaeota genome without an identifiable carbon fixation pathway, indicating that this mesophilic phylum encompasses more diverse metabolisms than previously thought. Furthermore, we report genetic evidence suggestive of sulfite and/or organosulfonate reduction by Thermoplasmata Bg1. In deep peat, inorganic TEAs are often depleted to extremely low levels, yet the anaerobic respiration predicted for two abundant archaeal members suggests organic electron acceptors such as fumarate and organosulfonate (enriched in humic substances) may be important for respiration and C mineralization in peatlands.

  13. High rate biological nutrient removal from high strength wastewater using anaerobic-circulating fluidized bed bioreactor (A-CFBBR).

    Science.gov (United States)

    Andalib, Mehran; Nakhla, George; Zhu, Jesse

    2012-08-01

    Biological nutrient removal (BNR) from high strength wastewater was investigated using a newly developed integrated anaerobic fluidized bed (AF) with circulating fluidized bed bioreactor henceforth called A-CFBBR. The A-CFBBR showed 99.7%COD removal, 84% nitrogen removal, with a very low sludge yield of 0.017 g VSS/g COD while treating a synthetic wastewater containing 10,700 mg COD/L and 250 mg NH(3)-N/L over a period of 6 months. The system was operated at an organic loading rate (OLR) of 35 kg COD/m(3)(AF) d and nitrogen loading rate (NLR) of 1.1 kg N/m(3)(CFBBR) d at a hydraulic retention time (HRT) of less than 12 h in the A-CFBBR. Microbial communities analysis using DGGE confirmed the presence of both AOBs and NOBs in the riser and downer. Pseudomonas putida and Pseudomonas fluorescence were the dominant denitrifiers present in the downer. Methanogenic activity was accomplished by a microbial mixture of archaea and bacteria in the anaerobic column.

  14. Regulation of multiple carbon monoxide consumption pathways in anaerobic bacteria

    Directory of Open Access Journals (Sweden)

    Stephen M Techtmann

    2011-07-01

    Full Text Available Carbon monoxide (CO, well known as a toxic gas, is increasingly recognized as a key metabolite and signaling molecule. Microbial utilization of CO is quite common, evidenced by the rapid escalation in description of new species of CO-utilizing bacteria and archaea. Carbon monoxide dehydrogenase (CODH, the protein complex that enables anaerobic CO utilization has been well-characterized from an increasing number of microorganisms, however the regulation of multiple CO-related gene clusters in single isolates remains unexplored. Many species are extroraordinarily resistant to high CO concentrations, thiriving under pure CO at more than one atmosphere. We hypothesized that, in strains that can grow exclusively on CO, both carbon acquisition via the CODH/Acetyl CoA synthase complex and energy conservation via a CODH-linked hydrogenase must be differentially regulated in response to the availability of CO. The CO-sensing transcriptional activator, CooA is present in most CO-oxidizing bacteria. Here we present a genomic and phylogenetic survey of CODH operons and cooA genes found in CooA-containing bacteria. Two distinct groups of CooA homologs were found: One clade (CooA-1 is found in the majority of CooA containing bacteria, whereas the other clade (CooA-2 is found only in genomes that encode multiple CODH clusters, suggesting that the CooA-2 might be important for cross-regulation of competing CODH operons. Recombinant CooA-1 and CooA-2 regulators from the prototypical CO-utilizing bacterium Carboxydothermus hydrogenoformans were purified, and promoter binding analyses revealed that CooA-1 specifically regulates the hydrogenase-linked CODH, whereas CooA-2 is able to regulate both the hydrogenase-linked CODH and the CODH/ACS operons. These studies point to the ability of dual CooA homologs to partition CO into divergent CO-utilizing pathways resulting in efficient consumption of a single limiting growth substrate available across a wide range of

  15. Application of Ventilation Air Methane Oxidization and Waste Heat Utilization Technology in Shanxi Lu’an Gaohe Coal Mine%乏风氧化及余热利用技术在山西潞安高河煤矿的应用

    Institute of Scientific and Technical Information of China (English)

    贾剑

    2014-01-01

    A large amount of coal mine ventilation air methane was directly exhausted into the atmosPhere,which not only intensified the greenhouse effect,but also caused the energy consumPtion,and if an aPProPriate technology was aPPlied to make full use of the mine ventilation air methane,huge benefits in energy saving and environmental Protection would be Produced. This PaPer described the mine ventilation air methane oxidation and the waste heat utilization technology in the home and abroad, emPhatically described the design and aPPlication of the Power generation Project with the mine ventilation methane oxidation in Lu’an Gaohe Mine in Shanxi Province,including the collecting and mixing system of the mine ventilation air methane,the safe delivery system of low-concentration gas,the oxidation system of the mine ventilation air methane,the utilization system of the waste heat and so on,and analyzed the significance of the successful construction of this Project.%大量煤矿乏风瓦斯的直接排空,在加剧温室效应的同时亦造成能源的浪费,而通过采用合适的技术对乏风瓦斯加以利用,将产生巨大的节能环保效益。介绍了国内外煤矿乏风瓦斯氧化及余热利用技术,重点介绍了山西潞安高河煤矿的乏风瓦斯氧化发电项目的设计及应用情况,包括乏风收集及掺混系统、低浓度瓦斯输送安全保障系统、乏风氧化系统、余热利用系统等,并分析了该项目建设成功的意义。

  16. Biogas production and methanogenic archaeal community in mesophilic and thermophilic anaerobic co-digestion processes.

    Science.gov (United States)

    Yu, D; Kurola, J M; Lähde, K; Kymäläinen, M; Sinkkonen, A; Romantschuk, M

    2014-10-01

    Over 258 Mt of solid waste are generated annually in Europe, a large fraction of which is biowaste. Sewage sludge is another major waste fraction. In this study, biowaste and sewage sludge were co-digested in an anaerobic digestion reactor (30% and 70% of total wet weight, respectively). The purpose was to investigate the biogas production and methanogenic archaeal community composition in the anaerobic digestion reactor under meso- (35-37 °C) and thermophilic (55-57 °C) processes and an increasing organic loading rate (OLR, 1-10 kg VS m(-3) d(-1)), and also to find a feasible compromise between waste treatment capacity and biogas production without causing process instability. In summary, more biogas was produced with all OLRs by the thermophilic process. Both processes showed a limited diversity of the methanogenic archaeal community which was dominated by Methanobacteriales and Methanosarcinales (e.g. Methanosarcina) in both meso- and thermophilic processes. Methanothermobacter was detected as an additional dominant genus in the thermophilic process. In addition to operating temperatures, the OLRs, the acetate concentration, and the presence of key substrates like propionate also affected the methanogenic archaeal community composition. A bacterial cell count 6.25 times higher than archaeal cell count was observed throughout the thermophilic process, while the cell count ratio varied between 0.2 and 8.5 in the mesophilic process. This suggests that the thermophilic process is more stable, but also that the relative abundance between bacteria and archaea can vary without seriously affecting biogas production.

  17. The effect of outside conditions on anaerobic ammonia oxidation reaction

    Institute of Scientific and Technical Information of China (English)

    YANG Min; WANG Shu-bo

    2016-01-01

    Organic carbon, inorganic carbon, temperature, pH and ORP are all to have a certain influence on the anaerobic ammonia oxidation reaction. We can draw some conclusions on the optimum conditions of anaerobic ammonia oxidation reaction. The optimum temperature of the anaerobic ammonia oxidation reaction is 30-35℃. And the optimum pH of the anaerobic ammonia reaction is 7.5-8.3. The presence of organic matters can affect the anaerobic ammonia reaction, and different organic matters have different influence on it. The concentration of the inorganic carbon also exist great influence on the reaction. High inorganic carbon concentration also can inhibit anaerobic ammonia oxidation reaction.

  18. Metabolic interactions between methanogenic consortia and anaerobic respiring bacteria

    DEFF Research Database (Denmark)

    Stams, A.J.; Oude Elferink, S.J.; Westermann, Peter

    2003-01-01

    Most types of anaerobic respiration are able to outcompete methanogenic consortia for common substrates if the respective electron acceptors are present in sufficient amounts. Furthermore, several products or intermediate compounds formed by anaerobic respiring bacteria are toxic to methanogenic...... consortia. Despite the potentially adverse effects, only few inorganic electron acceptors potentially utilizable for anaerobic respiration have been investigated with respect to negative interactions in anaerobic digesters. In this chapter we review competitive and inhibitory interactions between anaerobic...... respiring populations and methanogenic consortia in bioreactors. Due to the few studies in anaerobic digesters, many of our discussions are based upon studies of defined cultures or natural ecosystems...

  19. 嗜盐古菌Haloferax sp.H4蛋白质表达差异研究%Study on the Protein Ecpression Difference of Halophilic Archaea Haloferax sp.H4

    Institute of Scientific and Technical Information of China (English)

    刘杰; 高凯; 陈晨; 陈绍兴

    2011-01-01

    [目的]研究嗜盐古菌Haloferax sp.H4在不同环境中的蛋白表达差异.[方法]采用变性聚丙烯酰胺凝胶电泳(SDS-PAGE)检测不同NaCl浓度、pH、温度、有氧和无氧条件下的H4菌株蛋白表达差异.[结果]H4菌株在不同NaCl浓度、有氧和无氧条件下的蛋白表达存在明显特异性;而在不同pH和温度条件下,其蛋白表这差异性不明显.[结论]嗜盐古菌对不同环境因子的调控方式可能存在差异.%[Objective]The research aimed to study the protein expression difference of halophilic archaea Haloferax sp.H4 under the different environments.[Method]SDS-PAGE was used to detect the porotein expression difference of H4strain under the different NaCl concentration,PH value,temperature,aerobic and anaerobic conditions.[Result]The protein expression of H4strain had the obvious specificity underthe different NaCl concentration,aerobic and anaerobic conditions.But under the different pH value and temperature conditions,the protein expression different wasn't obvious.[Conclusion]Maybe the regulation manner of halophilic arehaea on the different environmental factors had the difference.

  20. Metagenomic analysis reveals the contribution of anaerobic methanotroph-1b in the oxidation of methane at the Ulleung Basin, East Sea of Korea.

    Science.gov (United States)

    Lee, Jin-Woo; Kwon, Kae Kyoung; Bahk, Jang-Jun; Lee, Dong-Hun; Lee, Hyun Sook; Kang, Sung Gyun; Lee, Jung-Hyun

    2016-12-01

    We have previously identified a sulfate methane transition zone (SMTZ) within the methane hydrate-bearing sediment in the Ulleung Basin, East Sea of Korea, and the presence of ANME-1b group in the sediment has been shown by phylogenetic analysis of a 16S rRNA gene. Herein, we describe taxonomic and functional profiling in the SMTZ sample by metagenomic analysis, comparing with that of surface sediment. Metagenomic sequences of 115 Mbp and 252 Mbp were obtained from SMTZ and surface sediments, respectively. The taxonomic profiling using BLASTX against the SEED within MG-RAST showed the prevalence of methanogens (19.1%), such as Methanosarcinales (12.0%) and Methanomicrobiales (4.1%) predominated within the SMTZ metagenome. A number of 185,200 SMTZ reads (38.9%) and 438,484 surface reads (62.5%) were assigned to functional categories, and methanogenesis-related reads were statistically significantly overrepresented in the SMTZ metagenome. However, the mapping analysis of metagenome reads to the reference genomes, most of the sequences of the SMTZ metagenome were mapped to ANME-1 draft genomes, rather than those of methanogens. Furthermore, the two copies of the methyl-coenzyme M reductase gene (mcrA) segments of the SMTZ metagenome were clustered with ANME-1b in the phylogenetic cluster. These results indicate that ANME-1b reads were miss-annotated to methanogens due to limitation of database. Many of key genes necessary for reverse methanogenesis were present in the SMTZ metagenome, except for N (5),N (10)-methenyl-H4MPT reductase (mer) and CoB-CoM heterodisulfide reductase subunits D and E (hdrDE). These data suggest that the ANME-1b represents the primary player the anaerobic methane oxidation in the SMTZ, of the methane hydrate-bearing sediment at the Ulleung Basin, East Sea of Korea.

  1. Performance and molecular evaluation of an anaerobic system with suspended biomass for treating wastewater with high fat content after enzymatic hydrolysis.

    Science.gov (United States)

    Rosa, Daniela R; Duarte, Iolanda C S; Saavedra, N Katia; Varesche, Maria B; Zaiat, Marcelo; Cammarota, Magali C; Freire, Denise M G

    2009-12-01

    The effect of a lipase-rich fungal enzymatic preparation, produced by a Penicillium sp. during solid-state fermentation, was evaluated in an anaerobic digester treating dairy wastewater with 1200 mg of oil and grease/L. The oil and grease hydrolysis step was carried out with 0.1% (w/v) of solid enzymatic preparation at 30 degrees C for 24 h, and resulted in a final free acid concentration eight times higher than the initial value. The digester operated in sequential batches of 48 h at 30 degrees C for 245 days, and had high chemical oxygen demand (COD) removal efficiencies (around 90%) when fed with pre-hydrolyzed wastewater. However, when the pre-hydrolysis step was removed, the anaerobic digester performed poorly (with an average COD removal of 32%), as the oil and grease accumulated in the biomass and effluent oil and grease concentration increased throughout the operational period. PCR-DGGE analysis of the Bacteria and Archaea domains revealed remarkable differences in the microbial profiles in trials conducted with and without the pre-hydrolysis step, indicating that differences observed in overall parameters were intrinsically related to the microbial diversity of the anaerobic sludge.

  2. Archaea and Bacteria Acclimate to High Total Ammonia in a Methanogenic Reactor Treating Swine Waste

    Directory of Open Access Journals (Sweden)

    Sofia Esquivel-Elizondo

    2016-01-01

    Full Text Available Inhibition by ammonium at concentrations above 1000 mgN/L is known to harm the methanogenesis phase of anaerobic digestion. We anaerobically digested swine waste and achieved steady state COD-removal efficiency of around 52% with no fatty-acid or H2 accumulation. As the anaerobic microbial community adapted to the gradual increase of total ammonia-N (NH3-N from 890±295 to 2040±30 mg/L, the Bacterial and Archaeal communities became less diverse. Phylotypes most closely related to hydrogenotrophic Methanoculleus (36.4% and Methanobrevibacter (11.6%, along with acetoclastic Methanosaeta (29.3%, became the most abundant Archaeal sequences during acclimation. This was accompanied by a sharp increase in the relative abundances of phylotypes most closely related to acetogens and fatty-acid producers (Clostridium, Coprococcus, and Sphaerochaeta and syntrophic fatty-acid Bacteria (Syntrophomonas, Clostridium, Clostridiaceae species, and Cloacamonaceae species that have metabolic capabilities for butyrate and propionate fermentation, as well as for reverse acetogenesis. Our results provide evidence countering a prevailing theory that acetoclastic methanogens are selectively inhibited when the total ammonia-N concentration is greater than ~1000 mgN/L. Instead, acetoclastic and hydrogenotrophic methanogens coexisted in the presence of total ammonia-N of ~2000 mgN/L by establishing syntrophic relationships with fatty-acid fermenters, as well as homoacetogens able to carry out forward and reverse acetogenesis.

  3. ANAEROBIC BIOLOGICAL TREATMENT OF PRODUCED WATER

    Energy Technology Data Exchange (ETDEWEB)

    John R. Gallagher

    2001-07-31

    During the production of oil and gas, large amounts of water are brought to the surface and must be disposed of in an environmentally sensitive manner. This is an especially difficult problem in offshore production facilities where space is a major constraint. The chief regulatory criterion for produced water is oil and grease. Most facilities have little trouble meeting this criterion using conventional oil-water separation technologies. However, some operations have significant amounts of naphthenic acids in the water that behave as oil and grease but are not well removed by conventional technologies. Aerobic biological treatment of naphthenic acids in simulated-produced water has been demonstrated by others; however, the system was easily overloaded by the large amounts of low-molecular-weight organic acids often found in produced waters. The objective of this research was to determine the ability of an anaerobic biological system to treat these organic acids in a simulated produced water and to examine the potential for biodegradation of the naphthenic acids in the anaerobic environment. A small fixed-film anaerobic biological reactor was constructed and adapted to treat a simulated produced water. The bioreactor was tubular, with a low-density porous glass packing material. The inocula to the reactor was sediment from a produced-water holding pond from a municipal anaerobic digester and two salt-loving methanogenic bacteria. During start-up, the feed to the reactor contained glucose as well as typical produced-water components. When glucose was used, rapid gas production was observed. However, when glucose was eliminated and the major organic component was acetate, little gas was generated. Methane production from acetate may have been inhibited by the high salt concentrations, by sulfide, or because of the lack, despite seeding, of microbes capable of converting acetate to methane. Toluene, a minor component of the produced water (0.1 g/L) was removed in the

  4. Oxygen Effects in Anaerobic Digestion - II

    Directory of Open Access Journals (Sweden)

    Deshai Botheju

    2010-04-01

    Full Text Available Standard models describing bio-gasification using anaerobic digestion do not include necessary processes to describe digester dynamics under the conditions of oxygen presence. Limited oxygenation in anaerobic digestion can sometimes be beneficial. The oxygen effects included anaerobic digestion model, ADM 1-Ox, was simulated against experimental data obtained from laboratory scale anaerobic digesters operated under different oxygenation conditions. ADM 1-Ox predictions are generally in good agreement with the trends of the experimental data. ADM 1-Ox simulations suggest the existence of an optimum oxygenation level corresponding to a peak methane yield. The positive impact of oxygenation on methane yield is more pronounced at conditions characterized by low hydrolysis rate coefficients (slowly degradable feed and low biomass concentrations. The optimum oxygenation point moves towards zero when the hydrolysis rate coefficient and the biomass concentration increase. Accordingly, the impact of oxygenation on methane yield can either be positive or negative depending on the digestion system characteristics. The developed ADM 1-Ox model can therefore be a valuable tool for recognizing suitable operating conditions for achieving the maximum benefits from partial aeration in anaerobic digestion.

  5. Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis.

    Science.gov (United States)

    Ravin, Nikolai V; Mardanov, Andrey V; Beletsky, Alexey V; Kublanov, Ilya V; Kolganova, Tatiana V; Lebedinsky, Alexander V; Chernyh, Nikolai A; Bonch-Osmolovskaya, Elizaveta A; Skryabin, Konstantin G

    2009-04-01

    Desulfurococcus kamchatkensis is an anaerobic organotrophic hyperthermophilic crenarchaeon isolated from a terrestrial hot spring. Its genome consists of a single circular chromosome of 1,365,223 bp with no extrachromosomal elements. A total of 1,474 protein-encoding genes were annotated, among which 205 are exclusive for D. kamchatkensis. The search for a replication origin site revealed a single region coinciding with a global extreme of the nucleotide composition disparity curve and containing a set of crenarchaeon-type origin recognition boxes. Unlike in most archaea, two genes encoding homologs of the eukaryotic initiator proteins Orc1 and Cdc6 are located distantly from this site. A number of mobile elements are present in the genome, including seven transposons representing IS607 and IS200/IS605 families and multiple copies of miniature inverted repeat transposable elements. Two large clusters of regularly interspaced repeats are present; none of the spacer sequences matches known archaeal extrachromosomal elements, except one spacer matches the sequence of a resident gene of D. kamchatkensis. Many of the predicted metabolic enzymes are associated with the fermentation of peptides and sugars, including more than 30 peptidases with diverse specificities, a number of polysaccharide degradation enzymes, and many transporters. Consistently, the genome encodes both enzymes of the modified Embden-Meyerhof pathway of glucose oxidation and a set of enzymes needed for gluconeogenesis. The genome structure and content reflect the organism's nutritionally diverse, competitive natural environment, which is periodically invaded by viruses and other mobile elements.

  6. Membrane biofilm development improves COD removal in anaerobic membrane bioreactor wastewater treatment.

    Science.gov (United States)

    Smith, Adam L; Skerlos, Steven J; Raskin, Lutgarde

    2015-09-01

    Membrane biofilm development was evaluated to improve psychrophilic (15°C) anaerobic membrane bioreactor (AnMBR) treatment of domestic wastewater. An AnMBR containing three replicate submerged membrane housings with separate permeate collection was operated at three levels of membrane fouling by independently controlling biogas sparging for each membrane unit. High membrane fouling significantly improved permeate quality, but resulted in dissolved methane in the permeate at a concentration two to three times the equilibrium concentration predicted by Henry's law. Illumina sequencing of 16S rRNA targeting Bacteria and Archaea and reverse transcription-quantitative polymerase chain reaction targeting the methyl coenzyme-M reductase (mcrA) gene in methanogens indicated that the membrane biofilm was enriched in highly active methanogens and syntrophic bacteria. Restoring fouled membranes to a transmembrane pressure (TMP) near zero by increasing biogas sparging did not disrupt the biofilm's treatment performance, suggesting that microbes in the foulant layer were tightly adhered and did not significantly contribute to TMP. Dissolved methane oversaturation persisted without high TMP, implying that methanogenesis in the biofilm, rather than high TMP, was the primary driving force in methane oversaturation. The results describe an attractive operational strategy to improve treatment performance in low-temperature AnMBR by supporting syntrophy and methanogenesis in the membrane biofilm through controlled membrane fouling.

  7. Isotope fractionation during the anaerobic consumption of acetate by methanogenic and sulfate-reducing microorganisms

    Science.gov (United States)

    Gövert, D.; Conrad, R.

    2009-04-01

    During the anaerobic degradation of organic matter in anoxic sediments and soils acetate is the most important substrate for the final step in production of CO2 and/or CH4. Sulfate-reducing bacteria (SRB) and methane-producing archaea both compete for the available acetate. Knowledge about the fractionation of 13C/12C of acetate carbon by these microbial groups is still limited. Therefore, we determined carbon isotope fractionation in different cultures of acetate-utilizing SRB (Desulfobacter postgatei, D. hydrogenophilus, Desulfobacca acetoxidans) and methanogens (Methanosarcina barkeri, M. acetivorans). Including literature values (e.g., Methanosaeta concilii), isotopic enrichment factors (epsilon) ranged between -35 and +2 permil, possibly involving equilibrium isotope effects besides kinetic isotope effects. The values of epsilon were dependent on the acetate-catabolic pathway of the particular microorganism, the methyl or carboxyl position of acetate, and the relative availability or limitation of the substrate acetate. Patterns of isotope fractionation in anoxic lake sediments and rice field soil seem to reflect the characteristics of the microorganisms actively involved in acetate catabolism. Hence, it might be possible using environmental isotopic information to determine the type of microbial metabolism converting acetate to CO2 and/or CH4.

  8. Biocatalytic methanation of hydrogen and carbon dioxide in an anaerobic three-phase system.

    Science.gov (United States)

    Burkhardt, M; Koschack, T; Busch, G

    2015-02-01

    A new type of anaerobic trickle-bed reactor was used for biocatalytic methanation of hydrogen and carbon dioxide under mesophilic temperatures and ambient pressure in a continuous process. The conversion of gaseous substrates through immobilized hydrogenotrophic methanogenic archaea in a biofilm is a unique feature of this type of reactor. Due to the formation of a three-phase system on the carrier surface and operation as a plug flow reactor without gas recirculation, a complete reaction could be observed. With a methane concentration higher than c(CH4) = 98%, the product gas exhibits a very high quality. A specific methane production of P(CH4) = 1.49 Nm(3)/(m(3)(SV) d) was achieved at a hydraulic loading rate of LR(H2) = 6.0 Nm(3)/(m(3)(SV) d). The relation between trickle flow through the reactor and productivity could be shown. An application for methane enrichment in combination with biogas facilities as a source of carbon dioxide has also been positively proven.

  9. Molecular tools for investigating ANME community structure and function

    Energy Technology Data Exchange (ETDEWEB)

    Hallam, Steven J.; Page, Antoine P.; Constan, Lea; Song, Young C.; Norbeck, Angela D.; Brewer, Heather M.; Pasa-Tolic, Ljiljana

    2011-05-20

    Methane production and consumption in anaerobic marine sediments 1 is catalyzed by a series of reversible tetramethanopterin (H4MPT)-linked C1 transfer reactions. Although many of these reactions are conserved between one-carbon compound utilizing microorganisms, two remain diagnostic for archaeal methane metabolism. These include reactions catalyzed by N5-methyltetrahydromethanopterin: coenzyme M methyltransferase and methyl coenzyme M reductase. The latter enzyme is central to C-H bond formation and cleavage underlying methanogenic and reverse methanogenic phenotypes. Here we describe a set of novel tools for the detection and functional analysis of H4MPT-linked C1 transfer reactions mediated by uncultivated anaerobic methane oxidizing archaea (ANME). These tools include polymerase chain reaction primers targeting ANME methyl coenzyme M reductase subunit A subgroups and protein extraction methods from marine sediments compatible with high-resolution mass spectrometry for profiling population structure and functional dynamics. [910, 1,043

  10. Anaerobic lipid degradation through acidification and methanization.

    Science.gov (United States)

    Kim, Ijung; Kim, Sang-Hyoun; Shin, Hang-Sik; Jung, Jin-Young

    2010-01-01

    In biological wastewater treatment high lipid concentration is known to inhibit microorganisms and cause active biomass flotation. To reduce lipid inhibition, a two-phase anaerobic system, consisting of an anaerobic sequencing batch reactor (ASBR) and an upflow anaerobic sludge blanket (UASB) reactor, was applied to synthetic dairy wastewater. During 153 days of operation, the two-phase system showed stable performance in lipid degradation. In the ASBR, a 13% lipid removal efficiency and 10% double bond removal efficiency were maintained. In the UASB, the chemical oxygen demand (COD), lipid and volatile fatty acid (VFA) removal efficiencies were more than 80%, 70% and 95%, respectively, up to organic loading rate 6.5 g COD/L/day. There were no operational problems such as serious scum formation or sludge washout. Protein degradation occurred prior to degradation during acidogenesis.

  11. Kinetics and modeling of anaerobic digestion process

    DEFF Research Database (Denmark)

    2003-01-01

    Anaerobic digestion modeling started in the early 1970s when the need for design and efficient operation of anaerobic systems became evident. At that time not only was the knowledge about the complex process of anaerobic digestion inadequate but also there were computational limitations. Thus......, the first models were very simple and consisted of a limited number of equations. During the past thirty years much research has been conducted on the peculiarities of the process and on the factors that influence it on the one hand while an enormous progress took place in computer science on the other....... The combination of both parameters resulted in the development of more and more concise and complex models. In this chapter the most important models found in the literature are described starting from the simplest and oldest to the more recent and complex ones....

  12. Multivariate monitoring of anaerobic co-digestion

    DEFF Research Database (Denmark)

    Madsen, Michael; Holm-Nielsen, Jens Bo

    Anaerobic digestion processes for production of renewable energy in the form of biogas, and in the future hydrogen, are becoming increasingly important worldwide. Sustainable solutions for renewable energy production systems are given high political priority, amongst other things due to global...... warming and environmental concerns. Anaerobic digestion applied in agriculture can simultaneously convert heterogeneous biomasses and wastes from the primary agricultural sector and from the bio processing industries, for instance food processing, pharma, and biofuel production, into valuable organic...... fertiliser and renewable energy. Meanwhile, in order for the biogas sector to become a significant player in the energy supply chain, the anaerobic digestion process has to be controlled to a greater extent than what is implemented as state-of-the-art today. Through application of the philosophy behind...

  13. The effect of tannic compounds on anaerobic wastewater treatment.

    NARCIS (Netherlands)

    Field, J.A.

    1989-01-01

    Anaerobic wastewater treatment is an alternative to the conventional aerobic treatment processes for the removal of easily biodegradable organic matter in medium to high strength industrial wastestreams. Anaerobic treatment has several advantages, however one important disadvantage is the high sensi

  14. Succession of lignocellulolytic bacterial consortia bred anaerobically from lake sediment

    NARCIS (Netherlands)

    Korenblum, Elisa; Jiménez Avella, Diego; van Elsas, Jan

    2016-01-01

    Anaerobic bacteria degrade lignocellulose in various anoxic and organically rich environments, often in a syntrophic process. Anaerobic enrichments of bacterial communities on a recalcitrant lignocellulose source were studied combining polymerase chain reaction–denaturing gradient gel electrophoresi

  15. Robust regulation of anaerobic digestion processes.

    Science.gov (United States)

    Mailleret, L; Bernard, O; Steyer, J P

    2003-01-01

    This paper deals with the problem of controlling anaerobic digestion processes. A two-step (i.e. acidogenesis-methanization) mass balance model is considered for a 1 m3 fixed bed digester treating industrial wine distillery wastewater. The control law aims at regulating the organic pollution level while avoiding washout of biomass. To this end, a simple output feedback controller is considered which regulates a variable strongly related to the Chemical Oxygen Demand (COD). Numerical simulations assuming noisy measurements first illustrate the robustness of this control procedure. Then, the regulating procedure is implemented on the considered anaerobic digestion process in order to validate and demonstrate its efficiency in real life experiments.

  16. Anaerobic bacteria, the colon and colitis.

    Science.gov (United States)

    Roediger, W E

    1980-02-01

    Anaerobic bacteria constitute more than 90% of the bacteria in the colon. An anaerobic environment is needed to maintain their growth and the production of short-chain fatty acids by these bacteria from carbohydrates. Short-chain fatty acids are rapidly absorbed and essential for metabolic as well as functional welfare of the colonic mucosa. The importance of these acids in water absorption and in the patogenesis of colitis is discussed in relation to the concept of "energy deficiency diseases" of the colonic mucosa.

  17. The Pasteur effect in facultative anaerobic metazoa.

    Science.gov (United States)

    Schmidt, H; Kamp, G

    1996-05-15

    The existence and the regulatory mechanisms of the Pasteur effect in facultative anaerobic metazoa are discussed. There are three reasons for the controversy surrounding this phenomenon. 1) The different definitions of the Pasteur effect, 2) the antagonistic effect of metabolic depression and its species specific response to hypoxia, as well as 3) the laboratory-specific differences in the experimental procedures for analyzing the Pasteur effect and its regulation. This review aims to clarify the confusion about the existence of the Pasteur effect in facultative anaerobic metazoa and to offer possible molecular mechanisms.

  18. The Application of Biomarker Genes for DNA/RNA-Stable Isotope Probing of Active Methanotrophs Responsible for Aerobic Methane Oxidation in Six Paddy Soils%基于核酸DNA/RNA同位素示踪技术的水稻土甲烷氧化微生物研究

    Institute of Scientific and Technical Information of China (English)

    郑燕; 贾仲君

    2016-01-01

    Rice fields are major source of atmospheric methane(CH4). However,30%~90% of CH4 produced in paddy soils is oxidized by methanotrophs before it escapes to the atmosphere. China holds the largest rice production in the world,but it remains largely unknown about the active methane oxidizers in paddy soils. In this study,soil microcosms of six paddy soil incubated with 13CH4 were constructed to assess active methanotrophs by tracing the isotopically labeled 13C-DNA/RNA. Six paddy soils collected from Yingtan City of Jiangxi Province(YT),Ziyang City of Sichuan Province(ZY),Jiaxing City of Zhejiang Province(JX),Changshu City of Jiangsu Province(CS),Yangzhou City of Jiangsu Province(YZ), and Wuchang City of Heilongjiang Province(WC),were incubated with 400 µmol-1 L labeled 13CH4 or unlabeled 12CH4 to determine aerobic methane oxidation kinetics. The destructive sampling was conducted when 400 µmol-1 L CH4 was consumed. 13C-DNA and 13C-RNA were obtained through ultracentrifugation of total DNA and RNA,respectively. Clone library of pmoA genes from 13C-DNA and 16S rRNA genes from 13C-RNA were constructed to analyze composition of active methanotrophic community. After ultracentrifugation of total DNA and RNA,the agarose gel electrophoresis of pmoA gene amplicons and methanotrophic 16S rRNA reverse transcription amplicons from the fractionated DNA and rRNA,respectively,were performed, indicating the incorporation of 13C-substrate into methanotrophs during the aerobic methane oxidation. DNA-SIP and rRNA-SIP each have their advantages. In contrast to DNA,the incorporation of labeled substrate into rRNA is much faster,and a greater unspecific background of ‘heavy’ nucleic acid was observed in ′heavy′fractions in rRNA-SIP than DNA-SIP,indicating the more efficient separation for DNA.. The separation of differentially labeled rRNA was effective,however,it was not as quantitative as for DNA. This resulted in a greater unspecific background of ‘heavy’ rRNA in

  19. Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures

    Directory of Open Access Journals (Sweden)

    Pride David T

    2008-09-01

    Full Text Available Abstract Background Metagenomic analysis provides a rich source of biological information for otherwise intractable viral communities. However, study of viral metagenomes has been hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences. We sought to develop algorithms for examination of viral metagenomes to identify the origin of sequences independent of BLAST algorithms. We chose viral metagenomes obtained from two hot springs, Bear Paw and Octopus, in Yellowstone National Park, as they represent simple microbial populations where comparatively large contigs were obtained. Thermal spring metagenomes have high proportions of sequences without significant Genbank homology, which has hampered identification of viruses and their linkage with hosts. To analyze each metagenome, we developed a method to classify DNA fragments using genome signature-based phylogenetic classification (GSPC, where metagenomic fragments are compared to a database of oligonucleotide signatures for all previously sequenced Bacteria, Archaea, and viruses. Results From both Bear Paw and Octopus hot springs, each assembled contig had more similarity to other metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a genome signature common to each of these extreme environments. While viral metagenomes from Bear Paw and Octopus share some similarity, the genome signatures from each locale are largely unique. GSPC using a microbial database predicts most of the Octopus metagenome has archaeal signatures, while bacterial signatures predominate in Bear Paw; a finding consistent with those of Genbank BLAST. When using a viral database, the majority of the Octopus metagenome is predicted to belong to archaeal virus Families Globuloviridae and Fuselloviridae, while none of the Bear Paw metagenome is predicted to belong to archaeal viruses. As expected, when microbial and viral databases are combined, each of

  20. Extremely halophilic archaea from ancient salt sediments and their possible survival in halite fluid inclusions

    Science.gov (United States)

    Stan-Lotter, H.; Fendrihan, S.; Gerbl, F. W.; Dornmayr-Pfaffenhuemer, M.; Frethem, C.

    2008-09-01

    Halophilic archaebacteria (haloarchaea) thrive in environments with salt concentrations approaching saturation, such as natural brines, marine solar salterns and alkaline salt lakes; they have also been isolated from ancient subsurface salt sediments of great geological age (195-280 million years) and some of those strains were described as novel species (1). The cells survived perhaps while being enclosed within small fluid inclusions in the halite. The characterization of subsurface microbial life is of astrobiological relevance since extraterrestrial halite has been detected and since microbial life on Mars, if existent, may have retreated into the subsurface. We attempted to simulate the embedding process of extremely halophilic archaea and to analyse any cellular changes which might occur. When enclosing haloarchaea in laboratory grown halite, cells accumulated preferentially in fluid inclusions, as could be demonstrated by pre-staining with fluorescent dyes. With increased time of embedding, rod-shaped cells of Halobacterium salinarum strains were found to assume roundish morphologies. Upon dissolution of the salt crystals, these spheres were stable and viable for months when kept in buffers containing 4 M NaCl. Scanning electron microscopy (SEM) following fixation with glutaraldehyde suggested a potentially gradual transformation from rods to spheres. This notion was supported by fluorescence microscopy of Halobacterium cells, following embedding in halite and staining with SYTO 9. One-dimensional protein patterns of rods and spheres, following SDS polyacrylamide gel electrophoresis, were similar except that the S-layer protein appeared reduced by about 15 - 20 % in spheres. The reddish-orange pigmentation of spheres was much lighter compared to that of rod-shaped cells, suggesting lowered concentrations of carotenoids; this was confirmed by extraction and spectrometry of pigments. The data suggested that Halobacterium cells are capable of forming specific

  1. The Influence of Hydration on Anaerobic Performance: A Review

    Science.gov (United States)

    Kraft, Justin A.; Green, James M.; Bishop, Phillip A.; Richardson, Mark T.; Neggers, Yasmin H.; Leeper, James D.

    2012-01-01

    This review examines the influence of dehydration on muscular strength and endurance and on single and repeated anaerobic sprint bouts. Describing hydration effects on anaerobic performance is difficult because various exercise modes are dominated by anaerobic energy pathways, but still contain inherent physiological differences. The critical…

  2. Stability of anaerobic reactors under micro-aeration conditions

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez-Polanco, M.; Perez, S.; Diaz, I.; Fernandez-Polanco, F.

    2009-07-01

    Oxidation of sulphide in anaerobic bioreactors by introducing limited amounts of oxygen provides a relatively simple strategy for reducing the levels of sulphite in anaerobic digesters (biogas and effluent). The introduction of limited amounts of air is a general practice in agricultural anaerobic digesters, it is estimated that worldwide over 3.000 units are operated under such conditions. (Author)

  3. Anaerobic Digestion. Student Manual. Biological Treatment Process Control.

    Science.gov (United States)

    Carnegie, John W., Ed.

    This student manual contains the textual material for a four-lesson unit on anaerobic digestion control. Areas addressed include: (1) anaerobic sludge digestion (considering the nature of raw sludge, purposes of anaerobic digestion, the results of digestion, types of equipment, and other topics); (2) digester process control (considering feeding…

  4. Optimization and microbial community analysis for production of biogas from solid waste residues of palm oil mill industry by solid-state anaerobic digestion.

    Science.gov (United States)

    Suksong, Wantanasak; Kongjan, Prawit; Prasertsan, Poonsuk; Imai, Tsuyoshi; O-Thong, Sompong

    2016-08-01

    This study investigated the improvement of biogas production from solid-state anaerobic digestion (SS-AD) of oil palm biomass by optimizing of total solids (TS) contents, feedstock to inoculum (F:I) ratios and carbon to nitrogen (C:N) ratios. Highest methane yield from EFB, OPF and OPT of 358, 280 and 324m(3)CH4ton(-1)VS, respectively, was achieved at TS content of 16%, C:N ratio of 30:1 and F:I ratio of 2:1. The main contribution to methane from biomass was the degradation of cellulose and hemicellulose. The highest methane production of 72m(3)CH4ton(-1) biomass was achieved from EFB. Bacteria community structure in SS-AD process of oil palm biomass was dominated by Ruminococcus sp. and Clostridium sp., while archaea community was dominated by Methanoculleus sp. Oil palm biomass has great potential for methane production via SS-AD.

  5. Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota

    Science.gov (United States)

    Kublanov, Ilya V.; Sigalova, Olga M.; Gavrilov, Sergey N.; Lebedinsky, Alexander V.; Rinke, Christian; Kovaleva, Olga; Chernyh, Nikolai A.; Ivanova, Natalia; Daum, Chris; Reddy, T.B.K.; Klenk, Hans-Peter; Spring, Stefan; Göker, Markus; Reva, Oleg N.; Miroshnichenko, Margarita L.; Kyrpides, Nikos C.; Woyke, Tanja; Gelfand, Mikhail S.; Bonch-Osmolovskaya, Elizaveta A.

    2017-01-01

    The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis

  6. Optimisation of the two-phase dry-thermophilic anaerobic digestion process of sulphate-containing municipal solid waste: population dynamics.

    Science.gov (United States)

    Zahedi, S; Sales, D; Romero, L I; Solera, R

    2013-11-01

    Microbial population dynamics and anaerobic digestion (AD) process to eight different hydraulic retention times (HRTs) (from 25d to 3.5d) in two-phase dry-thermophilic AD from sulphate-containing solid waste were investigated. Maximum values of gas production (1.9 ± 0.2 l H2/l/d; 5.4 ± 0.3 l CH4/l/d and 82 ± 9 ml H2S/l/d) and microbial activities were obtained at 4.5d HRT; where basically comprised hydrolysis step in the first phase (HRT=1.5d) and acidogenic step finished in the second phase as well as acetogenic-methanogenic steps (HRT=3d). In the first phase, hydrolytic-acidogenic bacteria (HABs) was the main group (44-77%) and Archaea, acetogens and sulphate-reducing bacteria (SRBs) contents were not significant; in the second phase (except to 2d HRT), microbial population was able to adapt to change in substrate and HRTs to ensure the proper functioning of the system and both acetogens and Archaea were dominated over SRBs. Decreasing HRT resulted in an increase in microbial activities.

  7. Sulphate reduction experiment: SURE-1

    Energy Technology Data Exchange (ETDEWEB)

    Pedersen, K.; Arlinger, J.; Bengtsson, A.; Edlund, J.; Eriksson, L.; Hallbeck, L.; Johansson, J.; Paeaejaervi, A.; Rabe, L. [Microbial Analytics Sweden AB, Moelnlycke (Sweden)

    2013-11-15

    It was previously concluded that opposing gradients of sulphate and methane, observations of 16S rDNA sequences displaying great similarity to those of anaerobic methane-oxidizing Archaea, and a peak in sulphide concentration in groundwater from a depth of 250-350 m in Olkiluoto, Finland, indicated proper conditions for methane oxidation with sulphate. In the present research (SURE-1), pressure-resistant, gas-tight circulating systems were constructed to enable the investigation of attached and unattached anaerobic microbial populations from a depth of 327 m in Olkiluoto under in situ pressure (2.4 MPa), diversity, dissolved gas, and hydrochemical conditions of groundwater station ONKPVA6. Three parallel flow cell cabinets were configured to allow observation of the influence on microbial metabolic activity of 11 mM methane, 11 mM methane plus 10 mM H{sub 2}, or 2.1 mM O{sub 2} plus 7.9 mM N{sub 2} (i.e., air). The concentrations of these gases and of organic acids and carbon, sulphur chemistry, pH and E{sub h}, ATP, numbers of cultivable microorganisms, and total numbers of cells and bacteriophages were subsequently recorded under batch conditions for 105 d. The system containing H{sub 2} and methane displayed microbial reduction of 0.7 mM sulphate to sulphide, while the system containing only methane produced 0.2 mM reduced sulphate. The system containing added air became inhibited and displayed no signs of microbial activity. Added H{sub 2} and methane induced increasing numbers of lysogenic bacteriophages per cell. It appears possible that a microbial anaerobic methane-oxidizing process coupled to acetate formation and sulphate reduction may be ongoing in aquifers at a depth of 250-350 m in Olkiluoto, but clear evidence of such an AOM process was not obtained. (orig.)

  8. Environmental impacts of anaerobic digestion and the use of anaerobic residues as soil amendment

    Energy Technology Data Exchange (ETDEWEB)

    Mosey, F.E. [VFA Services Ltd., Herts (United Kingdom)

    1996-01-01

    This paper defines the environmental role of anaerobic digestion within the overall objective of recovering energy from renewable biomass resources. Examples and opportunities for incorporating anaerobic digestion into biomass-to-energy schemes are discussed, together with environmental aspects of anaerobic digestion plants. These include visual, public amenity, pathogens and public health, odor control, and gaseous emissions. Digestate disposal and the benefits of restrictions on recycling organic wastes and biomass residues back to the land are discussed, particularly as they relate to American and European codes of practice and environmental legislation. The paper concludes that anaerobic digestion, if performed in purpose-designed reactors that efficiently recover and use biogas, is an environmentally benign process that can enhance energy recovery and aid the beneficial land use of plant residues in many biomass-to-energy schemes.

  9. Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria.

    Science.gov (United States)

    Ziegler, Sibylle; Dolch, Kerstin; Geiger, Katharina; Krause, Susanne; Asskamp, Maximilian; Eusterhues, Karin; Kriews, Michael; Wilhelms-Dick, Dorothee; Goettlicher, Joerg; Majzlan, Juraj; Gescher, Johannes

    2013-09-01

    Biofilms can provide a number of different ecological niches for microorganisms. Here, a multispecies biofilm was studied in which pyrite-oxidizing microbes are the primary producers. Its stability allowed not only detailed fluorescence in situ hybridization (FISH)-based characterization of the microbial population in different areas of the biofilm but also to integrate these results with oxygen and pH microsensor measurements conducted before. The O2 concentration declined rapidly from the outside to the inside of the biofilm. Hence, part of the population lives under microoxic or anoxic conditions. Leptospirillum ferrooxidans strains dominate the microbial population but are only located in the oxic periphery of the snottite structure. Interestingly, archaea were identified only in the anoxic parts of the biofilm. The archaeal community consists mainly of so far uncultured Thermoplasmatales as well as novel ARMAN (Archaeal Richmond Mine Acidophilic Nanoorganism) species. Inductively coupled plasma analysis and X-ray absorption near edge structure spectra provide further insight in the biofilm characteristics but revealed no other major factors than oxygen affecting the distribution of bacteria and archaea. In addition to catalyzed reporter deposition FISH and oxygen microsensor measurements, microautoradiographic FISH was used to identify areas in which active CO2 fixation takes place. Leptospirilla as well as acidithiobacilli were identified as primary producers. Fixation of gaseous CO2 seems to proceed only in the outer rim of the snottite. Archaea inhabiting the snottite core do not seem to contribute to the primary production. This work gives insight in the ecological niches of acidophilic microorganisms and their role in a consortium. The data provided the basis for the enrichment of uncultured archaea.

  10. A simple and sensitive quality control method of the anaerobic atmosphere for identification and antimicrobial susceptibility testing of anaerobic bacteria

    DEFF Research Database (Denmark)

    Justesen, Tage; Justesen, Ulrik Stenz

    2013-01-01

    The maintenance of a strict anaerobic atmosphere is essential for the culture of strict anaerobic bacteria. We describe a simple and sensitive quality control method of the anaerobic atmosphere, based on the measurement of the zone diameter around a 5-μg metronidazole disk when testing an aerotol...

  11. 生活垃圾填埋场甲烷自然减排的新途径——厌氧与好氧的共氧化作用%New Way for Natural Mitigation of Methane in Domestic Waste Landfill Sites: Co-oxidation of Anaerobic and Aerobic Oxidation

    Institute of Scientific and Technical Information of China (English)

    周海燕; 韩丹

    2011-01-01

    通过证实生活垃圾填埋场中甲烷厌氧氧化与好氧氧化的共存,提出了甲烷自然减排的新途径.分别选取暴雨过后垃圾填埋表层30~60 cm的覆土、1.5 m以下的垃圾以及底层矿化垃圾做硫酸盐还原菌阳性反应实验,结果表明:生活垃圾填埋体不同填埋层都存在不同数量级的硫酸盐还原菌,且底层矿化垃圾中的硫酸盐还原菌的数量最多,表层覆土中最少.颗粒大小比例为50%:50%的垃圾样品表现出最佳的甲烷好氧与厌氧氧化效果,且厌氧氧化在共氧化作用中的比例达到20%以上.含水率为25%时,矿化垃圾中微生物活性最大,好氧与厌氧氧化甲烷速率均达到最大;当含水率接近70%时,甲烷厌氧氧化的贡献率可达30%以上.外源甲烷的补充可以驯化甲烷氧化微生物,其中甲烷好氧氧化时间最大可缩短50%;而甲烷通入量超过2 mL后,甲烷好氧与厌氧氧化均受到抑制.%A new way for natural mitigation of methane was put forward by authenticating co-oxidation of anaerobic and aerobic oxidation of methane in domestic waste landfill sites. The soil at 30-60 cm, the waste below 1.5 m from the surface, and the aged waste at the bottom, were selected for the experiments of sulfate-reducing bacteria positive reaction. The results showed that sulfate-reducing bacteria nearly existed in all landfill layers of waste landfill bodies, and aged waste at the bottom contained most, the surface soil contained least. Waste samples with 50%: 50% of coarse and fine particle size proportion showed the best methane oxidation effect of aerobic and anaerobic oxidation, and anaerobic oxidation accounted for above 20%. Microbial activity in aged waste and its methane co-oxidation rate both reached the maximum value as moisture content was 25%. Anaerobic oxidation rate could reach more than 30% as moisture content was close to 70%. Supplement of exogenous methane could culture methane-oxidizing bacteria

  12. Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

    KAUST Repository

    Kyrpides, Nikos C.

    2014-08-05

    Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet\\'s most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet\\'s genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

  13. Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics.

    Directory of Open Access Journals (Sweden)

    Rika E Anderson

    Full Text Available The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts' functional capabilities.

  14. Genomes of two new ammonia-oxidizing archaea enriched from deep marine sediments.

    Directory of Open Access Journals (Sweden)

    Soo-Je Park

    Full Text Available Ammonia-oxidizing archaea (AOA are ubiquitous and abundant and contribute significantly to the carbon and nitrogen cycles in the ocean. In this study, we assembled AOA draft genomes from two deep marine sediments from Donghae, South Korea, and Svalbard, Arctic region, by sequencing the enriched metagenomes. Three major microorganism clusters belonging to Thaumarchaeota, Epsilonproteobacteria, and Gammaproteobacteria were deduced from their 16S rRNA genes, GC contents, and oligonucleotide frequencies. Three archaeal genomes were identified, two of which were distinct and were designated Ca. "Nitrosopumilus koreensis" AR1 and "Nitrosopumilus sediminis" AR2. AR1 and AR2 exhibited average nucleotide identities of 85.2% and 79.5% to N. maritimus, respectively. The AR1 and AR2 genomes contained genes pertaining to energy metabolism and carbon fixation as conserved in other AOA, but, conversely, had fewer heme-containing proteins and more copper-containing proteins than other AOA. Most of the distinctive AR1 and AR2 genes were located in genomic islands (GIs that were not present in other AOA genomes or in a reference water-column metagenome from the Sargasso Sea. A putative gene cluster involved in urea utilization was found in the AR2 genome, but not the AR1 genome, suggesting niche specialization in marine AOA. Co-cultured bacterial genome analysis suggested that bacterial sulfur and nitrogen metabolism could be involved in interactions with AOA. Our results provide fundamental information concerning the metabolic potential of deep marine sedimentary AOA.

  15. Genomes of two new ammonia-oxidizing archaea enriched from deep marine sediments.

    Science.gov (United States)

    Park, Soo-Je; Ghai, Rohit; Martín-Cuadrado, Ana-Belén; Rodríguez-Valera, Francisco; Chung, Won-Hyong; Kwon, KaeKyoung; Lee, Jung-Hyun; Madsen, Eugene L; Rhee, Sung-Keun

    2014-01-01

    Ammonia-oxidizing archaea (AOA) are ubiquitous and abundant and contribute significantly to the carbon and nitrogen cycles in the ocean. In this study, we assembled AOA draft genomes from two deep marine sediments from Donghae, South Korea, and Svalbard, Arctic region, by sequencing the enriched metagenomes. Three major microorganism clusters belonging to Thaumarchaeota, Epsilonproteobacteria, and Gammaproteobacteria were deduced from their 16S rRNA genes, GC contents, and oligonucleotide frequencies. Three archaeal genomes were identified, two of which were distinct and were designated Ca. "Nitrosopumilus koreensis" AR1 and "Nitrosopumilus sediminis" AR2. AR1 and AR2 exhibited average nucleotide identities of 85.2% and 79.5% to N. maritimus, respectively. The AR1 and AR2 genomes contained genes pertaining to energy metabolism and carbon fixation as conserved in other AOA, but, conversely, had fewer heme-containing proteins and more copper-containing proteins than other AOA. Most of the distinctive AR1 and AR2 genes were located in genomic islands (GIs) that were not present in other AOA genomes or in a reference water-column metagenome from the Sargasso Sea. A putative gene cluster involved in urea utilization was found in the AR2 genome, but not the AR1 genome, suggesting niche specialization in marine AOA. Co-cultured bacterial genome analysis suggested that bacterial sulfur and nitrogen metabolism could be involved in interactions with AOA. Our results provide fundamental information concerning the metabolic potential of deep marine sedimentary AOA.

  16. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

    Science.gov (United States)

    Kyrpides, Nikos C; Hugenholtz, Philip; Eisen, Jonathan A; Woyke, Tanja; Göker, Markus; Parker, Charles T; Amann, Rudolf; Beck, Brian J; Chain, Patrick S G; Chun, Jongsik; Colwell, Rita R; Danchin, Antoine; Dawyndt, Peter; Dedeurwaerdere, Tom; DeLong, Edward F; Detter, John C; De Vos, Paul; Donohue, Timothy J; Dong, Xiu-Zhu; Ehrlich, Dusko S; Fraser, Claire; Gibbs, Richard; Gilbert, Jack; Gilna, Paul; Glöckner, Frank Oliver; Jansson, Janet K; Keasling, Jay D; Knight, Rob; Labeda, David; Lapidus, Alla; Lee, Jung-Sook; Li, Wen-Jun; Ma, Juncai; Markowitz, Victor; Moore, Edward R B; Morrison, Mark; Meyer, Folker; Nelson, Karen E; Ohkuma, Moriya; Ouzounis, Christos A; Pace, Norman; Parkhill, Julian; Qin, Nan; Rossello-Mora, Ramon; Sikorski, Johannes; Smith, David; Sogin, Mitch; Stevens, Rick; Stingl, Uli; Suzuki, Ken-Ichiro; Taylor, Dorothea; Tiedje, Jim M; Tindall, Brian; Wagner, Michael; Weinstock, George; Weissenbach, Jean; White, Owen; Wang, Jun; Zhang, Lixin; Zhou, Yu-Guang; Field, Dawn; Whitman, William B; Garrity, George M; Klenk, Hans-Peter

    2014-08-01

    Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

  17. Diversity and Distribution of Archaea in the Mangrove Sediment of Sundarbans

    Directory of Open Access Journals (Sweden)

    Anish Bhattacharyya

    2015-01-01

    Full Text Available Mangroves are among the most diverse and productive coastal ecosystems in the tropical and subtropical regions. Environmental conditions particular to this biome make mangroves hotspots for microbial diversity, and the resident microbial communities play essential roles in maintenance of the ecosystem. Recently, there has been increasing interest to understand the composition and contribution of microorganisms in mangroves. In the present study, we have analyzed the diversity and distribution of archaea in the tropical mangrove sediments of Sundarbans using 16S rRNA gene amplicon sequencing. The extraction of DNA from sediment samples and the direct application of 16S rRNA gene amplicon sequencing resulted in approximately 142 Mb of data from three distinct mangrove areas (Godkhali, Bonnie camp, and Dhulibhashani. The taxonomic analysis revealed the dominance of phyla Euryarchaeota and Thaumarchaeota (Marine Group I within our dataset. The distribution of different archaeal taxa and respective statistical analysis (SIMPER, NMDS revealed a clear community shift along the sampling stations. The sampling stations (Godkhali and Bonnie camp with history of higher hydrocarbon/oil pollution showed different archaeal community pattern (dominated by haloarchaea compared to station (Dhulibhashani with nearly pristine environment (dominated by methanogens. It is indicated that sediment archaeal community patterns were influenced by environmental conditions.

  18. Extremely halophilic archaea from ancient salt sediments and their long term survival.

    Science.gov (United States)

    Stan-Lotter, Helga; Fendrihan, Sergiu; Dornmayr-Pfaffenhuemer, Marion

    Halophilic archaebacteria (haloarchaea) thrive in environments with salt concentrations approaching saturation, such as natural brines, marine solar salterns and alkaline salt lakes; they have also been isolated from rock salt of great geological age (195-250 million years) and some of those strains were described as novel species (1). The cells survived perhaps while being enclosed within small fluid inclusions in the halite. When simulating the embedding process of haloarchaea in laboratory-grown salt crystals, cells accumulated preferentially in fluid inclusions, as could be demonstrated by pre-staining with fluorescent dyes. The issue of extreme long term microbial survival in rock salt has considerable implications for the search for extraterrestrial life. Halite has been found in Martian meteorites, salts are present on the Martian surface and there is good evidence for a salty ocean on the Jovian moon Europa. Therefore the search for halophilic prokaryotic life in such environments appears plausible. The development of detection methods for subsurface haloarchaea, which might also be applicable to samples from future missions to space, is important and some examples such as fluorescence microscopy methods with novel dyes will be described. (1) Fendrihan, S., Legat, A., Gruber, C., Pfaffenhuemer, M., Weidler, G., Gerbl, F., Stan- Lotter, H. (2006) Extremely halophilic archaea and the issue of long term microbial survival. Reviews in Environmental Science and Bio/technology 5, 1569-1605.

  19. Geographical Distribution of Methanogenic Archaea in Nine Representative Paddy Soils in China

    Science.gov (United States)

    Zu, Qianhui; Zhong, Linghao; Deng, Ye; Shi, Yu; Wang, Baozhan; Jia, Zhongjun; Lin, Xiangui; Feng, Youzhi

    2016-01-01

    Paddy field methanogenic archaea are responsible for methane (CH4) production and contribute significantly to climate change. The information regarding the spatial variations in the abundance, the diversity and the composition of such ecologically important microbes, however, is quite limited at large scale. In this investigation, we studied the abundance, alpha diversity and geographical distribution of methanogenic archaeal communities in nine representative paddy sites, along a large latitudinal gradient in China, using pyrosequencing and real-time quantitative PCR. It is found that all paddy soils harbor constant methanogenic archaeal constituents, which is dominated by family Methanocellaceae (37.3%), Methanobacteriaceae (22.1%), Methanosaetaceae (17.2%), and Methanosarcinaceae (9.8%). Methanogenic archaeal abundance is primarily influenced by soil C (R = 0.612, P = 0.001) and N (R = 0.673, P = 0.001) contents, as well as alpha diversity by soil pH (PD: R = -0.552, P = 0.006; Chao1: R = -0.615, P = 0.002). Further exploration revealed that both spatial distance (R = 0.3469, P = 0.001, partial mental test) and soil chemical variables mainly about soil C and N (R = 0.2847, P = 0.001) are the two major factors affecting methanogenic archaeal community composition distribution in paddy soils. This finding will allow us to develop a better picture of the biogeographic ranges of these ecologically important microbes and get deeper insights into their ecology. PMID:27679621

  20. Dynamics of ammonia-oxidizing Archaea and Bacteria in contrasted freshwater ecosystems.

    Science.gov (United States)

    Hugoni, Mylène; Etien, Sandrine; Bourges, Antoine; Lepère, Cécile; Domaizon, Isabelle; Mallet, Clarisse; Bronner, Gisèle; Debroas, Didier; Mary, Isabelle

    2013-05-01

    Thaumarchaeota have been recognized as the main drivers of aerobic ammonia oxidation in many ecosystems. However, little is known about the role of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) in lacustrine ecosystems. In this study, the photic zone of three contrasted freshwater ecosystems located in France was sampled during two periods: winter homothermy (H) and summer thermal stratification (TS), to investigate the distribution of planktonic AOA and AOB. We showed that AOB were predominant in nutrient-rich ecosystems, whereas AOA dominated when ammonia concentrations were the lowest and during winter, which could provide a favorable environment for their growth. Moreover, analyses of archaeal libraries revealed the ubiquity of the thaumarchaeal I.1a clade associated with higher diversity of AOA in the most nutrient-poor lake. More generally, this work assesses the presence of AOA in lakes, but also highlights the existence of clades typically associated with lacustrine and hot spring ecosystems and specific ecological niches occupied by these microorganisms.

  1. Archaea rather than bacteria control nitrification in two agricultural acidic soils.

    Science.gov (United States)

    Gubry-Rangin, Cécile; Nicol, Graeme W; Prosser, James I

    2010-12-01

    Nitrification is a central component of the global nitrogen cycle. Ammonia oxidation, the first step of nitrification, is performed in terrestrial ecosystems by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Published studies indicate that soil pH may be a critical factor controlling the relative abundances of AOA and AOB communities. In order to determine the relative contributions of AOA and AOB to ammonia oxidation in two agricultural acidic Scottish soils (pH 4.5 and 6), the influence of acetylene (a nitrification inhibitor) was investigated during incubation of soil microcosms at 20 °C for 1 month. High rates of nitrification were observed in both soils in the absence of acetylene. Quantification of respective amoA genes (a key functional gene for ammonia oxidizers) demonstrated significant growth of AOA, but not AOB. A significant positive relationship was found between nitrification rate and AOA, but not AOB growth. AOA growth was inhibited in the acetylene-containing microcosms. Moreover, AOA transcriptional activity decreased significantly in the acetylene-containing microcosms compared with the control, whereas no difference was observed for the AOB transcriptional activity. Consequently, growth and activity of only archaeal but not bacterial ammonia oxidizer communities strongly suggest that AOA, but not AOB, control nitrification in these two acidic soils.

  2. Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions.

    Science.gov (United States)

    Di, Hong J; Cameron, Keith C; Shen, Ju-Pei; Winefield, Chris S; O'Callaghan, Maureen; Bowatte, Saman; He, Ji-Zheng

    2010-06-01

    Nitrification is a key process of the nitrogen (N) cycle in soil with major environmental implications. The recent discovery of ammonia-oxidizing archaea (AOA) questions the traditional assumption of the dominant role of ammonia-oxidizing bacteria (AOB) in nitrification. We investigated AOB and AOA growth and nitrification rate in two different layers of three grassland soils treated with animal urine substrate and a nitrification inhibitor [dicyandiamide (DCD)]. We show that AOB were more abundant in the topsoils than in the subsoils, whereas AOA were more abundant in one of the subsoils. AOB grew substantially when supplied with a high dose of urine substrate, whereas AOA only grew in the Controls without the urine-N substrate. AOB growth and the amoA gene transcription activity were significantly inhibited by DCD. Nitrification rates were much higher in the topsoils than in the subsoils and were significantly related to AOB abundance, but not to AOA abundance. These results suggest that AOB and AOA prefer different soil N conditions to grow: AOB under high ammonia (NH(3)) substrate and AOA under low NH(3) substrate conditions.

  3. Isolation and characterization of halophilic bacteria and archaea from salt ponds in Hangu Saltworks, Tianjin, China

    Science.gov (United States)

    Deng, Yuangao; Xu, Gaochao; Sui, Liying

    2015-07-01

    A total of 26 isolates were obtained from solar salt ponds of different salinities (100, 150, 200, and 250) in Hangu Saltworks Co. Ltd., Tianjin, China. Phylogenetic analysis of 16S rRNA gene sequences indicated that five bacteria genera Halomonas, Salinicoccus, Oceanobacillus, Gracibacillus, and Salimicrobium and one archaea genera Halorubrum were present. The genus Halomonas was predominant with eight strains distributed in a salinity range of 100-200, followed by Halorubrum with six strains in salinity 250. Based on the genus and original sampling salinity, eight bacterial and two archaeal isolates were selected for further morphological, physiological, and biochemical characterization. All of the bacterial strains were moderately halophilic with the optimal salinity for growth being either 50 or 100, while two archaeal strains were extremely halophilic with an optimal growth salinity of 200. Additionally, we put forth strain SM.200-5 as a new candidate Salimicrobium species based on the phylogenic analysis of the 16S rRNA gene sequence and its biochemical characteristics when compared with known related species.

  4. A virus of hyperthermophilic archaea with a unique architecture among DNA viruses.

    Science.gov (United States)

    Rensen, Elena Ilka; Mochizuki, Tomohiro; Quemin, Emmanuelle; Schouten, Stefan; Krupovic, Mart; Prangishvili, David

    2016-03-01

    Viruses package their genetic material in diverse ways. Most known strategies include encapsulation of nucleic acids into spherical or filamentous virions with icosahedral or helical symmetry, respectively. Filamentous viruses with dsDNA genomes are currently associated exclusively with Archaea. Here, we describe a filamentous hyperthermophilic archaeal virus, Pyrobaculum filamentous virus 1 (PFV1), with a type of virion organization not previously observed in DNA viruses. The PFV1 virion, 400 ± 20 × 32 ± 3 nm, contains an envelope and an inner core consisting of two structural units: a rod-shaped helical nucleocapsid formed of two 14-kDa major virion proteins and a nucleocapsid-encompassing protein sheath composed of a single major virion protein of 18 kDa. The virion organization of PFV1 is superficially similar to that of negative-sense RNA viruses of the family Filoviridae, including Ebola virus and Marburg virus. The linear dsDNA of PFV1 carries 17,714 bp, including 60-bp-long terminal inverted repeats, and contains 39 predicted ORFs, most of which do not show similarities to sequences in public databases. PFV1 is a lytic virus that completely disrupts the host cell membrane at the end of the infection cycle.

  5. Ammonia-oxidizing bacteria and archaea in groundwater treatment and drinking water distribution systems.

    Science.gov (United States)

    van der Wielen, Paul W J J; Voost, Stefan; van der Kooij, Dick

    2009-07-01

    The ammonia-oxidizing prokaryote (AOP) community in three groundwater treatment plants and connected distribution systems was analyzed by quantitative real-time PCR and sequence analysis targeting the amoA gene of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Results demonstrated that AOB and AOA numbers increased during biological filtration of ammonia-rich anoxic groundwater, and AOP were responsible for ammonium removal during treatment. In one of the treatment trains at plant C, ammonia removal correlated significantly with AOA numbers but not with AOB numbers. Thus, AOA were responsible for ammonia removal in water treatment at one of the studied plants. Furthermore, an observed negative correlation between the dissolved organic carbon (DOC) concentration in the water and AOA numbers suggests that high DOC levels might reduce growth of AOA. AOP entered the distribution system in numbers ranging from 1.5 x 10(3) to 6.5 x 10(4) AOPs ml(-1). These numbers did not change during transport in the distribution system despite the absence of a disinfectant residual. Thus, inactive AOP biomass does not seem to be degraded by heterotrophic microorganisms in the distribution system. We conclude from our results that AOA can be commonly present in distribution systems and groundwater treatment, where they can be responsible for the removal of ammonia.

  6. Phylogenetic- and genome-derived insight into the evolution of N-glycosylation in Archaea.

    Science.gov (United States)

    Kaminski, Lina; Lurie-Weinberger, Mor N; Allers, Thorsten; Gophna, Uri; Eichler, Jerry

    2013-08-01

    N-glycosylation, the covalent attachment of oligosaccharides to target protein Asn residues, is a post-translational modification that occurs in all three domains of life. In Archaea, the N-linked glycans that decorate experimentally characterized glycoproteins reveal a diversity in composition and content unequaled by their bacterial or eukaryal counterparts. At the same time, relatively little is known of archaeal N-glycosylation pathways outside of a handful of model strains. To gain insight into the distribution and evolutionary history of the archaeal version of this universal protein-processing event, 168 archaeal genome sequences were scanned for the presence of aglB, encoding the known archaeal oligosaccharyltransferase, an enzyme key to N-glycosylation. Such analysis predicts the presence of AglB in 166 species, with some species seemingly containing multiple versions of the protein. Phylogenetic analysis reveals that the events leading to aglB duplication occurred at various points during archaeal evolution. In many cases, aglB is found as part of a cluster of putative N-glycosylation genes. The presence, arrangement and nucleotide composition of genes in aglB-based clusters in five species of the halophilic archaeon Haloferax points to lateral gene transfer as contributing to the evolution of archaeal N-glycosylation.

  7. Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics.

    Science.gov (United States)

    Anderson, Rika E; Sogin, Mitchell L; Baross, John A

    2014-01-01

    The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, collected by size fractionation of high temperature fluids from a diffuse flow hydrothermal vent. We detected a high enrichment of mobile elements and proviruses in the cellular fraction relative to microorganisms in other environments. We observed a relatively high abundance of genes related to energy metabolism as well as cofactors and vitamins in the viral fraction compared to the cellular fraction, which suggest encoding of auxiliary metabolic genes on viral genomes. Moreover, the observation of stronger purifying selection in the viral versus cellular gene pool suggests viral strategies that promote prolonged host integration. Our results demonstrate that there is great potential for hydrothermal vent viruses to integrate into hosts, facilitate horizontal gene transfer, and express or transfer genes that manipulate the hosts' functional capabilities.

  8. Differential response of ammonia-oxidizing archaea and bacteria to the wetting of salty arid soil.

    Science.gov (United States)

    Sher, Yonatan; Ronen, Zeev; Nejidat, Ali

    2016-08-01

    Ammonia-oxidizing archaea and bacteria (AOA, AOB) catalyze the first and rate-limiting step of nitrification. To examine their differential responses to the wetting of dry and salty arid soil, AOA and AOB amoA genes (encoding subunit A of the ammonia monooxygenase) and transcripts were enumerated in dry (summer) and wet (after the first rainfall) soil under the canopy of halophytic shrubs and between the shrubs. AOA and AOB were more abundant under shrub canopies than between shrubs in both the dry and wetted soil. Soil wetting caused a significant decrease in AOB abundance under the canopy and an increase of AOA between the shrubs. The abundance of the archaeal amoA gene transcript was similar for both the wet and dry soil, and the transcript-to-gene ratios were water content. In contrast, the bacterial amoA transcript-to-gene ratios were between 78 and 514. The lowest ratio was in dry soil under the canopy and the highest in the soil between the shrubs. The results suggest that the AOA are more resilient to stress conditions and maintain a basic activity in arid ecosystems, while the AOB are more responsive to changes in the biotic and abiotic conditions.

  9. General trends in selectively driven codon usage biases in the domain archaea.

    Science.gov (United States)

    Iriarte, Andrés; Jara, Eugenio; Leytón, Lucía; Diana, Leticia; Musto, Héctor

    2014-10-01

    Since the advent of rapid techniques for sequencing DNA in the mid 70's, it became clear that all codons coding for the same amino acid are not used according to neutral expectations. In the last 30 years, several theories were proposed for explaining this fact. However, the most important concepts were the result of analyses carried out in Bacteria, and unicellular and multicellular eukaryotes like mammals (in other words, in two of the three Domains of life). In this communication, we study the main forces that shape codon usage in Archaeae under an evolutionary perspective. This is important because, as known, the orthologous genes related with the informational system in this Domain (replication, transcription and translation) are more similar to eukaryotes than to Bacteria. Our results show that the effect of selection acting at the level of translation is present in the Domain but mainly restricted to only a phylum (Euryarchaeota) and therefore is not as extended as in Bacteria. Besides, we describe the phylogenetic distribution of translational optimal codons and estimate the effect of selection acting at the level of accuracy. Finally, we discuss these results under some peculiarities that characterize this Domain.

  10. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

    Directory of Open Access Journals (Sweden)

    Nikos C Kyrpides

    2014-08-01

    Full Text Available Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance. However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000. This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

  11. Lessons from the genomes of extremely acidophilic bacteria and archaea with special emphasis on bioleaching microorganisms.

    Science.gov (United States)

    Cárdenas, Juan Pablo; Valdés, Jorge; Quatrini, Raquel; Duarte, Francisco; Holmes, David S

    2010-10-01

    This mini-review describes the current status of recent genome sequencing projects of extremely acidophilic microorganisms and highlights the most current scientific advances emerging from their analysis. There are now at least 56 draft or completely sequenced genomes of acidophiles including 30 bacteria and 26 archaea. There are also complete sequences for 38 plasmids, 29 viruses, and additional DNA sequence information of acidic environments is available from eight metagenomic projects. A special focus is provided on the genomics of acidophiles from industrial bioleaching operations. It is shown how this initial information provides a rich intellectual resource for microbiologists that has potential to open innovative and efficient research avenues. Examples presented illustrate the use of genomic information to construct preliminary models of metabolism of individual microorganisms. Most importantly, access to multiple genomes allows the prediction of metabolic and genetic interactions between members of the bioleaching microbial community (ecophysiology) and the investigation of major evolutionary trends that shape genome architecture and evolution. Despite these promising beginnings, a major conclusion is that the genome projects help focus attention on the tremendous effort still required to understand the biological principles that support life in extremely acidic environments, including those that might allow engineers to take appropriate action designed to improve the efficiency and rate of bioleaching and to protect the environment.

  12. Characterization and antimicrobial potential of extremely halophilic archaea isolated from hypersaline environments of the Algerian Sahara.

    Science.gov (United States)

    Quadri, Inès; Hassani, Imene Ikrame; l'Haridon, Stéphane; Chalopin, Morgane; Hacène, Hocine; Jebbar, Mohamed

    2016-01-01

    Halophilic archaea were isolated from different chotts and sebkha, dry salt lakes and salt flat respectively, of the Algerian Sahara and characterized using phenotypic and phylogenetic approaches. From 102 extremely halophilic strains isolated, forty three were selected and studied. These strains were also screened for their antagonistic potential and the production of hydrolytic enzymes. Sequencing of the 16S rRNA genes and phylogenetic analysis allowed the identification of 10 archaeal genera within the class