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Sample records for anaerobic methane-oxidizing archaea

  1. Energy Metabolism during Anaerobic Methane Oxidation in ANME Archaea

    Science.gov (United States)

    McGlynn, Shawn E.

    2017-01-01

    Anaerobic methane oxidation in archaea is often presented to operate via a pathway of “reverse methanogenesis”. However, if the cumulative reactions of a methanogen are run in reverse there is no apparent way to conserve energy. Recent findings suggest that chemiosmotic coupling enzymes known from their use in methylotrophic and acetoclastic methanogens—in addition to unique terminal reductases—biochemically facilitate energy conservation during complete CH4 oxidation to CO2. The apparent enzyme modularity of these organisms highlights how microbes can arrange their energy metabolisms to accommodate diverse chemical potentials in various ecological niches, even in the extreme case of utilizing “reverse” thermodynamic potentials. PMID:28321009

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

    Science.gov (United States)

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

    2016-01-01

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

  3. Biomarker evidence for widespread anaerobic methane oxidation in Mediterranean sediments by a consortium of methanogenic archaea and bacteria : The Medinaut Shipboard Scientific Party

    NARCIS (Netherlands)

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

    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

  4. Community Composition and Ultrastructure of a Nitrate-Dependent Anaerobic Methane-Oxidizing Enrichment Culture.

    Science.gov (United States)

    Gambelli, Lavinia; Guerrero-Cruz, Simon; Mesman, Rob J; Cremers, Geert; Jetten, Mike S M; Op den Camp, Huub J M; Kartal, Boran; Lueke, Claudia; van Niftrik, Laura

    2018-02-01

    Methane is a very potent greenhouse gas and can be oxidized aerobically or anaerobically through microbe-mediated processes, thus decreasing methane emissions in the atmosphere. Using a complementary array of methods, including phylogenetic analysis, physiological experiments, and light and electron microscopy techniques (including electron tomography), we investigated the community composition and ultrastructure of a continuous bioreactor enrichment culture, in which anaerobic oxidation of methane (AOM) was coupled to nitrate reduction. A membrane bioreactor was seeded with AOM biomass and continuously fed with excess methane. After 150 days, the bioreactor reached a daily consumption of 10 mmol nitrate · liter -1 · day -1 The biomass consisted of aggregates that were dominated by nitrate-dependent anaerobic methane-oxidizing " Candidatus Methanoperedens"-like archaea (40%) and nitrite-dependent anaerobic methane-oxidizing " Candidatus Methylomirabilis"-like bacteria (50%). The " Ca Methanoperedens" spp. were identified by fluorescence in situ hybridization and immunogold localization of the methyl-coenzyme M reductase (Mcr) enzyme, which was located in the cytoplasm. The " Ca Methanoperedens" sp. aggregates consisted of slightly irregular coccoid cells (∼1.5-μm diameter) which produced extruding tubular structures and putative cell-to-cell contacts among each other. " Ca Methylomirabilis" sp. bacteria exhibited the polygonal cell shape typical of this genus. In AOM archaea and bacteria, cytochrome c proteins were localized in the cytoplasm and periplasm, respectively, by cytochrome staining. Our results indicate that AOM bacteria and archaea might work closely together in the process of anaerobic methane oxidation, as the bacteria depend on the archaea for nitrite. Future studies will be aimed at elucidating the function of the cell-to-cell interactions in nitrate-dependent AOM. IMPORTANCE Microorganisms performing nitrate- and nitrite-dependent anaerobic

  5. Biogeochemical and molecular signatures of anaerobic methane oxidation in a marine sediment.

    Science.gov (United States)

    Thomsen, T R; Finster, K; Ramsing, N B

    2001-04-01

    Anaerobic methane oxidation was investigated in 6-m-long cores of marine sediment from Aarhus Bay, Denmark. Measured concentration profiles for methane and sulfate, as well as in situ rates determined with isotope tracers, indicated that there was a narrow zone of anaerobic methane oxidation about 150 cm below the sediment surface. Methane could account for 52% of the electron donor requirement for the peak sulfate reduction rate detected in the sulfate-methane transition zone. Molecular signatures of organisms present in the transition zone were detected by using selective PCR primers for sulfate-reducing bacteria and for Archaea. One primer pair amplified the dissimilatory sulfite reductase (DSR) gene of sulfate-reducing bacteria, whereas another primer (ANME) was designed to amplify archaeal sequences found in a recent study of sediments from the Eel River Basin, as these bacteria have been suggested to be anaerobic methane oxidizers (K. U. Hinrichs, J. M. Hayes, S. P. Sylva, P. G. Brewer, and E. F. DeLong, Nature 398:802-805, 1999). Amplification with the primer pairs produced more amplificate of both target genes with samples from the sulfate-methane transition zone than with samples from the surrounding sediment. Phylogenetic analysis of the DSR gene sequences retrieved from the transition zone revealed that they all belonged to a novel deeply branching lineage of diverse DSR gene sequences not related to any previously described DSR gene sequence. In contrast, DSR gene sequences found in the top sediment were related to environmental sequences from other estuarine sediments and to sequences of members of the genera Desulfonema, Desulfococcus, and Desulfosarcina. Phylogenetic analysis of 16S rRNA sequences obtained with the primers targeting the archaeal group of possible anaerobic methane oxidizers revealed two clusters of ANME sequences, both of which were affiliated with sequences from the Eel River Basin.

  6. 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

  7. Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Methylomirabilis Bioreactor Enrichment Culture

    NARCIS (Netherlands)

    Gambelli, L.; Cremers, G.; Mesman, R.; Guerrero, S.; Dutilh, B.E.; Jetten, M.S.; Camp, H.J. Op den; Niftrik, L. van

    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

  8. Subgroup characteristics of marine methane-oxidizing ANME-2 archaea and their syntrophic partners revealed by integrated multimodal analytical microscopy.

    Science.gov (United States)

    McGlynn, Shawn E; Chadwick, Grayson L; O'Neill, Ariel; Mackey, Mason; Thor, Andrea; Deerinck, Thomas J; Ellisman, Mark H; Orphan, Victoria J

    2018-04-06

    Phylogenetically diverse environmental ANME archaea and sulfate-reducing bacteria cooperatively catalyze the anaerobic oxidation of methane oxidation (AOM) in multi-celled consortia within methane seep environments. To better understand these cells and their symbiotic associations, we applied a suite of electron microscopy approaches including correlative f luorescence i n s itu h ybridization - e lectron m icroscopy (FISH-EM), t ransmission e lectron m icroscopy (TEM), and s erial b lock face scanning e lectron m icroscopy 3D reconstructions (SBEM). FISH-EM of methane seep derived consortia revealed phylogenetic variability in terms of cell morphology, ultrastructure, and storage granules. Representatives of the ANME-2b clade, but not other ANME-2 groups, contained polyphosphate-like granules, while some bacteria associated with ANME-2a/2c contained two distinct phases of iron mineral chains resembling magnetosomes. 3D segmentation of two ANME-2 consortia types revealed cellular volumes of ANME and their symbiotic partners which were larger than previous estimates based on light microscopy. Phosphorous granule containing ANME (tentatively ANME-2b) were larger than both ANME with no granules and partner bacteria. This cell type was observed with up to 4 granules per cell and the volume of the cell was larger in proportion to the number of granules inside it, but the percent of the cell occupied by these granules did not vary with granule number. These results illuminate distinctions between ANME-2 archaeal lineages and partnering bacterial populations that are apparently unified in their capability of performing anaerobic methane oxidation. Importance Methane oxidation in anaerobic environments can be accomplished by a number of archaeal groups, some of which live in syntrophic relationships with bacteria in structured consortia. Little is known as to the distinguishing characteristics of these groups. Here we applied imaging approaches to better understand the

  9. Nitrogen source effects on the denitrifying anaerobic methane oxidation culture and anaerobic ammonium oxidation bacteria enrichment process.

    Science.gov (United States)

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

    2017-05-01

    The co-culture system of denitrifying anaerobic methane oxidation (DAMO) and anaerobic ammonium oxidation (Anammox) has a potential application in wastewater treatment plant. This study explored the effects of permutation and combination of nitrate, nitrite, and ammonium on the culture enrichment from freshwater sediments. The co-existence of NO 3 - , NO 2 - , and NH 4 + shortened the enrichment time from 75 to 30 days and achieved a total nitrogen removal rate of 106.5 mg/L/day on day 132. Even though ammonium addition led to Anammox bacteria increase and a higher nitrogen removal rate, DAMO bacteria still dominated in different reactors with the highest proportion of 64.7% and the maximum abundance was 3.07 ± 0.25 × 10 8 copies/L (increased by five orders of magnitude) in the nitrite reactor. DAMO bacteria showed greater diversity in the nitrate reactor, and one was similar to M. oxyfera; DAMO bacteria in the nitrite reactor were relatively unified and similar to M. sinica. Interestingly, no DAMO archaea were found in the nitrate reactor. This study will improve the understanding of the impact of nitrogen source on DAMO and Anammox co-culture enrichment.

  10. 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...

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

    Science.gov (United States)

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

    2015-10-01

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

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

    Science.gov (United States)

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

    2014-12-23

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

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

    Science.gov (United States)

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

    2014-01-01

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

  14. 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.

  15. Anaerobic methane oxidation rates at the sulfate-methane transition in marine sediments from Kattegat and Skagerrak (Denmark)

    International Nuclear Information System (INIS)

    Iversen, N.; Jorgensen, B.B.

    1985-01-01

    Concomitant radiotracer measurements were made of in situ rates of sulfate reduction and anaerobic methane oxidation in 2-3-m-long sediment cores. Methane accumulated to high concentrations (> 1 mM CH 4 ) only below the sulfate zone, at 1 m or deeper in the sediment. Sulfate reduction showed a broad maximum below the sediment surface and a smaller, narrow maximum at the sulfate-methane transition. Methane oxidation was low (0.002-0.1 nmol CH 4 cm -3 d -1 ) throughout the sulfate zone and showed a sharp maximum at the sulfate-methane transition, coinciding with the sulfate reduction maximum. Total anaerobic methane oxidation at two stations was 0.83 and 1.16 mmol CH 4 m -2 d -1 , of which 96% was confined to the sulfate-methane transition. All the methane that was calculated to diffuse up into the sulfate-methane transition was oxidized in this zone. The methane oxidation was equivalent to 10% of the electron donor requirement for the total measured sulfate reduction. A third station showed high sulfate concentrations at all depths sampled and the total methane oxidation was only 0.013 mmol m -2 d -1 . From direct measurements of rates, concentration gradients, and diffusion coefficients, simple calculations were made of sulfate and methane fluxes and of methane production rates

  16. New molecular method to detect denitrifying anaerobic methane oxidation bacteria from different environmental niches.

    Science.gov (United States)

    Xu, Sai; Lu, Wenjing; Muhammad, Farooq Mustafa; Liu, Yanting; Guo, Hanwen; Meng, Ruihong; Wang, Hongtao

    2018-03-01

    The denitrifying anaerobic methane oxidation is an ecologically important process for reducing the potential methane emission into the atmosphere. The responsible bacterium for this process was Candidatus Methylomirabilis oxyfera belonging to the bacterial phylum of NC10. In this study, a new pair of primers targeting all the five groups of NC10 bacteria was designed to amplify NC10 bacteria from different environmental niches. The results showed that the group A was the dominant NC10 phylum bacteria from the sludges and food waste digestate while in paddy soil samples, group A and group B had nearly the same proportion. Our results also indicated that NC10 bacteria could exist in a high pH environment (pH9.24) from the food waste treatment facility. The Pearson relationship analysis showed that the pH had a significant positive relationship with the NC10 bacterial diversity (pbacteria. Copyright © 2017. Published by Elsevier B.V.

  17. Potential roles of anaerobic ammonium and methane oxidation in the nitrogen cycle of wetland ecosystems.

    Science.gov (United States)

    Zhu, Guibing; Jetten, Mike S M; Kuschk, Peter; Ettwig, Katharina F; Yin, Chengqing

    2010-04-01

    Anaerobic ammonium oxidation (anammox) and anaerobic methane oxidation (ANME coupled to denitrification) with nitrite as electron acceptor are two of the most recent discoveries in the microbial nitrogen cycle. Currently the anammox process has been relatively well investigated in a number of natural and man-made ecosystems, while ANME coupled to denitrification has only been observed in a limited number of freshwater ecosystems. The ubiquitous presence of anammox bacteria in marine ecosystems has changed our knowledge of the global nitrogen cycle. Up to 50% of N(2) production in marine sediments and oxygen-depleted zones may be attributed to anammox bacteria. However, there are only few indications of anammox in natural and constructed freshwater wetlands. In this paper, the potential role of anammox and denitrifying methanotrophic bacteria in natural and artificial wetlands is discussed in relation to global warming. The focus of the review is to explore and analyze if suitable environmental conditions exist for anammox and denitrifying methanotrophic bacteria in nitrogen-rich freshwater wetlands.

  18. Effect of inoculum sources on the enrichment of nitrite-dependent anaerobic methane-oxidizing bacteria.

    Science.gov (United States)

    He, Zhanfei; Cai, Chen; Shen, Lidong; Lou, Liping; Zheng, Ping; Xu, Xinhua; Hu, Baolan

    2015-01-01

    Nitrite-dependent anaerobic methane oxidation (n-damo) is a newly discovered biological process that couples anaerobic oxidation of methane (AOM) to nitrite reduction. In this study, three different inocula, methanogenic sludge, paddy soil, and freshwater sediment were used to enrich n-damo bacteria in three sequencing batch reactors (SBRs), and three n-damo enrichment cultures, C1, C2 and C3, were obtained, respectively. After 500 days of incubation, Methylomirabilis oxyfera-like bacteria and n-damo activities were observed in cultures C1, C2, and C3, and the specific activities were 0.8 ± 0.1, 1.4 ± 0.1, and 1.0 ± 0.1 μmol CH4 h(-1) g(-1) VSS, respectively. The copy numbers of 16S rRNA genes from cultures C1, C2, and C3 were 5.0 ± 0.4 × 10(8), 6.1 ± 0.1 × 10(9), and 1.0 ± 0.2 × 10(9) copies g(-1) dry weight, respectively. The results indicated that paddy soil is an excellent inoculum for n-damo bacterial enrichment. This work expanded the alternative source of n-damo inoculum and benefited the further research of n-damo process.

  19. 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.

  20. In Situ Bioremediation of 1,4-Dioxane by Methane Oxidizing Bacteria in Coupled Anaerobic-Aerobic Zones

    Science.gov (United States)

    2016-02-11

    FINAL REPORT In Situ Bioremediation of 1,4-Dioxane by Methane Oxidizing Bacteria in Coupled Anaerobic-Aerobic Zones SERDP Project ER-2306...volatile organic compound (CVOCs), ethene and ethane in groundwater at Raritan Arsenal Area 18C after in situ bioremediation . 4 List of...aquifers, the bioremediation approach most commonly used for chlorinated solvents. The ability of methanotrophs to biodegrade 1,4-dioxane was

  1. Enrichment of sulfate reducing anaerobic methane oxidizing community dominated by ANME-1 from Ginsburg Mud Volcano (Gulf of Cadiz) sediment in a biotrickling filter.

    Science.gov (United States)

    Bhattarai, Susma; Cassarini, Chiara; Rene, Eldon R; Zhang, Yu; Esposito, Giovanni; Lens, Piet N L

    2018-07-01

    This study was performed to enrich anaerobic methane-oxidizing archaea (ANME) present in sediment from the Ginsburg Mud Volcano (Gulf of Cadiz) in a polyurethane foam packed biotrickling filter (BTF). The BTF was operated at 20 (±2) °C, ambient pressure with continuous supply of methane for 248 days. Sulfate reduction with simultaneous sulfide production (accumulating ∼7 mM) after 200 days of BTF operation evidenced anaerobic oxidation of methane (AOM) coupled to sulfate reduction. High-throughput sequence analysis of 16S rRNA genes showed that after 248 days of BTF operation, the ANME clades enriched to more than 50% of the archaeal sequences, including ANME-1b (40.3%) and ANME-2 (10.0%). Enrichment of the AOM community was beneficial to Desulfobacteraceae, which increased from 0.2% to 1.8%. Both the inoculum and the BTF enrichment contained large populations of anaerobic sulfur oxidizing bacteria, suggesting extensive sulfur cycling in the BTF. Copyright © 2018 Elsevier Ltd. All rights reserved.

  2. 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. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  3. Co-existence of Anaerobic Ammonium Oxidation Bacteria and Denitrifying Anaerobic Methane Oxidation Bacteria in Sewage Sludge: Community Diversity and Seasonal Dynamics

    DEFF Research Database (Denmark)

    Xu, Sai; Lu, Wenjing; Mustafa, Muhammad Farooq

    2017-01-01

    Anaerobic ammonium oxidation (ANAMMOX) and denitrifying anaerobic methane oxidation (DAMO) have been recently discovered as relevant processes in the carbon and nitrogen cycles of wastewater treatment plants. In this study, the seasonal dynamics of ANAMMOX and DAMO bacterial community structures......, and an unknown cluster was primarily detected in autumn and winter. Similar patterns of seasonal variation in the community structure of DAMO bacteria were also observed. Group B was the dominant in spring and summer, whereas in autumn and winter, group A and group B presented almost the same proportion...

  4. 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

    . Anaerobic methane oxidation regulates methane emissions in marine sediments and appears to occur through a reversal of a methane-producing metabolism. We tested the assumption that ANME are obligate methanotrophs by detecting and quantifying gene transcription of ANME-1 across zones of methane oxidation...

  5. Methane oxidation in anoxic lake waters

    Science.gov (United States)

    Su, Guangyi; Zopfi, Jakob; Niemann, Helge; Lehmann, Moritz

    2017-04-01

    Freshwater habitats such as lakes are important sources of methante (CH4), however, most studies in lacustrine environments so far provided evidence for aerobic methane oxidation only, and little is known about the importance of anaerobic oxidation of CH4 (AOM) in anoxic lake waters. In marine environments, sulfate reduction coupled to AOM by archaea has been recognized as important sinks of CH4. More recently, the discorvery of anaerobic methane oxidizing denitrifying bacteria represents a novel and possible alternative AOM pathway, involving reactive nitrogen species (e.g., nitrate and nitrite) as electron acceptors in the absence of oxygen. We investigate anaerobic methane oxidation in the water column of two hydrochemically contrasting sites in Lake Lugano, Switzerland. The South Basin displays seasonal stratification, the development of a benthic nepheloid layer and anoxia during summer and fall. The North Basin is permanently stratified with anoxic conditions below 115m water depth. Both Basins accumulate seasonally (South Basin) or permanently (North Basin) large amounts of CH4 in the water column below the chemocline, providing ideal conditions for methanotrophic microorganisms. Previous work revealed a high potential for aerobic methane oxidation within the anoxic water column, but no evidence for true AOM. Here, we show depth distribution data of dissolved CH4, methane oxidation rates and nutrients at both sites. In addition, we performed high resolution phylogenetic analyses of microbial community structures and conducted radio-label incubation experiments with concentrated biomass from anoxic waters and potential alternative electron acceptor additions (nitrate, nitrite and sulfate). First results from the unamended experiments revealed maximum activity of methane oxidation below the redoxcline in both basins. While the incubation experiments neither provided clear evidence for NOx- nor sulfate-dependent AOM, the phylogenetic analysis revealed the

  6. Anaerobic Methane-Oxidizing Microbial Community in a Coastal Marine Sediment: Anaerobic Methanotrophy Dominated by ANME-3.

    Science.gov (United States)

    Bhattarai, Susma; Cassarini, Chiara; Gonzalez-Gil, Graciela; Egger, Matthias; Slomp, Caroline P; Zhang, Yu; Esposito, Giovanni; Lens, Piet N L

    2017-10-01

    The microbial community inhabiting the shallow sulfate-methane transition zone in coastal sediments from marine Lake Grevelingen (The Netherlands) was characterized, and the ability of the microorganisms to carry out anaerobic oxidation of methane coupled to sulfate reduction was assessed in activity tests. In vitro activity tests of the sediment with methane and sulfate demonstrated sulfide production coupled to the simultaneous consumption of sulfate and methane at approximately equimolar ratios over a period of 150 days. The maximum sulfate reduction rate was 5 μmol sulfate per gram dry weight per day during the incubation period. Diverse archaeal and bacterial clades were retrieved from the sediment with the majority of them clustered with Euryarchaeota, Thaumarcheota, Bacteroidetes, and Proteobacteria. The 16S rRNA gene sequence analysis showed that the sediment from marine Lake Grevelingen contained anaerobic methanotrophic Archaea (ANME) and methanogens as archaeal clades with a role in the methane cycling. ANME at the studied site mainly belong to the ANME-3 clade. This study provides one of the few reports for the presence of ANME-3 in a shallow coastal sediment. Sulfate-reducing bacteria from Desulfobulbus clades were found among the sulfate reducers, however, with very low relative abundance. Desulfobulbus has previously been commonly found associated with ANME, whereas in our study, ANME-3 and Desulfobulbus were not observed simultaneously in clusters, suggesting the possibility of independent AOM by ANME-3.

  7. Illumina sequencing-based analysis of a microbial community enriched under anaerobic methane oxidation condition coupled to denitrification revealed coexistence of aerobic and anaerobic methanotrophs.

    Science.gov (United States)

    Siniscalchi, Luciene Alves Batista; Leite, Laura Rabelo; Oliveira, Guilherme; Chernicharo, Carlos Augusto Lemos; de Araújo, Juliana Calabria

    2017-07-01

    Methane is produced in anaerobic environments, such as reactors used to treat wastewaters, and can be consumed by methanotrophs. The composition and structure of a microbial community enriched from anaerobic sewage sludge under methane-oxidation condition coupled to denitrification were investigated. Denaturing gradient gel electrophoresis (DGGE) analysis retrieved sequences of Methylocaldum and Chloroflexi. Deep sequencing analysis revealed a complex community that changed over time and was affected by methane concentration. Methylocaldum (8.2%), Methylosinus (2.3%), Methylomonas (0.02%), Methylacidiphilales (0.45%), Nitrospirales (0.18%), and Methanosarcinales (0.3%) were detected. Despite denitrifying conditions provided, Nitrospirales and Methanosarcinales, known to perform anaerobic methane oxidation coupled to denitrification (DAMO) process, were in very low abundance. Results demonstrated that aerobic and anaerobic methanotrophs coexisted in the reactor together with heterotrophic microorganisms, suggesting that a diverse microbial community was important to sustain methanotrophic activity. The methanogenic sludge was a good inoculum to enrich methanotrophs, and cultivation conditions play a selective role in determining community composition.

  8. Dissolved methane oxidation and competition for oxygen in down-flow hanging sponge reactor for post-treatment of anaerobic wastewater treatment.

    Science.gov (United States)

    Hatamoto, Masashi; Miyauchi, Tomo; Kindaichi, Tomonori; Ozaki, Noriatsu; Ohashi, Akiyoshi

    2011-11-01

    Post-treatment of anaerobic wastewater was undertaken to biologically oxidize dissolved methane, with the aim of preventing methane emission. The performance of dissolved methane oxidation and competition for oxygen among methane, ammonium, organic matter, and sulfide oxidizing bacteria were investigated using a lab-scale closed-type down-flow hanging sponge (DHS) reactor. Under the oxygen abundant condition of a hydraulic retention time of 2h and volumetric air supply rate of 12.95m(3)-airm(-3)day(-1), greater than 90% oxidation of dissolved methane, ammonium, sulfide, and organic matter was achieved. With reduction in the air supply rate, ammonium oxidation first ceased, after which methane oxidation deteriorated. Sulfide oxidation was disrupted in the final step, indicating that COD and sulfide oxidation occurred prior to methane oxidation. A microbial community analysis revealed that peculiar methanotrophic communities dominating the Methylocaldum species were formed in the DHS reactor operation. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

    KAUST Repository

    Meulepas, Roel J.W.; Jagersma, Christian G.; Zhang, Yu; Petrillo, Michele; Cai, Hengzhe; Buisman, Cees J.N.; Stams, Alfons J.M.; Lens, Piet N.L.

    2010-01-01

    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

  10. Community composition and ultrastructure of a nitrate-dependent anaerobic methane-oxidizing enrichment culture

    NARCIS (Netherlands)

    Gambelli, L.; Guerrero-Cruz, Simon; Mesman, R.; Cremers, G.; Jetten, M.S.M.; Camp, H.J.M. op den; Lueke, Claudia; Niftrik, L.A.M.P. van

    2017-01-01

    Methane is a very potent greenhouse gas and can be oxidized aerobically or anaerobically through microbial-mediated processes, thus decreasing methane emissions to the atmosphere. Using a complementary array of methods including phylogenetic analysis, physiological experiments, and light and

  11. Dissolved methane oxidation and competition for oxygen in down-flow hanging sponge reactor for post-treatment of anaerobic wastewater treatment

    OpenAIRE

    Hatamoto, Masashi; Miyauchi, Tomo; Kindaichi, Tomonori; Ozaki, Noriatsu; Ohashi, Akiyoshi

    2011-01-01

    Post-treatment of anaerobic wastewater was undertaken to biologically oxidize dissolved methane, with the aim of preventing methane emission. The performance of dissolved methane oxidation and competition for oxygen among methane, ammonium, organic matter, and sulfide oxidizing bacteria were investigated using a lab-scale closed-type down-flow hanging sponge (OHS) reactor. Under the oxygen abundant condition of a hydraulic retention time of 2 h and volumetric air supply rate of 12.95 m(3)-air...

  12. Spatial and temporal distribution of nitrite-dependent anaerobic methane-oxidizing bacteria in an intertidal zone of the East China Sea.

    Science.gov (United States)

    Wang, Jiaqi; Shen, Lidong; He, Zhanfei; Hu, Jiajie; Cai, Zhaoyang; Zheng, Ping; Hu, Baolan

    2017-11-01

    Nitrite-dependent anaerobic methane oxidation (N-DAMO), which couples anaerobic methane oxidation and nitrite reduction, is a recently discovered bioprocess coupling microbial nitrogen and carbon cycles. The discovery of this microbial process challenges the traditional knowledge of global methane sinks and nitrogen losses. In this study, the abundance and activity of N-DAMO bacteria were investigated and their contributions to methane sink and nitrogen loss were estimated in different seasons and different partitions of an intertidal zone of the East China Sea. The results showed that N-DAMO bacteria were extensively and continuously present in the intertidal zone, with the number of cells ranging from 5.5 × 10 4 to 2.8 × 10 5 copy g -1 soil and the potential activity ranging from 0.52 to 5.7 nmol CO 2  g -1 soil day -1 , contributing 5.0-36.6% of nitrite- and sulfate-dependent anaerobic methane oxidation in the intertidal zone. The N-DAMO activity and its contribution to the methane consumption were highest in the spring and in the low intertidal zone. These findings showed that the N-DAMO process is an important methane and nitrogen sink in the intertidal zone and varies with the seasons and the partitions of the intertidal zone.

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

    Science.gov (United States)

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

    2014-01-01

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

  14. Current advances in molecular methods for detection of nitrite-dependent anaerobic methane oxidizing bacteria in natural environments.

    Science.gov (United States)

    Chen, Jing; Dick, Richard; Lin, Jih-Gaw; Gu, Ji-Dong

    2016-12-01

    Nitrite-dependent anaerobic methane oxidation (n-damo) process uniquely links microbial nitrogen and carbon cycles. Research on n-damo bacteria progresses quickly with experimental evidences through enrichment cultures. Polymerase chain reaction (PCR)-based methods for detecting them in various natural ecosystems and engineered systems play a very important role in the discovery of their distribution, abundance, and biodiversity in the ecosystems. Important characteristics of n-damo enrichments were obtained and their key significance in microbial nitrogen and carbon cycles was investigated. The molecular methods currently used in detecting n-damo bacteria were comprehensively reviewed and discussed for their strengths and limitations in applications with a wide range of samples. The pmoA gene-based PCR primers for n-damo bacterial detection were evaluated and, in particular, several incorrectly stated PCR primer nucleotide sequences in the published papers were also pointed out to allow correct applications of the PCR primers in current and future investigations. Furthermore, this review also offers the future perspectives of n-damo bacteria based on current information and methods available for a better acquisition of new knowledge about this group of bacteria.

  15. Anaerobic methane oxidation and aerobic methane production in an east African great lake (Lake Kivu)

    DEFF Research Database (Denmark)

    Roland, Fleur A.E.; Morana, Cédric; Darchambeau, François

    2018-01-01

    We investigated CH4 oxidation in the water column of Lake Kivu, a deep meromictic tropical lake with CH4-rich anoxic deep waters. Depth profiles of dissolved gases (CH4 and N2O) and a diversity of potential electron acceptors for anaerobic CH4 oxidation (NO3 −, SO4 2−, Fe and Mn oxides) were dete...

  16. Thermodynamic and Kinetic Requirements in Anaerobic Methane Oxidizing Consortia Exclude Hydrogen, Acetate, and Methanol as Possible Electron Shuttles.

    Science.gov (United States)

    Sørensen, K.B.; Finster, K.; Ramsing, N.B.

    2001-07-01

    Anaerobic methane oxidation (AMO) has long remained an enigma in microbial ecology. In the process the net reaction appears to be an oxidation of methane with sulfate as electron acceptor. In order to explain experimental data such as effects of inhibitors and isotopic signals in biomarkers it has been suggested that the process is carried out by a consortium of bacteria using an unknown compound to shuttle electrons between the participants. The overall change in free energy during AMO with sulfate is very small (?22 kJ mol-1) at in situ concentrations of methane and sulfate. In order to share the available free energy between the members of the consortium, the concentration of the intermediate electron shuttle compound becomes crucial. Diffusive flux of a substrate (i.e, the electron shuttle) between bacteria requires a stable concentration gradient where the concentration is higher in the producing organism than in the consuming organism. Since changes in concentrations cause changes in reaction free energies, the diffusive flux of a catabolic product/substrate between bacteria is associated with a net loss of available energy. This restricts maximal inter-bacterial distances in consortia composed of stationary bacteria. A simple theoretical model was used to describe the relationship between inter-bacterial distances and the energy lost due to concentration differences in consortia. Key parameters turned out to be the permissible concentration range of the electron shuttle in the consortium (i.e., the concentration range that allows both participants to gain sufficient energy) and the stoichiometry of the partial reactions. The model was applied to two known consortia degrading ethanol and butyrate and to four hypothetical methane-oxidizing consortia (MOC) based on interspecies transfer of hydrogen, methanol, acetate, or formate, respectively. In the first three MOCs the permissible distances between producers and consumers of the transferred compounds were

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

    Science.gov (United States)

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

    2012-01-01

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

  18. 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.

  19. High abundance and diversity of nitrite-dependent anaerobic methane-oxidizing bacteria in a paddy field profile.

    Science.gov (United States)

    Zhou, Leiliu; Wang, Yu; Long, Xi-En; Guo, Jianhua; Zhu, Guibing

    2014-11-01

    The discovery of nitrite-dependent anaerobic methane oxidation (n-damo) mediated by 'Candidatus Methylomirabilis oxyfera' with nitrite and methane as substrates has connected biogeochemical carbon and nitrogen cycles in a new way. The paddy fields often carry substantial methane and nitrate, thus may be a favorable habitat for n-damo bacteria. In this paper, the vertical-temporal molecular fingerprints of M. oxyfera-like bacteria, including abundance and community composition, were investigated in a paddy soil core in Jiangyin, near the Yangtze River. Through qPCR investigation, high abundance of M. oxyfera-like bacteria up to 1.0 × 10(8) copies (g d.w.s.)(-1) in summer and 8.5 × 10(7) copies (g d.w.s.)(-1) in winter was observed in the ecotone of soil and groundwater in the paddy soil core, which was the highest in natural environments to our knowledge. In the ecotone, the ratio of M. oxyfera-like bacteria to total bacteria reached peak values of 2.80% in summer and 4.41% in winter. Phylogenetic analysis showed n-damo bacteria in the paddy soil were closely related to M. oxyfera and had high diversity in the soil/groundwater ecotone. All of the results indicated the soil/groundwater ecotone of the Jiangyin paddy field was a favorable environment for the growth of n-damo bacteria. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  20. Assessing the High Temperature, High Pressure Subsurface for Anaerobic Methane Oxidation

    Science.gov (United States)

    Harris, R. L.; Bartlett, D.; Byrnes, A. W.; Walsh, K. M.; Lau, C. Y. M.; Onstott, T. C.

    2017-12-01

    The anaerobic oxidation of methane (AOM) is an important sink in the global methane (CH4) budget. ANMEs are known to oxidize CH4 either independently or in consortia with bacteria, coupling the reduction of electron acceptors such as, SO42-, NO2-, NO3-, Mn4+, or Fe3+. To further constrain the contribution of AOM to the global CH4 budget, it is important to assess unexplored environments where AOM is thermodynamically possible such as the high pressure, high temperature deep biosphere. Provided plausible electron acceptor availability, increased temperature and pCH4 yield favorable Gibbs free energies for AOM reactions and the production of ATP (Fig. 1). To date, only sulfate-dependent AOM metabolism has been documented under high temperature conditions (50-72˚C), and AOM has not been assessed above 10.1 MPa. Given that ANMEs share close phylogenetic and metabolic heritage with methanogens and that the most heat-tolerant microorganism known is a barophilic methanogen, there possibly exist thermophilic ANMEs. Here we describe preliminary results from high pressure, high temperature stable isotope tracer incubation experiments on deep biosphere samples. Deep sub-seafloor sediments collected by IODP 370 from the Nankai Trough (257 - 865 m below seafloor) and deep fracture fluid from South Africa (1339 m below land surface) were incubated anaerobically in hydrostatic pressure vessels at 40 MPa in simulated in situ temperatures (40˚ - 80˚C). Sediments and fracture fluid were incubated in sulfate-free artificial seawater, a 2:98 13CH4:N2 headspace, and treated with one of the potential electron acceptors listed above in addition to kill and endogenous activity (i.e. no added electron acceptor) controls. Stable isotope analysis of dissolved inorganic carbon (DIC) suggests that AOM occurred within 60 days of incubation for all investigated electron acceptors and temperatures except 50˚C. Sulfate-dependent AOM rates are consistent with those previously reported in the

  1. 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.

  2. Co-existence of Anaerobic Ammonium Oxidation Bacteria and Denitrifying Anaerobic Methane Oxidation Bacteria in Sewage Sludge: Community Diversity and Seasonal Dynamics.

    Science.gov (United States)

    Xu, Sai; Lu, Wenjing; Mustafa, Muhammad Farooq; Caicedo, Luis Miguel; Guo, Hanwen; Fu, Xindi; Wang, Hongtao

    2017-11-01

    Anaerobic ammonium oxidation (ANAMMOX) and denitrifying anaerobic methane oxidation (DAMO) have been recently discovered as relevant processes in the carbon and nitrogen cycles of wastewater treatment plants. In this study, the seasonal dynamics of ANAMMOX and DAMO bacterial community structures and their abundance in sewage sludge collected from wastewater treatment plants were analysed. Results indicated that ANAMMOX and DAMO bacteria co-existed in sewage sludge in different seasons and their abundance was positively correlated (P bacteria in autumn and winter indicated that these seasons were the preferred time to favour the growth of ANAMMOX and DAMO bacteria. The community structure of ANNAMOX and DAMO bacteria could also shift with seasonal changes. The "Candidatus Brocadia" genus of ANAMMOX bacteria was mainly recovered in spring and summer, and an unknown cluster was primarily detected in autumn and winter. Similar patterns of seasonal variation in the community structure of DAMO bacteria were also observed. Group B was the dominant in spring and summer, whereas in autumn and winter, group A and group B presented almost the same proportion. The redundancy analysis revealed that pH and nitrate were the most significant factors affecting community structures of these two groups (P < 0.01). This study reported the diversity of ANAMMOX and DAMO in wastewater treatment plants that may be the basis for new nitrogen removal technologies.

  3. A Metagenomics-Based Metabolic Model of Nitrate-Dependent Anaerobic Oxidation of Methane by Methanoperedens-Like Archaea

    Science.gov (United States)

    Arshad, Arslan; Speth, Daan R.; de Graaf, Rob M.; Op den Camp, Huub J. M.; Jetten, Mike S. M.; Welte, Cornelia U.

    2015-01-01

    Methane oxidation is an important process to mitigate the emission of the greenhouse gas methane and further exacerbating of climate forcing. Both aerobic and anaerobic microorganisms have been reported to catalyze methane oxidation with only a few possible electron acceptors. Recently, new microorganisms were identified that could couple the oxidation of methane to nitrate or nitrite reduction. Here we investigated such an enrichment culture at the (meta) genomic level to establish a metabolic model of nitrate-driven anaerobic oxidation of methane (nitrate-AOM). Nitrate-AOM is catalyzed by an archaeon closely related to (reverse) methanogens that belongs to the ANME-2d clade, tentatively named Methanoperedens nitroreducens. Methane may be activated by methyl-CoM reductase and subsequently undergo full oxidation to carbon dioxide via reverse methanogenesis. All enzymes of this pathway were present and expressed in the investigated culture. The genome of the archaeal enrichment culture encoded a variety of enzymes involved in an electron transport chain similar to those found in Methanosarcina species with additional features not previously found in methane-converting archaea. Nitrate reduction to nitrite seems to be located in the pseudoperiplasm and may be catalyzed by an unusual Nar-like protein complex. A small part of the resulting nitrite is reduced to ammonium which may be catalyzed by a Nrf-type nitrite reductase. One of the key questions is how electrons from cytoplasmically located reverse methanogenesis reach the nitrate reductase in the pseudoperiplasm. Electron transport in M. nitroreducens probably involves cofactor F420 in the cytoplasm, quinones in the cytoplasmic membrane and cytochrome c in the pseudoperiplasm. The membrane-bound electron transport chain includes F420H2 dehydrogenase and an unusual Rieske/cytochrome b complex. Based on genome and transcriptome studies a tentative model of how central energy metabolism of nitrate-AOM could work is

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

    Science.gov (United States)

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

    2014-12-01

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

  5. 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.

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

    Science.gov (United States)

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

    2015-01-01

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

  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. Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction.

    Science.gov (United States)

    Scheller, Silvan; Yu, Hang; Chadwick, Grayson L; McGlynn, Shawn E; Orphan, Victoria J

    2016-02-12

    The oxidation of methane with sulfate is an important microbial metabolism in the global carbon cycle. In marine methane seeps, this process is mediated by consortia of anaerobic methanotrophic archaea (ANME) that live in syntrophy with sulfate-reducing bacteria (SRB). The underlying interdependencies within this uncultured symbiotic partnership are poorly understood. We used a combination of rate measurements and single-cell stable isotope probing to demonstrate that ANME in deep-sea sediments can be catabolically and anabolically decoupled from their syntrophic SRB partners using soluble artificial oxidants. The ANME still sustain high rates of methane oxidation in the absence of sulfate as the terminal oxidant, lending support to the hypothesis that interspecies extracellular electron transfer is the syntrophic mechanism for the anaerobic oxidation of methane. Copyright © 2016, American Association for the Advancement of Science.

  9. Distribution and characteristic of nitrite-dependent anaerobic methane oxidation bacteria by comparative analysis of wastewater treatment plants and agriculture fields in northern China

    Directory of Open Access Journals (Sweden)

    Zhen Hu

    2016-12-01

    Full Text Available Nitrite-dependent anaerobic methane oxidation (n-damo is a recently discovered biological process which has been arousing global attention because of its potential in minimizing greenhouse gases emissions. In this study, molecular biological techniques and potential n-damo activity batch experiments were conducted to investigate the presence and diversity of M. oxyfera bacteria in paddy field, corn field, and wastewater treatment plant (WWTP sites in northern China, as well as lab-scale n-damo enrichment culture. N-damo enrichment culture showed the highest abundance of M. oxyfera bacteria, and positive correlation was observed between potential n-damo rate and abundance of M. oxyfera bacteria. Both paddy field and corn field sites were believed to be better inoculum than WWTP for the enrichment of M. oxyfera bacteria due to their higher abundance and the diversity of M. oxyfera bacteria. Comparative analysis revealed that long biomass retention time, low NH ${}_{4}^{+}$ 4 + and high NO ${}_{2}^{-}$ 2 − content were suitable for the growth of M. oxyfera bacteria.

  10. Molecular and stable isotopic evidence for the occurrence of nitrite-dependent anaerobic methane-oxidizing bacteria in the mangrove sediment of Zhangjiang Estuary, China.

    Science.gov (United States)

    Zhang, Manping; Luo, Yi; Lin, Li'an; Lin, Xiaolan; Hetharua, Buce; Zhao, Weijun; Zhou, Mengkai; Zhan, Qing; Xu, Hong; Zheng, Tianling; Tian, Yun

    2018-03-01

    Nitrite-dependent anaerobic methane oxidation (n-damo), which is mediated by "Candidatus Methylomirabilis oxyfera-like" bacteria, is unique in linking the carbon and nitrogen cycles. However, the niche and activity of n-damo bacteria in the mangrove ecosystem have not been confirmed. Here, we report the occurrence of the n-damo process in the mangrove wetland of the Zhangjiang Estuary, China. The widespread occurrence of n-damo bacteria in mangrove wetland was confirmed using real-time quantitative polymerase chain reaction (qPCR) assay, which showed that the abundance of Methylomirabilis oxyfera-like bacterial 16S rRNA and pmoA genes ranged from 2.43 × 10 6 to 2.09 × 10 7 and 2.07 × 10 6 to 3.38 × 10 7 copies per gram of dry soil in the examined sediment cores. The highest amount of targeting genes was all detected in the upper layer (0-20 cm). Phylogenetic analyses of n-damo bacterial 16S rRNA and pmoA genes illustrated the depth-specific distribution and high diversity of n-damo bacteria in the mangrove wetland. Stable isotope experiments further confirmed the occurrence of n-damo in the examined mangrove sediments, and the potential n-damo rates ranged from 25.93 to 704.08 nmol CO 2 per gram of dry soil per day at different depths of the sediment cores, with the n-damo being more active in the upper layer of the mangrove sediments. These results illustrate the existence of active M. oxyfera-like bacteria and indicate that the n-damo process is a previously overlooked microbial methane sink in the mangrove wetlands.

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

    Directory of Open Access Journals (Sweden)

    Pengze Yan

    Full Text Available 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±0.11×10(3 to 2.10±0.13×10(5 copies g(-1 (dry weight, and the pmoA gene abundance ranged from 8.63±0.50×10(3 to 1.83±0.18×10(5 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.

  12. 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±0.11×10(3) to 2.10±0.13×10(5) copies g(-1) (dry weight), and the pmoA gene abundance ranged from 8.63±0.50×10(3) to 1.83±0.18×10(5) 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.

  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

    2017-01-18

    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 (NO 3 - ) 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 NO 3 - 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 13 CO 2 production confimed DAMO did occur in both the paddy-peatland and the undisturbed peatland, the rates of which increased with NO 3 - additions, but decreased logarithmically with time. When NO 3 - was added, there were no significant differences between the CH 4 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 NO 3 - applied and the depth to which it penetrates into the anoxic layer.

  14. Biogeochemical evidence that thermophilic Archaea mediate the anaerobic oxidation of methane

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Schouten, S.; Wakeham, S.G.; Hopmans, E.C.

    2003-01-01

    Distributions and isotopic analyses of lipids from sediment cores at a hydrothermally active site in the Guaymas Basin with a steep sedimentary temperature gradient revealed the presence of archaea that oxidize methane anaerobically. The presence of strongly 13C-depleted lipids at greater depths in

  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. Archaea.

    Science.gov (United States)

    Eme, Laura; Doolittle, W Ford

    2015-10-05

    A headline on the front page of the New York Times for November 3, 1977, read "Scientists Discover a Way of Life That Predates Higher Organisms". The accompanying article described a spectacular claim by Carl Woese and George Fox to have discovered a third form of life, a new 'domain' that we now call Archaea. It's not that these microbes were unknown before, nor was it the case that their peculiarities had gone completely unnoticed. Indeed, Ralph Wolfe, in the same department at the University of Illinois as Woese, had already discovered how it was that methanogens (uniquely on the planet) make methane, and the bizarre adaptations that allow extremely halophilic archaea (then called halobacteria) and thermoacidophiles to live in the extreme environments where they do were already under investigation in many labs. But what Woese and Fox had found was that these organisms were related to each other not just in their 'extremophily' but also phylogenetically. And, most surprisingly, they were only remotely related to the rest of the prokaryotes, which we now call the domain Bacteria (Figure 1). Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Genome Analysis of a Limnobacter sp. Identified in an Anaerobic Methane-Consuming Cell Consortium

    OpenAIRE

    Chen, Ying; Feng, Xiaoyuan; He, Ying; Wang, Fengping

    2016-01-01

    Species of Limnobacter genus are widespread in a variety of environments, yet knowledges upon their metabolic potentials and mechanisms of environmental adaptation are limited. In this study, a cell aggregate containing Limnobacter and anaerobic methanotrophic archaea (ANME) was captured from an enriched anaerobic methane oxidizing (AOM) microbial community. A genomic bin of Limnobacter was obtained and analyzed, which provides the first metabolic insights into Limnobacter from an AOM environ...

  18. Genome analysis of a Limnobacter sp. identified in an anaerobic methane-consuming cell consortium

    OpenAIRE

    Ying Chen; Ying Chen; Ying Chen; Xiaoyuan Feng; Xiaoyuan Feng; Ying He; Ying He; Fengping Wang; Fengping Wang

    2016-01-01

    Species of Limnobacter genus are widespread in a variety of environments, yet knowledges upon their metabolic potentials and mechanisms of environmental adaptation are limited. In this study, a cell aggregate containing Limnobacter and anaerobic methanotrophic archaea (ANME) was captured from an enriched anaerobic methane oxidizing (AOM) microbial community. A genomic bin of Limnobacter was obtained and analyzed, which provides the first metabolic insights into Limnobacter from an AOM environ...

  19. A mechanistic model on methane oxidation in the rice rhizosphere

    NARCIS (Netherlands)

    Bodegom, van P.M.; Leffelaar, P.A.; Goudriaan, J.

    2001-01-01

    A mechanistic model is presented on the processes leading to methane oxidation in rice rhizosphere. The model is driven by oxygen release from a rice root into anaerobic rice soil. Oxygen is consumed by heterotrophic and methanotrophic respiration, described by double Monod kinetics, and by iron

  20. 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

  1. 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

  2. Could Methane Oxidation in Lakes Be Enhanced by Eutrophication?

    Science.gov (United States)

    Van Grinsven, S.; Villanueva, L.; Harrison, J.; S Sinninghe Damsté, J.

    2017-12-01

    Climate change and eutrophication both affect aquatic ecosystems. Eutrophication is caused by high nutrient inputs, leading to algal blooms, oxygen depletion and disturbances of the natural balances in aquatic systems. Methane, a potent greenhouse gas produced biologically by anaerobic degradation of organic matter, is often released from the sediments of lakes and marine systems to overlying water and the atmosphere. Methane oxidation, a microbial methane consumption process, can limit methane emission from lakes and reservoirs by 50-80%. Here, we studied methane oxidation in a seasonally stratified reservoir: Lacamas Lake in Washington, USA. We found this lake has a large summer storage capacity of methane in its deep water layer, with a very active microbial community capable of oxidizing exceptionally high amounts of methane. The natural presence of terminal electron acceptors is, however, too low to support these high potential rates. Addition of eutrophication-related nutrients such as nitrate and sulfate increased the methane removal rates by 4 to 7-fold. The microbial community was studied using 16S rRNA gene amplicon sequencing and preliminary results indicate the presence of a relatively unknown facultative anaerobic methane oxidizer of the genus Methylomonas, capable of using nitrate as an electron donor. Experiments in which anoxic and oxic conditions were rapidly interchanged showed this facultative anaerobic methane oxidizer has an impressive flexibility towards large, rapid changes in environmental conditions and this feature might be key to the unexpectedly high methane removal rates in eutrophied and anoxic watersheds.

  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. Enrichment of anaerobic nitrate-dependent methanotrophic ?Candidatus Methanoperedens nitroreducens? archaea from an Italian paddy field soil

    OpenAIRE

    Vaksmaa, Annika; Guerrero-Cruz, Simon; van Alen, Theo A.; Cremers, Geert; Ettwig, Katharina F.; L?ke, Claudia; Jetten, Mike S. M.

    2017-01-01

    Paddy fields are a significant source of methane and contribute up to 20% of total methane emissions from wetland ecosystems. These inundated, anoxic soils featuring abundant nitrogen compounds and methane are an ideal niche for nitrate-dependent anaerobic methanotrophs. After 2?years of enrichment with a continuous supply of methane and nitrate as the sole electron donor and acceptor, a stable enrichment dominated by ?Candidatus Methanoperedens nitroreducens? archaea and ?Candidatus Methylom...

  5. 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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Thermophilic archaea activate butane via alkyl-coenzyme M formation.

    Science.gov (United States)

    Laso-Pérez, Rafael; Wegener, Gunter; Knittel, Katrin; Widdel, Friedrich; Harding, Katie J; Krukenberg, Viola; Meier, Dimitri V; Richter, Michael; Tegetmeyer, Halina E; Riedel, Dietmar; Richnow, Hans-Hermann; Adrian, Lorenz; Reemtsma, Thorsten; Lechtenfeld, Oliver J; Musat, Florin

    2016-11-17

    The anaerobic formation and oxidation of methane involve unique enzymatic mechanisms and cofactors, all of which are believed to be specific for C 1 -compounds. Here we show that an anaerobic thermophilic enrichment culture composed of dense consortia of archaea and bacteria apparently uses partly similar pathways to oxidize the C 4 hydrocarbon butane. The archaea, proposed genus 'Candidatus Syntrophoarchaeum', show the characteristic autofluorescence of methanogens, and contain highly expressed genes encoding enzymes similar to methyl-coenzyme M reductase. We detect butyl-coenzyme M, indicating archaeal butane activation analogous to the first step in anaerobic methane oxidation. In addition, Ca. Syntrophoarchaeum expresses the genes encoding β-oxidation enzymes, carbon monoxide dehydrogenase and reversible C 1 methanogenesis enzymes. This allows for the complete oxidation of butane. Reducing equivalents are seemingly channelled to HotSeep-1, a thermophilic sulfate-reducing partner bacterium known from the anaerobic oxidation of methane. Genes encoding 16S rRNA and methyl-coenzyme M reductase similar to those identifying Ca. Syntrophoarchaeum were repeatedly retrieved from marine subsurface sediments, suggesting that the presented activation mechanism is naturally widespread in the anaerobic oxidation of short-chain hydrocarbons.

  7. Methane oxidation coupled to oxygenic photosynthesis in anoxic waters

    Science.gov (United States)

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

    2015-01-01

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

  8. Influence of four antimicrobials on methane-producing archaea and sulfate-reducing bacteria in anaerobic granular sludge.

    Science.gov (United States)

    Du, Jingru; Hu, Yong; Qi, Weikang; Zhang, Yanlong; Jing, Zhaoqian; Norton, Michael; Li, Yu-You

    2015-12-01

    The influence of Cephalexin (CLX), Tetracycline (TC), Erythromycin (ERY) and Sulfathiazole (ST) on methane-producing archaea (MPA) and sulfate-reducing bacteria (SRB) in anaerobic sludge was investigated using acetate or ethanol as substrate. With antimicrobial concentrations below 400mgL(-1), the relative specific methanogenic activity (SMA) was above 50%, so that the antimicrobials exerted slight effects on archaea. However ERY and ST at 400mgL(-1) caused a 74.5% and 57.6% inhibition to specific sulfidogenic activity (SSA) when the sludge granules were disrupted and ethanol used as substrate. After disruption, microbial tolerance to antimicrobials decreased, but the rate at which MPA utilized acetate and ethanol increased from 0.95gCOD·(gVSS⋅d)(-1) to 1.45gCOD·(gVSS⋅d)(-1) and 0.90gCOD·(gVSS⋅d)(-1) to 1.15gCOD·(gVSS⋅d)(-1) respectively. The ethanol utilization rate for SRB also increased after disruption from 0.35gCOD·(gVSS⋅d)(-1) to 0.46gCOD·(gVSS⋅d)(-1). Removal rates for CLX approaching 20.0% and 25.0% were obtained used acetate and ethanol respectively. The disintegration of granules improved the CLX removal rate to 65% and 78%, but ST was not removed during this process. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea.

    Science.gov (United States)

    Skennerton, Connor T; Chourey, Karuna; Iyer, Ramsunder; Hettich, Robert L; Tyson, Gene W; Orphan, Victoria J

    2017-08-01

    The anaerobic oxidation of methane by anaerobic methanotrophic (ANME) archaea in syntrophic partnership with deltaproteobacterial sulfate-reducing bacteria (SRB) is the primary mechanism for methane removal in ocean sediments. The mechanism of their syntrophy has been the subject of much research as traditional intermediate compounds, such as hydrogen and formate, failed to decouple the partners. Recent findings have indicated the potential for extracellular electron transfer from ANME archaea to SRB, though it is unclear how extracellular electrons are integrated into the metabolism of the SRB partner. We used metagenomics to reconstruct eight genomes from the globally distributed SEEP-SRB1 clade of ANME partner bacteria to determine what genomic features are required for syntrophy. The SEEP-SRB1 genomes contain large multiheme cytochromes that were not found in previously described free-living SRB and also lack periplasmic hydrogenases that may prevent an independent lifestyle without an extracellular source of electrons from ANME archaea. Metaproteomics revealed the expression of these cytochromes at in situ methane seep sediments from three sites along the Pacific coast of the United States. Phylogenetic analysis showed that these cytochromes appear to have been horizontally transferred from metal-respiring members of the Deltaproteobacteria such as Geobacter and may allow these syntrophic SRB to accept extracellular electrons in place of other chemical/organic electron donors. IMPORTANCE Some archaea, known as anaerobic methanotrophs, are capable of converting methane into carbon dioxide when they are growing syntopically with sulfate-reducing bacteria. This partnership is the primary mechanism for methane removal in ocean sediments; however, there is still much to learn about how this syntrophy works. Previous studies have failed to identify the metabolic intermediate, such as hydrogen or formate, that is passed between partners. However, recent analysis of

  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

    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...... 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....

  11. 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'.

  12. Methanogenic archaea

    International Nuclear Information System (INIS)

    Joblin, K.N.

    2005-01-01

    This chapter outlines procedures for enumerating, isolating, culturing and storing methanogens from ruminal digesta. The methanogens, a large and diverse group of Archaea, have unique features that separate them from the bacteria and the eukaryotes. They are the only recognized ruminal microbes belonging to the Archaea and are an integral part of the rumen microbial ecosystem. By scavenging hydrogen gas, methanogens play a key ecological role in keeping the partial pressure of hydrogen low so that fermentation can proceed efficiently. Although about 70 methanogenic species belonging to 2 1 genera have been identified from anaerobic environments, and a range of different methanogens co-exist in the rumen, to date only seven ruminal species have been isolated and purified. The population densities of methanogens in the rumen appear to be influenced by diet, and in particular by the fibre content of the diet. Sheep and cattle fed diets rich in concentrates contained 10 7 -10 8 and 10 8 - 10 9 ruminal methanogens/g, respectively, whereas sheep and dairy cows grazing pasture contained 10 9 -10 10 ruminal methanogens/g (G.N. Jarvis and K.N. Joblin, unpublished data). With careful application, methanogen population densities can readily be determined using culture methods. These appear to be similar to the population densities determined by culture-independent methods (P. Evans and K.N. Joblin, unpublished data)

  13. Genome analysis of a Limnobacter sp. identified in an anaerobic methane-consuming cell consortium

    Directory of Open Access Journals (Sweden)

    Ying Chen

    2016-12-01

    Full Text Available Species of Limnobacter genus are widespread in a variety of environments, yet knowledges upon their metabolic potentials and mechanisms of environmental adaptation are limited. In this study, a cell aggregate containing Limnobacter and anaerobic methanotrophic archaea (ANME was captured from an enriched anaerobic methane oxidizing (AOM microbial community. A genomic bin of Limnobacter was obtained and analyzed, which provides the first metabolic insights into Limnobacter from an AOM environment. This Limnobacter was found to contain genes involved in the Embden-Meyerhof pathway, the citrate cycle, citronellol degradation, and transporters of various organic substances, indicating a potentially heterotrophic lifestyle. A number of genes involved in sulfur oxidization, oxidative phosphorylation and ethanol fermentation that serve both aerobic and anaerobic purposes have been found in Limnobacter. This work suggests that in the AOM environment, Limnobacter strains may live on the organic substances produced through AOM activity and subsequently may contribute to the AOM community by providing sulfate from sulfur oxidation.

  14. Effects of trace volatile organic compounds on methane oxidation

    Directory of Open Access Journals (Sweden)

    Chiemchaisri Wilai

    2001-01-01

    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 oxidation

  15. Associative patterns among anaerobic fungi, methanogenic archaea, and bacterial communities in response to changes in diet and age in the rumen of dairy cows.

    Science.gov (United States)

    Kumar, Sanjay; Indugu, Nagaraju; Vecchiarelli, Bonnie; Pitta, Dipti W

    2015-01-01

    The rumen microbiome represents a complex microbial genetic web where bacteria, anaerobic rumen fungi (ARF), protozoa and archaea work in harmony contributing to the health and productivity of ruminants. We hypothesized that the rumen microbiome shifts as the dairy cow advances in lactations and these microbial changes may contribute to differences in productivity between primiparous (first lactation) and multiparous (≥second lactation) cows. To this end, we investigated shifts in the ruminal ARF and methanogenic communities in both primiparous (n = 5) and multiparous (n = 5) cows as they transitioned from a high forage to a high grain diet upon initiation of lactation. A total of 20 rumen samples were extracted for genomic DNA, amplified using archaeal and fungal specific primers, sequenced on a 454 platform and analyzed using QIIME. Community comparisons (Bray-Curtis index) revealed the effect of diet (P bacteria, ARF and archaea revealed syntrophic interactions both within and between microbial domains in response to change in diet as well as age of dairy cows. Notably, these interactions were numerous and complex in multiparous cows, supporting our hypothesis that the rumen microbiome also matures with age to sustain the growing metabolic needs of the host. This study provides a broader picture of the ARF and methanogenic populations in the rumen of dairy cows and their co-occurrence implicates specific relationships between different microbial domains in response to diet and age.

  16. Effect of biowaste sludge maturation on the diversity of thermophilic bacteria and archaea in an anaerobic reactor.

    Science.gov (United States)

    Goberna, M; Insam, H; Franke-Whittle, I H

    2009-04-01

    Prokaryotic diversity was investigated near the inlet and outlet of a plug-flow reactor. After analyzing 800 clones, 50 bacterial and 3 archaeal phylogenetic groups were defined. Clostridia (>92%) dominated among bacteria and Methanoculleus (>90%) among archaea. Significant changes in pH and volatile fatty acids did not invoke a major shift in the phylogenetic groups. We suggest that the environmental filter imposed by the saline conditions (20 g liter(-1)) selected a stable community of halotolerant and halophilic prokaryotes.

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

    Science.gov (United States)

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

    2015-10-22

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

  18. Associative patterns among anaerobic fungi, methanogenic archaea and bacterial communities in response to changes in diet and age in the rumen of dairy cows

    Directory of Open Access Journals (Sweden)

    Sanjay eKumar

    2015-07-01

    Full Text Available The rumen microbiome represents a complex microbial genetic web where bacteria, anaerobic rumen fungi (ARF, protozoa and archaea work in harmony contributing to the health and productivity of ruminants. We hypothesized that the rumen microbiome shifts as the dairy cow advances in lactations and these microbial changes may contribute to differences in productivity between primiparous (first lactation and multiparous (≥ second lactation cows. To this end, we investigated shifts in the ruminal ARF and methanogenic communities in both primiparous (n=5 and multiparous (n=5 cows as they transitioned from a high forage to a high grain diet upon initiation of lactation. A total of 20 rumen samples were extracted for genomic DNA, amplified using archaeal and fungal specific primers, sequenced on a 454 platform and analyzed using QIIME. Community comparisons (Bray-Curtis index revealed the effect of diet (P < 0.01 on ARF composition, while archaeal communities differed between primiparous and multiparous cows (P < 0.05. Among ARF, several lineages were unclassified, however, phylum Neocallimastigomycota showed the presence of three known genera. Abundance of Cyllamyces and Caecomyces shifted with diet whereas, Orpinomyces was influenced by both diet and age. Methanobrevibacter constituted the most dominant archaeal genus across all samples. Co-occurrence analysis incorporating taxa from bacteria, ARF and archaea revealed syntrophic interactions both within and between microbial domains in response to change in diet as well as age of dairy cows. Notably, these interactions were numerous and complex in multiparous cows supporting our hypothesis that the rumen microbiome also matures with age to sustain the growing metabolic needs of the host. This study provides a broader picture of the ARF and methanogenic populations in the rumen of dairy cows and their co-occurrence implicates specific relationships between different microbial domains in response to

  19. Enhancement of anaerobic acidogenesis by integrating an electrochemical system into an acidogenic reactor: effect of hydraulic retention times (HRT) and role of bacteria and acidophilic methanogenic Archaea.

    Science.gov (United States)

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

    2015-03-01

    In this study, an acidogenic reactor packed with a pair of Fe-carbon electrodes (R1) was developed to enhance anaerobic acidogenesis of organic wastewater at short hydraulic retention times. The results indicated that the acidogenic efficiency was improved by settling a bio-electrochemical system. When hydraulic retention times decreased from 12 to 3h, R1 showed 18.9% more chemical oxygen demand removal and 13.8% more acidification efficiency. After cutting off the voltage of R1, the COD removal decreased by about 5%. Coupling of Fe(2+) leaching and electric field accelerated the hydrolysis of polysaccharide, relieving its accumulation in the sludge phase. Several acidophilic methanogenic Archaea such as Methanosarcina sp. were enriched in R1, which was favorable for consuming organic acids and preventing excessive pH decline. Thus, the developed acidogenic reactor with Fe-carbon electrodes is expected to be potentially effective and useful for wastewater treatment. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

    DEFF Research Database (Denmark)

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

    2009-01-01

    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...... 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...

  1. Anaerobic methanotrophic communities thrive in deep submarine permafrost.

    Science.gov (United States)

    Winkel, Matthias; Mitzscherling, Julia; Overduin, Pier P; Horn, Fabian; Winterfeld, Maria; Rijkers, Ruud; Grigoriev, Mikhail N; Knoblauch, Christian; Mangelsdorf, Kai; Wagner, Dirk; Liebner, Susanne

    2018-01-22

    Thawing submarine permafrost is a source of methane to the subsurface biosphere. Methane oxidation in submarine permafrost sediments has been proposed, but the responsible microorganisms remain uncharacterized. We analyzed archaeal communities and identified distinct anaerobic methanotrophic assemblages of marine and terrestrial origin (ANME-2a/b, ANME-2d) both in frozen and completely thawed submarine permafrost sediments. Besides archaea potentially involved in anaerobic oxidation of methane (AOM) we found a large diversity of archaea mainly belonging to Bathyarchaeota, Thaumarchaeota, and Euryarchaeota. Methane concentrations and δ 13 C-methane signatures distinguish horizons of potential AOM coupled either to sulfate reduction in a sulfate-methane transition zone (SMTZ) or to the reduction of other electron acceptors, such as iron, manganese or nitrate. Analysis of functional marker genes (mcrA) and fluorescence in situ hybridization (FISH) corroborate potential activity of AOM communities in submarine permafrost sediments at low temperatures. Modeled potential AOM consumes 72-100% of submarine permafrost methane and up to 1.2 Tg of carbon per year for the total expected area of submarine permafrost. This is comparable with AOM habitats such as cold seeps. We thus propose that AOM is active where submarine permafrost thaws, which should be included in global methane budgets.

  2. Termites facilitate methane oxidation and shape the methanotrophic community

    NARCIS (Netherlands)

    Ho, A.; Erens, H.; Mujinya, B.B.; Boeckx, P.; Baert, G.; Schneider, B.; Frenzel, P.; Boon, N.; Van Ranst, E.

    2013-01-01

    Termite-derived methane contributes 3-4% to the total methane budget globally. Termites are not known to harbor methane-oxidizing microorganisms (methanotrophs). However, a considerable fraction of methane produced can be consumed by methanotrophs that inhabit the mound material. Yet, methanotroph

  3. Termites facilitate methane oxidation and shape the methanotrophic community.

    Science.gov (United States)

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

    2013-12-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

  5. A laboratory study of anaerobic oxidation of methane in the presence of methane hydrate

    Science.gov (United States)

    Solem, R.; Bartlett, D.; Kastner, M.; Valentine, D.

    2003-12-01

    In order to mimic and study the process of anaerobic methane oxidation in methane hydrate regions we developed four high-pressure anaerobic bioreactors, designed to incubate environmental sediment samples, and enrich for populations of microbes associated with anaerobic methane oxidation (AMO). We obtained sediment inocula from a bacterial mat at the southern Hydrate Ridge, Cascadia, having cell counts approaching 1010 cells/cc. Ultimately, our goal is to produce an enriched culture of these microbes for characterization of the biochemical processes and chemical fluxes involved, as well as the unique adaptations required for, AMO. Molecular phylogenetic information along with results from fluorescent in situ hybridization indicate that consortia of Archaea and Bacteria are present which are related to those previously described for marine sediment AMO environments. Using a medium of enriched seawater and sediment in a 3:1 ratio, the system was incubated at 4° C under 43 atm of methane pressure; the temperature and pressure were kept constant. We have followed the reactions for seven months, particularly the vigorous consumption rates of dissolved sulfate and alkalinity production, as well as increases in HS-, and decreases in Ca concentrations. We also monitored the dissolved inorganic C (DIC) δ 13C values. The data were reproduced, and indicated that the process is extremely sensitive to changes in methane pressure. The rates of decrease in sulfate and increase in alkalinity concentrations were complimentary and showed considerable linearity with time. When the pressure in the reactor was decreased below the methane hydrate stability field, following the methane hydrate dissociation, sulfate reduction abruptly decreased. When the pressure was restored all the reactions returned to their previous rates. Much of the methane oxidation activity in the reactor is believed to occur in association with the methane hydrate. Upon the completion of one of the experiments

  6. Methane-oxidizing seawater microbial communities from an Arctic shelf

    Science.gov (United States)

    Uhlig, Christiane; Kirkpatrick, John B.; D'Hondt, Steven; Loose, Brice

    2018-06-01

    Marine microbial communities can consume dissolved methane before it can escape to the atmosphere and contribute to global warming. Seawater over the shallow Arctic shelf is characterized by excess methane compared to atmospheric equilibrium. This methane originates in sediment, permafrost, and hydrate. Particularly high concentrations are found beneath sea ice. We studied the structure and methane oxidation potential of the microbial communities from seawater collected close to Utqiagvik, Alaska, in April 2016. The in situ methane concentrations were 16.3 ± 7.2 nmol L-1, approximately 4.8 times oversaturated relative to atmospheric equilibrium. The group of methane-oxidizing bacteria (MOB) in the natural seawater and incubated seawater was > 97 % dominated by Methylococcales (γ-Proteobacteria). Incubations of seawater under a range of methane concentrations led to loss of diversity in the bacterial community. The abundance of MOB was low with maximal fractions of 2.5 % at 200 times elevated methane concentration, while sequence reads of non-MOB methylotrophs were 4 times more abundant than MOB in most incubations. The abundances of MOB as well as non-MOB methylotroph sequences correlated tightly with the rate constant (kox) for methane oxidation, indicating that non-MOB methylotrophs might be coupled to MOB and involved in community methane oxidation. In sea ice, where methane concentrations of 82 ± 35.8 nmol kg-1 were found, Methylobacterium (α-Proteobacteria) was the dominant MOB with a relative abundance of 80 %. Total MOB abundances were very low in sea ice, with maximal fractions found at the ice-snow interface (0.1 %), while non-MOB methylotrophs were present in abundances similar to natural seawater communities. The dissimilarities in MOB taxa, methane concentrations, and stable isotope ratios between the sea ice and water column point toward different methane dynamics in the two environments.

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

    OpenAIRE

    Lawton, Thomas J.; Rosenzweig, Amy C.

    2016-01-01

    Biological conversion of natural gas to liquids (Bio-GTL) represents an immense economic opportunity. In nature, aerobic methanotrophic bacteria and anaerobic archaea are able to selectively oxidize methane using methane monooxygenase (MMO) and methyl coenzyme M reductase (MCR) enzymes. Although significant progress has been made toward genetically manipulating these organisms for biotechnological applications, the enzymes themselves are slow, complex, and not recombinantly tractable in tradi...

  8. Modeling of simultaneous anaerobic methane and ammonium oxidation in a membrane biofilm reactor.

    Science.gov (United States)

    Chen, Xueming; Guo, Jianhua; Shi, Ying; Hu, Shihu; Yuan, Zhiguo; Ni, Bing-Jie

    2014-08-19

    Nitrogen removal by using the synergy of denitrifying anaerobic methane oxidation (DAMO) and anaerobic ammonium oxidation (Anammox) microorganisms in a membrane biofilm reactor (MBfR) has previously been demonstrated experimentally. In this work, a mathematical model is developed to describe the simultaneous anaerobic methane and ammonium oxidation by DAMO and Anammox microorganisms in an MBfR for the first time. In this model, DAMO archaea convert nitrate, both externally fed and/or produced by Anammox, to nitrite, with methane as the electron donor. Anammox and DAMO bacteria jointly remove the nitrite fed/produced, with ammonium and methane as the electron donor, respectively. The model is successfully calibrated and validated using the long-term (over 400 days) dynamic experimental data from the MBfR, as well as two independent batch tests at different operational stages of the MBfR. The model satisfactorily describes the methane oxidation and nitrogen conversion data from the system. Modeling results show the concentration gradients of methane and nitrogen would cause stratification of the biofilm, where Anammox bacteria mainly grow in the biofilm layer close to the bulk liquid and DAMO organisms attach close to the membrane surface. The low surface methane loadings result in a low fraction of DAMO microorganisms, but the high surface methane loadings would lead to overgrowth of DAMO bacteria, which would compete with Anammox for nitrite and decrease the fraction of Anammox bacteria. The results suggest an optimal methane supply under the given condition should be applied not only to benefit the nitrogen removal but also to avoid potential methane emissions.

  9. 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

    2014-01-01

    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 δ13CDIC 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 (34ε = 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. PMID:25039851

  10. Bacteria and archaea communities in full-scale thermophilic and mesophilic anaerobic digesters treating food wastewater: Key process parameters and microbial indicators of process instability.

    Science.gov (United States)

    Lee, Joonyeob; Shin, Seung Gu; Han, Gyuseong; Koo, Taewoan; Hwang, Seokhwan

    2017-12-01

    In this study, four different mesophilic and thermophilic full-scale anaerobic digesters treating food wastewater (FWW) were monitored for 1-2years in order to investigate: 1) microbial communities underpinning anaerobic digestion of FWW, 2) significant factors shaping microbial community structures, and 3) potential microbial indicators of process instability. Twenty-seven bacterial genera were identified as abundant bacteria underpinning the anaerobic digestion of FWW. Methanosaeta harundinacea, M. concilii, Methanoculleus bourgensis, M. thermophilus, and Methanobacterium beijingense were revealed as dominant methanogens. Bacterial community structures were clearly differentiated by digesters; archaeal community structures of each digester were dominated by one or two methanogen species. Temperature, ammonia, propionate, Na + , and acetate in the digester were significant factors shaping microbial community structures. The total microbial populations, microbial diversity, and specific bacteria genera showed potential as indicators of process instability in the anaerobic digestion of FWW. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Methane oxidation at low temperatures in soil exposed to landfill gas

    DEFF Research Database (Denmark)

    Christophersen, Mette; Linderød, L.; Jensen, Pernille Erland

    2000-01-01

    soil moisture regimes, At 2 degreesC the methane oxidation rates were 0.005 to 0.17 mu mol g(-1) h(-1), and calculations showed that it was possible to oxidize all the produced methane at older landfills, even during the winter. Therefore, methane oxidation in top covers of landfills is an alternative...

  12. Intensive Ammonia and Methane Oxidation in Organic Liquid Manure Crusts

    DEFF Research Database (Denmark)

    Nielsen, Daniel Aagren; Nielsen, Lars Peter; Schramm, Andreas

    methane oxidizing bacteria (MOB) and are known to accumulate nitrite and nitrate, indicating the presence of ammonia oxidizers (AOB). We have surveyed six manure tanks with organic covers to investigate the prevalence of MOB and AOB and to link the potential activity with physical and chemical aspects...... characterized with respect to O2 availability by in situ profiling with electrochemical microsensors. Results show that oxygen penetration increased from few micrometers up to several centimetres with crust age. AOB and ammonium oxidation are ubiquitously present in well-developed manure crusts whereas MOB were...... also CH4 emission mitigation, an organic surface crust can be effective if populations of MOB and AOB are allowed to build up....

  13. 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...... methanol, but only for a limited time period of about 5 days. Several explanations for the discontinued degradation of TCE are given. An experiment carried out to re-activate the methane-oxidizing bacteria after 8 days of growth on methanol by adding methane did not immediately result in degradation...... of methane and TCE. During the first 10–15 days after the addition of methane a significant degradation of methane and a minor degradation of TCE were observed. This experiment revealed that the ability of mixed cultures of methane-oxidizing bacteria to degrade TCE varied significantly even though...

  14. Extreme nitrogen deposition can change methane oxidation rate in moist acidic tundra soil in Arctic regions

    Science.gov (United States)

    Lee, J.; Kim, J.; Kang, H.

    2017-12-01

    Recently, extreme nitrogen(N) deposition events are observed in Arctic regions where over 90% of the annual N deposition occurred in just a few days. Since Arctic ecosystems are typically N-limited, input of extremely high amount of N could substantially affect ecosystem processes. CH4 is a potent greenhouse gas that has 25 times greater global warming potential than CO2 over a 100-year time frame. Ammonium is known as an inhibitor of methane oxidation and nitrate also shows inhibitory effect on it in temperate ecosystems. However, effects of N addition on Arctic ecosystems are still elusive. We conducted a lab-scale incubation experiment with moist acidic tundra (MAT) soil from Council, Alaska to investigate the effect of extreme N deposition events on methane oxidation. Zero point five % methane was added to the head space to determine the potential methane oxidation rate of MAT soil. Three treatments (NH4NO3-AN, (NH4)2SO4-AS, KNO3-PN) were used to compare effects of ammonium, nitrate and salts. All treatments were added in 3 levels: 10μg N gd.w-1(10), 50μg N gd.w-1(50) and 100μg N gd.w-1(100). AN10 and AN50 increased methane oxidation rate 1.7, 6% respectively. However, AN100 shows -8.5% of inhibitory effect. In AS added samples, all 3 concentrations (AN10, AN50, AN100) stimulated methane oxidation rate with 4.7, 8.9, 4%, respectively. On the contrary, PN50 (-9%) and PN100 (-59.5%) exhibited a significant inhibitory effect. We also analyzed the microbial gene abundance and community structures of methane oxidizing bacteria using a DNA-based fingerprinting method (T-RFLP) Our study results suggest that NH4+ can stimulate methane oxidation in Arctic MAT soil, while NO3- can inhibit methane oxidation significantly.

  15. Systems Level Dissection of Anaerobic Methane Cycling: Quantitative Measurements of Single Cell Ecophysiology, Genetic Mechanisms, and Microbial Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Orphan, Victoria [California Inst. of Technology (CalTech), Pasadena, CA (United States); Tyson, Gene [University of Queensland, Brisbane Australia; Meile, Christof [University of Georgia, Athens, Georgia; McGlynn, Shawn [California Inst. of Technology (CalTech), Pasadena, CA (United States); Yu, Hang [California Inst. of Technology (CalTech), Pasadena, CA (United States); Chadwick, Grayson [California Inst. of Technology (CalTech), Pasadena, CA (United States); Marlow, Jeffrey [California Inst. of Technology (CalTech), Pasadena, CA (United States); Trembath-Reichert, Elizabeth [California Inst. of Technology (CalTech), Pasadena, CA (United States); Dekas, Anne [California Inst. of Technology (CalTech), Pasadena, CA (United States); Hettich, Robert [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Pan, Chongle [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Ellisman, Mark [University of California San Diego; Hatzenpichler, Roland [California Inst. of Technology (CalTech), Pasadena, CA (United States); Skennerton, Connor [California Inst. of Technology (CalTech), Pasadena, CA (United States); Scheller, Silvan [California Inst. of Technology (CalTech), Pasadena, CA (United States)

    2017-12-25

    The global biological CH4 cycle is largely controlled through coordinated and often intimate microbial interactions between archaea and bacteria, the majority of which are still unknown or have been only cursorily identified. Members of the methanotrophic archaea, aka ‘ANME’, are believed to play a major role in the cycling of methane in anoxic environments coupled to sulfate, nitrate, and possibly iron and manganese oxides, frequently forming diverse physical and metabolic partnerships with a range of bacteria. The thermodynamic challenges overcome by the ANME and their bacterial partners and corresponding slow rates of growth are common characteristics in anaerobic ecosystems, and, in stark contrast to most cultured microorganisms, this type of energy and resource limited microbial lifestyle is likely the norm in the environment. While we have gained an in-depth systems level understanding of fast-growing, energy-replete microorganisms, comparatively little is known about the dynamics of cell respiration, growth, protein turnover, gene expression, and energy storage in the slow-growing microbial majority. These fundamental properties, combined with the observed metabolic and symbiotic versatility of methanotrophic ANME, make these cooperative microbial systems a relevant (albeit challenging) system to study and for which to develop and optimize culture-independent methodologies, which enable a systems-level understanding of microbial interactions and metabolic networks. We used an integrative systems biology approach to study anaerobic sediment microcosms and methane-oxidizing bioreactors and expanded our understanding of the methanotrophic ANME archaea, their interactions with physically-associated bacteria, ecophysiological characteristics, and underlying genetic basis for cooperative microbial methane-oxidation linked with different terminal electron acceptors. Our approach is inherently multi-disciplinary and multi-scaled, combining transcriptional and

  16. Activity and diversity of methane-oxidizing bacteria in glacier forefields on siliceous and calcareous bedrock

    Directory of Open Access Journals (Sweden)

    P. A. Nauer

    2012-06-01

    Full Text Available The global methane (CH4 cycle is largely driven by methanogenic archaea and methane-oxidizing bacteria (MOB, but little is known about their activity and diversity in pioneer ecosystems. We conducted a field survey in forefields of 13 receding Swiss glaciers on both siliceous and calcareous bedrock to investigate and quantify CH4 turnover based on soil-gas CH4 concentration profiles, and to characterize the MOB community by sequencing and terminal restriction fragment length polymorphism (T-RFLP analysis of pmoA. Methane turnover was fundamentally different in the two bedrock categories. Of the 36 CH4 concentration profiles from siliceous locations, 11 showed atmospheric CH4 consumption at concentrations of ~1–2 μL L−1 with soil-atmosphere CH4 fluxes of –0.14 to –1.1 mg m−2 d−1. Another 11 profiles showed no apparent activity, while the remaining 14 exhibited slightly increased CH4 concentrations of ~2–10 μL L−1 , most likely due to microsite methanogenesis. In contrast, all profiles from calcareous sites suggested a substantial, yet unknown CH4 source below our sampling zone, with soil-gas CH4 concentrations reaching up to 1400 μL L−1. Remarkably, most soils oxidized ~90 % of the deep-soil CH4, resulting in soil-atmosphere fluxes of 0.12 to 31 mg m−2 d−1. MOB showed limited diversity in both siliceous and calcareous forefields: all identified pmoA sequences formed only 5 operational taxonomic units (OTUs at the species level and, with one exception, could be assigned to either Methylocystis or the as-yet-uncultivated Upland Soil Cluster γ (USCγ. The latter dominated T-RFLP patterns of all siliceous and most calcareous samples, while Methylocystis dominated in 4 calcareous samples. Members of Upland Soil

  17. Thermophilic anaerobic oxidation of methane by marine microbial consortia.

    Science.gov (United States)

    Holler, Thomas; Widdel, Friedrich; Knittel, Katrin; Amann, Rudolf; Kellermann, Matthias Y; Hinrichs, Kai-Uwe; Teske, Andreas; Boetius, Antje; Wegener, Gunter

    2011-12-01

    The anaerobic oxidation of methane (AOM) with sulfate controls the emission of the greenhouse gas methane from the ocean floor. AOM is performed by microbial consortia of archaea (ANME) associated with partners related to sulfate-reducing bacteria. In vitro enrichments of AOM were so far only successful at temperatures ≤25 °C; however, energy gain for growth by AOM with sulfate is in principle also possible at higher temperatures. Sequences of 16S rRNA genes and core lipids characteristic for ANME as well as hints of in situ AOM activity were indeed reported for geothermally heated marine environments, yet no direct evidence for thermophilic growth of marine ANME consortia was obtained to date. To study possible thermophilic AOM, we investigated hydrothermally influenced sediment from the Guaymas Basin. In vitro incubations showed activity of sulfate-dependent methane oxidation between 5 and 70 °C with an apparent optimum between 45 and 60 °C. AOM was absent at temperatures ≥75 °C. Long-term enrichment of AOM was fastest at 50 °C, yielding a 13-fold increase of methane-dependent sulfate reduction within 250 days, equivalent to an apparent doubling time of 68 days. The enrichments were dominated by novel ANME-1 consortia, mostly associated with bacterial partners of the deltaproteobacterial HotSeep-1 cluster, a deeply branching phylogenetic group previously found in a butane-amended 60 °C-enrichment culture of Guaymas sediments. The closest relatives (Desulfurella spp.; Hippea maritima) are moderately thermophilic sulfur reducers. Results indicate that AOM and ANME archaea could be of biogeochemical relevance not only in cold to moderate but also in hot marine habitats.

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

    International Nuclear Information System (INIS)

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

    1991-01-01

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

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

    International Nuclear Information System (INIS)

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

    2008-01-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

  1. 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...

  2. The nitrogen cycle in anaerobic methanotrophic mats of the Black Sea is linked to sulfate reduction and biomass decomposition.

    Science.gov (United States)

    Siegert, Michael; Taubert, Martin; Seifert, Jana; von Bergen-Tomm, Martin; Basen, Mirko; Bastida, Felipe; Gehre, Matthias; Richnow, Hans-Hermann; Krüger, Martin

    2013-11-01

    Anaerobic methanotrophic (ANME) mats host methane-oxidizing archaea and sulfate-reducing prokaryotes. Little is known about the nitrogen cycle in these communities. Here, we link the anaerobic oxidation of methane (AOM) to the nitrogen cycle in microbial mats of the Black Sea by using stable isotope probing. We used four different (15)N-labeled sources of nitrogen: dinitrogen, nitrate, nitrite and ammonium. We estimated the nitrogen incorporation rates into the total biomass and the methyl coenzyme M reductase (MCR). Dinitrogen played an insignificant role as nitrogen source. Assimilatory and dissimilatory nitrate reduction occurred. High rates of nitrate reduction to dinitrogen were stimulated by methane and sulfate, suggesting that oxidation of reduced sulfur compounds such as sulfides was necessary for AOM with nitrate as electron acceptor. Nitrate reduction to dinitrogen occurred also in the absence of methane as electron donor but at six times slower rates. Dissimilatory nitrate reduction to ammonium was independent of AOM. Ammonium was used for biomass synthesis under all conditions. The pivotal enzyme in AOM coupled to sulfate reduction, MCR, was synthesized from nitrate and ammonium. Results show that AOM coupled to sulfate reduction along with biomass decomposition drive the nitrogen cycle in the ANME mats of the Black Sea and that MCR enzymes are involved in this process. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  3. Archaea: Essential inhabitants of the human digestive microbiota

    Directory of Open Access Journals (Sweden)

    Vanessa Demonfort Nkamga

    2017-03-01

    Full Text Available Prokaryotes forming the domain of Archaea, named after their first discovery in extreme environments, are acknowledged but still neglected members of the human digestive tract microbiota. In this microbiota, cultured archaea comprise anaerobic methanogens: Methanobrevibacter smithii, Methanobrevibacter oralis, Methanobrevibacter massiliense, Methanosphaera stadtmanae, Methanobrevibacter arboriphilus, Methanobrevibacter millerae and Methanomassiliicoccus luminyensis; along with the non-methanogen halophilic Archaea Halopherax massiliense. Metagenomic analyses detected DNA sequences indicative of the presence of additional methanogenic and non-methanogenic halophilic Archaea in the human intestinal tract and oral cavity. Methanogens specifically metabolize hydrogen produced by anaerobic fermentation of carbohydrates into methane; further transforming heavy metals and metalloids into methylated derivatives, such as trimethylbismuth which is toxic for both human and bacterial cells. However, the role of Archaea as pathogens remains to be established. Future researches will aim to increase the repertoire of the human digestive tract Archaea and to understand their possible association with intestinal and extra-intestinal infections and diseases including weight regulation abnormalities. Keywords: Human-associated Archaea, Methanogens, Halophiles, Oral cavity, Intestinal tract

  4. Evidence of sulfate-dependent anaerobic methane oxidation... Wolfe & Wilkin data table vers 1

    Data.gov (United States)

    U.S. Environmental Protection Agency — Data file (.csv) including data plotted in manuscript figures: methane and sulfate concentrations, and stable isotope data for carbon, hydrogen, sulfur, and oxygen....

  5. Vertical and horizontal distribution of sediment nitrite-dependent methane-oxidizing organisms in a mesotrophic freshwater reservoir.

    Science.gov (United States)

    Long, Yan; Liu, Changbao; Lin, Hengliang; Li, Ningning; Guo, Qingwei; Xie, Shuguang

    2017-06-01

    In the present study, we investigated the spatial change of sediment nitrite-dependent anaerobic methane-oxidizing (n-damo) organisms in the mesotrophic freshwater Gaozhou Reservoir (6 different sampling locations and 2 sediment depths (0-5 cm, 5-10 cm)), one of the largest drinking water reservoirs in China. The abundance of sediment n-damo bacteria was quantified using quantitative polymerase chain reaction assay, while the richness, diversity, and composition of n-damo pmoA gene sequences were characterized using clone library analysis. Vertical and horizontal changes in sediment n-damo bacterial abundance occurred in Gaozhou Reservoir, with 1.37 × 10 5 to 8.24 × 10 5 n-damo 16S rRNA gene copies per gram of dry sediment. Considerable horizontal and vertical variations of n-damo pmoA gene diversity (Shannon index = 0.32-2.50) and composition also occurred in this reservoir. Various types of sediment n-damo pmoA genes existed in Gaozhou Reservoir. A small proportion of n-damo pmoA gene sequences (19.1%) were related to those recovered from "Candidatus Methylomirabilis oxyfera". Our results suggested that sediment n-damo pmoA gene diversity might be regulated by nitrite, while n-damo pmoA gene richness might be governed by multiple environmental factors, including total organic carbon, total phosphorus, nitrite, and total nitrogen.

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

    NARCIS (Netherlands)

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

    2016-01-01

    Soils serve as the biological sink of the potent greenhouse gas methane with exceptionally low concentrations of ~1.84 p.p.m.v. in the atmosphere. The as-yet-uncultivated methane-consuming bacteria have long been proposed to be responsible for this ‘high-affinity’ methane oxidation (HAMO). Here we

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

    NARCIS (Netherlands)

    Ganendra, G; De Muynck, W; Ho, A.; Hoefman, S.; De Vos, P.; Boeckx, P.; Boon, N.

    2014-01-01

    Biological treatment using methane-oxidizing bacteria (MOB) immobilized on six porous carrier materials have been used to mitigate methane emission. Experiments were performed with different MOB inoculated in building materials at high (similar to 20 % (v/v)) and low (similar to 100 ppmv) methane

  8. The Effect of Nitrogen and Argon Dilution on Methane Oxidation in Laminar Flames

    Czech Academy of Sciences Publication Activity Database

    Kozubková, M.; Kozubek, E.; Nevrlý, V.; Bitala, P.; Štěpánek, O.; Dlabka, J.; Vašinek, M.; Bojko, M.; Zelinger, Zdeněk; Kubát, Pavel; Grigorová, E.

    2012-01-01

    Roč. 42, č. 0 (2012), s. 1826-1839 E-ISSN 1877-7058. [International Congress of Chemical and Process Engineering CHISA 2012 /20./. Prague, 25.08.2012-29.08.2012] R&D Projects: GA MŠk LD12020 Institutional support: RVO:61388955 Keywords : dilution * methane oxidation * global chemistry Subject RIV: CF - Physical ; Theoretical Chemistry

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

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

    Directory of Open Access Journals (Sweden)

    Zhen Yan

    2017-02-01

    Full Text Available 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.

  12. Improved stratospheric atmosphere forecasts in the general circulation model through a methane oxidation parametrization

    Science.gov (United States)

    Wang, S.; Jun, Z.

    2017-12-01

    Climatic characteristics of tropical stratospheric methane have been well researched using various satellite data, and numerical simulations have furtherly conducted using chemical climatic models, while the impact of stratospheric methane oxidation on distribution of water vapor is not paid enough attention in general circulation models. Simulated values of water vapour in the tropical upper stratosphere, and throughout much of the extratropical stratosphere, were too low. Something must be done to remedy this deficiency in order to producing realistic stratospheric water vapor using a general circulation model including the whole stratosphere. Introduction of a simple parametrization of the upper-stratospheric moisture source due to methane oxidation and a sink due to photolysis in the mesosphere was conducted. Numerical simulations and analysis of the influence of stratospheric methane on the prediction of tropical stratospheric moisture and temperature fields were carried out. This study presents the advantages of methane oxidation parametrization in producing a realistic distribution of water vapour in the tropical stratosphere and analyzes the impact of methane chemical process on the general circulation model using two storm cases including a heavy rain in South China and a typhoon caused tropical storm.It is obvious that general circulation model with methane oxidation parametrization succeeds in simulating the water vapor and temperature in stratosphere. The simulating rain center value of contrast experiment is increased up to 10% than that of the control experiment. Introduction of methane oxidation parametrization has modified the distribution of water vapour and then producing a broadly realistic distribution of temperature. Objective weather forecast verifications have been performed using simulating results of one month, which demonstrate somewhat positive effects on the model skill. There is a certain extent impact of methane oxidation

  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] ~ 1.9 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.

  14. Acetate repression of methane oxidation by supplemental Methylocella silvestris in a peat soil microcosm.

    Science.gov (United States)

    Rahman, M Tanvir; Crombie, Andrew; Moussard, Hélène; Chen, Yin; Murrell, J Colin

    2011-06-01

    Methylocella spp. are facultative methanotrophs that grow on methane and multicarbon substrates, such as acetate. Acetate represses transcription of methane monooxygenase of Methylocella silvestris in laboratory culture. DNA stable-isotope probing (DNA-SIP) using (13)C-methane and (12)C-acetate, carried out with Methylocella-spiked peat soil, showed that acetate also repressed methane oxidation by Methylocella in environmental samples.

  15. Acetate Repression of Methane Oxidation by Supplemental Methylocella silvestris in a Peat Soil Microcosm ▿ †

    Science.gov (United States)

    Rahman, M. Tanvir; Crombie, Andrew; Moussard, Hélène; Chen, Yin; Murrell, J. Colin

    2011-01-01

    Methylocella spp. are facultative methanotrophs that grow on methane and multicarbon substrates, such as acetate. Acetate represses transcription of methane monooxygenase of Methylocella silvestris in laboratory culture. DNA stable-isotope probing (DNA-SIP) using 13C-methane and 12C-acetate, carried out with Methylocella-spiked peat soil, showed that acetate also repressed methane oxidation by Methylocella in environmental samples. PMID:21515721

  16. Acetate Repression of Methane Oxidation by Supplemental Methylocella silvestris in a Peat Soil Microcosm ▿ †

    OpenAIRE

    Rahman, M. Tanvir; Crombie, Andrew; Moussard, Hélène; Chen, Yin; Murrell, J. Colin

    2011-01-01

    Methylocella spp. are facultative methanotrophs that grow on methane and multicarbon substrates, such as acetate. Acetate represses transcription of methane monooxygenase of Methylocella silvestris in laboratory culture. DNA stable-isotope probing (DNA-SIP) using 13C-methane and 12C-acetate, carried out with Methylocella-spiked peat soil, showed that acetate also repressed methane oxidation by Methylocella in environmental samples.

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

    International Nuclear Information System (INIS)

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

    2004-01-01

    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

  18. 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...

  19. 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...

  20. Iron-Coupled Anaerobic Oxidation of Methane Performed by a Mixed Bacterial-Archaeal Community Based on Poorly Reactive Minerals.

    Science.gov (United States)

    Bar-Or, Itay; Elvert, Marcus; Eckert, Werner; Kushmaro, Ariel; Vigderovich, Hanni; Zhu, Qingzeng; Ben-Dov, Eitan; Sivan, Orit

    2017-11-07

    Anaerobic oxidation of methane (AOM) was shown to reduce methane emissions by over 50% in freshwater systems, its main natural contributor to the atmosphere. In these environments iron oxides can become main agents for AOM, but the underlying mechanism for this process has remained enigmatic. By conducting anoxic slurry incubations with lake sediments amended with 13 C-labeled methane and naturally abundant iron oxides the process was evidenced by significant 13 C-enrichment of the dissolved inorganic carbon pool and most pronounced when poorly reactive iron minerals such as magnetite and hematite were applied. Methane incorporation into biomass was apparent by strong uptake of 13 C into fatty acids indicative of methanotrophic bacteria, associated with increasing copy numbers of the functional methane monooxygenase pmoA gene. Archaea were not directly involved in full methane oxidation, but their crucial participation, likely being mediators in electron transfer, was indicated by specific inhibition of their activity that fully stopped iron-coupled AOM. By contrast, inhibition of sulfur cycling increased 13 C-methane turnover, pointing to sulfur species involvement in a competing process. Our findings suggest that the mechanism of iron-coupled AOM is accomplished by a complex microbe-mineral reaction network, being likely representative of many similar but hidden interactions sustaining life under highly reducing low energy conditions.

  1. Effects of inorganic electron acceptors on methanogenesis and methanotrophy and on the community structure of bacteria and archaea in sediments of a boreal lake

    Science.gov (United States)

    Rissanen, Antti J.; Karvinen, Anu; Nykänen, Hannu; Peura, Sari; Tiirola, Marja; Mäki, Anita; Kankaala, Paula

    2016-04-01

    occurred. Besides decreasing the availability of methanogenic substrates, the Mn4+/Fe3+ - induced changes in the bacterial community also probably decreased the H2:acetate - ratio in the substrate pool. This led to increase in the relative activity (mRNA level) of some operational taxonomic units assigned to aceticlastic Methanosaetaceae and decrease in the relative activity of hydrogenotrophic Methanoregulaceae in the sediment. CH4 oxidation (0.02 - 0.30 nmol gdw-1d-1 in anaerobic and 18 - 73 nmol gdw-1d-1in aerobic treatments) took place without EA additions and was enhanced only by O2. This suggests decoupling of the process from the reduction of other inorganic EAs. The results also indicate that Fe3+/Mn4+ - reduction did not increase CH4 oxidation via increased availability of SO42- by cryptic sulfur cycle or via increased availability of organic EAs. Furthermore, ANME - archaea were only ≤ 3% of sediment archaeal community and their relative activity was decreased during incubations. Thus, EA driving CH4 oxidation in the anoxic sediments of the lake remains unknown or the process was methanogen-driven via trace methane oxidation.

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

    Science.gov (United States)

    Yan, Zhen; Wang, Mingyu; Ferry, James G

    2017-02-07

    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 CO 2 -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 F 420 (F 420 H 2 ) as an electron donor. Remarkably, HdrA2B2C2 couples the previously unknown endergonic oxidation of F 420 H 2 and reduction of ferredoxin with the exergonic oxidation of F 420 H 2 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. Discovery of the archetype HdrA2B2C2 heterodisulfide reductase with categorically unique properties extends the understanding of this ancient family beyond CO 2

  3. 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.

  4. 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 CH 4 and CO 2 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.

  5. 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...... headspace CH4. First-order rate constants were used to evaluate the strength of inhibition. Nitrite was the most potent inhibitor, reducing methanotrophic activity by up to 70% at only 1 mM NO2–. MOB were least sensitive to NO3–, tolerating up to 30 mM NO3– at 100 ppmv CH4 and 50 mM NO3– at 10,000 ppmv CH4...

  6. 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.

  7. 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.

  8. Dissimilatory oxidation and reduction of elemental sulfur in thermophilic archaea.

    Science.gov (United States)

    Kletzin, Arnulf; Urich, Tim; Müller, Fabian; Bandeiras, Tiago M; Gomes, Cláudio M

    2004-02-01

    The oxidation and reduction of elemental sulfur and reduced inorganic sulfur species are some of the most important energy-yielding reactions for microorganisms living in volcanic hot springs, solfataras, and submarine hydrothermal vents, including both heterotrophic, mixotrophic, and chemolithoautotrophic, carbon dioxide-fixing species. Elemental sulfur is the electron donor in aerobic archaea like Acidianus and Sulfolobus. It is oxidized via sulfite and thiosulfate in a pathway involving both soluble and membrane-bound enzymes. This pathway was recently found to be coupled to the aerobic respiratory chain, eliciting a link between sulfur oxidation and oxygen reduction at the level of the respiratory heme copper oxidase. In contrast, elemental sulfur is the electron acceptor in a short electron transport chain consisting of a membrane-bound hydrogenase and a sulfur reductase in (facultatively) anaerobic chemolithotrophic archaea Acidianus and Pyrodictium species. It is also the electron acceptor in organoheterotrophic anaerobic species like Pyrococcus and Thermococcus, however, an electron transport chain has not been described as yet. The current knowledge on the composition and properties of the aerobic and anaerobic pathways of dissimilatory elemental sulfur metabolism in thermophilic archaea is summarized in this contribution.

  9. Methane oxidation in soil profiles of Dutch and Finnish coniferous forests with different soil texture and atmospheric nitrogen deposition

    NARCIS (Netherlands)

    Saari, A.; Martikainen, P.J.; Ferm, A.; Ruuskanen, J.; Boer, W. de; Troelstra, S.R.; Laanbroek, H.J.

    1997-01-01

    We studied methane oxidation capacity in soil profiles of Dutch and Finnish coniferous forests. The Finnish sites (n = 9) had nitrogen depositions from 3 to 36 kg N ha⁻¹ a⁻¹. The deposition of N on the Dutch sites (n = 13) was higher ranging from 50 to 92 kg N ha⁻¹ a⁻¹. The Dutch sites had also

  10. Methane oxidation in soil profiles of Dutch and Finnish coniferous forests with different soil texture and atmospheric nitrogen deposition

    NARCIS (Netherlands)

    Saari, A.; Martikainen, P.J.; Ferm, A.; Ruuskanen, J.; De Boer, W.; Troelstra, S.R.; Laanbroek, H.J.

    1997-01-01

    We studied methane oxidation capacity in soil profiles of Dutch and Finnish coniferous forests. The Finnish sites (n = 9) had nitrogen depositions from 3 to 36 kg N ha(-1) a(-1). The deposition of N on the Dutch sites (n = 13) was higher ranging from 50 to 92 kg N ha(-1) a(-1). The Dutch sites had

  11. Wood ant nests as hot spots of carbon dioxide production and cold spots of methane oxidation in temperate forests

    Czech Academy of Sciences Publication Activity Database

    Jílková, Veronika; Picek, T.; Cajthaml, Tomáš; Frouz, Jan

    2016-01-01

    Roč. 18, April (2016), EGU2016-4634 ISSN 1607-7962. [European Geosciences Union General Assembly 2016. 17.04.2016-22.04.2016, Vienna] Institutional support: RVO:60077344 ; RVO:61388971 Keywords : wood ant nests * hot spots of carbon dioxide production * cold spots of methane oxidation * temperate forests Subject RIV: DF - Soil Science

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

    NARCIS (Netherlands)

    Pan, Y.; Abell, G.C.J.; Bodelier, P.L.E.; Meima-Franke, M.; Sessitsch, A.; Bodrossy, L.

    2014-01-01

    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

  13. Assessment of the radio 3H-CH4 tracer technique to measure aerobic methane oxidation in the water column

    Czech Academy of Sciences Publication Activity Database

    Bussmann, I.; Matoušů, Anna; Osudar, R.; Mau, S.

    2015-01-01

    Roč. 13, č. 6 (2015), s. 312-327 ISSN 1541-5856 R&D Projects: GA ČR(CZ) GA13-00243S Institutional support: RVO:60077344 Keywords : methane * aerobic methane oxidation * methods * radiotracer Subject RIV: DA - Hydrology ; Limnology Impact factor: 2.008, year: 2015

  14. Improved methane removal in exhaust gas from biogas upgrading process using immobilized methane-oxidizing bacteria.

    Science.gov (United States)

    Sun, Meng-Ting; Yang, Zhi-Man; Fu, Shan-Fei; Fan, Xiao-Lei; Guo, Rong-Bo

    2018-05-01

    Methane in exhaust gas from biogas upgrading process, which is a greenhouse gas, could cause global warming. The biofilter with immobilized methane-oxidizing bacteria (MOB) is a promising approach for methane removal, and the selections of inoculated MOB culture and support material are vital for the biofilter. In this work, five MOB consortia were enriched at different methane concentrations. The MOB-20 consortium enriched at the methane concentration of 20.0% (v/v) was then immobilized on sponge and two particle sizes of volcanic rock in biofilters to remove methane in exhaust gas from biogas upgrading process. Results showed that the immobilized MOB performed more admirable methane removal capacity than suspended cells. The immobilized MOB on sponge reached the highest methane removal efficiency (RE) of 35%. The rough surface, preferable hydroscopicity, appropriate pore size and particle size of support material might favor the MOB immobilization and accordingly methane removal. Copyright © 2018 Elsevier Ltd. All rights reserved.

  15. The indirect global warming potential and global temperature change potential due to methane oxidation

    International Nuclear Information System (INIS)

    Boucher, Olivier; Collins, Bill; Friedlingstein, Pierre; Shine, Keith P

    2009-01-01

    Methane is the second most important anthropogenic greenhouse gas in the atmosphere next to carbon dioxide. Its global warming potential (GWP) for a time horizon of 100 years is 25, which makes it an attractive target for climate mitigation policies. Although the methane GWP traditionally includes the methane indirect effects on the concentrations of ozone and stratospheric water vapour, it does not take into account the production of carbon dioxide from methane oxidation. We argue here that this CO 2 -induced effect should be included for fossil sources of methane, which results in slightly larger GWP values for all time horizons. If the global temperature change potential is used as an alternative climate metric, then the impact of the CO 2 -induced effect is proportionally much larger. We also discuss what the correction term should be for methane from anthropogenic biogenic sources.

  16. Methane oxidation over noble metal catalysts as related to controlling natural gas vehicle exhaust emissions

    International Nuclear Information System (INIS)

    Oh, S.H.; Mitchell, P.J.; Siewert, R.M.

    1992-01-01

    Natural gas has considerable potential as an alternative automotive fuel. This paper reports on methane, the principal hydrocarbon species in natural-gas engine exhaust, which has extremely low photochemical reactivity but is a powerful greenhouse gas. Therefore, exhaust emissions of unburned methane from natural-gas vehicles are of particular concern. This laboratory reactor study evaluates noble metal catalysts for their potential in the catalytic removal of methane from natural-gas vehicle exhaust. Temperature run-up experiments show that the methane oxidation activity decreases in the order Pd/Al 2 O 3 > Rh/Al 2 O 3 > Pt/Al 2 O 3 . Also, for all the noble metal catalysts studied, methane conversion can be maximized by controlling the O 2 concentration of the feedstream at a point somewhat rich (reducing) of stoichiometry

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

    International Nuclear Information System (INIS)

    Mor, Suman; Visscher, Alex de; Ravindra, Khaiwal; Dahiya, R.P.; Chandra, A.; Cleemput, Oswald van

    2006-01-01

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

  18. Methane oxidation and attenuation of sulphur compounds in landfill top cover systems: Lab-scale tests.

    Science.gov (United States)

    Raga, Roberto; Pivato, Alberto; Lavagnolo, Maria Cristina; Megido, Laura; Cossu, Raffaello

    2018-03-01

    In this study, a top cover system is investigated as a control for emissions during the aftercare of new landfills and for old landfills where biogas energy production might not be profitable. Different materials were studied as landfill cover system in lab-scale columns: mechanical-biological pretreated municipal solid waste (MBP); mechanical-biological pretreated biowaste (PB); fine (PBS f ) and coarse (PBS c ) mechanical-biological pretreated mixtures of biowaste and sewage sludge, and natural soil (NS). The effectiveness of these materials in removing methane and sulphur compounds from a gas stream was tested, even coupled with activated carbon membranes. Concentrations of CO 2 , CH 4 , O 2 , N 2 , H 2 S and mercaptans were analysed at different depths along the columns. Methane degradation was assessed using mass balance and the results were expressed in terms of methane oxidation rate (MOR). The highest maximum and mean MOR were observed for MBP (17.2gCH 4 /m 2 /hr and 10.3gCH 4 /m 2 /hr, respectively). Similar values were obtained with PB and PBS c . The lowest values of MOR were obtained for NS (6.7gCH 4 /m 2 /hr) and PBS f (3.6gCH 4 /m 2 /hr), which may be due to their low organic content and void index, respectively. Activated membranes with high load capacity did not seem to have an influence on the methane oxidation process: MBP coupled with 220g/m 2 and 360g/m 2 membranes gave maximum MOR of 16.5gCH 4 /m 2 /hr and 17.4gCH 4 /m 2 /hr, respectively. Activated carbon membranes proved to be very effective on H 2 S adsorption. Furthermore, carbonyl sulphide, ethyl mercaptan and isopropyl mercaptan seemed to be easily absorbed by the filling materials. Copyright © 2017. Published by Elsevier B.V.

  19. Temporal variation of aerobic methane oxidation over a tidal cycle in a wetland of northern Taiwan.

    Science.gov (United States)

    Lee, T. Y.; Wang, P. L.; Lin, L. H.

    2017-12-01

    Aerobic methanotrophy plays an important role in controlling methane emitted from wetlands. However, the activity of aerobic methanotrophy regulated by temporal fluctuation of oxygen and methane supply in tidal wetlands is not well known. This study aims to examine the dynamics of methane fluxes and potential aerobic methane consumption rates in a tidal wetland of northern Taiwan, where the variation of environmental characteristics, such as sulfate and methane concentration in pore water has been demonstrated during a tidal cycle. Two field campaigns were carried out in December of 2016 and March of 2017. Fluxes of methane emission, methane concentrations in surface sediments and oxygen profiles were measured at different tidal phases. Besides, batch incubations were conducted on surface sediments in order to quantify potential microbial methane consumption rates and to derive the kinetic parameters for aerobic methanotrophy. Our results demonstrated temporal changes of the surface methane concentration and the methane emission flux during a tidal cycle, while the oxygen flux into the sediment was kept at a similar magnitude. The methane flux was low when the surface was exposed for both shortest and longest periods of time. The potential aerobic methane oxidation rate was high for sample collected from the surface sediments exposed the longest. No correlation could be found between the potential aerobic methane oxidation rate and either the oxygen downward flux or methane emission flux. The decoupled relationships between these observed rates and fluxes suggest that, rather than aerobic methanotrophy, heterotrophic respirations exert a profound control on oxygen flux, and the methane emission is not only been affected by methane consumption but also methane production at depths. The maximum potential rate and the half saturation concentration determined from the batch incubations were high for the surface sediments collected in low tide, suggesting that aerobic

  20. 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.

  1. Methane oxidation in an intensively cropped tropical rice field soil under long-term application of organic and mineral fertilizers.

    Science.gov (United States)

    Nayak, D R; Babu, Y Jagadeesh; Datta, A; Adhya, T K

    2007-01-01

    Methane (CH4) oxidation is the only known biological sink process for mitigating atmospheric and terrestrial emissions of CH4, a major greenhouse gas. Methane oxidation in an alluvial soil planted to rice (Oryza sativa L.) under long-term application of organic (compost with a C/N ratio of 21.71), and mineral fertilizers was measured in a field-cum-laboratory incubation study. Oxidation rates were quantified in terms of decrease in the concentration of CH4 in the headspace of incubation vessels and expressed as half-life (t(1)2) values. Methane oxidation rates significantly differed among the treatments and growth stages of the rice crop. Methane oxidation rates were high at the maximum tillering and maturity stages, whereas they were low at grain-filling stage. Methane oxidation was low (t(1)2) = 15.76 d) when provided with low concentration of CH4. On the contrary, high concentration of CH4 resulted in faster oxidation (t(1)2) = 6.67 d), suggesting the predominance of "low affinity oxidation" in rice fields. Methane oxidation was stimulated following the application of mineral fertilizers or compost implicating nutrient limitation as one of the factors affecting the process. Combined application of compost and mineral fertilizer, however, inhibited CH4 oxidation probably due to N immobilization by the added compost. The positive effect of mineral fertilizer on CH4 oxidation rate was evident only at high CH4 concentration (t(1)2 = 4.80 d), while at low CH4 concentration their was considerable suppression (t(1) = 17.60 d). Further research may reveal that long-term application of fertilizers, organic or inorganic, may not inhibit CH4 oxidation.

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

    KAUST Repository

    Meulepas, Roel J W; Jagersma, Christian G; Khadem, Ahmad F; Stams, Alfons J M; Lens, Piet N L

    2010-01-01

    Anaerobic oxidation of methane (AOM) coupled to sulfate reduction (SR) is assumed to be a syntrophic process, in which methanotrophic archaea produce an interspecies electron carrier (IEC), which is subsequently utilized by sulfate-reducing bacteria

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

    Directory of Open Access Journals (Sweden)

    Elizabeth Trembath-Reichert

    2016-04-01

    Full Text Available Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM. This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME and sulfate-reducing bacteria (SRB. These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag. Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to

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

    Science.gov (United States)

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

    2016-01-01

    Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co

  5. Evidence of sulfate-dependent anaerobic methane oxidation within an area impacted by coalbed methane-related gas migration

    Science.gov (United States)

    The rapid development of unconventional gas resources has been accompanied by an increase in public awareness regarding the potential effects of drilling operations on drinking water sources. Incidents have been reported involving blowouts (e.g., Converse County, WY; Lawrence Tow...

  6. 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...

  7. Characterization of methane oxidation in a simulated landfill cover system by comparing molecular and stable isotope mass balances.

    Science.gov (United States)

    Schulte, Marcel; Jochmann, Maik A; Gehrke, Tobias; Thom, Andrea; Ricken, Tim; Denecke, Martin; Schmidt, Torsten C

    2017-11-01

    Biological methane oxidation may be regarded as a method of aftercare treatment for landfills to reduce climate relevant methane emissions. It is of social and economic interest to estimate the behavior of bacterial methane oxidation in aged landfill covers due to an adequate long-term treatment of the gas emissions. Different approaches assessing methane oxidation in laboratory column studies have been investigated by other authors recently. However, this work represents the first study in which three independent approaches, ((i) mass balance, (ii) stable isotope analysis, and (iii) stoichiometric balance of product (CO 2 ) and reactant (CH 4 ) by CO 2 /CH 4 -ratio) have been compared for the estimation of the biodegradation by a robust statistical validation on a rectangular, wide soil column. Additionally, an evaluation by thermal imaging as a potential technique for the localization of the active zone of bacterial methane oxidation has been addressed in connection with stable isotope analysis and CO 2 /CH 4 -ratios. Although landfills can be considered as open systems the results for stable isotope analysis based on a closed system correlated better with the mass balance than calculations based on an open system. CO 2 /CH 4 -ratios were also in good agreement with mass balance. In general, highest values for biodegradation were determined from mass balance, followed by CO 2 /CH 4 -ratio, and stable isotope analysis. The investigated topsoil proved to be very suitable as a potential cover layer by removing up to 99% of methane for CH 4 loads of 35-65gm -2 d -1 that are typical in the aftercare phase of landfills. Finally, data from stable isotope analysis and the CO 2 /CH 4 -ratios were used to trace microbial activity within the reactor system. It was shown that methane consumption and temperature increase, as a cause of high microbial activity, correlated very well. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

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

    2006-01-01

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

  9. Regulation of methane oxidation in the facultative methanotroph Methylocella silvestris BL2.

    Science.gov (United States)

    Theisen, Andreas R; Ali, M Hanif; Radajewski, Stefan; Dumont, Marc G; Dunfield, Peter F; McDonald, Ian R; Dedysh, Svetlana N; Miguez, Carlos B; Murrell, J Colin

    2005-11-01

    The molecular regulation of methane oxidation in the first fully authenticated facultative methanotroph Methylocella silvestris BL2 was assessed during growth on methane and acetate. Problems of poor growth of Methylocella spp. in small-scale batch culture were overcome by growth in fermentor culture. The genes encoding soluble methane monooxygenase were cloned and sequenced, which revealed that the structural genes for soluble methane monooxygenase, mmoXYBZDC, were adjacent to two genes, mmoR and mmoG, encoding a sigma54 transcriptional activator and a putative GroEL-like chaperone, located downstream (3') of mmoC. Transcriptional analysis revealed that the genes were all cotranscribed from a sigma54-dependent promoter located upstream (5') of mmo X. The transcriptional start site was mapped. Transcriptional analysis of soluble methane monooxygenase genes and expression studies on fermentor grown cultures showed that acetate repressed transcription of sMMO in M. silvestris BL2. The possibility of the presence of a particulate, membrane-bound methane monooxygenase enzyme in M. silvestris BL2 and the copper-mediated regulation of soluble methane monooxygenase was investigated. Both were shown to be absent. A promoter probe vector was constructed and used to assay transcription of the promoter of the soluble methane monoxygenase genes of M. silvestris BL2 grown under various conditions and with different substrates. These data represent the first insights into the molecular physiology of a facultative methanotroph.

  10. A Singular Perturbation Problem for Steady State Conversion of Methane Oxidation in Reverse Flow Reactor

    Directory of Open Access Journals (Sweden)

    Aang Nuryaman

    2012-11-01

    Full Text Available The governing equations describing the methane oxidation process in reverse flow reactor are given by a set of convective-diffusion equations with a nonlinear reaction term, where temperature and methane conversion are dependent variables. In this study, the process is assumed to be one-dimensional pseudo homogeneous model and takes place with a certain reaction rate in which the whole process of reactor is still workable. Thus, the reaction rate can proceed at a fixed temperature. Under this condition, we restrict ourselves to solve the equations for the conversion only. From the available data, it turns out that the ratio of the diffusion term to the reaction term is small. Hence, this ratio is considered as small parameter in our model and this leads to a singular perturbation problem. In the vicinity of small parameter in front of higher order term, the numerical difficulties will be found. Here, we present an analytical solution by means of matched asymptotic expansions. Result shows that, up to and including the first order of approximation, the solution is in agreement with the exact and numerical solutions of the boundary value problem.

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

    Science.gov (United States)

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

    2016-09-01

    The rhizosphere is known as the most active biogeochemical layer of the soil. Therefore, it could be a beneficial environment for biotic methane oxidation. The aim of this study was to document - by means of batch incubation tests - the kinetics of CH4 oxidation in rhizosphere soils that were previously exposed to methane. Soils from three pre-exposure to CH4 zones were sampled: the never-before pre-exposed (NEX), the moderately pre-exposed (MEX) and the very pre-exposed (VEX). For each pre-exposure zone, the rhizosphere of several plant species was collected, pre-incubated, placed in glass vials and submitted to CH4 concentrations varying from 0.5% to 10%. The time to the beginning of CH4 consumption and the CH4 oxidation rate were recorded. The results showed that the fastest CH4 consumption occurred for the very pre-exposed rhizosphere. Specifically, a statistically significant difference in CH4 oxidation half-life was found between the rhizosphere of the VEX vegetated with a mixture of different plants and the NEX vegetated with ryegrass. This difference was attributed to the combined effect of the preconditioning level and plant species as well as to the organic matter content. Regardless of the preconditioning level, the oxidation rate values obtained in this study were comparable to those reported in the reviewed literature for mature compost. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

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

    2012-01-01

    Microbial oxidation is the only biological sink for atmospheric methane. We assessed seasonal changes in atmospheric methane oxidation and the underlying methanotrophic communities in grassland near Giessen (Germany), along a soil moisture gradient. Soil samples were taken from the surface layer (0–10 cm) of three sites in August 2007, November 2007, February 2008 and May 2008. The sites showed seasonal differences in hydrological parameters. Net uptake rates varied seasonally between 0 and 70 μg CH4 m−2 h−1. Greatest uptake rates coincided with lowest soil moisture in spring and summer. Over all sites and seasons, the methanotrophic communities were dominated by uncultivated methanotrophs. These formed a monophyletic cluster defined by the RA14, MHP and JR1 clades, referred to as upland soil cluster alphaproteobacteria (USCα)-like group. The copy numbers of pmoA genes ranged between 3.8 × 105–1.9 × 106 copies g−1 of soil. Temperature was positively correlated with CH4 uptake rates (P50 vol% and primarily related to members of the MHP clade. PMID:22189499

  13. Elimination of methane in exhaust gas from biogas upgrading process by immobilized methane-oxidizing bacteria.

    Science.gov (United States)

    Wu, Ya-Min; Yang, Jing; Fan, Xiao-Lei; Fu, Shan-Fei; Sun, Meng-Ting; Guo, Rong-Bo

    2017-05-01

    Biogas upgrading is essential for the comprehensive utilization of biogas as substitute of natural gas. However, the methane in the biogas can be fully recovered during the upgrading process of biogas, and the exhaust gas produced during biogas upgrading may contain a very low concentration of methane. If the exhaust gas with low concentration methane releases to atmosphere, it will be harmful to environment. In addition, the utilization of large amounts of digestate produced from biogas plant is another important issue for the development of biogas industry. In this study, solid digestate was used to produce active carbon, which was subsequently used as immobilized material for methane-oxidizing bacteria (MOB) in biofilter. Biofilter with MOB immobilized on active carbon was used to eliminate the methane in exhaust gas from biogas upgrading process. Results showed porous active carbon was successfully made from solid digestate. The final methane elimination capacity of immobilized MOB reached about 13molh -1 m -3 , which was more 4 times higher than that of MOB without immobilization. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. 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 CH 4 oxidation potential and biological characteristics with CH 4 concentration was studied in a landfill cover soil reactor (LCSR). The maximum rate of CH 4 oxidation reached 32.40 mol d -1 m -2 by providing sufficient O 2 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 CH 4 and O 2 . The values of [Formula: see text] (0.93-2.29%) and [Formula: see text] (140-524 nmol kg soil-DW -1 ·s -1 ) increased with CH 4 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 CH 4 concentration. These findings provide information for assessing CH 4 oxidation potential and changing of biological characteristics in landfill cover soil.

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

    Science.gov (United States)

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

    2012-06-01

    Microbial oxidation is the only biological sink for atmospheric methane. We assessed seasonal changes in atmospheric methane oxidation and the underlying methanotrophic communities in grassland near Giessen (Germany), along a soil moisture gradient. Soil samples were taken from the surface layer (0-10 cm) of three sites in August 2007, November 2007, February 2008 and May 2008. The sites showed seasonal differences in hydrological parameters. Net uptake rates varied seasonally between 0 and 70 μg CH(4) m(-2) h(-1). Greatest uptake rates coincided with lowest soil moisture in spring and summer. Over all sites and seasons, the methanotrophic communities were dominated by uncultivated methanotrophs. These formed a monophyletic cluster defined by the RA14, MHP and JR1 clades, referred to as upland soil cluster alphaproteobacteria (USCα)-like group. The copy numbers of pmoA genes ranged between 3.8 × 10(5)-1.9 × 10(6) copies g(-1) of soil. Temperature was positively correlated with CH(4) uptake rates (P50 vol% and primarily related to members of the MHP clade.

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

    Science.gov (United States)

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

    2014-04-01

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

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

    Science.gov (United States)

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

    2011-01-01

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

  18. Numerical modelling of methane oxidation efficiency and coupled water-gas-heat reactive transfer in a sloping landfill cover.

    Science.gov (United States)

    Feng, S; Ng, C W W; Leung, A K; Liu, H W

    2017-10-01

    Microbial aerobic methane oxidation in unsaturated landfill cover involves coupled water, gas and heat reactive transfer. The coupled process is complex and its influence on methane oxidation efficiency is not clear, especially in steep covers where spatial variations of water, gas and heat are significant. In this study, two-dimensional finite element numerical simulations were carried out to evaluate the performance of unsaturated sloping cover. The numerical model was calibrated using a set of flume model test data, and was then subsequently used for parametric study. A new method that considers transient changes of methane concentration during the estimation of the methane oxidation efficiency was proposed and compared against existing methods. It was found that a steeper cover had a lower oxidation efficiency due to enhanced downslope water flow, during which desaturation of soil promoted gas transport and hence landfill gas emission. This effect was magnified as the cover angle and landfill gas generation rate at the bottom of the cover increased. Assuming the steady-state methane concentration in a cover would result in a non-conservative overestimation of oxidation efficiency, especially when a steep cover was subjected to rainfall infiltration. By considering the transient methane concentration, the newly-modified method can give a more accurate oxidation efficiency. Copyright © 2017. Published by Elsevier Ltd.

  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. 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

  1. [Long-term storage of obligate anaerobic microorganisms in glycerol].

    Science.gov (United States)

    Briukhanov, A I; Netrusov, A I

    2006-01-01

    We evaluated the possibility of storing the cultures of obligate anaerobic microorganisms (clostridia. acetogenic and sulfate-reducing bacteria, and methanogenic archaea) in 25% glycerol at -70 degrees C for a long time (up to 3 years). This method of storage is adequate to preserve cell viability in most obligate anaerobes.

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

    Science.gov (United States)

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

    2009-11-01

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

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

    Science.gov (United States)

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

    2016-10-01

    Reported methane oxidation activity (MOA) varies widely for common landfill cover materials. Variation is expected due to differences in surface area, the composition of the substratum and culturing conditions. MOA per methanotrophic cell has been calculated in the study of natural systems such as lake sediments to examine the inherent conditions for methanotrophic activity. In this study, biomass normalised MOA (i.e., MOA per methanotophic cell) was measured on stabilised compost, a commonly used cover in landfills, and on graphite granules, an inert substratum widely used in microbial electrosynthesis studies. After initially enriching methanotrophs on both substrata, biomass normalised MOA was quantified under excess oxygen and limiting methane conditions in 160ml serum vials on both substrata and blends of the substrata. Biomass concentration was measured using the bicinchoninic acid assay for microbial protein. The biomass normalised MOA was consistent across all compost-to-graphite granules blends, but varied with time, reflecting the growth phase of the microorganisms. The biomass normalised MOA ranged from 0.069±0.006μmol CH4/mg dry biomass/h during active growth, to 0.024±0.001μmol CH4/mg dry biomass/h for established biofilms regardless of the substrata employed, indicating the substrata were equally effective in terms of inherent composition. The correlation of MOA with biomass is consistent with studies on methanotrophic activity in natural systems, but biomass normalised MOA varies by over 5 orders of magnitude between studies. This is partially due to different methods being used to quantify biomass, such as pmoA gene quantification and the culture dependent Most Probable Number method, but also indicates that long term exposure of materials to a supply of methane in an aerobic environment, as can occur in natural systems, leads to the enrichment and adaptation of types suitable for those conditions. Copyright © 2016 Elsevier Ltd. All rights

  4. Molecular biology of hyperthermophilic Archaea.

    Science.gov (United States)

    van der Oost, J; Ciaramella, M; Moracci, M; Pisani, F M; Rossi, M; de Vos, W M

    1998-01-01

    The sequences of a number of archaeal genomes have recently been completed, and many more are expected shortly. Consequently, the research of Archaea in general and hyperthermophiles in particular has entered a new phase, with many exciting discoveries to be expected. The wealth of sequence information has already led, and will continue to lead to the identification of many enzymes with unique properties, some of which have potential for industrial applications. Subsequent functional genomics will help reveal fundamental matters such as details concerning the genetic, biochemical and physiological adaptation of extremophiles, and hence give insight into their genomic evolution, polypeptide structure-function relations, and metabolic regulation. In order to optimally exploit many unique features that are now emerging, the development of genetic systems for hyperthermophilic Archaea is an absolute requirement. Such systems would allow the application of this class of Archaea as so-called "cell factories": (i) expression of certain archaeal enzymes for which no suitable conventional (mesophilic bacterial or eukaryal) systems are available, (ii) selection for thermostable variants of potentially interesting enzymes from mesophilic origin, and (iii) the development of in vivo production systems by metabolic engineering. An overview is given of recent insight in the molecular biology of hyperthermophilic Archaea, as well as of a number of promising developments that should result in the generation of suitable genetic systems in the near future.

  5. Early Microbial Evolution: The Age of Anaerobes.

    Science.gov (United States)

    Martin, William F; Sousa, Filipa L

    2015-12-18

    In this article, the term "early microbial evolution" refers to the phase of biological history from the emergence of life to the diversification of the first microbial lineages. In the modern era (since we knew about archaea), three debates have emerged on the subject that deserve discussion: (1) thermophilic origins versus mesophilic origins, (2) autotrophic origins versus heterotrophic origins, and (3) how do eukaryotes figure into early evolution. Here, we revisit those debates from the standpoint of newer data. We also consider the perhaps more pressing issue that molecular phylogenies need to recover anaerobic lineages at the base of prokaryotic trees, because O2 is a product of biological evolution; hence, the first microbes had to be anaerobes. If molecular phylogenies do not recover anaerobes basal, something is wrong. Among the anaerobes, hydrogen-dependent autotrophs--acetogens and methanogens--look like good candidates for the ancestral state of physiology in the bacteria and archaea, respectively. New trees tend to indicate that eukaryote cytosolic ribosomes branch within their archaeal homologs, not as sisters to them and, furthermore tend to root archaea within the methanogens. These are major changes in the tree of life, and open up new avenues of thought. Geochemical methane synthesis occurs as a spontaneous, abiotic exergonic reaction at hydrothermal vents. The overall similarity between that reaction and biological methanogenesis fits well with the concept of a methanogenic root for archaea and an autotrophic origin of microbial physiology. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

  6. Constraining the relationships between anaerobic oxidation of methane and sulfate reduction under in situ methane concentrations

    Science.gov (United States)

    Zhuang, G.; Wegener, G.; Joye, S. B.

    2017-12-01

    The anaerobic oxidation of methane (AOM) is an important microbial metabolism in the global carbon cycle. In marine methane seeps sediment, this process is mediated by syntrophic consortium that includes anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). Stoichiometrically in AOM methane oxidation should be coupled to sulfate reduction (SR) in a 1:1 ratio. However, weak coupling of AOM and SR in seep sediments was frequently observed from the ex situ rate measurements, and the metabolic dynamics of AOM and SR under in situ conditions remain poorly understood. Here we investigated the metabolic activity of AOM and SR with radiotracers by restoring in situ methane concentrations under pressure to constrain the in situ relationships between AOM and SR in the cold seep sediments of Gulf of Mexico as well as the sediment-free AOM enrichments cultivated from cold seep of Italian Island Elba or hydrothermal vent of Guaymas Basin5. Surprisingly, we found that AOM rates strongly exceeded those of SR when high pressures and methane concentrations were applied at seep sites of GC600 and GC767 in Gulf of Mexico. With the addition of molybdate, SR was inhibited but AOM was not affected, suggesting the potential coupling of AOM with other terminal processes. Amendments of nitrate, iron, manganese and AQDS to the SR-inhibited slurries did not stimulate or inhibit the AOM activity, indicating either those electron acceptors were not limiting for AOM in the sediments or AOM was coupled to other process (e.g., organic matter). In the ANME enrichments, higher AOM rates were also observed with the addition of high concentrations of methane (10mM and 50 mM). The tracer transfer of CO2 to methane, i.e., the back reaction of AOM, increased with increasing methane concentrations and accounted for 1%-5% of the AOM rates. AOM rates at 10 mM and 50 mM methane concentration were much higher than the SR rates, suggesting those two processes were not tightly coupled

  7. Studying gene regulation in methanogenic archaea.

    Science.gov (United States)

    Rother, Michael; Sattler, Christian; Stock, Tilmann

    2011-01-01

    Methanogenic archaea are a unique group of strictly anaerobic microorganisms characterized by their ability, and dependence, to convert simple C1 and C2 compounds to methane for growth. The major models for studying the biology of methanogens are members of the Methanococcus and Methanosarcina species. Recent development of sophisticated tools for molecular analysis and for genetic manipulation allows investigating not only their metabolism but also their cell cycle, and their interaction with the environment in great detail. One aspect of such analyses is assessment and dissection of methanoarchaeal gene regulation, for which, at present, only a handful of cases have been investigated thoroughly, partly due to the great methodological effort required. However, it becomes more and more evident that many new regulatory paradigms can be unraveled in this unique archaeal group. Here, we report both molecular and physiological/genetic methods to assess gene regulation in Methanococcus maripaludis and Methanosarcina acetivorans, which should, however, be applicable for other methanogens as well. Copyright © 2011 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    D'Imperio, Ludovica

    2014-05-01

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

  9. Rain increases methane production and methane oxidation in a boreal thermokarst bog

    Science.gov (United States)

    Neumann, R. B.; Moorberg, C.; Turner, J.; Wong, A.; Waldrop, M. P.; Euskirchen, E. S.; Edgar, C.; Turetsky, M. R.

    2017-12-01

    Bottom-up biogeochemical models of wetland methane emissions simulate the response of methane production, oxidation and transport to wetland conditions and environmental forcings. One reason for mismatches between bottom-up and top-down estimates of emissions is incomplete knowledge of factors and processes that control microbial rates and methane transport. To advance mechanistic understanding of wetland methane emissions, we conducted a multi-year field investigation and plant manipulation experiment in a thermokarst bog located near Fairbanks, Alaska. The edge of the bog is experiencing active permafrost thaw, while the center of the bog thawed 50 to 100 years ago. Our study, which captured both an average year and two of the wettest years on record, revealed how rain interacts with vascular vegetation and recently thawed permafrost to affect methane emissions. In the floating bog, rain water warmed and oxygenated the subsurface, but did not alter soil saturation. The warmer peat temperatures increased both microbial methane production and plant productivity at the edge of the bog near the actively thawing margin, but minimally altered microbial and plant activity in the center of the bog. These responses indicate processes at the edge of the bog were temperature limited while those in the center were not. The compounding effect of increased microbial activity and plant productivity at the edge of the bog doubled methane emissions from treatments with vascular vegetation during rainy years. In contrast, methane emissions from vegetated treatments in the center of the bog did not change with rain. The oxygenating influence of rain facilitated greater methane oxidation in treatments without vascular vegetation, which offset warming-induced increases in methane production at the edge of the bog and decreased methane emissions in the center of the bog. These results elucidate the complex and spatially variable response of methane production and oxidation in

  10. A record of aerobic methane oxidation in tropical Africa over the last 2.5 Ma

    Science.gov (United States)

    Spencer-Jones, Charlotte L.; Wagner, Thomas; Talbot, Helen M.

    2017-12-01

    Methane and CO2 are climatically active greenhouse gases (GHG) and are powerful drivers of rapid global warming. Comparable to the Arctic, the tropics store large volumes of labile sedimentary carbon that is vulnerable to climate change. However, little is known about this labile carbon reservoir, in particular the behaviour of high methane-producing environments (e.g. wetlands), and their role in driving or responding to past periods of global climate change. In this study, we use a microbial biomarker approach that traces continental aerobic methane oxidation (AMO) from sedimentary organic matter in deep-sea fan sediments off the Congo River to reconstruct the link between central African methane cycling and continental export during key periods of global Pleistocene warmth. We use 35-amino bacteriohopanepolyols (BHPs), specifically aminobacteriohopane-31,32,33,34-tetrol (aminotetrol) and 35-aminobacteriohopane-30,31,32,33,34-pentol (aminopentol) as diagnostic molecular markers for AMO (CH4 oxidation markers) and the prevalence of continental wetland environments. BHPs were analysed in sediments from the Congo fan (ODP 1075) dated to 2.5 Ma. High resolution studies of key warm marine isotope stages (MIS) 5, 11 and 13 are included to test the relationship between CH4 oxidation markers in sediments at different levels of elevated global atmospheric GHG. This study presents the oldest reported occurrence, to date, of 35-amino BHPs up to 200 m below sea floor (∼2.5 Ma) with no strong degradation signature observed. Low concentrations of CH4 oxidation markers identified between 1.7 Ma and 1 Ma suggest a reduction in wetland extent in tropical Africa in response to more arid environmental conditions. Correlation of high resolution CH4 oxidation marker signatures with global atmospheric GHG concentrations during MIS 5, 11 and 13 further emphasize periods of enhanced tropical C cycling. However, subsequent analysis would be required to further extrapolate the relative

  11. Taxonomic, phylogenetic, and ecological diversity of methanogenic Archaea

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, J.-L.; Ollivier, B. [Universite de Provence, Marseille (France). Laboratoire de Microbiologist; Patel, B.K.C. [Griffith University, Brisbane (Australia). Microbial Discovery Research Unit

    2000-07-01

    Methanogens are strict anaerobes which share a complex biochemistry for methane synthesis as part of their energy metabolism. The discovery of the unique biochemical and genetic properties of these organisms led to the concept of Archaebacteria at the end of the seventies and the proposal in 1990 for the domain Archaea. A number of studies have provided evidence that they are of economic value. The successive petroleum crisis since 1973 has led to great interest in alternative forms of energy, including recovery of methane via anaerobic digestion of wastes. Improvements in the design of digestors have been made possible by advances in understanding the ecology and physiology of methanogens. In the cattle industry, the knowledge of the fermentation processes in the rumen demonstrated a net loss of energy via the methanogenesis, and inhibitors such as Rumensin have been developed to enhance meat yields. Oil companies try to distinguish between natural gas produced by methanogens or by the thermocatalytic reactions associated with petroleum generation. Finally, studies on the global distribution of methane in the earth's atmosphere are increasing due to the sudden awareness of its possible role in the enhancement of the greenhouse effect from CO-2 accumulation, and on the reversal of stratospheric ozone depletion. This paper summarizes the recent knowledge of methanogenic Archaea with emphasis on their taxonomy and ecology. (author)

  12. 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

  13. Novel metabolic pathways in Archaea.

    Science.gov (United States)

    Sato, Takaaki; Atomi, Haruyuki

    2011-06-01

    The Archaea harbor many metabolic pathways that differ to previously recognized classical pathways. Glycolysis is carried out by modified versions of the Embden-Meyerhof and Entner-Doudoroff pathways. Thermophilic archaea have recently been found to harbor a bi-functional fructose-1,6-bisphosphate aldolase/phosphatase for gluconeogenesis. A number of novel pentose-degrading pathways have also been recently identified. In terms of anabolic metabolism, a pathway for acetate assimilation, the methylaspartate cycle, and two CO2-fixing pathways, the 3-hydroxypropionate/4-hydroxybutyrate cycle and the dicarboxylate/4-hydroxybutyrate cycle, have been elucidated. As for biosynthetic pathways, recent studies have clarified the enzymes responsible for several steps involved in the biosynthesis of inositol phospholipids, polyamine, coenzyme A, flavin adeninedinucleotide and heme. By examining the presence/absence of homologs of these enzymes on genome sequences, we have found that the majority of these enzymes and pathways are specific to the Archaea. Copyright © 2011 Elsevier Ltd. All rights reserved.

  14. Production of biogenic manganese oxides coupled with methane oxidation in a bioreactor for removing metals from wastewater.

    Science.gov (United States)

    Matsushita, Shuji; Komizo, Daisuke; Cao, Linh Thi Thuy; Aoi, Yoshiteru; Kindaichi, Tomonori; Ozaki, Noriatsu; Imachi, Hiroyuki; Ohashi, Akiyoshi

    2018-03-01

    Biogenic manganese oxide (BioMnO x ) can efficiently adsorb various minor metals. The production of BioMnO x in reactors to remove metals during wastewater treatment processes is a promising biotechnological method. However, it is difficult to preferentially enrich manganese-oxidizing bacteria (MnOB) to produce BioMnO x during wastewater treatment processes. A unique method of cultivating MnOB using methane-oxidizing bacteria (MOB) to produce soluble microbial products is proposed here. MnOB were successfully enriched in a methane-fed reactor containing MOB. BioMnO x production during the wastewater treatment process was confirmed. Long-term continual operation of the reactor allowed simultaneous removal of Mn(II), Co(II), and Ni(II). The Co(II)/Mn(II) and Ni(II)/Mn(II) removal ratios were 53% and 19%, respectively. The degree to which Mn(II) was removed indicated that the enriched MnOB used utilization-associated products and/or biomass-associated products. Microbial community analysis revealed that methanol-oxidizing bacteria belonging to the Hyphomicrobiaceae family played important roles in the oxidation of Mn(II) by using utilization-associated products. Methane-oxidizing bacteria were found to be inhibited by MnO 2 , but the maximum Mn(II) removal rate was 0.49 kg m -3  d -1 . Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Effect of the environment on horizontal gene transfer between bacteria and archaea.

    Science.gov (United States)

    Fuchsman, Clara A; Collins, Roy Eric; Rocap, Gabrielle; Brazelton, William J

    2017-01-01

    Horizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted). We investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell & Gaasterland, 2007), to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits) and transferred genes (identified by DarkHorse) were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids. Anaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of genes from the archaea to the bacteria. In

  16. Effect of the environment on horizontal gene transfer between bacteria and archaea

    Directory of Open Access Journals (Sweden)

    Clara A. Fuchsman

    2017-09-01

    Full Text Available Background Horizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted. Results We investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell & Gaasterland, 2007, to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits and transferred genes (identified by DarkHorse were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids. Conclusions Anaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of

  17. Characterization of technetium(vII) reduction by cell suspensions of thermophilic bacteria and archaea.

    Science.gov (United States)

    Chernyh, Nikolay A; Gavrilov, Sergei N; Sorokin, Vladimir V; German, Konstantin E; Sergeant, Claire; Simonoff, Monique; Robb, Frank; Slobodkin, Alexander I

    2007-08-01

    Washed cell suspensions of the anaerobic hyperthermophilic archaea Thermococcus pacificus and Thermoproteus uzoniensis and the anaerobic thermophilic gram-positive bacteria Thermoterrabacterium ferrireducens and Tepidibacter thalassicus reduced technetium [(99)Tc(VII)], supplied as soluble pertechnetate with molecular hydrogen as an electron donor, forming highly insoluble Tc(IV)-containing grayish-black precipitate. Apart from molecular hydrogen, T. ferrireducens reduced Tc(VII) with lactate, glycerol, and yeast extract as electron donors, and T. thalassicus reduced it with peptone. Scanning electron microscopy and X-ray microanalysis of cell suspensions of T. ferrireducens showed the presence of Tc-containing particles attached to the surfaces of non-lysed cells. This is the first report on the reduction in Tc(VII) by thermophilic microorganisms of the domain Bacteria and by archaea of the phylum Euryarchaeota.

  18. Influence of capillary barrier effect on biogas distribution at the base of passive methane oxidation biosystems: Parametric study.

    Science.gov (United States)

    Ahoughalandari, Bahar; Cabral, Alexandre R

    2017-05-01

    The efficiency of methane oxidation in passive methane oxidation biosystems (PMOBs) is influenced by, among other things, the intensity and distribution of the CH 4 loading at the base of the methane oxidation layer (MOL). Both the intensity and distribution are affected by the capillary barrier that results from the superposition of the two materials constituting the PMOB, namely the MOL and the gas distribution layer (GDL). The effect of capillary barriers on the unsaturated flow of water has been well documented in the literature. However, its effect on gas flow through PMOBs is still poorly documented. In this study, sets of numerical simulations were performed to evaluate the effect of unsaturated hydraulic characteristics of the MOL material on the value and distribution of moisture and hence, the ease and uniformity in the distribution of the upward flow of biogas along the GDL-MOL interface. The unsaturated hydraulic parameters of the materials used to construct the experimental field plot at the St-Nicephore landfill (Quebec, Canada) were adopted to build the reference simulation of the parametric study. The behavior of the upward flow of biogas for this particular material was analyzed based on its gas intrinsic permeability function, which was obtained in the laboratory. The parameters that most influenced the distribution and the ease of biogas flow at the base of the MOL were the saturated hydraulic conductivity and pore size distribution of the MOL material, whose effects were intensified as the slope of the interface increased. The effect of initial dry density was also assessed herein. Selection of the MOL material must be made bearing in mind that these three parameters are key in the effort to prevent unwanted restriction in the upward flow of biogas, which may result in the redirection of biogas towards the top of the slope, leading to high CH 4 fluxes (hotspots). In a well-designed PMOB, upward flow of biogas across the GDL-MOL interface is

  19. Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy.

    Science.gov (United States)

    Ruff, S Emil; Kuhfuss, Hanna; Wegener, Gunter; Lott, Christian; Ramette, Alban; Wiedling, Johanna; Knittel, Katrin; Weber, Miriam

    2016-01-01

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

  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. Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy

    Science.gov (United States)

    Ruff, S. Emil; Kuhfuss, Hanna; Wegener, Gunter; Lott, Christian; Ramette, Alban; Wiedling, Johanna; Knittel, Katrin; Weber, Miriam

    2016-01-01

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

  2. Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment

    Directory of Open Access Journals (Sweden)

    Ellen M. Black

    2017-07-01

    Full Text Available Targeted qPCR and non-targeted amplicon sequencing of 16S rRNA genes within sediment layers identified the anaerobic ammonium oxidation (anammox niche and characterized microbial community changes attributable to freshwater mussels. Anammox bacteria were normally distributed (Shapiro-Wilk normality test, W-statistic =0.954, p = 0.773 between 1 and 15 cm depth and were increased by a factor of 2.2 (p < 0.001 at 3 cm below the water-sediment interface when mussels were present. Amplicon sequencing of sediment at depths relevant to mussel burrowing (3 and 5 cm showed that mussel presence reduced observed species richness (p = 0.005, Chao1 diversity (p = 0.005, and Shannon diversity (p < 0.001, with more pronounced decreases at 5 cm depth. A non-metric, multidimensional scaling model showed that intersample microbial species diversity varied as a function of mussel presence, indicating that sediment below mussels harbored distinct microbial communities. Mussel presence corresponded with a 4-fold decrease in a majority of operational taxonomic units (OTUs classified in the phyla Gemmatimonadetes, Actinobacteria, Acidobacteria, Plantomycetes, Chloroflexi, Firmicutes, Crenarcheota, and Verrucomicrobia. 38 OTUs in the phylum Nitrospirae were differentially abundant (p < 0.001 with mussels, resulting in an overall increase from 25% to 35%. Nitrogen (N-cycle OTUs significantly impacted by mussels belonged to anammmox genus Candidatus Brocadia, ammonium oxidizing bacteria family Nitrosomonadaceae, ammonium oxidizing archaea genus Candidatus Nitrososphaera, nitrite oxidizing bacteria in genus Nitrospira, and nitrate- and nitrite-dependent anaerobic methane oxidizing organisms in the archaeal family “ANME-2d” and bacterial phylum “NC10”, respectively. Nitrosomonadaceae (0.9-fold (p < 0.001 increased with mussels, while NC10 (2.1-fold (p < 0.001, ANME-2d (1.8-fold (p < 0.001, and Candidatus Nitrososphaera (1.5-fold (p < 0

  3. 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...... crusts indicates that there is a potential for stimulating the process by manipulation of gas phase composition above the stored slurry....

  4. Composition of methane-oxidizing bacterial communities as a function of nutrient loading in the Florida everglades.

    Science.gov (United States)

    Chauhan, Ashvini; Pathak, Ashish; Ogram, Andrew

    2012-10-01

    Agricultural runoff of phosphorus (P) in the northern Florida Everglades has resulted in several ecosystem level changes, including shifts in the microbial ecology of carbon cycling, with significantly higher methane being produced in the nutrient-enriched soils. Little is, however, known of the structure and activities of methane-oxidizing bacteria (MOB) in these environments. To address this, 0 to 10 cm plant-associated soil cores were collected from nutrient-impacted (F1), transition (F4), and unimpacted (U3) areas, sectioned in 2-cm increments, and methane oxidation rates were measured. F1 soils consumed approximately two-fold higher methane than U3 soils; additionally, most probable numbers of methanotrophs were 4-log higher in F1 than U3 soils. Metabolically active MOB containing pmoA sequences were characterized by stable-isotope probing using 10 % (v/v) (13)CH(4). pmoA sequences, encoding the alpha subunit of methane monooxygenase and related to type I methanotrophs, were identified from both impacted and unimpacted soils. Additionally, impacted soils also harbored type II methanotrophs, which have been shown to exhibit preferences for high methane concentrations. Additionally, across all soils, novel pmoA-type sequences were also detected, indicating presence of MOB specific to the Everglades. Multivariate statistical analyses confirmed that eutrophic soils consisted of metabolically distinct MOB community that is likely driven by nutrient enrichment. This study enhances our understanding on the biological fate of methane being produced in productive wetland soils of the Florida Everglades and how nutrient-enrichment affects the composition of methanotroph bacterial communities.

  5. Regulation of transcription in hyperthermophilic archaea

    NARCIS (Netherlands)

    Brinkman, A.B.

    2002-01-01

    The aim of the research presented here was to insight in the mechanisms by which transcription in hyperthermophilic archaea is regulated. To accomplish this, we have aimed (I) to identify transcriptional regulatory proteins from hyperthermophilic archaea, (II) to characterize these

  6. Unique features of glycolysis in Archaea

    NARCIS (Netherlands)

    Verhees, C.H.; Kengen, S.W.M.; Tuininga, J.E.; Schut, G.J.; Adams, M.W.W.; Vos, de W.M.; Oost, van der J.

    2003-01-01

    An early divergence in evolution has resulted in two prokaryotic domains, the Bacteria and the Archaea. Whereas the central metabolic routes of bacteria and eukaryotes are generally well-conserved, variant pathways have developed in Archaea involving several novel enzymes with a distinct control. A

  7. 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

  8. Anaerobic bacteria

    Science.gov (United States)

    Anaerobic bacteria are bacteria that do not live or grow when oxygen is present. In humans, these bacteria ... Brook I. Diseases caused by non-spore-forming anaerobic bacteria. In: Goldman L, Schafer AI, eds. Goldman-Cecil ...

  9. Industrial relevance of thermophilic Archaea.

    Science.gov (United States)

    Egorova, Ksenia; Antranikian, Garabed

    2005-12-01

    The dramatic increase of newly isolated extremophilic microorganisms, analysis of their genomes and investigations of their enzymes by academic and industrial laboratories demonstrate the great potential of extremophiles in industrial (white) biotechnology. Enzymes derived from extremophiles (extremozymes) are superior to the traditional catalysts because they can perform industrial processes even under harsh conditions, under which conventional proteins are completely denatured. In particular, enzymes from thermophilic and hyperthermophilic Archaea have industrial relevance. Despite intensive investigations, our knowledge of the structure-function relationships of their enzymes is still limited. Information concerning the molecular properties of their enzymes and genes has to be obtained to be able to understand the mechanisms that are responsible for catalytic activity and stability at the boiling point of water.

  10. 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.

  11. 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.

  12. Microbiological Hydrogen Production by Anaerobic Fermentation and Photosynthetic Process

    International Nuclear Information System (INIS)

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

    2009-01-01

    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)

  13. 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.

  14. 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...

  15. Bioprospecting Archaea: Focus on Extreme Halophiles

    KAUST Repository

    Antunes, André ; Simõ es, Marta F.; Grö tzinger, Stefan W.; Eppinger, Jö rg; Braganç a, Judith; Bajic, Vladimir B.

    2016-01-01

    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

  16. 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.

  17. 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

  18. ?Altiarchaeales?: Uncultivated Archaea from the Subsurface

    OpenAIRE

    Probst, Alexander J.; Moissl-Eichinger, Christine

    2015-01-01

    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. ...

  19. 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.

  20. Methane Oxidation to Methanol Catalyzed by Cu-Oxo Clusters Stabilized in NU-1000 Metal-Organic Framework.

    Science.gov (United States)

    Ikuno, Takaaki; Zheng, Jian; Vjunov, Aleksei; Sanchez-Sanchez, Maricruz; Ortuño, Manuel A; Pahls, Dale R; Fulton, John L; Camaioni, Donald M; Li, Zhanyong; Ray, Debmalya; Mehdi, B Layla; Browning, Nigel D; Farha, Omar K; Hupp, Joseph T; Cramer, Christopher J; Gagliardi, Laura; Lercher, Johannes A

    2017-08-02

    Copper oxide clusters synthesized via atomic layer deposition on the nodes of the metal-organic framework (MOF) NU-1000 are active for oxidation of methane to methanol under mild reaction conditions. Analysis of chemical reactivity, in situ X-ray absorption spectroscopy, and density functional theory calculations are used to determine structure/activity relations in the Cu-NU-1000 catalytic system. The Cu-loaded MOF contained Cu-oxo clusters of a few Cu atoms. The Cu was present under ambient conditions as a mixture of ∼15% Cu + and ∼85% Cu 2+ . The oxidation of methane on Cu-NU-1000 was accompanied by the reduction of 9% of the Cu in the catalyst from Cu 2+ to Cu + . The products, methanol, dimethyl ether, and CO 2 , were desorbed with the passage of 10% water/He at 135 °C, giving a carbon selectivity for methane to methanol of 45-60%. Cu oxo clusters stabilized in NU-1000 provide an active, first generation MOF-based, selective methane oxidation catalyst.

  1. Rare branched fatty acids characterize the lipid composition of the intra-aerobic methane oxidizer "Candidatus Methylomirabilis oxyfera".

    Science.gov (United States)

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

    2012-12-01

    The recently described bacterium "Candidatus Methylomirabilis oxyfera" couples the oxidation of the important greenhouse gas methane to the reduction of nitrite. The ecological significance of "Ca. Methylomirabilis oxyfera" is still underexplored, as our ability to identify the presence of this bacterium is thus far limited to DNA-based techniques. Here, we investigated the lipid composition of "Ca. Methylomirabilis oxyfera" to identify new, gene-independent biomarkers for the environmental detection of this bacterium. Multiple "Ca. Methylomirabilis oxyfera" enrichment cultures were investigated. In all cultures, the lipid profile was dominated up to 46% by the fatty acid (FA) 10-methylhexadecanoic acid (10MeC(16:0)). Furthermore, a unique FA was identified that has not been reported elsewhere: the monounsaturated 10-methylhexadecenoic acid with a double bond at the Δ7 position (10MeC(16:1Δ7)), which comprised up to 10% of the total FA profile. We propose that the typical branched fatty acids 10MeC(16:0) and 10MeC(16:1Δ7) are key and characteristic components of the lipid profile of "Ca. Methylomirabilis oxyfera." The successful detection of these fatty acids in a peatland from which one of the enrichment cultures originated supports the potential of these unique lipids as biomarkers for the process of nitrite-dependent methane oxidation in the environment.

  2. A novel surface-enhanced Raman scattering (SERS) detection for natural gas exploration using methane-oxidizing bacteria.

    Science.gov (United States)

    Liang, Weiwei; Chen, Qiao; Peng, Fang; Shen, Aiguo; Hu, Jiming

    2018-07-01

    Methane-oxidizing bacteria (MOB), a unique group of Gram-negative bacteria utilizing methane as a sole source of carbon and energy, have been proved to be a biological indicator for gas prospecting. Field and cultivation-free detection of MOB is important but still challenging in current microbial prospecting of oil and gas (MPOG) system. Herein, SERS was used for the first time to our knowledge to investigate two species of methanotrophs and four closely relevant bacteria that universally coexisted in the upper soil of natural gas. A special but very simple approach was utilized to make silver nanoparticles (Ag NPs) sufficiently contact with every single bacterial cell, and highly strong and distinct Raman signals free from any native fluorescence have been obtained, and successfully utilized for distinguishing MOB from other species. A more convincing multi-Raman criterion based on single Raman bands, and further the entire Raman spectrum in combination with statistical analysis (e.g., principal component analysis (PCA)), which were found capable of classifying MOB related bacterial cells in soil with an accuracy of 100%. This study therefore demonstrated sensitive and rapid SERS measurement technique accompanied by complete Raman database of various gas reservoirs related bacteria could aid field exploration of natural gas reservoir. Copyright © 2018 Elsevier B.V. All rights reserved.

  3. Anaerobic Oxidation of Methane in a French meromictic lake (Lake Pavin): Who is responsible?

    Science.gov (United States)

    Grossi, V.; Attard, E.; Birgel, D.; Schaeffer, P.; Jézéquel, D.; Lehours, A.

    2012-12-01

    Methane is an important greenhouse gas and its biogeochemical cycle is of primary significance to the global carbon cycle. The Anaerobic Oxidation of Methane (AOM) has been estimated to be responsible for >90% of methane consumption. This biogeochemical process has been increasingly documented during the last two decades but the underlying microbial processes and their key agents remain incompletely understood. Freshwater lakes account for 2-10% of the total emissions of methane and are therefore an important part of the global methane cycle. Lake Pavin is a French meromictic crater lake with unusual hydrological characteristics: its morphology (depth >92m, mean diameter 750m) induce that waters below 60m are never mixed with overlying waters and remain permanently anoxic. The deep anoxic waters of Lake Pavin contain high concentrations (i.e. 4 mM) of methane but, contrary to other aquatic systems, almost no methane escapes from the lake. Previous biogeochemical and modeling studies suggest that methane is preferentially consumed within the oxic-anoxic transition zone (ca. 55-60 m depth) but that ca. 30% of methane oxidation occurs in the anoxic part of the lake. Phylogenetic (16S rRNA) analyses showed that ANME generally involved in AOM (ANME-1, -2 and -3) are not present in Lake Pavin. Other archaeal groups that do not have any cultured representatives so far appear well represented in the anoxic parts of the lake but their implication in AOM is not demonstrated. The analysis of lipid biomarkers using GC-MS and LC-MS revealed the presence of a low diversity of archaeal-specific biomarkers in the superficial sediments and in the anoxic waters of the lake. Archaeol and caldarcheaol (GDGT-0) are the two main archaeal core lipids detected; other biomarkers generally present in ANME such as pentamethylicosane or hydroxyarchaeol are not present. However, the stable carbon isotopic composition of archaeol (δ13C = -18‰) and of the biphytane chain of GDGT-0 (δ13C

  4. 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.

  5. Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog.

    Science.gov (United States)

    Dedysh, Svetlana N; Khmelenina, Valentina N; Suzina, Natalia E; Trotsenko, Yuri A; Semrau, Jeremy D; Liesack, Werner; Tiedje, James M

    2002-01-01

    A novel genus and species, Methylocapsa acidiphila gen. nov., sp. nov., are proposed for a methane-oxidizing bacterium isolated from an acidic Sphagnum peat bog. This bacterium, designated strain B2T, represents aerobic, gram-negative, colourless, non-motile, curved coccoids that form conglomerates covered by an extracellular polysaccharide matrix. The cells use methane and methanol as sole sources of carbon and energy and utilize the serine pathway for carbon assimilation. Strain B2T is a moderately acidophilic organism with growth between pH 4.2 and 7.2 and at temperatures from 10 to 30 degrees C. The cells possess a well-developed system of intracytoplasmic membranes (ICM) packed in parallel on only one side of the cell membrane. This type of ICM structure represents a novel arrangement, which was termed type III. The resting cells are Azotobacter-type cysts. Strain B2T is capable of atmospheric nitrogen fixation; it possesses particulate methane monooxygenase and does not express soluble methane monooxygenase. The major phospholipid fatty acid is 18:1omega7c and the major phospholipids are phosphatidylglycerols. The G+C content of the DNA is 63.1 mol%. This bacterium belongs to the alpha-subclass of the Proteobacteria and is most closely related to the acidophilic methanotroph Methylocella palustris KT (97.3% 16S rDNA sequence similarity). However, the DNA-DNA hybridization value between strain B2T and Methylocella palustris K(T) is only 7%. Thus, strain B2T is proposed to comprise a novel genus and species, Methylocapsa acidiphila gen. nov., sp. nov. Strain B2T (= DSM 13967T = NCIMB 13765T) is the type strain.

  6. Systematic Identification of Promoters for Methane Oxidation Catalysts Using Size- and Composition-Controlled Pd-Based Bimetallic Nanocrystals.

    Science.gov (United States)

    Willis, Joshua J; Goodman, Emmett D; Wu, Liheng; Riscoe, Andrew R; Martins, Pedro; Tassone, Christopher J; Cargnello, Matteo

    2017-08-30

    Promoters enhance the performance of catalytic active phases by increasing rates, stability, and/or selectivity. The process of identifying promoters is in most cases empirical and relies on testing a broad range of catalysts prepared with the random deposition of active and promoter phases, typically with no fine control over their localization. This issue is particularly relevant in supported bimetallic systems, where two metals are codeposited onto high-surface area materials. We here report the use of colloidal bimetallic nanocrystals to produce catalysts where the active and promoter phases are colocalized to a fine extent. This strategy enables a systematic approach to study the promotional effects of several transition metals on palladium catalysts for methane oxidation. In order to achieve these goals, we demonstrate a single synthetic protocol to obtain uniform palladium-based bimetallic nanocrystals (PdM, M = V, Mn, Fe, Co, Ni, Zn, Sn, and potentially extendable to other metal combinations) with a wide variety of compositions and sizes based on high-temperature thermal decomposition of readily available precursors. Once the nanocrystals are supported onto oxide materials, thermal treatments in air cause segregation of the base metal oxide phase in close proximity to the Pd phase. We demonstrate that some metals (Fe, Co, and Sn) inhibit the sintering of the active Pd metal phase, while others (Ni and Zn) increase its intrinsic activity compared to a monometallic Pd catalyst. This procedure can be generalized to systematically investigate the promotional effects of metal and metal oxide phases for a variety of active metal-promoter combinations and catalytic reactions.

  7. 2009 Archaea: Ecology, Metabolism & Molecular Biology GRC

    Energy Technology Data Exchange (ETDEWEB)

    Furlow, Julie Maupin- [Univ. of Florida, Gainesville, FL (United States)

    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.

  8. 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.

  9. Diversity of Archaea in Brazilian savanna soils.

    Science.gov (United States)

    Catão, E; Castro, A P; Barreto, C C; Krüger, R H; Kyaw, C M

    2013-07-01

    Although the richness of Bacteria and Fungi in Cerrado' soils has been reported, here we report, for the first time, the archaeal community in Cerrado's soils. DNA extracted from soil of two distinct vegetation types, a dense subtype of sensu strict (cerrado denso) and riverbank forest (mata de galeria), was used to amplify Archaea-specific 16S rRNA gene. All of the fragments sequenced were classified as Archaea into the phylum Thaumarchaeota, predominantly affiliated to groups I.1b and I.1c. Sequences affiliated to the group I.1a were found only in the soil from riverbank forest. Soils from 'cerrado denso' had greater Archaea richness than those from 'mata de galeria' based on the richness indexes and on the rarefaction curve. β-Diversity analysis showed significant differences between the sequences from the two soil areas studied because of their different thaumarchaeal group composition. These results provide information about the third domain of life from Cerrado soils.

  10. 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.

  11. Archaea: Evolution, Physiology, and Molecular Biology

    DEFF Research Database (Denmark)

    field, including an account by Carl Woese of his original discovery of the Archaea (until 1990 termed archaebacteria) and the initially mixed reactions of the scientific community. The review chapters and specialized articles address the emerging significance of the Archaea within a broader scientific......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 Munich...

  12. 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?.

  13. Enrichment of denitrifying methanotrophic bacteria for application after direct low-temperature anaerobic sewage treatment

    Energy Technology Data Exchange (ETDEWEB)

    Kampman, Christel, E-mail: christel.kampman@wur.nl [Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen (Netherlands); Hendrickx, Tim L.G. [Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen (Netherlands); Luesken, Francisca A.; Alen, Theo A. van; Op den Camp, Huub J.M.; Jetten, Mike S.M. [Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Zeeman, Grietje; Buisman, Cees J.N.; Temmink, Hardy [Sub-department of Environmental Technology, Wageningen University, P.O. Box 17, 6700 AA, Wageningen (Netherlands)

    2012-08-15

    Highlights: Black-Right-Pointing-Pointer A new concept for low-temperature anaerobic sewage treatment is proposed. Black-Right-Pointing-Pointer In this concept, denitrification and methane oxidation are performed by Methylomirabilis oxyfera. Black-Right-Pointing-Pointer The bacteria were enriched from fresh water sediment using sequencing fed-batch reactors. Black-Right-Pointing-Pointer The volumetric consumption rate has to be increased by an order of magnitude for practical application. Black-Right-Pointing-Pointer Further research should focus on systems with improved biomass retention. - Abstract: Despite many advantages of anaerobic sewage treatment over conventional activated sludge treatment, it has not yet been applied in temperate zones. This is especially because effluent from low-temperature anaerobic treatment contains nitrogen and dissolved methane. The presence of nitrogen and methane offers the opportunity to develop a reactor in which methane is used as electron donor for denitrification. Such a reactor could be used in a new concept for low-temperature anaerobic sewage treatment, consisting of a UASB-digester system, a reactor for denitrification coupled to anaerobic methane oxidation, and a nitritation reactor. In the present study denitrifying methanotrophic bacteria similar to 'Candidatus Methylomirabilis oxyfera' were enriched. Maximum volumetric nitrite consumption rates were 33.5 mg NO{sub 2}{sup -}-N/L d (using synthetic medium) and 37.8 mg NO{sub 2}{sup -}-N/L d (using medium containing effluent from a sewage treatment plant), which are similar to the maximum rate reported so far. Though the goal was to increase the rates, in both reactors, after reaching these maximum rates, volumetric nitrite consumption rates decreased in time. Results indicate biomass washout may have significantly decelerated enrichment. Therefore, to obtain higher volumetric consumption rates, further research should focus on systems with complete biomass

  14. Enrichment of denitrifying methanotrophic bacteria for application after direct low-temperature anaerobic sewage treatment

    International Nuclear Information System (INIS)

    Kampman, Christel; Hendrickx, Tim L.G.; Luesken, Francisca A.; Alen, Theo A. van; Op den Camp, Huub J.M.; Jetten, Mike S.M.; Zeeman, Grietje; Buisman, Cees J.N.; Temmink, Hardy

    2012-01-01

    Highlights: ► A new concept for low-temperature anaerobic sewage treatment is proposed. ► In this concept, denitrification and methane oxidation are performed by Methylomirabilis oxyfera. ► The bacteria were enriched from fresh water sediment using sequencing fed-batch reactors. ► The volumetric consumption rate has to be increased by an order of magnitude for practical application. ► Further research should focus on systems with improved biomass retention. - Abstract: Despite many advantages of anaerobic sewage treatment over conventional activated sludge treatment, it has not yet been applied in temperate zones. This is especially because effluent from low-temperature anaerobic treatment contains nitrogen and dissolved methane. The presence of nitrogen and methane offers the opportunity to develop a reactor in which methane is used as electron donor for denitrification. Such a reactor could be used in a new concept for low-temperature anaerobic sewage treatment, consisting of a UASB-digester system, a reactor for denitrification coupled to anaerobic methane oxidation, and a nitritation reactor. In the present study denitrifying methanotrophic bacteria similar to ‘Candidatus Methylomirabilis oxyfera’ were enriched. Maximum volumetric nitrite consumption rates were 33.5 mg NO 2 − -N/L d (using synthetic medium) and 37.8 mg NO 2 − -N/L d (using medium containing effluent from a sewage treatment plant), which are similar to the maximum rate reported so far. Though the goal was to increase the rates, in both reactors, after reaching these maximum rates, volumetric nitrite consumption rates decreased in time. Results indicate biomass washout may have significantly decelerated enrichment. Therefore, to obtain higher volumetric consumption rates, further research should focus on systems with complete biomass retention.

  15. Isolation and characterization of extreme halophilic archaea

    Energy Technology Data Exchange (ETDEWEB)

    Franze, Madlen; Cherkouk, Andrea [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). HZDR Young Investigator Group

    2017-06-01

    Extreme halophilic archaea from the family Halobactereacea represent a dominant part of the microbial community present in saline soils as well as rock salts. By using a culture-dependent approach different Haloarchaea could be isolated and were phylogenetic analysed. Interestingly, isolates closely related to different Halobacterium spp. were found in both environments.

  16. Isolation and characterization of extreme halophilic archaea

    International Nuclear Information System (INIS)

    Franze, Madlen; Cherkouk, Andrea

    2017-01-01

    Extreme halophilic archaea from the family Halobactereacea represent a dominant part of the microbial community present in saline soils as well as rock salts. By using a culture-dependent approach different Haloarchaea could be isolated and were phylogenetic analysed. Interestingly, isolates closely related to different Halobacterium spp. were found in both environments.

  17. Lipidomic Analysis: From Archaea to Mammals

    Czech Academy of Sciences Publication Activity Database

    Řezanka, Tomáš; Kolouchová, I.; Gharwalová, L.; Palyzová, Andrea; Sigler, Karel

    2018-01-01

    Roč. 53, č. 1 (2018), s. 5-25 ISSN 0024-4201 R&D Projects: GA ČR(CZ) GA17-00027S Institutional support: RVO:61388971 Keywords : Algae * Animals * Archaea Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 1.934, year: 2016

  18. 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

  19. 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.

  20. Anaerobic oxidation of methane coupled to thiosulfate reduction in a biotrickling filter.

    Science.gov (United States)

    Cassarini, Chiara; Rene, Eldon R; Bhattarai, Susma; Esposito, Giovanni; Lens, Piet N L

    2017-09-01

    Microorganisms from an anaerobic methane oxidizing sediment were enriched with methane gas as the substrate in a biotrickling filter (BTF) using thiosulfate as electron acceptor for 213days. Thiosulfate disproportionation to sulfate and sulfide were the dominating sulfur conversion process in the BTF and the sulfide production rate was 0.5mmoll -1 day -1 . A specific group of sulfate reducing bacteria (SRB), belonging to the Desulforsarcina/Desulfococcus group, was enriched in the BTF. The BTF biomass showed maximum sulfate reduction rate (0.38mmoll -1 day -1 ) with methane as sole electron donor, measured in the absence of thiosulfate in the BTF. Therefore, a BTF fed with thiosulfate as electron acceptor can be used to enrich SRB of the DSS group and activate the inoculum for anaerobic oxidation of methane coupled to sulfate reduction. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. 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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. 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

    2016-01-01

    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. PMID:27112502

  3. Halophilic archaea on Earth and in space: growth and survival under extreme conditions.

    Science.gov (United States)

    Oren, Aharon

    2014-12-13

    Salts are abundant on Mars, and any liquid water that is present or may have been present on the planet is expected to be hypersaline. Halophilic archaea (family Halobacteriaceae) are the microorganisms best adapted to life at extremes of salinity on Earth. This paper reviews the properties of the Halobacteriaceae that may make the group good candidates for life also on Mars. Many species resist high UV and gamma radiation levels; one species has survived exposure to vacuum and radiation during a space flight; and there is at least one psychrotolerant species. Halophilic archaea may survive for millions of years within brine inclusions in salt crystals. Many species have different modes of anaerobic metabolism, and some can use light as an energy source using the light-driven proton pump bacteriorhodopsin. They are also highly tolerant to perchlorate, recently shown to be present in Martian soils, and some species can even use perchlorate as an electron acceptor to support anaerobic growth. The presence of characteristic carotenoid pigments (α-bacterioruberin and derivatives) makes the Halobacteriaceae easy to identify by Raman spectroscopy. Thus, if present on Mars, such organisms may be detected by Raman instrumentation planned to explore Mars during the upcoming ExoMars mission. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  4. Diversity of bacteria and archaea from two shallow marine hydrothermal vents from Vulcano Island.

    Science.gov (United States)

    Antranikian, Garabed; Suleiman, Marcel; Schäfers, Christian; Adams, Michael W W; Bartolucci, Simonetta; Blamey, Jenny M; Birkeland, Nils-Kåre; Bonch-Osmolovskaya, Elizaveta; da Costa, Milton S; Cowan, Don; Danson, Michael; Forterre, Patrick; Kelly, Robert; Ishino, Yoshizumi; Littlechild, Jennifer; Moracci, Marco; Noll, Kenneth; Oshima, Tairo; Robb, Frank; Rossi, Mosè; Santos, Helena; Schönheit, Peter; Sterner, Reinhard; Thauer, Rudolf; Thomm, Michael; Wiegel, Jürgen; Stetter, Karl Otto

    2017-07-01

    To obtain new insights into community compositions of hyperthermophilic microorganisms, defined as having optimal growth temperatures of 80 °C and above, sediment and water samples were taken from two shallow marine hydrothermal vents (I and II) with temperatures of 100 °C at Vulcano Island, Italy. A combinatorial approach of denaturant gradient gel electrophoresis (DGGE) and metagenomic sequencing was used for microbial community analyses of the samples. In addition, enrichment cultures, growing anaerobically on selected polysaccharides such as starch and cellulose, were also analyzed by the combinatorial approach. Our results showed a high abundance of hyperthermophilic archaea, especially in sample II, and a comparable diverse archaeal community composition in both samples. In particular, the strains of the hyperthermophilic anaerobic genera Staphylothermus and Thermococcus, and strains of the aerobic hyperthermophilic genus Aeropyrum, were abundant. Regarding the bacterial community, ε-Proteobacteria, especially the genera Sulfurimonas and Sulfurovum, were highly abundant. The microbial diversity of the enrichment cultures changed significantly by showing a high dominance of archaea, particularly the genera Thermococcus and Palaeococcus, depending on the carbon source and the selected temperature.

  5. Perspectives on biotechnological applications of archaea

    Science.gov (United States)

    Schiraldi, Chiara; Giuliano, Mariateresa; De Rosa, Mario

    2002-01-01

    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. PMID:15803645

  6. Cell architecture and flagella of hyperthermophilic Archaea

    OpenAIRE

    Bellack, Annett

    2011-01-01

    Earlier studies indicated that flagella might play a crucial role in motility, adhesion, and cell-cell contacts of Archaea. Thus, the ultrastructural and functional characterization of flagella and their anchoring in the cell are crucial for understanding the archaeal cell organization in general. To address this topic, Pyrococcus furiosus was chosen as a suitable model organism. However, in the course of this study, morphological changes of this strain, cultured continuously for several y...

  7. Pathways and bioenergetics of anaerobic carbon monoxide fermentation.

    OpenAIRE

    Martijn eDiender; Alfons J.M. Stams; Alfons J.M. Stams; Diana Z. Sousa

    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, ...

  8. The unique features of glycolytic pathways in Archaea.

    OpenAIRE

    Verhees, Corné H; Kengen, Servé W M; Tuininga, Judith E; Schut, Gerrit J; Adams, Michael W W; De Vos, Willem M; Van Der Oost, John

    2003-01-01

    An early divergence in evolution has resulted in two prokaryotic domains, the Bacteria and the Archaea. Whereas the central metabolic routes of bacteria and eukaryotes are generally well-conserved, variant pathways have developed in Archaea involving several novel enzymes with a distinct control. A spectacular example of convergent evolution concerns the glucose-degrading pathways of saccharolytic archaea. The identification, characterization and comparison of the glycolytic enzymes of a vari...

  9. Visible-light-assisted SLCs template synthesis of sea anemone-like Pd/PANI nanocomposites with high electrocatalytic activity for methane oxidation in acidic medium

    Science.gov (United States)

    Tan, De-Xin; Wang, Yan-Li

    2018-03-01

    Sea anemone-like palladium (Pd)/polyaniline (PANI) nanocomposites were synthesized via visible-light-assisted swollen liquid crystals (SLCs) template method. The resulting samples were characterized by transmission electron microscopy (TEM), selected area electron diffraction (SAED), energy dispersive spectrometer (EDS), x-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), ultraviolet-visible (UV–vis) absorption spectroscopy and Fourier transform infrared (FT-IR) spectroscopy, respectively. The electrocatalytic properties of Pd/PANI nanocomposites modified glass carbon electrode (GCE) for methane oxidation were investigated by cycle voltammetry (CV) and chronoamperometry. Those dispersed sea anemone-like Pd/PANI nanocomposites had an average diameter of 320 nm. The obtained Pd nanoparticles with an average diameter of about 45 nm were uniformly distributed in PANI matrix. Sea anemone-like Pd/PANI nanocomposites exhibited excellent electrocatalytic activity and stability for oxidation of methane (CH4).

  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...

  11. Exocellular electron transfer in anaerobic microbial communities.

    Science.gov (United States)

    Stams, Alfons J M; de Bok, Frank A M; Plugge, Caroline M; van Eekert, Miriam H A; Dolfing, Jan; Schraa, Gosse

    2006-03-01

    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 syntrophic consortia of proton-reducing acetogenic bacteria and hydrogen-consuming methanogenic archaea. Anaerobic microorganisms that use insoluble electron acceptors for growth, such as iron- and manganese-oxide as well as inert graphite electrodes in microbial fuel cells, also transfer electrons exocellularly. Soluble compounds, like humic substances, quinones, phenazines and riboflavin, can function as exocellular electron mediators enhancing this type of anaerobic respiration. However, direct electron transfer by cell-cell contact is important as well. This review addresses the mechanisms of exocellular electron transfer in anaerobic microbial communities. There are fundamental differences but also similarities between electron transfer to another microorganism or to an insoluble electron acceptor. The physical separation of the electron donor and electron acceptor metabolism allows energy conservation in compounds as methane and hydrogen or as electricity. Furthermore, this separation is essential in the donation or acceptance of electrons in some environmental technological processes, e.g. soil remediation, wastewater purification and corrosion.

  12. 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.

  13. Role of Mn2+ and compatible solutes in the radiation resistance of thermophilic bacteria and archaea.

    Science.gov (United States)

    Webb, Kimberly M; DiRuggiero, Jocelyne

    2012-01-01

    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 Mn(2+)-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.

  14. Iron-mediated anaerobic oxidation of methane in brackish coastal sediments.

    Science.gov (United States)

    Egger, Matthias; Rasigraf, Olivia; Sapart, Célia J; Jilbert, Tom; Jetten, Mike S M; Röckmann, Thomas; van der Veen, Carina; Bândă, Narcisa; Kartal, Boran; Ettwig, Katharina F; Slomp, Caroline P

    2015-01-06

    Methane is a powerful greenhouse gas and its biological conversion in marine sediments, largely controlled by anaerobic oxidation of methane (AOM), is a crucial part of the global carbon cycle. However, little is known about the role of iron oxides as an oxidant for AOM. Here we provide the first field evidence for iron-dependent AOM in brackish coastal surface sediments and show that methane produced in Bothnian Sea sediments is oxidized in distinct zones of iron- and sulfate-dependent AOM. At our study site, anthropogenic eutrophication over recent decades has led to an upward migration of the sulfate/methane transition zone in the sediment. Abundant iron oxides and high dissolved ferrous iron indicate iron reduction in the methanogenic sediments below the newly established sulfate/methane transition. Laboratory incubation studies of these sediments strongly suggest that the in situ microbial community is capable of linking methane oxidation to iron oxide reduction. Eutrophication of coastal environments may therefore create geochemical conditions favorable for iron-mediated AOM and thus increase the relevance of iron-dependent methane oxidation in the future. Besides its role in mitigating methane emissions, iron-dependent AOM strongly impacts sedimentary iron cycling and related biogeochemical processes through the reduction of large quantities of iron oxides.

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

    Science.gov (United States)

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

    2015-08-15

    Anaerobic oxidation of methane (AOM) coupled to nitrite reduction is a novel AOM process that is mediated by denitrifying methanotrophs. To date, enrichments of these denitrifying methanotrophs have been confined to freshwater systems; however, the recent findings of 16S rRNA and pmoA gene sequences in marine sediments suggest a possible occurrence of AOM coupled to nitrite reduction in marine systems. In this research, a marine denitrifying methanotrophic culture was obtained after 20 months of enrichment. Activity testing and quantitative PCR (qPCR) analysis were then conducted and showed that the methane oxidation activity and the number of NC10 bacteria increased correlatively during the enrichment period. 16S rRNA gene sequencing indicated that only bacteria in group A of the NC10 phylum were enriched and responsible for the resulting methane oxidation activity, although a diverse community of NC10 bacteria was harbored in the inoculum. Fluorescence in situ hybridization showed that NC10 bacteria were dominant in the enrichment culture after 20 months. The effect of salinity on the marine denitrifying methanotrophic culture was investigated, and the apparent optimal salinity was 20.5‰, which suggested that halophilic bacterial AOM coupled to nitrite reduction was obtained. Moreover, the apparent substrate affinity coefficients of the halophilic denitrifying methanotrophs were determined to be 9.8 ± 2.2 μM for methane and 8.7 ± 1.5 μM for nitrite. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  16. ADP-dependent Phosphofructokinases in Mesophilic and Thermophilic Methanogenic Archaea

    NARCIS (Netherlands)

    Verhees, C.H.; Tuininga, J.E.; Kengen, S.W.M.; Stams, A.J.M.; Oost, van der J.; Vos, de W.M.

    2001-01-01

    Phosphofructokinase (PFK) is a key enzyme of the glycolytic pathway in all domains of life. Two related PFKs, ATP-dependent and PPi-dependent PFK, have been distinguished in bacteria and eucarya, as well as in some archaea. Hyperthermophilic archaea of the order Thermococcales, including Pyrococcus

  17. Isoprenoid biosynthesis in Archaea - Biochemical and evolutionary implications

    NARCIS (Netherlands)

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

    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,

  18. Molecular characterization of anaerobic sulfur-oxidizing microbial communities in up-flow anaerobic sludge blanket reactor treating municipal sewage.

    Science.gov (United States)

    Aida, Azrina A; Hatamoto, Masashi; Yamamoto, Masamitsu; Ono, Shinya; Nakamura, Akinobu; Takahashi, Masanobu; Yamaguchi, Takashi

    2014-11-01

    A novel wastewater treatment system consisting of an up-flow anaerobic sludge blanket (UASB) reactor and a down-flow hanging sponge (DHS) reactor with sulfur-redox reaction was developed for treatment of municipal sewage under low-temperature conditions. In the UASB reactor, a novel phenomenon of anaerobic sulfur oxidation occurred in the absence of oxygen, nitrite and nitrate as electron acceptors. The microorganisms involved in anaerobic sulfur oxidation have not been elucidated. Therefore, in this study, we studied the microbial communities existing in the UASB reactor that probably enhanced anaerobic sulfur oxidation. Sludge samples collected from the UASB reactor before and after sulfur oxidation were used for cloning and terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes of the bacterial and archaeal domains. The microbial community structures of bacteria and archaea indicated that the genus Smithella and uncultured bacteria within the phylum Caldiserica were the dominant bacteria groups. Methanosaeta spp. was the dominant group of the domain archaea. The T-RFLP analysis, which was consistent with the cloning results, also yielded characteristic fingerprints for bacterial communities, whereas the archaeal community structure yielded stable microbial community. From these results, it can be presumed that these major bacteria groups, genus Smithella and uncultured bacteria within the phylum Caldiserica, probably play an important role in sulfur oxidation in UASB reactors. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  19. Translation termination in pyrrolysine-utilizing archaea.

    Science.gov (United States)

    Alkalaeva, Elena; Eliseev, Boris; Ambrogelly, Alexandre; Vlasov, Peter; Kondrashov, Fyodor A; Gundllapalli, Sharath; Frolova, Lyudmila; Söll, Dieter; Kisselev, Lev

    2009-11-03

    Although some data link archaeal and eukaryotic translation, the overall mechanism of protein synthesis in archaea remains largely obscure. Both archaeal (aRF1) and eukaryotic (eRF1) single release factors recognize all three stop codons. The archaeal genus Methanosarcinaceae contains two aRF1 homologs, and also uses the UAG stop to encode the 22nd amino acid, pyrrolysine. Here we provide an analysis of the last stage of archaeal translation in pyrrolysine-utilizing species. We demonstrated that only one of two Methanosarcina barkeri aRF1 homologs possesses activity and recognizes all three stop codons. The second aRF1 homolog may have another unknown function. The mechanism of pyrrolysine incorporation in the Methanosarcinaceae is discussed.

  20. A marine microbial consortium apparently mediating anaerobic oxidation of methane

    DEFF Research Database (Denmark)

    Boetius, A.; Ravenschlag, K.; Schubert, CJ

    2000-01-01

    microorganisms mediating this reaction have not yet been isolated, and the pathway of anaerobic oxidation of methane is insufficiently understood. Recent data suggest that certain archaea reverse the process of methanogenesis by interaction with sulphate-reducing bacteria(5-7). Here we provide microscopic...... cells and are surrounded by sulphate-reducing bacteria. These aggregates were abundant in gas-hydrate-rich sediments with extremely high rates of methane-based sulphate reduction, and apparently mediate anaerobic oxidation of methane.......A large fraction of globally produced methane is converted to CO2 by anaerobic oxidation in marine sediments(1). Strong geochemical evidence for net methane consumption in anoxic sediments is based on methane profiles(2), radiotracer experiments(3) and stable carbon isotope data(4). But the elusive...

  1. Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs.

    Science.gov (United States)

    Dedysh, S N; Liesack, W; Khmelenina, V N; Suzina, N E; Trotsenko, Y A; Semrau, J D; Bares, A M; Panikov, N S; Tiedje, J M

    2000-05-01

    A new genus, Methylocella, and a new species, Methylocella palustris, are proposed for three strains of methane-oxidizing bacteria isolated from acidic Sphagnum peat bogs. These bacteria are aerobic, Gram-negative, colourless, non-motile, straight and curved rods that utilize the serine pathway for carbon assimilation, multiply by normal cell division and contain intracellular poly-beta-hydroxybutyrate granules (one at each pole). These strains use methane and methanol as sole sources of carbon and energy and are moderately acidophilic organisms with growth between pH 4.5 and pH 7.0, the optimum being at pH 5.0-5.5. The temperature range for growth is 10-28 degrees C with the optimum at 15-20 degrees C. The intracytoplasmic membrane system is different from those of type I and II methanotrophs. Cells contain an extensive periplasmic space and a vesicular membrane system connected to the cytoplasmic membrane. The strains grew only on media with a low salt content (0.2-0.5 g l(-1)). All three strains were found to possess soluble methane monooxygenase and are able to fix atmospheric nitrogen via an oxygen-sensitive nitrogenase. No products were observed in a PCR with particulate methane monooxygenase-targeted primers; hybridization with a pmoA probe was also negative. The major phospholipid fatty acids are 18:1 acids. The G+C content of the DNA is 61.2 mol%. The three strains share identical 16S rRNA gene sequences and represent a novel lineage of methane-oxidizing bacteria within the alpha-subclass of the class Proteobacteria and are only moderately related to type II methanotrophs of the Methylocystis-Methylosinus group. The three strains are most closely related to the acidophilic heterotrophic bacterium Beijerinckia indica subsp. indica (96.5% 16S rDNA sequence similarity). Collectively, these strains comprise a new species and genus Methylocella palustris gen. nov., sp. nov.; strain KT (= ATCC 700799T) is the type strain.

  2. Protein Ser/Thr/Tyr phosphorylation in the Archaea.

    Science.gov (United States)

    Kennelly, Peter J

    2014-04-04

    The third domain of life, the Archaea (formerly Archaebacteria), is populated by a physiologically diverse set of microorganisms, many of which reside at the ecological extremes of our global environment. Although ostensibly prokaryotic in morphology, the Archaea share much closer evolutionary ties with the Eukarya than with the superficially more similar Bacteria. Initial genomic, proteomic, and biochemical analyses have revealed the presence of "eukaryotic" protein kinases and phosphatases and an intriguing set of serine-, threonine-, and tyrosine-phosphorylated proteins in the Archaea that may offer new insights into this important regulatory mechanism.

  3. A novel polygeneration process to co-produce ethylene and electricity from shale gas with zero CO2 emissions via methane oxidative coupling

    International Nuclear Information System (INIS)

    Khojasteh Salkuyeh, Yaser; Adams, Thomas A.

    2015-01-01

    Highlights: • Development of an ethylene plant from shale gases with zero CO 2 emissions. • Oxidative coupling of methane is used for the conversion of gas to ethylene. • Polygeneration strategy is used to improve the profitability of plant. - Abstract: A techno-economic analysis of a novel process to co-produce ethylene and electricity using a recently developed methane oxidative coupling catalyst is presented. Several design variants are considered, featuring the use of traditional gas turbines, chemical looping combustion, and 100% carbon dioxide capture. Mass and energy balance simulations were carried out using Aspen Plus simulations, and particle swarm optimization was used to determine the optimal process design under a variety of market scenarios. A custom model for the gas turbine section was used to ensure that the negative impacts of various cooling strategies were factored into the analysis. The results show that by synergistically co-producing power and ethylene using this catalyst, ethylene can be produced at costs close to traditional steam cracking methods with nearly zero carbon dioxide emissions, even when factoring in the relatively poor conversion and selectivity of the chosen catalyst

  4. 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.

  5. A criterion based on computational singular perturbation for the identification of quasi steady state species: A reduced mechanism for methane oxidation with NO chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Tianfeng; Law, Chung K. [Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544 (United States)

    2008-09-15

    A criterion based on computational singular perturbation (CSP) is proposed to effectively distinguish the quasi steady state (QSS) species from the fast species induced by reactions in partial equilibrium. Together with the method of directed relation graph (DRG), it was applied to the reduction of GRI-Mech 3.0 for methane oxidation, leading to the development of a 19-species reduced mechanism with 15 lumped steps, with the concentrations of the QSS species solved analytically for maximum computational efficiency. Compared to the 12-step and 16-species augmented reduced mechanism (ARM) previously developed by Sung, Law and Chen, three species, namely O, CH{sub 3}OH, and CH{sub 2}CO, are now excluded from the QSS species list. The reduced mechanism was validated with a variety of phenomena including perfectly stirred reactors, auto-ignition, and premixed and non-premixed flames, with the worst-case error being less than 10% over a wide range of parameters. This mechanism was then supplemented with the reactions involving NO formation, followed by validations in both homogeneous and diffusive systems. (author)

  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. Diversity of the DNA Replication System in the Archaea Domain

    Directory of Open Access Journals (Sweden)

    Felipe Sarmiento

    2014-01-01

    Full Text Available The precise and timely duplication of the genome is essential for cellular life. It is achieved by DNA replication, a complex process that is conserved among the three domains of life. Even though the cellular structure of archaea closely resembles that of bacteria, the information processing machinery of archaea is evolutionarily more closely related to the eukaryotic system, especially for the proteins involved in the DNA replication process. While the general DNA replication mechanism is conserved among the different domains of life, modifications in functionality and in some of the specialized replication proteins are observed. Indeed, Archaea possess specific features unique to this domain. Moreover, even though the general pattern of the replicative system is the same in all archaea, a great deal of variation exists between specific groups.

  8. A pursuit of lineage-specific and niche-specific proteome features in the world of archaea.

    Science.gov (United States)

    Roy Chowdhury, Anindya; Dutta, Chitra

    2012-06-12

    Archaea evoke interest among researchers for two enigmatic characteristics -a combination of bacterial and eukaryotic components in their molecular architectures and an enormous diversity in their life-style and metabolic capabilities. Despite considerable research efforts, lineage- specific/niche-specific molecular features of the whole archaeal world are yet to be fully unveiled. The study offers the first large-scale in silico proteome analysis of all archaeal species of known genome sequences with a special emphasis on methanogenic and sulphur-metabolising archaea. Overall amino acid usage in archaea is dominated by GC-bias. But the environmental factors like oxygen requirement or thermal adaptation seem to play important roles in selection of residues with no GC-bias at the codon level. All methanogens, irrespective of their thermal/salt adaptation, show higher usage of Cys and have relatively acidic proteomes, while the proteomes of sulphur-metabolisers have higher aromaticity and more positive charges. Despite of exhibiting thermophilic life-style, korarchaeota possesses an acidic proteome. Among the distinct trends prevailing in COGs (Cluster of Orthologous Groups of proteins) distribution profiles, crenarchaeal organisms display higher intra-order variations in COGs repertoire, especially in the metabolic ones, as compared to euryarchaea. All methanogens are characterised by a presence of 22 exclusive COGs. Divergences in amino acid usage, aromaticity/charge profiles and COG repertoire among methanogens and sulphur-metabolisers, aerobic and anaerobic archaea or korarchaeota and nanoarchaeota, as elucidated in the present study, point towards the presence of distinct molecular strategies for niche specialization in the archaeal world.

  9. A pursuit of lineage-specific and niche-specific proteome features in the world of archaea

    Directory of Open Access Journals (Sweden)

    Roy Chowdhury Anindya

    2012-06-01

    Full Text Available Abstract Background Archaea evoke interest among researchers for two enigmatic characteristics –a combination of bacterial and eukaryotic components in their molecular architectures and an enormous diversity in their life-style and metabolic capabilities. Despite considerable research efforts, lineage- specific/niche-specific molecular features of the whole archaeal world are yet to be fully unveiled. The study offers the first large-scale in silico proteome analysis of all archaeal species of known genome sequences with a special emphasis on methanogenic and sulphur-metabolising archaea. Results Overall amino acid usage in archaea is dominated by GC-bias. But the environmental factors like oxygen requirement or thermal adaptation seem to play important roles in selection of residues with no GC-bias at the codon level. All methanogens, irrespective of their thermal/salt adaptation, show higher usage of Cys and have relatively acidic proteomes, while the proteomes of sulphur-metabolisers have higher aromaticity and more positive charges. Despite of exhibiting thermophilic life-style, korarchaeota possesses an acidic proteome. Among the distinct trends prevailing in COGs (Cluster of Orthologous Groups of proteins distribution profiles, crenarchaeal organisms display higher intra-order variations in COGs repertoire, especially in the metabolic ones, as compared to euryarchaea. All methanogens are characterised by a presence of 22 exclusive COGs. Conclusions Divergences in amino acid usage, aromaticity/charge profiles and COG repertoire among methanogens and sulphur-metabolisers, aerobic and anaerobic archaea or korarchaeota and nanoarchaeota, as elucidated in the present study, point towards the presence of distinct molecular strategies for niche specialization in the archaeal world.

  10. Evolutionary insights from studies on viruses of hyperthermophilic archaea.

    Science.gov (United States)

    Prangishvili, David

    2003-05-01

    The morphological diversity of viruses which parasitize hyperthermophilic archaea thriving at temperatures > or = 80 degrees C appears to exceed that of viruses of prokaryotes living at lower temperatures. Based on assumptions of the existence of viruses in the prebiotic phase of evolution and hot origins of cellular life, we suggest that this remarkable diversity could have its source in ancestral diversity of viral morphotypes in hot environments. Attempts are made to trace evolutionary relationships of viruses of hyperthermophilic archaea with other viruses.

  11. Widespread Disulfide Bonding in Proteins from Thermophilic Archaea

    OpenAIRE

    Jorda, Julien; Yeates, Todd O.

    2011-01-01

    Disulfide bonds are generally not used to stabilize proteins in the cytosolic compartments of bacteria or eukaryotic cells, owing to the chemically reducing nature of those environments. In contrast, certain thermophilic archaea use disulfide bonding as a major mechanism for protein stabilization. Here, we provide a current survey of completely sequenced genomes, applying computational methods to estimate the use of disulfide bonding across the Archaea. Microbes belonging to the Crenarchaea...

  12. 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.

  13. Biological oxidation of dissolved methane in effluents from anaerobic reactors using a down-flow hanging sponge reactor.

    Science.gov (United States)

    Hatamoto, Masashi; Yamamoto, Hiroki; Kindaichi, Tomonori; Ozaki, Noriatsu; Ohashi, Akiyoshi

    2010-03-01

    Anaerobic wastewater treatment plants discharge dissolved methane, which is usually not recovered. To prevent emission of methane, which is a greenhouse gas, we utilized an encapsulated down-flow hanging sponge reactor as a post-treatment to biologically oxidize dissolved methane. Within 3 weeks after reactor start-up, methane removal efficiency of up to 95% was achieved with a methane removal rate of 0.8 kg COD m(-3) day(-1) at an HRT of 2 h. After increasing the methane-loading rate, the maximum methane removal rate reached 2.2 kg COD m(-3) day(-1) at an HRT of 0.5 h. On the other hand, only about 10% of influent ammonium was oxidized to nitrate during the first period, but as airflow was increased to 2.5 L day(-1), nitrification efficiency increased to approximately 70%. However, the ammonia oxidation rate then decreased with an increase in the methane-loading rate. These results indicate that methane oxidation occurred preferentially over ammonium oxidation in the reactor. Cloning of the 16S rRNA and pmoA genes as well as phylogenetic and T-RFLP analyses revealed that type I methanotrophs were the dominant methane oxidizers, whereas type II methanotrophs were detected only in minor portion of the reactor. Copyright 2009 Elsevier Ltd. All rights reserved.

  14. Livestock Anaerobic Digester Database

    Science.gov (United States)

    The Anaerobic Digester Database provides basic information about anaerobic digesters on livestock farms in the United States, organized in Excel spreadsheets. It includes projects that are under construction, operating, or shut down.

  15. Anaerobes in pleuropulmonary infections

    Directory of Open Access Journals (Sweden)

    De A

    2002-01-01

    Full Text Available A total of 76 anaerobes and 122 aerobes were isolated from 100 patients with pleuropulmonary infections, e.g. empyema (64, pleural effusion (19 and lung abscess (13. In 14% of the patients, only anaerobes were recovered, while a mixture of aerobes and anaerobes was encountered in 58%. From all cases of lung abscess, anaerobic bacteria were isolated, alone (04 or along with aerobic bacteria (13. From empyema and pleural effusion cases, 65.6% and 68.4% anaerobes were recovered respectively. Amongst anaerobes, gram negative anaerobic bacilli predominated (Prevotella melaninogenicus 16, Fusobacterium spp. 10, Bacteroides spp. 9, followed by gram positive anaerobic cocci (Peptostreptococcus spp. 31. Coliform bacteria (45 and Pseudomonas aeruginosa (42 were the predominant aerobic isolates.

  16. Identity and diversity of archaeal communities during anaerobic co-digestion of chicken feathers and other animal wastes.

    Science.gov (United States)

    Xia, Yun; Massé, Daniel I; McAllister, Tim A; Kong, Yunhong; Seviour, Robert; Beaulieu, Carole

    2012-04-01

    Digestion of raw feathers in anaerobic digesters inoculated with adapted swine manure, slaughterhouse sludge or dairy manure was investigated using twelve 42-L anaerobic digesters at 25°C. After 120days 74%, 49% and 40% added feathers were converted to methane in swine manure, dairy manure and slaughterhouse sludge anaerobic digesters respectively. 16S rRNA gene clone library analyses identified twenty-one operational taxonomic units containing clone sequences from 5 genera, 5 families and 2 phyla of members of the Archaea from 158 sequenced clones. Fluorescence insitu hybridization revealed that methanogens from the Methanomicrobiales, Methanosarcinales and Methanobacteriales constituted a major fraction (>78%) of these Archaea. A high correlation was seen between the distribution of functional archaeal groups and the NH(3)-N levels of digester mixed liquors. The compositions of archaeal communities fed different substrates were statistically significantly different (P<0.05). Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

  17. Density functional theory analysis of the reaction pathway for methane oxidation to acetic acid catalyzed by Pd2+ in sulfuric acid.

    Science.gov (United States)

    Chempath, Shaji; Bell, Alexis T

    2006-04-12

    Density functional theory has been used to investigate the thermodynamics and activation barriers associated with the direct oxidation of methane to acetic acid catalyzed by Pd2+ cation in concentrated sulfuric acid. Pd2+ cations in such solutions are ligated by two bisulfate anions and by one or two molecules of sulfuric acid. Methane oxidation is initiated by the addition of CH4 across one of the Pd-O bonds of a bisulfate ligand to form Pd(HSO4)(CH3)(H2SO4)2. The latter species will react with CO to produce Pd(HSO4)(CH3CO)(H2SO4)2. The most likely path to the final products is found to be via oxidation of Pd(HSO4)(CH3)(H2SO4)2 and Pd(HSO4)(CH3CO)(H2SO4)2 to form Pd(eta2-HSO4)(HSO4)2(CH3)(H2SO4) and Pd(eta2-HSO4)(HSO4)2(CH3CO)(H2SO4), respectively. CH3HSO4 or CH3COHSO4 is then produced by reductive elimination from the latter two species, and CH(3)COOH is then formed by hydrolysis of CH3COHSO4. The loss of Pd2+ from solution to form Pd(0) or Pd-black is predicted to occur via reduction with CO. This process is offset, though, by reoxidation of palladium by either H2SO4 or O2.

  18. 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.

  19. 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.

  20. Anaerobic Digestion: Process

    DEFF Research Database (Denmark)

    Angelidaki, Irini; Batstone, Damien J.

    2011-01-01

    Organic waste may degrade anaerobically in nature as well as in engineered systems. The latter is called anaerobic digestion or biogasification. Anaerobic digestion produces two main outputs: An energy-rich gas called biogas and an effluent. The effluent, which may be a solid as well as liquid...... 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...

  1. Vitamin and amino acid auxotrophy in anaerobic consortia operating under methanogenic condition

    OpenAIRE

    Eiler, Alexander; Bertilsson, Stefan; Berry, David; Wendeberg, Anneli; Foght, Julia; Tan, Boonfei; Buck, Moritz; Hubalek, Valeria

    2017-01-01

    Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in crude oil reservoirs and petroleum contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance1. Using micromanipulation combined with shotgun metagenomic approaches, we disentangled the genomes of complex consortia inside a short chain alkane deg...

  2. Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions

    OpenAIRE

    Valerie Hubalek; Moritz Buck; BoonFei Tan; Julia Foght; Annelie Wendeberg; David Berry; Stefan Bertilsson; Alexander Eiler; Karen G. Lloyd

    2017-01-01

    ABSTRACT Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-ch...

  3. Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota

    OpenAIRE

    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; G?ker, Markus; Reva, Oleg N.; Miroshnichenko, Margarita L.

    2017-01-01

    © 2017 Kublanov, Sigalova, Gavrilov, Lebedinsky, Rinke, Kovaleva, Chernyh, Ivanova, Daum, Reddy, Klenk, Spring, Göker, Reva, Miroshnichenko, Kyrpides, Woyke, Gelfand, Bonch-Osmolovskaya. 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 impl...

  4. 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).

  5. The unique features of glycolytic pathways in Archaea.

    Science.gov (United States)

    Verhees, Corné H; Kengen, Servé W M; Tuininga, Judith E; Schut, Gerrit J; Adams, Michael W W; De Vos, Willem M; Van Der Oost, John

    2003-10-15

    An early divergence in evolution has resulted in two prokaryotic domains, the Bacteria and the Archaea. Whereas the central metabolic routes of bacteria and eukaryotes are generally well-conserved, variant pathways have developed in Archaea involving several novel enzymes with a distinct control. A spectacular example of convergent evolution concerns the glucose-degrading pathways of saccharolytic archaea. The identification, characterization and comparison of the glycolytic enzymes of a variety of phylogenetic lineages have revealed a mosaic of canonical and novel enzymes in the archaeal variants of the Embden-Meyerhof and the Entner-Doudoroff pathways. By means of integrating results from biochemical and genetic studies with recently obtained comparative and functional genomics data, the structure and function of the archaeal glycolytic routes, the participating enzymes and their regulation are re-evaluated.

  6. Physiological Evidence for Isopotential Tunneling in the Electron Transport Chain of Methane-Producing Archaea.

    Science.gov (United States)

    Duszenko, Nikolas; Buan, Nicole R

    2017-09-15

    supramolecular complexes to optimize electron and carbon flow to control biomass synthesis and the production of methane. Worldwide, methanogens are used to generate renewable methane for heat, electricity, and transportation. Our observations suggest Methanosarcina acetivorans , but not Methanosarcina barkeri , has electrically quantized membranes. Escherichia coli , a model facultative anaerobe, has optimal electron transport at the stationary phase but not during exponential growth. This study also suggests the metabolic efficiency of bacteria and archaea can be improved using exogenously supplied lipophilic electron carriers. The enhancement of methanogen electron transport through methanophenazine has the potential to increase renewable methane production at an industrial scale. Copyright © 2017 American Society for Microbiology.

  7. A six-well plate method: less laborious and effective method for cultivation of obligate anaerobic microorganisms.

    Science.gov (United States)

    Nakamura, Kohei; Tamaki, Hideyuki; Kang, Myung Suk; Mochimaru, Hanako; Lee, Sung-Taik; Nakamura, Kazunori; Kamagata, Yoichi

    2011-01-01

    We developed a simple, less laborious method to cultivate and isolate obligate anaerobic microorganisms using a six-well plate together with the AnaeroPack System, designated as the six-well plate method. The cultivation efficiency of this method, based on colony-forming units, colony formation time, and colony size, was evaluated with four authentic obligate anaerobes (two methanogenic archaea and two sulfate-reducing bacteria). The method was found to be comparable to or even better than the roll tube method, a technique that is commonly used at present for the cultivation of obligate anaerobes. Further experiments using 21 representative obligate anaerobes demonstrated that all examined anaerobes (11 methanogens, 5 sulfate- or thiosulfate-reducing bacteria, and 5 syntrophs) could form visible colonies on the six-well plate and that these colonies could be successfully subcultured in fresh liquid media. Using this method, an unidentified sulfate-reducing bacterium was successfully isolated from an environmental sample.

  8. Aerobic and anaerobic methanotrophic communities in urban landscape wetland.

    Science.gov (United States)

    Chen, Sili; Chen, Jianfei; Chang, Sha; Yi, Hao; Huang, Dawei; Xie, Shuguang; Guo, Qingwei

    2018-01-01

    Both aerobic methane-oxidizing bacteria (MOB) and nitrite-dependent anaerobic methane oxidation (n-damo) organisms can be important methane sinks in a wetland. However, the influences of the vegetation type on aerobic MOB and n-damo communities in wetland, especially in constructed wetland, remain poorly understood. The present study investigated the influences of the vegetation type on both aerobic MOB and n-damo organisms in a constructed urban landscape wetland. Sediments were collected from eight sites vegetated with different plant species. The abundance (1.19-3.27 × 10 7 pmoA gene copies per gram dry sediment), richness (Chao1 estimator = 16.3-81.5), diversity (Shannon index = 2.10-3.15), and structure of the sediment aerobic MOB community were found to vary considerably with sampling site. In contrast, n-damo community abundance (8.74 × 10 5 -4.80 × 10 6 NC10 16S rRNA gene copies per gram dry sediment) changed slightly with the sampling site. The richness (Chao1 estimator = 1-11), diversity (Shannon index = 0-0.78), and structure of the NC10 16S rRNA gene-based n-damo community illustrated slight site-related changes, while the spatial changes of the pmoA gene-based n-damo community richness (Chao1 estimator = 1-8), diversity (Shannon index = 0-0.99), and structure were considerable. The vegetation type could have a profound impact on the wetland aerobic MOB community and had a stronger influence on the pmoA-based n-damo community than on the NC10 16S-based one in urban wetland. Moreover, the aerobic MOB community had greater abundance and higher richness and diversity than the n-damo community. Methylocystis (type II MOB) predominated in urban wetland, while no known type I MOB species was detected. In addition, the ratio of total organic carbon to total nitrogen (C/N) might be a determinant of sediment n-damo community diversity and aerobic MOB richness.

  9. 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

  10. 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

  11. Anaerobic treatment techniques

    International Nuclear Information System (INIS)

    Boehnke, B.; Bischofsberger, W.; Seyfried, C.F.

    1993-01-01

    This practical and theoretical guide presents the current state of knowledge in anaerobic treatment of industrial effluents with a high organic pollutant load and sewage sludges resulting from the treatment of municipal and industrial waste water. Starting from the microbiological bases of anaerobic degradation processes including a description and critical evaluation of executed plants, the book evolves the process-technical bases of anaerobic treatment techniques, derives relative applications, and discusses these with reference to excuted examples. (orig./UWA). 232 figs [de

  12. MTH1745, a protein disulfide isomerase-like protein from thermophilic archaea, Methanothermobacter thermoautotrophicum involving in stress response.

    Science.gov (United States)

    Ding, Xia; Lv, Zhen-Mei; Zhao, Yang; Min, Hang; Yang, Wei-Jun

    2008-01-01

    MTH1745 is a putative protein disulfide isomerase characterized with 151 amino acid residues and a CPAC active-site from the anaerobic archaea Methanothermobacter thermoautotrophicum. The potential functions of MTH1745 are not clear. In the present study, we show a crucial role of MTH1745 in protecting cells against stress which may be related to its functions as a disulfide isomerase and its chaperone properties. Using real-time polymerase chain reaction analyses, the level of MTH1745 messenger RNA (mRNA) in the thermophilic archaea M. thermoautotrophicum was found to be stress-induced in that it was significantly higher under low (50 degrees C) and high (70 degrees C) growth temperatures than under the optimal growth temperature for the organism (65 degrees C). Additionally, the expression of MTH1745 mRNA was up-regulated by cold shock (4 degrees C). Furthermore, the survival of MTH1745 expressing Escherichia coli cells was markedly higher than that of control cells in response to heat shock (51.0 degrees C). These results indicated that MTH1745 plays an important role in the resistance of stress. By assay of enzyme activities in vitro, MTH1745 also exhibited a chaperone function by promoting the functional folding of citrate synthase after thermodenaturation. On the other hand, MTH1745 was also shown to function as a disulfide isomerase on the refolding of denatured and reduced ribonuclease A. On the basis of its single thioredoxin domain, function as a disulfide isomerase, and its chaperone activity, we suggest that MTH1745 may be an ancient protein disulfide isomerase. These studies may provide clues to the understanding of the function of protein disulfide isomerase in archaea.

  13. On the Response of Halophilic Archaea to Space Conditions

    Science.gov (United States)

    Leuko, Stefan; Rettberg, Petra; Pontifex, Ashleigh L.; Burns, Brendan P.

    2014-01-01

    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. PMID:25370029

  14. Engineering of β-glycosidases from hyperthermophilic Archaea

    NARCIS (Netherlands)

    Kaper, T.

    2001-01-01

    Hyperthermophilic Archaea are microorganisms that grow optimally above 80°C. To be able to live at these temperature extremes their cell components display extreme resistance towards thermal degradation. This characteristic is an attractive feature

  15. 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

  16. Nitrogen metabolism and kinetics of ammonia-oxidizing archaea.

    Science.gov (United States)

    Martens-Habbena, Willm; Stahl, David A

    2011-01-01

    The discovery of ammonia-oxidizing mesophilic and thermophilic Group I archaea changed the century-old paradigm that aerobic ammonia oxidation is solely mediated by two small clades of Beta- and Gammaproteobacteria. Group I archaea are extremely diverse and ubiquitous in marine and terrestrial environments, accounting for 20-30% of the microbial plankton in the global oceans. Recent studies indicated that many of these organisms carry putative ammonia monooxygenase genes and are more abundant than ammonia-oxidizing bacteria in most natural environments suggesting a potentially significant role in the nitrogen cycle. The isolation of Nitrosopumilus maritimus strain SCM1 provided the first direct evidence that Group I archaea indeed gain energy from ammonia oxidation. To characterize the physiology of this archaeal nitrifier, we developed a respirometry setup particularly suited for activity measurements in dilute microbial cultures with extremely low oxygen uptake rates. Here, we describe the setup and review the kinetic experiments conducted with N. maritimus and other nitrifying microorganisms. These experiments demonstrated that N. maritimus is adapted to grow on ammonia concentrations found in oligotrophic open ocean environments, far below the survival threshold of ammonia-oxidizing bacteria. The described setup and experimental procedures should facilitate physiological studies on other nitrifying archaea and oligotrophic microorganisms in general. Copyright © 2011 Elsevier Inc. All rights reserved.

  17. Bacteria, not archaea, restore nitrification in a zinc contaminated soil.

    NARCIS (Netherlands)

    Mertens, J.; Broos, K.; Wakelin, S.A.; Kowalchuk, G.A.; Springael, D.; Smolders, E.

    2009-01-01

    Biological ammonia oxidation had long been thought to be mediated solely by discrete clades of Β- and γ-proteobacteria (ammonia-oxidizing bacteria; AOB). However, ammonia-oxidizing Crenarchaeota (ammonia-oxidizing archaea; AOA) have recently been identified and proposed to be the dominant agents of

  18. 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.

  19. Confocal Raman microspectroscopy reveals a convergence of the chemical composition in methanogenic archaea from a Siberian permafrost-affected soil.

    Science.gov (United States)

    Serrano, Paloma; Hermelink, Antje; Lasch, Peter; de Vera, Jean-Pierre; König, Nicole; Burckhardt, Oliver; Wagner, Dirk

    2015-12-01

    Methanogenic archaea are widespread anaerobic microorganisms responsible for the production of biogenic methane. Several new species of psychrotolerant methanogenic archaea were recently isolated from a permafrost-affected soil in the Lena Delta (Siberia, Russia), showing an exceptional resistance against desiccation, osmotic stress, low temperatures, starvation, UV and ionizing radiation when compared to methanogens from non-permafrost environments. To gain a deeper insight into the differences observed in their resistance, we described the chemical composition of methanogenic strains from permafrost and non-permafrost environments using confocal Raman microspectroscopy (CRM). CRM is a powerful tool for microbial identification and provides fingerprint-like information about the chemical composition of the cells. Our results show that the chemical composition of methanogens from permafrost-affected soils presents a high homology and is remarkably different from strains inhabiting non-permafrost environments. In addition, we performed a phylogenetic reconstruction of the studied strains based on the functional gene mcrA to prove the different evolutionary relationship of the permafrost strains. We conclude that the permafrost methanogenic strains show a convergent chemical composition regardless of their genotype. This fact is likely to be the consequence of a complex adaptive process to the Siberian permafrost environment and might be the reason underlying their resistant nature. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  20. New insight into stratification of anaerobic methanotrophs in cold seep sediments.

    Science.gov (United States)

    Roalkvam, Irene; Jørgensen, Steffen Leth; Chen, Yifeng; Stokke, Runar; Dahle, Håkon; Hocking, William Peter; Lanzén, Anders; Haflidason, Haflidi; Steen, Ida Helene

    2011-11-01

    Methane seepages typically harbor communities of anaerobic methane oxidizers (ANME); however, knowledge about fine-scale vertical variation of ANME in response to geochemical gradients is limited. We investigated microbial communities in sediments below a white microbial mat in the G11 pockmark at Nyegga by 16S rRNA gene tag pyrosequencing and real-time quantitative PCR. A vertical stratification of dominating ANME communities was observed at 4 cmbsf (cm below seafloor) and below in the following order: ANME-2a/b, ANME-1 and ANME-2c. The ANME-1 community was most numerous and comprised single or chains of cells with typical rectangular morphology, accounting up to 89.2% of the retrieved 16S rRNA gene sequences. Detection rates for sulfate-reducing Deltaproteobacteria possibly involved in anaerobic oxidation of methane were low throughout the core. However, a correlation in the abundance of Candidate division JS-1 with ANME-2 was observed, indicating involvement in metabolisms occurring in ANME-2-dominated horizons. The white microbial mat and shallow sediments were dominated by organisms affiliated with Sulfurovum (Epsilonproteobacteria) and Methylococcales (Gammaproteobacteria), suggesting that aerobic oxidation of sulfur and methane is taking place. In intermediate horizons, typical microbial groups associated with methane seeps were recovered. The data are discussed with respect to co-occurring microbial assemblages and interspecies interactions. FEMS Microbiology Ecology © 2011 Federation of Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original Norwegian works.

  1. Microbial anaerobic methane cycling in the subseafloor at the Von Damm hydrothermal vent field, Mid-Cayman Rise

    Science.gov (United States)

    Huber, J. A.; Reveillaud, J. C.; Stepanauskas, R.; McDermott, J. M.; Sylva, S. P.; Seewald, J.

    2013-12-01

    The Mid-Cayman Rise (MCR) is Earth's deepest and slowest spreading mid-ocean ridge located in the western Caribbean. With an axial rift valley floor at a depth of ~4200-6500 m, it represents one of the deepest sections of ridge crest worldwide. In 2009, the world's deepest hydrothermal vents (Piccard at 4960 m) and an ultramafic-influenced system only 20 km away on top of an oceanic core complex (Von Damm at 2350 m) were discovered along the MCR. Each site is hosted in a distinct geologic setting with different thermal and chemical regimes. The Von Damm site is a particularly interesting location to examine chemolithoautotrophic subseafloor microbial communities due to the abundant hydrogen, methane, and organic compounds in the venting fluids. Here, we used a combination of stable isotope tracing, next-generation sequencing, and single cell techniques to determine the identity, activity, and genomic repertoire of subseafloor anaerobic archaea involved in methane cycling in hydrothermal fluids venting at the Von Damm site. Molecular sequencing of phylogenetic marker genes revealed the presence of diverse archaea that both generate and consume methane across a geochemical and thermal spectrum of vents. Stable isotope tracing experiments were used to detect biological utilization of formate and dissolved inorganic carbon, and methane generation at 70 °C under anaerobic conditions. Results indicate that methanogenesis with formate as a substrate is occurring at 70 °C at two Von Damm sites, Ginger Castle and the Main Orifice. The results are consistent with thermodynamic predictions for carbon speciation at the temperatures encountered at the ultramafic-hosted Von Damm, where formate is predicted to be thermodynamically stable, and may thus serve as a an important source of carbon. Diverse thermophilic methanogenic archaea belonging to the genera Methanothermococcus were detected at all vent sites with both 16S rRNA tag sequencing and single cell sorting. Other

  2. Comparative Analysis of Performance and Microbial Characteristics Between High-Solid and Low-Solid Anaerobic Digestion of Sewage Sludge Under Mesophilic Conditions.

    Science.gov (United States)

    Lu, Qin; Yi, Jing; Yang, Dianhai

    2016-01-01

    High-solid anaerobic digestion of sewage sludge achieves highly efficient volatile solid reduction, and production of volatile fatty acid (VFA) and methane compared with conventional low-solid anaerobic digestion. In this study, the potential mechanisms of the better performance in high-solid anaerobic digestion of sewage sludge were investigated by using 454 high-throughput pyrosequencing and real-time PCR to analyze the microbial characteristics in sewage sludge fermentation reactors. The results obtained by 454 high-throughput pyrosequencing revealed that the phyla Chloroflexi, Bacteroidetes, and Firmicutes were the dominant functional microorganisms in high-solid and low-solid anaerobic systems. Meanwhile, the real-time PCR assays showed that high-solid anaerobic digestion significantly increased the number of total bacteria, which enhanced the hydrolysis and acidification of sewage sludge. Further study indicated that the number of total archaea (dominated by Methanosarcina) in a high-solid anaerobic fermentation reactor was also higher than that in a low-solid reactor, resulting in higher VFA consumption and methane production. Hence, the increased key bacteria and methanogenic archaea involved in sewage sludge hydrolysis, acidification, and methanogenesis resulted in the better performance of high-solid anaerobic sewage sludge fermentation.

  3. 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...

  4. Bacteria and archaea paleomicrobiology of the dental calculus: a review.

    Science.gov (United States)

    Huynh, H T T; Verneau, J; Levasseur, A; Drancourt, M; Aboudharam, G

    2016-06-01

    Dental calculus, a material observed in the majority of adults worldwide, emerged as a source for correlating paleomicrobiology with human health and diet. This mini review of 48 articles on the paleomicrobiology of dental calculus over 7550 years discloses a secular core microbiota comprising nine bacterial phyla - Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, TM7, Synergistetes, Chloroflexi, Fusobacteria, Spirochetes - and one archaeal phylum Euryarchaeota; and some accessory microbiota that appear and disappear according to time frame. The diet residues and oral microbes, including bacteria, archaea, viruses and fungi, consisting of harmless organisms and pathogens associated with local and systemic infections have been found trapped in ancient dental calculus by morphological approaches, immunolabeling techniques, isotope analyses, fluorescent in situ hybridization, DNA-based approaches, and protein-based approaches. These observations led to correlation of paleomicrobiology, particularly Streptococcus mutans and archaea, with past human health and diet. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  5. Structural and physicochemical properties of polar lipids from thermophilic archaea.

    Science.gov (United States)

    Ulrih, Natasa Poklar; Gmajner, Dejan; Raspor, Peter

    2009-08-01

    The essential general features required for lipid membranes of extremophilic archaea to fulfill biological functions are that they are in the liquid crystalline phase and have extremely low permeability of solutes that is much less temperature sensitive due to a lack of lipid-phase transition and highly branched isoprenoid chains. Many accumulated data indicate that the organism's response to extremely low pH is the opposite of that to high temperature. The high temperature adaptation does not require the tetraether lipids, while the adaptation of thermophiles to acidic environment requires the tetraether polar lipids. The presence of cyclopentane rings and the role of polar heads are not so straightforward regarding the correlations between fluidity and permeability of the lipid membrane. Due to the unique lipid structures and properties of archaeal lipids, they are a valuable resource in the development of novel biotechnological processes. This microreview focuses primarily on structural and physicochemical properties of polar lipids of (hyper)thermophilic archaea.

  6. Widespread Disulfide Bonding in Proteins from Thermophilic Archaea

    Directory of Open Access Journals (Sweden)

    Julien Jorda

    2011-01-01

    Full Text Available Disulfide bonds are generally not used to stabilize proteins in the cytosolic compartments of bacteria or eukaryotic cells, owing to the chemically reducing nature of those environments. In contrast, certain thermophilic archaea use disulfide bonding as a major mechanism for protein stabilization. Here, we provide a current survey of completely sequenced genomes, applying computational methods to estimate the use of disulfide bonding across the Archaea. Microbes belonging to the Crenarchaeal branch, which are essentially all hyperthermophilic, are universally rich in disulfide bonding while lesser degrees of disulfide bonding are found among the thermophilic Euryarchaea, excluding those that are methanogenic. The results help clarify which parts of the archaeal lineage are likely to yield more examples and additional specific data on protein disulfide bonding, as increasing genomic sequencing efforts are brought to bear.

  7. Widespread disulfide bonding in proteins from thermophilic archaea.

    Science.gov (United States)

    Jorda, Julien; Yeates, Todd O

    2011-01-01

    Disulfide bonds are generally not used to stabilize proteins in the cytosolic compartments of bacteria or eukaryotic cells, owing to the chemically reducing nature of those environments. In contrast, certain thermophilic archaea use disulfide bonding as a major mechanism for protein stabilization. Here, we provide a current survey of completely sequenced genomes, applying computational methods to estimate the use of disulfide bonding across the Archaea. Microbes belonging to the Crenarchaeal branch, which are essentially all hyperthermophilic, are universally rich in disulfide bonding while lesser degrees of disulfide bonding are found among the thermophilic Euryarchaea, excluding those that are methanogenic. The results help clarify which parts of the archaeal lineage are likely to yield more examples and additional specific data on protein disulfide bonding, as increasing genomic sequencing efforts are brought to bear.

  8. 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...... phylogenetic distribution of proteorhodopsins reflects their significant light-dependent fitness contributions, which drive the photoprotein's lateral acquisition and retention, but constrain its dispersal to the photic zone....

  9. Identification of a mismatch-specific endonuclease in hyperthermophilic Archaea

    OpenAIRE

    Ishino, Sonoko; Nishi, Yuki; Oda, Soichiro; Uemori, Takashi; Sagara, Takehiro; Takatsu, Nariaki; Yamagami, Takeshi; Shirai, Tsuyoshi; Ishino, Yoshizumi

    2016-01-01

    The common mismatch repair system processed by MutS and MutL and their homologs was identified in Bacteria and Eukarya. However, no evidence of a functional MutS/L homolog has been reported for archaeal organisms, and it is not known whether the mismatch repair system is conserved in Archaea. Here, we describe an endonuclease that cleaves double-stranded DNA containing a mismatched base pair, from the hyperthermophilic archaeon Pyrococcus furiosus. The corresponding gene revealed that the act...

  10. Diversity of Ammonia Oxidizing Archaea in Tropical Compost Systems

    OpenAIRE

    Vidya eDe Gannes; Gaius eEudoxie; David H Dyer; William James Hickey

    2012-01-01

    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 p...

  11. Selenoproteins in Archaea and Gram-positive bacteria.

    Science.gov (United States)

    Stock, Tilmann; Rother, Michael

    2009-11-01

    Selenium is an essential trace element for many organisms by serving important catalytic roles in the form of the 21st co-translationally inserted amino acid selenocysteine. It is mostly found in redox-active proteins in members of all three domains of life and analysis of the ever-increasing number of genome sequences has facilitated identification of the encoded selenoproteins. Available data from biochemical, sequence, and structure analyses indicate that Gram-positive bacteria synthesize and incorporate selenocysteine via the same pathway as enterobacteria. However, recent in vivo studies indicate that selenocysteine-decoding is much less stringent in Gram-positive bacteria than in Escherichia coli. For years, knowledge about the pathway of selenocysteine synthesis in Archaea and Eukarya was only fragmentary, but genetic and biochemical studies guided by analysis of genome sequences of Sec-encoding archaea has not only led to the characterization of the pathways but has also shown that they are principally identical. This review summarizes current knowledge about the metabolic pathways of Archaea and Gram-positive bacteria where selenium is involved, about the known selenoproteins, and about the respective pathways employed in selenoprotein synthesis.

  12. 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.

  13. Assessing methane oxidation under landfill covers and its contribution to the above atmospheric CO2 levels: The added value of the isotope (δ13C and δ18O CO2; δ13C and δD CH4) approach

    International Nuclear Information System (INIS)

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

    2012-01-01

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

  14. Respiratory transformation of nitrous oxide (N2O) to dinitrogen by Bacteria and Archaea.

    Science.gov (United States)

    Zumft, Walter G; Kroneck, Peter M H

    2007-01-01

    N2O is a potent greenhouse gas and stratospheric reactant that has been steadily on the rise since the beginning of industrialization. It is an obligatory inorganic metabolite of denitrifying bacteria, and some production of N2O is also found in nitrifying and methanotrophic bacteria. We focus this review on the respiratory aspect of N2O transformation catalysed by the multicopper enzyme nitrous oxide reductase (N2OR) that provides the bacterial cell with an electron sink for anaerobic growth. Two types of Cu centres discovered in N2OR were both novel structures among the Cu proteins: the mixed-valent dinuclear Cu(A) species at the electron entry site of the enzyme, and the tetranuclear Cu(Z) centre as the first catalytically active Cu-sulfur complex known. Several accessory proteins function as Cu chaperone and ABC transporter systems for the biogenesis of the catalytic centre. We describe here the paradigm of Z-type N2OR, whose characteristics have been studied in most detail in the genera Pseudomonas and Paracoccus. Sequenced bacterial genomes now provide an invaluable additional source of information. New strains harbouring nos genes and capability of N2O utilization are being uncovered. This reveals previously unknown relationships and allows pattern recognition and predictions. The core nos genes, nosZDFYL, share a common phylogeny. Most principal taxonomic lineages follow the same biochemical and genetic pattern and share the Z-type enzyme. A modified N2OR is found in Wolinella succinogenes, and circumstantial evidence also indicates for certain Archaea another type of N2OR. The current picture supports the view of evolution of N2O respiration prior to the separation of the domains Bacteria and Archaea. Lateral nos gene transfer from an epsilon-proteobacterium as donor is suggested for Magnetospirillum magnetotacticum and Dechloromonas aromatica. In a few cases, nos gene clusters are plasmid borne. Inorganic N2O metabolism is associated with a diversity of

  15. Rice Cluster I, an Important Group of Archaea Producing Methane in Rice Fields

    Science.gov (United States)

    Conrad, R.

    2006-12-01

    Rice fields are an important source for the greenhouse gas methane. Methane is a major degradation product of organic matter in the anoxic soil, is partially oxidized in the rhizosphere and is emitted into the atmosphere through the aerenchyma system of the plants. Anaerobic degradation of organic matter by fermenting bacteria eventually results in the production of acetate and hydrogen, the two major substrates for microbial methanogenesis. The community of methanogenic archaea consists of several major orders or families including hydrogen-utilizing Rice Cluster-I (RC-I). Environmental conditions affect the methanogenic degradation process and the community structure of the methanogenic archaea in soil and rhizosphere. For example, populations of acetoclastic Methanosaetaceae and Methanosarcinaceae are enhanced by low and high acetate concentrations, respectively. Stable isotope probing of 16S rRNA showed that RC-I methanogens are mainly active on rice roots and at low H2 concentrations. Growth and population size is largely consistent with energetic conditions. RC-I methanogens on roots seem to be responsible for methane production from plant photosynthates that account for a major part of the emitted methane. Populations of RC-I methanogens in rice field soil are also enhanced at elevated temperatures (40-50°C). Moderately thermophilic members of RC-I methanogens or other methanogenic families were found to be ubiquitously present in soils from rice fields and river marshes. The genome of a RC-I methanogen was completely sequenced out of an enrichment culture using a metagenome approach. Genes found are consistent with life in the rhizosphere and in temporarily drained, oxic soil. We found that the methanogenic community structure on the rice roots is mainly determined by the respective community structure of the soil, but is in addition affected by the rice cultivar. Rice microcosms in which soil and rice roots are mainly colonized by RC-I methanogens produce

  16. Expanding diversity of potential bacterial partners of the methanotrophic ANME archaea using Magneto-FISH

    Science.gov (United States)

    Trembath-Reichert, E.; Green-Saxena, A.; Steele, J. A.; Orphan, V. J.

    2012-12-01

    Sulfate-coupled anaerobic oxidation of methane (AOM) in marine sediments is the major sink for methane in the oceans. This process is believed to be catalyzed by as yet uncultured syntrophic consortia of ANME archaea (affiliated with the Methanosarcinales) and sulfate-reducing bacteria belonging to the Desulfosarcina/Desulfococcus and Desulfobulbaceae. These syntrophic consortia have been described from methane-rich habitats worldwide and appear to be most concentrated in areas of high methane flux, such as cold seeps along continental margins. The extent of the diversity and ecophysiological potential of these microbial associations is still poorly constrained. In an effort to better characterize the diversity of microorganisms forming associations with different clades of methanotrophic ANME archaea (ANME-1, ANME-2a/b/c, ANME-3) and link these organisms to potentially diagnostic metabolic genes (e.g. mcrA, dsrAB, aprA), we employed a unique culture-independent whole cell capture technique which combines Fluorescence In Situ Hybridization with immuno-magnetic cell capture (Magneto-FISH). We used Magneto-FISH for targeted enrichment of specific ANME groups and their associated bacteria directly from formalin- and ethanol-fixed methane seep sediment. The identity and metabolic gene diversity of captured microorganisms were then assessed by clone library construction and sequencing. Diversity recovered from Magneto-FISH experiments using general and clade-specific ANME targeted probes show both the expected selectivity of the FISH probes (i.e. predominately ANME-2c subclade captured with an ANME-2c probe and multiple ANME groups recovered with the general probe targeting most ANME). Follow up FISH experiments were conducted to confirm physical associations between ANME and unique bacterial members (deltaproteobacteria and other non-sulfate reducing groups) that were common to multiple Magneto-FISH capture experiments. Analyses of metabolic gene diversity for archaeal

  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. 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.

  19. Sulfate reduction and methane oxidation activity below the sulfate-methane transition zone in Alaskan Beaufort Sea continental margin sediments: Implications for deep sulfur cycling

    Science.gov (United States)

    Treude, Tina; Krause, Stefan; Maltby, Johanna; Dale, Andrew W.; Coffin, Richard; Hamdan, Leila J.

    2014-11-01

    Two ∼6 m long sediment cores were collected along the ∼300 m isobath on the Alaskan Beaufort Sea continental margin. Both cores showed distinct sulfate-methane transition zones (SMTZ) at 105 and 120 cm below seafloor (cmbsf). Sulfate was not completely depleted below the SMTZ but remained between 30 and 500 μM. Sulfate reduction and anaerobic oxidation of methane (AOM) determined by radiotracer incubations were active throughout the methanogenic zone. Although a mass balance could not explain the source of sulfate below the SMTZ, geochemical profiles and correlation network analyses of biotic and abiotic data suggest a cryptic sulfur cycle involving iron, manganese and barite. Inhibition experiments with molybdate and 2-bromoethanesulfonate (BES) indicated decoupling of sulfate reduction and AOM and competition between sulfate reducers and methanogens for substrates. While correlation network analyses predicted coupling of AOM to iron reduction, the addition of manganese or iron did not stimulate AOM. Since none of the classical archaeal anaerobic methanotrophs (ANME) were abundant, the involvement of unknown or unconventional phylotypes in AOM is conceivable. The resistance of AOM activity to inhibitors implies deviation from conventional enzymatic pathways. This work suggests that the classical redox cascade of electron acceptor utilization based on Gibbs energy yields does not always hold in diffusion-dominated systems, and instead biotic processes may be more strongly coupled to mineralogy.

  20. 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

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

    Science.gov (United States)

    Liebner, Susanne; Svenning, Mette M.

    2013-04-01

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

  2. Diversity of halophilic archaea in fermented foods and human intestines and their application.

    Science.gov (United States)

    Lee, Han-Seung

    2013-12-01

    Archaea are prokaryotic organisms distinct from bacteria in the structural and molecular biological sense, and these microorganisms are known to thrive mostly at extreme environments. In particular, most studies on halophilic archaea have been focused on environmental and ecological researches. However, new species of halophilic archaea are being isolated and identified from high salt-fermented foods consumed by humans, and it has been found that various types of halophilic archaea exist in food products by culture-independent molecular biological methods. In addition, even if the numbers are not quite high, DNAs of various halophilic archaea are being detected in human intestines and much interest is given to their possible roles. This review aims to summarize the types and characteristics of halophilic archaea reported to be present in foods and human intestines and to discuss their application as well.

  3. Microbial community analysis of ambient temperature anaerobic digesters

    Energy Technology Data Exchange (ETDEWEB)

    Ciotola, R. [Ohio State Univ., Columbus, OH (United States). Dept. of Food, Agriculture and Biological Engineering

    2010-07-01

    This paper reported on a study in which designs for Chinese and Indian fixed-dome anaerobic digesters were modified in an effort to produce smaller and more affordable digesters. While these types of systems are common in tropical regions of developing countries, they have not been used in colder climates because of the low biogas yield during the winter months. Although there is evidence that sufficient biogas production can be maintained in colder temperatures through design and operational changes, there is a lack of knowledge about the seasonal changes in the composition of the microbial communities in ambient temperature digesters. More knowledge is needed to design and operate systems for maximum biogas yield in temperate climates. The purpose of this study was to cultivate a microbial community that maximizes biogas production at psychrophilic temperatures. The study was conducted on a 300 gallon experimental anaerobic digester on the campus of Ohio State University. Culture-independent methods were used on weekly samples collected from the digester in order to examine microbial community response to changes in ambient temperature. Microbial community profiles were established using universal bacterial and archaeal primers that targeted the 16S rRNA gene. In addition to the methanogenic archaea, this analysis also targeted some of the other numerically and functionally important microbial taxa in anaerobic digesters, such as hydrolytic, fermentative, acetogenic and sulfate reducing bacteria. According to preliminary results, the composition of the microbial community shifts with changes in seasonal temperature.

  4. Microbial examination of anaerobic sludge adaptation to animal slurry.

    Science.gov (United States)

    Moset, V; Cerisuelo, A; Ferrer, P; Jimenez, A; Bertolini, E; Cambra-López, M

    2014-01-01

    The objective of this study was to evaluate changes in the microbial population of anaerobic sludge digesters during the adaptation to pig slurry (PS) using quantitative real-time polymerase chain reaction (qPCR) and qualitative scanning electron microscopy (SEM). Additionally, the relationship between microbial parameters and sludge physicochemical composition and methane yield was examined. Results showed that the addition of PS to an unadapted thermophilic anaerobic digester caused an increase in volatile fatty acids (VFA) concentration, a decrease in removal efficiency and CH4 yield. Additionally, increases in total bacteria and total archaea were observed using qPCR. Scanning electron micrographs provided a general overview of the sludge's cell morphology, morphological diversity and degree of organic matter degradation. A change in microbial morphotypes from homogeneous cell morphologies to a higher morphological diversity, similar to that observed in PS, was observed with the addition of PS by SEM. Therefore, the combination of qPCR and SEM allowed expanding the knowledge about the microbial adaptation to animal slurry in thermophilic anaerobic digesters.

  5. Are high rates of sulphate reduction associated with anaerobic oxidation of methane

    Energy Technology Data Exchange (ETDEWEB)

    Devol, A H; Ahmed, S I

    1981-01-01

    Classical models of sulphur diagenesis in marine sediments are based on the assumption that the rate of sulphate reduction is first order with respect to oxidizable particulate organic carbon (POC). This assumption requires that oxidizable POC, sulphate concentration and the sulphate reduction rate be highest at the top of the sulphate reduction zone and decrease exponentially with increasing sediment depth. However, to explain recent observations of concave upwards methane distributions, the anaerobic consumption of methane has been proposed. Furthermore, it has been proposed that this consumption takes place near the bottom of the sulphate reducing zone where sulphate concentrations are low. Thus, if sulphate reducing bacteria are associated with the anaerobic oxidation of methane, a peak in sulphate reduction rate might be expected in this deep consumption zone. The importance of the process in sedimentary sulphur diagenesis is indicated by calculations estimating that 30 to 75% of the downward sulphate flux at depth may be consumed by methane oxidation within this zone. We present here profiles of sulphate reduction rate in anoxic sediments that show distinct local maxima at the depth where the anaerobic oxidation of methane would be expected. Our measurements were made during July and August 1978 in Saanich Inlet, an anoxic fjord located on the south-east of Vancouver Island, British Columbia. The inlet has a shallow sill (approx 70 m) which restricts circulation of the deeper water (maximum depth 225 m) inside the basin to the extent that for about 8 months of the year the bottom waters contain hydrogen sulphide, the inlet is an ideal location for studying sedimentary sulphate reduction because reactions with oxygen and the effects of burrowing organisms can be neglected.

  6. 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.

  7. Environmental control on anaerobic oxidation of methane in the gassy sediments of Eckernforde Bay (German Baltic)

    DEFF Research Database (Denmark)

    Treude, T.; Kruger, M.; Boetius, A.

    2005-01-01

    We investigated the effect of seasonal environmental changes on the rate and distribution of anaerobic oxidation of methane (AOM) in Eckernforde Bay sediments (German Baltic Sea) and identified organisms that are likely to be involved in the process. Surface sediments were sampled during September...... of methane were measured in vitro. AOM changed seasonally within the upper 20 cm of the sediment, with rates being between 1 and 14 nmol cm(-3) d(-1). Its distribution is suggested to be controlled by oxygen and sulfate penetration, temperature, as well as methane supply, leading to a shallow AOM zone during...... AOM in Eckerntorde Bay. These archaea are known also from other marine methane-rich locations. However, they were not directly associated with sulfate-reducing bacteria. AOM is possibly mediated solely by these archaea that show a mesophilic physiology according to the seasonal temperature changes...

  8. Anaerobic prosthetic joint infection.

    Science.gov (United States)

    Shah, Neel B; Tande, Aaron J; Patel, Robin; Berbari, Elie F

    2015-12-01

    In an effort to improve mobility and alleviate pain from degenerative and connective tissue joint disease, an increasing number of individuals are undergoing prosthetic joint replacement in the United States. Joint replacement is a highly effective intervention, resulting in improved quality of life and increased independence [1]. By 2030, it is predicted that approximately 4 million total hip and knee arthroplasties will be performed yearly in the United States [2]. One of the major complications associated with this procedure is prosthetic joint infection (PJI), occurring at a rate of 1-2% [3-7]. In 2011, the Musculoskeletal Infectious Society created a unifying definition for prosthetic joint infection [8]. The following year, the Infectious Disease Society of America published practice guidelines that focused on the diagnosis and management of PJI. These guidelines focused on the management of commonly encountered organisms associated with PJI, including staphylococci, streptococci and select aerobic Gram-negative bacteria. However, with the exception of Propionibacterium acnes, management of other anaerobic organisms was not addressed in these guidelines [1]. Although making up approximately 3-6% of PJI [9,10], anaerobic microorganisms cause devastating complications, and similar to the more common organisms associated with PJI, these bacteria also result in significant morbidity, poor outcomes and increased health-care costs. Data on diagnosis and management of anaerobic PJI is mostly derived from case reports, along with a few cohort studies [3]. There is a paucity of published data outlining factors associated with risks, diagnosis and management of anaerobic PJI. We therefore reviewed available literature on anaerobic PJI by systematically searching the PubMed database, and collected data from secondary searches to determine information on pathogenesis, demographic data, clinical features, diagnosis and management. We focused our search on five commonly

  9. Diversity and stratification of archaea in a hypersaline microbial mat.

    Science.gov (United States)

    Robertson, Charles E; Spear, John R; Harris, J Kirk; Pace, Norman R

    2009-04-01

    The Guerrero Negro (GN) hypersaline microbial mats have become one focus for biogeochemical studies of stratified ecosystems. The GN mats are found beneath several of a series of ponds of increasing salinity that make up a solar saltern fed from Pacific Ocean water pumped from the Laguna Ojo de Liebre near GN, Baja California Sur, Mexico. Molecular surveys of the laminated photosynthetic microbial mat below the fourth pond in the series identified an enormous diversity of bacteria in the mat, but archaea have received little attention. To determine the bulk contribution of archaeal phylotypes to the pond 4 study site, we determined the phylogenetic distribution of archaeal rRNA gene sequences in PCR libraries based on nominally universal primers. The ratios of bacterial/archaeal/eukaryotic rRNA genes, 90%/9%/1%, suggest that the archaeal contribution to the metabolic activities of the mat may be significant. To explore the distribution of archaea in the mat, sequences derived using archaeon-specific PCR primers were surveyed in 10 strata of the 6-cm-thick mat. The diversity of archaea overall was substantial albeit less than the diversity observed previously for bacteria. Archaeal diversity, mainly euryarchaeotes, was highest in the uppermost 2 to 3 mm of the mat and decreased rapidly with depth, where crenarchaeotes dominated. Only 3% of the sequences were specifically related to known organisms including methanogens. While some mat archaeal clades corresponded with known chemical gradients, others did not, which is likely explained by heretofore-unrecognized gradients. Some clades did not segregate by depth in the mat, indicating broad metabolic repertoires, undersampling, or both.

  10. 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.

  11. Anaerobic digestion of spent mushroom substrate under thermophilic conditions: performance and microbial community analysis.

    Science.gov (United States)

    Xiao, Zheng; Lin, Manhong; Fan, Jinlin; Chen, Yixuan; Zhao, Chao; Liu, Bin

    2018-01-01

    Spent mushroom substrate (SMS) is the residue of edible mushroom production occurring in huge amounts. The SMS residue can be digested for biogas production in the mesophilic anaerobic digestion. In the present study, performance of batch thermophilic anaerobic digestion (TAD) of SMS was investigated as well as the interconnected microbial population structure changes. The analyzed batch TAD process lasted for 12 days with the cumulative methane yields of 177.69 mL/g volatile solid (VS). Hydrolytic activities of soluble sugar, crude protein, and crude fat in SMS were conducted mainly in the initial phase, accompanied by the excessive accumulation of volatile fatty acids and low methane yield. Biogas production increased dramatically from days 4 to 6. The degradation rates of cellulose and hemicellulose were 47.53 and 55.08%, respectively. The high-throughput sequencing of 16S rRNA gene amplicons revealed that Proteobacteria (56.7%-62.8%) was the dominant phylum in different fermentative stages, which was highly specific compared with other anaerobic processes of lignocellulosic materials reported in the literature. Crenarchaeota was abundant in the archaea. The most dominant genera of archaea were retrieved as Methanothermobacter and Methanobacterium, but the latter decreased sharply with time. This study shows that TAD is a feasible method to handle the waste SMS.

  12. 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

  13. 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...

  14. Computational Modeling of Fluctuations in Energy and Metabolic Pathways of Methanogenic Archaea

    Energy Technology Data Exchange (ETDEWEB)

    Luthey-Schulten, Zaida [Univ. of Illinois, Urbana-Champaign, IL (United States). Dept. of Chemistry; Carl R. Woese Inst. for Genomic Biology

    2017-01-04

    The methanogenic archaea, anaerobic microbes that convert CO2 and H2 and/or other small organic fermentation products into methane, play an unusually large role in the global carbon cycle. As they perform the final step in the anaerobic breakdown of biomass, methanogens are a biogenic source of an estimated one billion tons methane each year. Depending on the location, produced methane can be considered as either a greenhouse gas (agricultural byproduct), sequestered carbon storage (methane hydrate deposits), or a potential energy source (organic wastewater treatment). These microbes therefore represent an important target for biotechnology applications. Computational models of methanogens with predictive power are useful aids in the adaptation of methanogenic systems, but need to connect processes of wide-ranging time and length scales. In this project, we developed several computational methodologies for modeling the dynamic behavior of entire cells that connects stochastic reaction-diffusion dynamics of individual biochemical pathways with genome-scale modeling of metabolic networks. While each of these techniques were in the realm of well-defined computational methods, here we integrated them to develop several entirely new approaches to systems biology. The first scientific aim of the project was to model how noise in a biochemical pathway propagates into cellular phenotypes. Genetic circuits have been optimized by evolution to regulate molecular processes despite stochastic noise, but the effect of such noise on a cellular biochemical networks is currently unknown. An integrated stochastic/systems model of Escherichia coli species was created to analyze how noise in protein expression gives—and therefore noise in metabolic fluxes—gives rise to multiple cellular phenotype in isogenic population. After the initial work developing and validating methods that allow characterization of the heterogeneity in the model organism E. coli, the project shifted toward

  15. Anaerobes in bacterial vaginosis

    Directory of Open Access Journals (Sweden)

    Aggarwal A

    2003-01-01

    Full Text Available Four hundred high vaginal swabs were taken from patients attending gynaecology and obstetrics department of Govt. medical college, Amritsar. The patients were divided into four groups i.e. women in pregnancy (Group I, in labour/post partum (Group II, with abnormal vaginal discharge or bacterial vaginosis (Group III and asymptomatic women as control (Group IV. Anaerobic culture of vaginal swabs revealed that out of 400 cases, 212(53% were culture positive. Maximum isolation of anaerobes was in group III (84% followed by group II (56%, group I (36% and control group (15%. Gram positive anaerobes (69.2% out numbered gram negatives (30.8%. Among various isolates Peptostreptococcus spp. and Bacteroides spp. were predominant.

  16. Evolution of microorganisms in thermophilic-dry anaerobic digestion.

    Science.gov (United States)

    Montero, B; Garcia-Morales, J L; Sales, D; Solera, R

    2008-05-01

    Microbial population dynamics were studied during the start-up and stabilization periods in thermophilic-dry anaerobic digestion at lab-scale. The experimental protocol was defined to quantify Eubacteria and Archaea using Fluorescent in situ hybridization (FISH) in a continuously stirred tank reactor (CSTR), without recycling solids. The reactor was subjected to a programme of steady-state operation over a range of the retention times from 40 to 25 days, with an organic loading rate between 4.42 and 7.50 kg volatile solid/m3/day. Changes in microbial concentrations were linked to traditional performance parameters such as biogas production and VS removal. The relations of Eubacteria:Archaea and H2-utilising methanogens:acetate-utilising methanogens were 88:12 and 11:1, respectively, during start-up stage. Hydrogenotrophic methanogens, although important in the initial phase of the reactor start-up, were displaced by acetoclastic methanogens at steady-state, thus their relation were 7:32, respectively. The methane yield coefficient, the methane content in the biogas and VS removal were stabilized around 0.30 LCH4/gCOD, 50% and 80%, respectively. Methanogenic population correlated well with performance measurements.

  17. Anaerobic Ammonium-Oxidizing Bacteria: Unique Microorganisms with Exceptional Properties

    Science.gov (United States)

    Jetten, Mike S. M.

    2012-01-01

    Summary: Anaerobic ammonium-oxidizing (anammox) bacteria defy many microbiological concepts and share numerous properties with both eukaryotes and archaea. Among their most intriguing characteristics are their compartmentalized cell plan and archaeon-like cell wall. Here we review our current knowledge about anammox cell biology. The anammox cell is divided into three separate compartments by bilayer membranes. The anammox cell consists of (from outside to inside) the cell wall, paryphoplasm, riboplasm, and anammoxosome. Not much is known about the composition or function of both the anammox cell wall and the paryphoplasm compartment. The cell wall is proposed to be proteinaceous and to lack both peptidoglycan and an outer membrane typical of Gram-negative bacteria. The function of the paryphoplasm is unknown, but it contains the cell division ring. The riboplasm resembles the standard cytoplasmic compartment of other bacteria; it contains ribosomes and the nucleoid. The anammoxosome occupies most of the cell volume and is a so-called “prokaryotic organelle” analogous to the eukaryotic mitochondrion. This is the site where the anammox reaction takes place, coupled over the curved anammoxosome membrane, possibly giving rise to a proton motive force and subsequent ATP synthesis. With these unique properties, anammox bacteria are food for thought concerning the early evolution of the domains Bacteria, Archaea, and Eukarya. PMID:22933561

  18. Terminal processes in the anaerobic degradation of an algal-bacterial mat in a high-sulfate hot spring

    International Nuclear Information System (INIS)

    Ward, D.M.; Olson, G.J.

    1980-01-01

    The algal-bacterial mat of a high-sulfate hot spring (Bath Lake) provided an environment in which to compare terminal processes involved in anaerobic decomposition. Sulfate reduction was found to dominate methane production, as indicated by comparison of initial electron flow through the two processes, rapid conversion of [2- 14 C]acetate to 14 CO 2 and not to 14 CH 4 , and the lack of rapid reduction of NaH 14 CO 3 to 14 CH 4 . Sulfate reduction was the dominant process at all depth intervals, but a marked decrease of sulfate reduction and sulfate-reducing bacteria was observed with depth. Concurrent methanogenesis was indicated by the presence of viable methanogenic bacteria and very low but detectable rates of methane production. A marked increase in methane production was observed after sulfate depletion despite high concentrations of sulfide (>1.25 mM), indicating that methanogenesis was not inhibited by sulfide in the natural environment. Although a sulfate minimum and sulfide maximum occurred in the region of maximal sulfate reduction, the absence of sulfate depletion in interstitial water suggests that methanogenesis is always severely limited in Bath Lake sediments. Low initial methanogenesis was not due to anaerobic methane oxidation

  19. Perspectives for anaerobic digestion

    DEFF Research Database (Denmark)

    Ahring, Birgitte Kiær

    2003-01-01

    The modern society generates large amounts of waste that represent a tremendous threat to the environment and human and animal health. To prevent and control this, a range of different waste treatment and disposal methods are used. The choice of method must always be based on maximum safety...... to the soil. Anaerobic digestion (AD) is one way of achieving this goal and it will furthermore, reduce energy consumption or may even be net energy producing. This chapter aims at provide a basic understanding of the world in which anaerobic digestion is operating today. The newest process developments...

  20. A Novel Type of Polyhedral Viruses Infecting Hyperthermophilic Archaea.

    Science.gov (United States)

    Liu, Ying; Ishino, Sonoko; Ishino, Yoshizumi; Pehau-Arnaudet, Gérard; Krupovic, Mart; Prangishvili, David

    2017-07-01

    Encapsidation of genetic material into polyhedral particles is one of the most common structural solutions employed by viruses infecting hosts in all three domains of life. Here, we describe a new virus of hyperthermophilic archaea, Sulfolobus polyhedral virus 1 (SPV1), which condenses its circular double-stranded DNA genome in a manner not previously observed for other known viruses. The genome complexed with virion proteins is wound up sinusoidally into a spherical coil which is surrounded by an envelope and further encased by an outer polyhedral capsid apparently composed of the 20-kDa virion protein. Lipids selectively acquired from the pool of host lipids are integral constituents of the virion. None of the major virion proteins of SPV1 show similarity to structural proteins of known viruses. However, minor structural proteins, which are predicted to mediate host recognition, are shared with other hyperthermophilic archaeal viruses infecting members of the order Sulfolobales The SPV1 genome consists of 20,222 bp and contains 45 open reading frames, only one-fifth of which could be functionally annotated. IMPORTANCE Viruses infecting hyperthermophilic archaea display a remarkable morphological diversity, often presenting architectural solutions not employed by known viruses of bacteria and eukaryotes. Here we present the isolation and characterization of Sulfolobus polyhedral virus 1, which condenses its genome into a unique spherical coil. Due to the original genomic and architectural features of SPV1, the virus should be considered a representative of a new viral family, "Portogloboviridae." Copyright © 2017 American Society for Microbiology.

  1. 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

  2. Proteasomes in the archaea: from structure to function.

    Science.gov (United States)

    Maupin-Furlow, J A; Wilson, H L; Kaczowka, S J; Ou, M S

    2000-09-01

    Survival of cells is critically dependent on their ability to rapidly adapt to changes in the natural environment no matter how 'extreme'the habitat. An interplay between protein folding and hydrolysis is emerging as a central mechanism for stress survival and proper cell function. In eucaryotic cells, most proteins destined for destruction are covalently modified by the ubiquitin-system and then degraded in an energy-dependent mechanism by the 26S proteasome, a multicatalytic protease. The 26S proteasome is composed of a 20S proteolytic core and 19S cap (PA700) regulator which includes six AAA+ ATPase subunits. Related AAA+ proteins and 20S proteasomes are found in the archaea and Gram positive actinomycetes. In general, 20S proteasomes form a barrel-shaped nanocompartment with narrow openings which isolate rather non-specific proteolytic active-sites to the interior of the cylinder and away from interaction with cytosolic proteins. The proteasome-associated AAA+ proteins are predicted to form ring-like structures which unfold substrate proteins for entry into the central proteolytic 20S chamber resulting in an energy-dependent and processive destruction of the protein. Detailed biochemical and biophysical analysis as well as identification of proteasomes in archaea with developed genetic tools are providing a foundation for understanding the biological role of the proteasome in these unusual organisms.

  3. CRISPR loci reveal networks of gene exchange in archaea.

    Science.gov (United States)

    Brodt, Avital; Lurie-Weinberger, Mor N; Gophna, Uri

    2011-12-21

    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. 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. 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. This article was reviewed by: Profs. W. Ford Doolittle, John van der Oost, Christa Schleper (nominated by board member Prof. J Peter Gogarten).

  4. The impact of genomics on research in diversity and evolution of archaea.

    Science.gov (United States)

    Mardanov, A V; Ravin, N V

    2012-08-01

    Since the definition of archaea as a separate domain of life along with bacteria and eukaryotes, they have become one of the most interesting objects of modern microbiology, molecular biology, and biochemistry. Sequencing and analysis of archaeal genomes were especially important for studies on archaea because of a limited availability of genetic tools for the majority of these microorganisms and problems associated with their cultivation. Fifteen years since the publication of the first genome of an archaeon, more than one hundred complete genome sequences of representatives of different phylogenetic groups have been determined. Analysis of these genomes has expanded our knowledge of biology of archaea, their diversity and evolution, and allowed identification and characterization of new deep phylogenetic lineages of archaea. The development of genome technologies has allowed sequencing the genomes of uncultivated archaea directly from enrichment cultures, metagenomic samples, and even from single cells. Insights have been gained into the evolution of key biochemical processes in archaea, such as cell division and DNA replication, the role of horizontal gene transfer in the evolution of archaea, and new relationships between archaea and eukaryotes have been revealed.

  5. 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.

  6. Bio digester : anaerobic methanogenesis

    NARCIS (Netherlands)

    Bullema, Marten; Hulzen, Hans; Keizer, Melvin; Pruisscher, Gerlof; Smint, Martin; Vincent, Helene

    2014-01-01

    As part of the theme 13 and 14, our group have to realize a project in the field of the renewable energy. This project consist of the design of a bio-digester for the canteen of Zernikeplein. Gert Hofstede is our client. To produce energy, a bio-digester uses the anaerobic digestion, which is made

  7. Anaerobic biotransformation of estrogens

    International Nuclear Information System (INIS)

    Czajka, Cynthia P.; Londry, Kathleen L.

    2006-01-01

    Estrogens are important environmental contaminants that disrupt endocrine systems and feminize male fish. We investigated the potential for anaerobic biodegradation of the estrogens 17-α-ethynylestradiol (EE2) and 17-β-estradiol (E2) in order to understand their fate in aquatic and terrestrial environments. Cultures were established using lake water and sediment under methanogenic, sulfate-, iron-, and nitrate-reducing conditions. Anaerobic degradation of EE2 (added at 5 mg/L) was not observed in multiple trials over long incubation periods (over three years). E2 (added at 5 mg/L) was transformed to estrone (E1) under all four anaerobic conditions (99-176 μg L -1 day -1 ), but the extent of conversion was different for each electron acceptor. The oxidation of E2 to E1 was not inhibited by E1. Under some conditions, reversible inter-conversion of E2 and E1 was observed, and the final steady state concentration of E2 depended on the electron-accepting condition but was independent of the total amount of estrogens added. In addition, racemization occurred and E1 was also transformed to 17-α-estradiol under all but nitrate-reducing conditions. Although E2 could be readily transformed to E1 and in many cases 17-α-estradiol under anaerobic conditions, the complete degradation of estrogens under these conditions was minimal, suggesting that they would accumulate in anoxic environments

  8. 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.

  9. Anaerobic treatment in Italy

    Energy Technology Data Exchange (ETDEWEB)

    Del Borghi, M; Solisio, C; Ferrailo, G

    1984-02-01

    In Italy, environmental protection and energy conservation have become very important since the increase in oil prices. The law requires that all waste waters have a B.O.D. of 40 mg/l by 1986 so there has been an expansion of purification plants since 1976, using anaerobic digestion. The report deals with the current state of anaerobic treatment in Italy with particular reference to (1) animal wastes. In intensive holdings, anaerobic digestion leads to a decrease in pollution and an increase in biogas generation which can be used to cover the energy demand of the process. The factors which influence the builders of digestors for farms are considered. (2) Non toxic industrial wastes. These are the waste waters emanating from the meat packing, brewing, pharmaceutical and chemical industries. Particular reference is made to the distillery plants using anaerobic treatment prior to aerobic digestion. (3) Urban wastes. The advantages and the disadvantages are considered and further research and development is recommended. 20 references.

  10. Anaerobic biological treatment

    International Nuclear Information System (INIS)

    Speece, R.E.

    1990-01-01

    The Enso-Fenox process has been very successfully used to remove chlorinated phenolic compounds from pulp bleaching effluents. It is a two-stage anaerobic/aerobic process consisting of a nonmethanogenic anaerobic fluidized bed followed by a trickling filter. Studies have been conducted on reductive dechlorination of chlorinated aromatic compounds under anaerobic conditions with chlorinated phenols as the sole carbon and energy source. Approximately 40% of the added chlorophenols was converted to CH 4 and CO 2 . Substrate loading rates were 20 mg/L/d at hydraulic detention times of 2-4 days with 90% substrate conversion efficiency. Reductive dechlorination of mono, di-, tri-, and pentachlorophenols has been demonstrated in anaerobic sewage sludge. The following constituents were tested in the laboratory at their approximate concentrations in coal conversion wastewater (CCWW) and were anaerobically degraded in serum bottles: 1,000 mg/L phenol; 500 mg/L resorcinol; 1,000 mg/L benzoic acid; 500 mg/L p-cresol; 200 mg/L pyridine; 2,000 mg/L benzoic acid; 250 mg/L 40 methylcatechol; 500 mg/L 4-ethylpyridine; and 2,000 mg/L hexanoic acid. A petrochemical may initially exhibit toxicity to an unacclimated population of methane-fermenting bacteria, but with acclimation the toxicity may be greatly reduced or disappear. In addition, the microorganisms may develop the capacity to actually degrade compounds which showed initial toxicity. Since biomass digestion requires a complete consortium of bacteria, it is relevant to study the effect of a given process as well as to individual steps within the process. A toxicant can inhibit the rate-limiting step and/or change the step that is rate-limiting. Both manifestations of toxicity can severely affect the overall process

  11. Mrp Antiporters Have Important Roles in Diverse Bacteria and Archaea.

    Science.gov (United States)

    Ito, Masahiro; Morino, Masato; Krulwich, Terry A

    2017-01-01

    Mrp (Multiple resistance and pH) antiporter was identified as a gene complementing an alkaline-sensitive mutant strain of alkaliphilic Bacillus halodurans C-125 in 1990. At that time, there was no example of a multi-subunit type Na + /H + antiporter comprising six or seven hydrophobic proteins, and it was newly designated as the monovalent cation: proton antiporter-3 (CPA3) family in the classification of transporters. The Mrp antiporter is broadly distributed among bacteria and archaea, not only in alkaliphiles. Generally, all Mrp subunits, mrpA-G , are required for enzymatic activity. Two exceptions are Mrp from the archaea Methanosarcina acetivorans and the eubacteria Natranaerobius thermophilus , which are reported to sustain Na + /H + antiport activity with the MrpA subunit alone. Two large subunits of the Mrp antiporter, MrpA and MrpD, are homologous to membrane-embedded subunits of the respiratory chain complex I, NuoL, NuoM, and NuoN, and the small subunit MrpC has homology with NuoK. The functions of the Mrp antiporter include sodium tolerance and pH homeostasis in an alkaline environment, nitrogen fixation in Schizolobium meliloti , bile salt tolerance in Bacillus subtilis and Vibrio cholerae , arsenic oxidation in Agrobacterium tumefaciens , pathogenesis in Pseudomonas aeruginosa and Staphylococcus aureus , and the conversion of energy involved in metabolism and hydrogen production in archaea. In addition, some Mrp antiporters transport K + and Ca 2+ instead of Na + , depending on the environmental conditions. Recently, the molecular structure of the respiratory chain complex I has been elucidated by others, and details of the mechanism by which it transports protons are being clarified. Based on this, several hypotheses concerning the substrate transport mechanism in the Mrp antiporter have been proposed. The MrpA and MrpD subunits, which are homologous to the proton transport subunit of complex I, are involved in the transport of protons and their

  12. 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

  13. 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

  14. 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. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

    International Nuclear Information System (INIS)

    Tong, Hui; Liu, Chengshuai; Li, Fangbai; Luo, Chunling; Chen, Manjia; Hu, Min

    2015-01-01

    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 13 CH 4 and 13 CO 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

  16. 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.

  17. Diversity of halophilic archaea from six hypersaline environments in Turkey.

    Science.gov (United States)

    Ozcan, Birgul; Ozcengiz, Gulay; Coleri, Arzu; Cokmus, Cumhur

    2007-06-01

    The diversity of archaeal strains from six hypersaline environments in Turkey was analyzed by comparing their phenotypic characteristics and 16S rDNA sequences. Thirty-three isolates were characterized in terms of their phenotypic properties including morphological and biochemical characteristics, susceptibility to different antibiotics, and total lipid and plasmid contents, and finally compared by 16S rDNA gene sequences. The results showed that all isolates belong to the family Halobacteriaceae. Phylogenetic analyses using approximately 1,388 bp comparisions of 16S rDNA sequences demonstrated that all isolates clustered closely to species belonging to 9 genera, namely Halorubrum (8 isolates), Natrinema (5 isolates), Haloarcula (4 isolates), Natronococcus (4 isolates), Natrialba (4 isolates), Haloferax (3 isolates), Haloterrigena (3 isolates), Halalkalicoccus (1 isolate), and Halomicrobium (1 isolate). The results revealed a high diversity among the isolated halophilic strains and indicated that some of these strains constitute new taxa of extremely halophilic archaea.

  18. Evolvability of thermophilic proteins from archaea and bacteria.

    Science.gov (United States)

    Takano, Kazufumi; Aoi, Atsushi; Koga, Yuichi; Kanaya, Shigenori

    2013-07-16

    Proteins from thermophiles possess high thermostability. The stabilization mechanisms differ between archaeal and bacterial proteins, whereby archaeal proteins are mainly stabilized via hydrophobic interactions and bacterial proteins by ion pairs. High stability is an important factor in promoting protein evolution, but the precise means by which different stabilization mechanisms affect the evolution process remain unclear. In this study, we investigated a random mutational drift of esterases from thermophilic archaea and bacteria at high temperatures. Our results indicate that mutations in archaeal proteins lead to improved function with no loss of stability, while mutant bacterial proteins are largely destabilized with decreased activity at high temperatures. On the basis of these findings, we suggest that archaeal proteins possess higher "evolvability" than bacterial proteins under temperature selection and are additionally able to evolve into eukaryotic proteins.

  19. Identification of a mismatch-specific endonuclease in hyperthermophilic Archaea.

    Science.gov (United States)

    Ishino, Sonoko; Nishi, Yuki; Oda, Soichiro; Uemori, Takashi; Sagara, Takehiro; Takatsu, Nariaki; Yamagami, Takeshi; Shirai, Tsuyoshi; Ishino, Yoshizumi

    2016-04-20

    The common mismatch repair system processed by MutS and MutL and their homologs was identified in Bacteria and Eukarya. However, no evidence of a functional MutS/L homolog has been reported for archaeal organisms, and it is not known whether the mismatch repair system is conserved in Archaea. Here, we describe an endonuclease that cleaves double-stranded DNA containing a mismatched base pair, from the hyperthermophilic archaeon Pyrococcus furiosus The corresponding gene revealed that the activity originates from PF0012, and we named this enzyme Endonuclease MS (EndoMS) as the mismatch-specific Endonuclease. The sequence similarity suggested that EndoMS is the ortholog of NucS isolated from Pyrococcus abyssi, published previously. Biochemical characterizations of the EndoMS homolog from Thermococcus kodakarensis clearly showed that EndoMS specifically cleaves both strands of double-stranded DNA into 5'-protruding forms, with the mismatched base pair in the central position. EndoMS cleaves G/T, G/G, T/T, T/C and A/G mismatches, with a more preference for G/T, G/G and T/T, but has very little or no effect on C/C, A/C and A/A mismatches. The discovery of this endonuclease suggests the existence of a novel mismatch repair process, initiated by the double-strand break generated by the EndoMS endonuclease, in Archaea and some Bacteria. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. 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.

  1. The Non-Coding Regulatory RNA Revolution in Archaea

    Directory of Open Access Journals (Sweden)

    Diego Rivera Gelsinger

    2018-03-01

    Full Text Available Small non-coding RNAs (sRNAs are ubiquitously found in the three domains of life playing large-scale roles in gene regulation, transposable element silencing and defense against foreign elements. While a substantial body of experimental work has been done to uncover function of sRNAs in Bacteria and Eukarya, the functional roles of sRNAs in Archaea are still poorly understood. Recently, high throughput studies using RNA-sequencing revealed that sRNAs are broadly expressed in the Archaea, comprising thousands of transcripts within the transcriptome during non-challenged and stressed conditions. Antisense sRNAs, which overlap a portion of a gene on the opposite strand (cis-acting, are the most abundantly expressed non-coding RNAs and they can be classified based on their binding patterns to mRNAs (3′ untranslated region (UTR, 5′ UTR, CDS-binding. These antisense sRNAs target many genes and pathways, suggesting extensive roles in gene regulation. Intergenic sRNAs are less abundantly expressed and their targets are difficult to find because of a lack of complete overlap between sRNAs and target mRNAs (trans-acting. While many sRNAs have been validated experimentally, a regulatory role has only been reported for very few of them. Further work is needed to elucidate sRNA-RNA binding mechanisms, the molecular determinants of sRNA-mediated regulation, whether protein components are involved and how sRNAs integrate with complex regulatory networks.

  2. 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.

  3. High rates of anaerobic oxidation of methane, ethane and propane coupled to thiosulphate reduction.

    Science.gov (United States)

    Suarez-Zuluaga, Diego A; Weijma, Jan; Timmers, Peer H A; Buisman, Cees J N

    2015-03-01

    Anaerobic methane oxidation coupled to sulphate reduction and the use of ethane and propane as electron donors by sulphate-reducing bacteria represent new opportunities for the treatment of streams contaminated with sulphur oxyanions. However, growth of microbial sulphate-reducing populations with methane, propane or butane is extremely slow, which hampers research and development of bioprocesses based on these conversions. Thermodynamic calculations indicate that the growth rate with possible alternative terminal electron acceptors such as thiosulphate and elemental sulphur may be higher, which would facilitate future research. Here, we investigate the use of these electron acceptors for oxidation of methane, ethane and propane, with marine sediment as inoculum. Mixed marine sediments originating from Aarhus Bay (Denmark) and Eckernförde Bay (Germany) were cultivated anaerobically at a pH between 7.2 and 7.8 and a temperature of 15 °C in the presence of methane, ethane and propane and various sulphur electron acceptors. The sulphide production rates in the conditions with methane, ethane and propane with sulphate were respectively 2.3, 2.2 and 1.8 μmol S L(-1) day(-1). For sulphur, no reduction was demonstrated. For thiosulphate, the sulphide production rates were up to 50 times higher compared to those of sulphate, with 86.2, 90.7 and 108.1 μmol S L(-1) day(-1) for methane, ethane and propane respectively. This sulphide production was partly due to disproportionation, 50 % for ethane but only 7 and 14 % for methane and propane respectively. The oxidation of the alkanes in the presence of thiosulphate was confirmed by carbon dioxide production. This is, to our knowledge, the first report of thiosulphate use as electron acceptor with ethane and propane as electron donors. Additionally, these results indicate that thiosulphate is a promising electron acceptor to increase start-up rates for sulphate-reducing bioprocesses coupled to short-chain alkane oxidation.

  4. 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.

  5. Early anaerobic metabolisms

    DEFF Research Database (Denmark)

    Canfield, Donald Eugene; Rosing, Minik T; Bjerrum, Christian

    2006-01-01

    probably driven by the cycling of H2 and Fe2+ through primary production conducted by anoxygenic phototrophs. Interesting and dynamic ecosystems would have also been driven by the microbial cycling of sulphur and nitrogen species, but their activity levels were probably not so great. Despite the diversity......Before the advent of oxygenic photosynthesis, the biosphere was driven by anaerobic metabolisms. We catalogue and quantify the source strengths of the most probable electron donors and electron acceptors that would have been available to fuel early-Earth ecosystems. The most active ecosystems were...... of potential early ecosystems, rates of primary production in the early-Earth anaerobic biosphere were probably well below those rates observed in the marine environment. We shift our attention to the Earth environment at 3.8Gyr ago, where the earliest marine sediments are preserved. We calculate, consistent...

  6. Anaerobic azo dye reduction

    OpenAIRE

    Zee, van der, F.P.

    2002-01-01

    Azo dyes, aromatic moieties linked together by azo (-N=N-) chromophores, represent the largest class of dyes used in textile-processing and other industries. The release of these compounds into the environment is undesirable, not only because of their colour, but also because many azo dyes and their breakdown products are toxic and/or mutagenic to life. To remove azo dyes from wastewater, a biological treatment strategy based on anaerobic reduction of the azo dye...

  7. 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.

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

    KAUST Repository

    Meulepas, Roel J W

    2010-05-06

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

  9. 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...

  10. [Anaerobic bacteria isolated from patients with suspected anaerobic infections].

    Science.gov (United States)

    Ercis, Serpil; Tunçkanat, Ferda; Hasçelik, Gülşen

    2005-10-01

    The study involved 394 clinical samples sent to the Clinical Microbiology Laboratory of Hacettepe University Adult Hospital between January 1997 and May 2004 for anaerobic cultivation. Since multiple cultures from the same clinical samples of the same patient were excluded, the study was carried on 367 samples. The anaerobic cultures were performed in anaerobic jar using AnaeroGen kits (Oxoid, Basingstoke, U.K.) or GENbox (bioMérieux, Lyon, France). The isolates were identified by both classical methods and "BBL Crystal System" (Becton Dickinson, U.S.A.). While no growth was detected in 120 (32.7%) of the clinical samples studied, in 144 samples (39.2%) only aerobes, in 28 (7.6%) only anaerobes and in 75 (20.5%) of the samples both aerobes and anaerobes were isolated. The number of the anaerobic isolates was 217 from 103 samples with anaerobic growth. Of these 103 samples 15 showed single bacterial growth whereas in 88 samples multiple bacterial isolates were detected. Anaerobic isolates consisted of 92 Gram negative bacilli (Bacteroides spp. 50, Prevotella spp. 14, Porphyromonas spp. 10, Fusobacterium spp. 7, Tisierella spp. 2, unidentified 9), 57 Gram positive bacilli (Clostridium spp.17, Propionibacterium spp. 16, Lactobacillus spp. 8, Actinomyces spp. 5, Eubacterium spp. 2, Bifidobacterium adolescentis 1, Mobiluncus mulieris 1, unidentified nonspore forming rods 7), 61 Gram positive cocci (anaerobic cocci 44, microaerophilic cocci 17), and 7 Gram negative cocci (Veillonella spp.). In conclusion, in the samples studied with prediagnosis of anaerobic infection, Bacteroides spp. (23%) were the most common bacteria followed by anaerobic Gram positive cocci (20.3%) and Clostridium spp (7.8%).

  11. Seeking key microorganisms for enhancing methane production in anaerobic digestion of waste sewage sludge.

    Science.gov (United States)

    Mustapha, Nurul Asyifah; Hu, Anyi; Yu, Chang-Ping; Sharuddin, Siti Suhailah; Ramli, Norhayati; Shirai, Yoshihito; Maeda, Toshinari

    2018-04-25

    Efficient approaches for the utilization of waste sewage sludge have been widely studied. One of them is to use it for the bioenergy production, specifically methane gas which is well-known to be driven by complex bacterial interactions during the anaerobic digestion process. Therefore, it is important to understand not only microorganisms for producing methane but also those for controlling or regulating the process. In this study, azithromycin analogs belonging to macrolide, ketolide, and lincosamide groups were applied to investigate the mechanisms and dynamics of bacterial community in waste sewage sludge for methane production. The stages of anaerobic digestion process were evaluated by measuring the production of intermediate substrates, such as protease activity, organic acids, the quantification of bacteria and archaea, and its community dynamics. All azithromycin analogs used in this study achieved a high methane production compared to the control sample without any antibiotic due to the efficient hydrolysis process and the presence of important fermentative bacteria and archaea responsible in the methanogenesis stage. The key microorganisms contributing to the methane production may be Clostridia, Cladilinea, Planctomycetes, and Alphaproteobacteria as an accelerator whereas Nitrosomonadaceae and Nitrospiraceae may be suppressors for methane production. In conclusion, the utilization of antibiotic analogs of macrolide, ketolide, and lincosamide groups has a promising ability in finding the essential microorganisms and improving the methane production using waste sewage sludge.

  12. New Lipids From Cultured Archaea and Environmental Samples

    Science.gov (United States)

    Summons, R. E.; Meyer-Dombard, D. R.; Bradley, A. S.; Hebting, Y.; Jahnke, L. L.; Embaye, T.; Orphan, V. J.

    2006-12-01

    The intact polar lipids of Archaea comprise cores with isoprenoid hydrocarbon chains with 20, 25 or 40 carbon atoms linked through ether bonds to glycerol. These cores can take the form of diethers or membrane- spanning tetraethers. Together with their wide array of polar head groups, these compounds are structurally diverse and potentially very useful as taxonomic markers for making assessments of microbial diversity independently of genomic approaches. Furthermore, the recalcitrant hydrocarbon chains of these lipids are the only really effective means to identify the presence of Archaea in ancient sedimentary environments. The advent of new LC-MS methods has enabled ready identification and quantification of intact polar lipids in cultures and environmental samples based on comparisons with appropriate standard compounds [1, 2]. However, these LC-MS analyses of intact lipids have also revealed the presence of additional compounds and it is likely that many of these represent chemical structures that are new to science. Elucidating these structures is a major analytical challenge because, generally, only minute amounts of material available for chemical characterization. In order to study these potentially new structures, one layer of information can be obtained by chemical degradation to remove and identify the polar head groups [2]. Cleavage of the ether bonds releases the hydrocarbon chains for their further characterization. One class of core lipids, the 3-hydroxyarchaeols, escaped detection for many years because strong acid treatments in the analysis protocols had destroyed hydroxyl-containing isoprenoid chains. We have now re-examined the lipids of a thermophilic methanogen, M. thermolithotrophicus, using mild procedures and avoiding strong acids. As well as the known compounds archaeol, sn-2-hydroxyarchaeol and sn-3-hydroxyarchaeol, we encountered dihydroxyarchaeol. Moreover, the hydroxylated archaeols were found to exist as a very complex mixture of

  13. Design and Synthesis of Archaea-Inspired Tetraether Lipids

    Science.gov (United States)

    Koyanagi, Takaoki

    Maintaining the correct ion homeostasis across membranes is a major challenge in both nature and artificial systems. Archaea, have evolved to solve membrane permeability problems to survive in extreme environments by incorporating unique structural features found in their lipid. Specifically, inclusion of phytanyl side chains, ether glycerol linkages, tethering of lipids, cycloalkanes, and different polar lipid headgroups into their lipid membrane are believed to contribute to membrane stability. We sought to gain a better understanding of the functional benefits attributed to these structural features to membrane stability to design a new class of synthetic Archaea inspired lipid membranes that can be used to overcome limitations (i.e. unstable in serum environment, high background leakage, and prone to hydrolysis) found in current lipid based technologies. Leakage experiments revealed liposomes made from GMGTPC (glycerol monoalkyl glycerol tetraether lipid with phosphatidylcholine headgroup) demonstrated a two order magnitude reduction in membrane leakage to small ions when compared with liposomes made from EggPC. Additionally, liposomes composed of GMGTPC-CH (cyclohexane integrated) lipid displayed an additional 40% decrease in membrane leakage to small ions when compared with liposomes made from GMGTPC lipids. Furthermore, leakage experiments revealed a higher degree of tolerance to headgroup modifications to membrane leakage for liposomes made from GMGT lipid analogs when compared with liposomes made from POPC. After designing an optimal tetraether lipid scaffold that incorporates key Archaeal structural features for membrane leakage, we explored to integrate strategies employed by eukaryotes to improve membrane properties (i.e. addition of cholesterol). Liposomes made from the hybrid lipid, GcGTPC-CH, displayed a five-fold decrease in membrane leakage when compared with liposomes made from GMGTPC-CH, while maintaining functional membrane properties similar to

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

    Science.gov (United States)

    Rodríguez, Elisa; Lopes, Alexandre; Fdz-Polanco, María; Stams, Alfons J M; García-Encina, Pedro A

    2012-03-01

    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 focused on the competitive and syntrophic interactions between the different microbial groups at varying influent substrate to sulfate ratios of 8, 4, and 2 and anaerobic or micro-aerobic conditions. Acetogens detected along the anaerobic phases at substrate to sulfate ratios of 8 and 4 seemed to be mainly involved in the fermentation of glucose and betaine, but they were substituted by other sugar or betaine degraders after oxygen application. Typical fatty acid degraders that grow in syntrophy with methanogens were not detected during the entire reactor run. Likely, sugar and betaine degraders outnumbered them in the DGGE analysis. The detected sulfate-reducing bacteria (SRB) belonged to the hydrogen-utilizing Desulfovibrio. The introduction of oxygen led to the formation of elemental sulfur (S(0)) and probably other sulfur compounds by sulfide-oxidizing bacteria (γ-Proteobacteria). It is likely that the sulfur intermediates produced from sulfide oxidation were used by SRB and other microorganisms as electron acceptors, as was supported by the detection of the sulfur respiring Wolinella succinogenes. Within the Archaea population, members of Methanomethylovorans and Methanosaeta were detected throughout the entire reactor operation. Hydrogenotrophic methanogens mainly belonging to the genus Methanobacterium were detected at the highest substrate to sulfate ratio but rapidly disappeared by increasing the sulfate concentration.

  15. The Peculiar Glycolytic Pathway in Hyperthermophylic Archaea : Understanding Its Whims by Experimentation In Silico

    NARCIS (Netherlands)

    Zhang, Y.; Kouril, T.; Snoep, J.L.; Siebers, B.; Barberis, M.; Westerhoff, H.V.

    2017-01-01

    Mathematical models are key to systems biology where they typically describe the topology and dynamics of biological networks, listing biochemical entities and their relationships with one another. Some (hyper)thermophilic Archaea contain an enzyme, called non-phosphorylating

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

    NARCIS (Netherlands)

    Rensen, Elena Ilka; Mochizuki, Tomohiro; Quemin, Emmanuelle; Schouten, S.; Krupovic, Mart; Prangishvili, David

    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.

  17. Genome-wide identification of SF1 and SF2 helicases from archaea.

    Science.gov (United States)

    Chamieh, Hala; Ibrahim, Hiba; Kozah, Juliana

    2016-01-15

    Archaea microorganisms have long been used as model organisms for the study of protein molecular machines. Archaeal proteins are particularly appealing to study since archaea, even though prokaryotic, possess eukaryotic-like cellular processes. Super Family I (SF1) and Super Family II (SF2) helicase families have been studied in many model organisms, little is known about their presence and distribution in archaea. We performed an exhaustive search of homologs of SF1 and SF2 helicase proteins in 95 complete archaeal genomes. In the present study, we identified the complete sets of SF1 and SF2 helicases in archaea. Comparative analysis between archaea, human and the bacteria E. coli SF1 and SF2 helicases, resulted in the identification of seven helicase families conserved among representatives of the domains of life. This analysis suggests that these helicase families are highly conserved throughout evolution. We highlight the conserved motifs of each family and characteristic domains of the detected families. Distribution of SF1/SF2 families show that Ski2-like, Lhr, Sfth and Rad3-like helicases are ubiquitous among archaeal genomes while the other families are specific to certain archaeal groups. We also report the presence of a novel SF2 helicase specific to archaea domain named Archaea Specific Helicase (ASH). Phylogenetic analysis indicated that ASH has evolved in Euryarchaeota and is evolutionary related to the Ski2-like family with specific characteristic domains. Our study provides the first exhaustive analysis of SF1 and SF2 helicases from archaea. It expands the variety of SF1 and SF2 archaeal helicases known to exist to date and provides a starting point for new biochemical and genetic studies needed to validate their biological functions. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. 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....

  19. Insights into Head-Tailed Viruses Infecting Extremely Halophilic Archaea

    Science.gov (United States)

    Pietilä, Maija K.; Laurinmäki, Pasi; Russell, Daniel A.; Ko, Ching-Chung; Jacobs-Sera, Deborah; Butcher, Sarah J.

    2013-01-01

    Extremophilic archaea, both hyperthermophiles and halophiles, dominate in habitats where rather harsh conditions are encountered. Like all other organisms, archaeal cells are susceptible to viral infections, and to date, about 100 archaeal viruses have been described. Among them, there are extraordinary virion morphologies as well as the common head-tailed viruses. Although approximately half of the isolated archaeal viruses belong to the latter group, no three-dimensional virion structures of these head-tailed viruses are available. Thus, rigorous comparisons with bacteriophages are not yet warranted. In the present study, we determined the genome sequences of two of such viruses of halophiles and solved their capsid structures by cryo-electron microscopy and three-dimensional image reconstruction. We show that these viruses are inactivated, yet remain intact, at low salinity and that their infectivity is regained when high salinity is restored. This enabled us to determine their three-dimensional capsid structures at low salinity to a ∼10-Å resolution. The genetic and structural data showed that both viruses belong to the same T-number class, but one of them has enlarged its capsid to accommodate a larger genome than typically associated with a T=7 capsid by inserting an additional protein into the capsid lattice. PMID:23283946

  20. 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

  1. Patterns of gene flow define species of thermophilic Archaea.

    Directory of Open Access Journals (Sweden)

    Hinsby Cadillo-Quiroz

    2012-02-01

    Full Text Available Despite a growing appreciation of their vast diversity in nature, mechanisms of speciation are poorly understood in Bacteria and Archaea. Here we use high-throughput genome sequencing to identify ongoing speciation in the thermoacidophilic Archaeon Sulfolobus islandicus. Patterns of homologous gene flow among genomes of 12 strains from a single hot spring in Kamchatka, Russia, demonstrate higher levels of gene flow within than between two persistent, coexisting groups, demonstrating that these microorganisms fit the biological species concept. Furthermore, rates of gene flow between two species are decreasing over time in a manner consistent with incipient speciation. Unlike other microorganisms investigated, we do not observe a relationship between genetic divergence and frequency of recombination along a chromosome, or other physical mechanisms that would reduce gene flow between lineages. Each species has its own genetic island encoding unique physiological functions and a unique growth phenotype that may be indicative of ecological specialization. Genetic differentiation between these coexisting groups occurs in large genomic "continents," indicating the topology of genomic divergence during speciation is not uniform and is not associated with a single locus under strong diversifying selection. These data support a model where species do not require physical barriers to gene flow but are maintained by ecological differentiation.

  2. Patterns of gene flow define species of thermophilic Archaea.

    Science.gov (United States)

    Cadillo-Quiroz, Hinsby; Didelot, Xavier; Held, Nicole L; Herrera, Alfa; Darling, Aaron; Reno, Michael L; Krause, David J; Whitaker, Rachel J

    2012-02-01

    Despite a growing appreciation of their vast diversity in nature, mechanisms of speciation are poorly understood in Bacteria and Archaea. Here we use high-throughput genome sequencing to identify ongoing speciation in the thermoacidophilic Archaeon Sulfolobus islandicus. Patterns of homologous gene flow among genomes of 12 strains from a single hot spring in Kamchatka, Russia, demonstrate higher levels of gene flow within than between two persistent, coexisting groups, demonstrating that these microorganisms fit the biological species concept. Furthermore, rates of gene flow between two species are decreasing over time in a manner consistent with incipient speciation. Unlike other microorganisms investigated, we do not observe a relationship between genetic divergence and frequency of recombination along a chromosome, or other physical mechanisms that would reduce gene flow between lineages. Each species has its own genetic island encoding unique physiological functions and a unique growth phenotype that may be indicative of ecological specialization. Genetic differentiation between these coexisting groups occurs in large genomic "continents," indicating the topology of genomic divergence during speciation is not uniform and is not associated with a single locus under strong diversifying selection. These data support a model where species do not require physical barriers to gene flow but are maintained by ecological differentiation.

  3. Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems.

    Science.gov (United States)

    Laskar, Folguni; Das Purkayastha, Sumi; Sen, Aniruddha; Bhattacharya, Mrinal K; Misra, Biswapriya B

    2018-02-01

    About half of the global methane (CH 4 ) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH 4 emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. 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. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  5. 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.

  6. The common ancestor of archaea and eukarya was not an archaeon.

    Science.gov (United States)

    Forterre, Patrick

    2013-01-01

    It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the "prokaryotic" phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other.

  7. The Common Ancestor of Archaea and Eukarya Was Not an Archaeon

    Directory of Open Access Journals (Sweden)

    Patrick Forterre

    2013-01-01

    Full Text Available It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario. I propose that the ancestors of archaea (and bacteria escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the “prokaryotic” phenotype (the thermoreduction hypothesis. Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction could explain why the archaeal and bacterial mobilomes somehow resemble each other.

  8. New perspectives in anaerobic digestion.

    NARCIS (Netherlands)

    Lier, van J.B.; Tilche, A.; Ahring, B.K.; Macarie, H.; Moletta, R.; Dohanyos, M.; Hulshoff Pol, L.W.; Lens, P.N.L.; Verstraete, W.

    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

  9. 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.

  10. 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

  11. Soil methane oxidation in a long-term no-tillage system in Southern BrazilOxidação de metano em solo a longo prazo sob plantio direto no Sul do Brasil

    Directory of Open Access Journals (Sweden)

    Cimélio Bayer

    2013-09-01

    Full Text Available Conservation management systems are usually suggested as alternative to restore the soil methane (CH4 oxidation capacity of degraded soils; however, little information is available on tropical and subtropical soils. Our objective was to evaluate the long-term (19 years effect of no-tillage (NT versus conventional tillage (CT management systems on CH4 fluxes in a formerly degraded Acrisol in Southern Brazil. Annual CH4 fluxes of two cropping systems [O/M-black oat (Avena strigosa/maize and V/M-vetch (Vigna sativa/maize] were measured in NT and CT soils. Static chambers were used for air sampling, while chromatography was used for CH4 analysis. Analysis of the historical dataset at this experimental site indicated improvements in soil quality under the NT system, especially in legume-based cropping system (V/M that exhibited the highest annual biomass input. CH4 fluxes ranged from −42 ± 2 to 38 ± 16 μg C m-2 h-1, and annual CH4 emissions ranged from −825 ± 117 (CT V/M to 453 ± 185 g C ha-1 (NT O/M. Thus, the annual CH4 oxidation capacity of the soil was not related to the soil quality produced by the soil management systems. On the basis of our results and published literature, we postulate that conservation management systems improve the methane oxidation and soil quality in distinct soil layers, which result in a slow effect of these management systems on the methane oxidation capacity. Sistemas conservacionistas de manejo de solo são considerados usualmente uma alternativa para restaurar a capacidade de solos agrícolas degradados em oxidar metano (CH4, mas escassa informação é disponível para solos tropicais e subtropicais. O objetivo do presente estudo foi avaliar o efeito de longo prazo (19 anos do plantio direto (PD nos fluxos de CH4 em um Argissolo Vermelho (Classificação Brasileira degradado da região Sul do Brasil, em comparação ao preparo convencional (PC. Fluxos anuais de CH4 do solo foram avaliados nos sistemas PD e

  12. Selected Topics in Anaerobic Bacteriology.

    Science.gov (United States)

    Church, Deirdre L

    2016-08-01

    Alteration in the host microbiome at skin and mucosal surfaces plays a role in the function of the immune system, and may predispose immunocompromised patients to infection. Because obligate anaerobes are the predominant type of bacteria present in humans at skin and mucosal surfaces, immunocompromised patients are at increased risk for serious invasive infection due to anaerobes. Laboratory approaches to the diagnosis of anaerobe infections that occur due to pyogenic, polymicrobial, or toxin-producing organisms are described. The clinical interpretation and limitations of anaerobe recovery from specimens, anaerobe-identification procedures, and antibiotic-susceptibility testing are outlined. Bacteriotherapy following analysis of disruption of the host microbiome has been effective for treatment of refractory or recurrent Clostridium difficile infection, and may become feasible for other conditions in the future.

  13. Respiration of arsenate and selenate by hyperthermophilic archaea.

    Science.gov (United States)

    Huber, R; Sacher, M; Vollmann, A; Huber, H; Rose, D

    2000-10-01

    A novel, strictly anaerobic, hyperthermophilic, facultative organotrophic archaeon was isolated from a hot spring at Pisciarelli Solfatara, Naples, Italy. The rod-shaped cells grew chemolithoautotrophically with carbon dioxide as carbon source, hydrogen as electron donor and arsenate, thiosulfate or elemental sulfur as electron acceptor. H2S was formed from sulfur or thiosulfate, arsenite from arsenate. Organotrophically, the new isolate grew optimally in the presence of an inorganic electron acceptor like sulfur, selenate or arsenate. Cultures, grown on arsenate and thiosulfate or arsenate and L-cysteine, precipitated realgar (As2S2). During growth on selenate, elemental selenium was produced. The G+C content of the DNA was 58.3 mol%. Due to 16S rRNA gene sequence analysis combined with physiological and morphological criteria, the new isolate belongs to the Thermoproteales order. It represents a new species within the genus Pyrobaculum, the type species of which we name Pyrobaculum arsenaticum (type strain PZ6*, DSM 13514, ATCC 700994). Comparative studies with different Pyrobaculum-species showed, that Pyrobaculum aerophilum was also able to grow organotrophically under anaerobic culture conditions in the presence of arsenate, selenate and selenite. During growth on selenite, elemental selenium was formed as final product. In contrast to P. arsenaticum, P. aerophilum could use selenate or arsenate for lithoautotrophic growth with carbon dioxide and hydrogen.

  14. 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.

  15. Anaerobic fungal populations

    International Nuclear Information System (INIS)

    Brookman, J.L.; Nicholson, M.J.

    2005-01-01

    The development of molecular techniques has greatly broadened our view of microbial diversity and enabled a more complete detection and description of microbial communities. The application of these techniques provides a simple means of following community changes, for example, Ishii et al. described transient and more stable inhabitants in another dynamic microbial system, compost. Our present knowledge of anaerobic gut fungal population diversity within the gastrointestinal tract is based upon isolation, cultivation and observations in vivo. It is likely that there are many species yet to be described, some of which may be non-culturable. We have observed a distinct difference in the ease of cultivation between the different genera, for example, Caecomyes isolates are especially difficult to isolate and maintain in vitro, a feature that is likely to result in the under representation of this genera in culture-based enumerations. The anaerobic gut fungi are the only known obligately anaerobic fungi. For the majority of their life cycles, they are found tightly associated with solid digesta in the rumen and/or hindgut. They produce potent fibrolytic enzymes and grow invasively on and into the plant material they are digesting making them important contributors to fibre digestion. This close association with intestinal digesta has made it difficult to accurately determine the amount of fungal biomass present in the rumen, with Orpin suggesting 8% contribution to the total microbial biomass, whereas Rezaeian et al. more recently gave a value of approximately 20%. It is clear that the rumen microbial complement is affected by dietary changes, and that the fungi are more important in digestion in the rumens of animals fed with high-fibre diets. It seems likely that the gut fungi play an important role within the rumen as primary colonizers of plant fibre, and so we are particularly interested in being able to measure the appearance and diversity of fungi on the plant

  16. Arsenic, Anaerobes, and Autotrophy.

    Science.gov (United States)

    Oremland, R. S.

    2008-12-01

    That microbes have resistance to the toxic arsenic oxyanions arsenite [As(III)] and arsenate [As(V)] has been recognized for some time. More recently it was shown that certain prokaryotes can demonstrate As- dependent growth by conserving the energy gained from the aerobic oxidation of As(III) to As(V), or from the reduction of As(V) to As(III) under anaerobic conditions. During the course of our field studies of two alkaline, hypersaline soda lakes (Mono Lake and Searles Lake, CA) we have discovered several new anaerobic chemo- and photo-autotrophic bacteria that can center their energy gain around the redox reactions between As(III) and As(V). Alkalilimnicola ehrlichii, isolated from the water column of Mono Lake is a nitrate-respiring, As(III)-oxidizing chemoautotroph of the gamma-proteobacteria that has a highly flexible metabolism. It can function either as a facultative anaerobe or as a chemo-autotroph, or as a heterotroph (Hoeft et al., 2007). In contrast, strain MLMS-1 of the delta-proteobacteria was also isolated from Mono Lake, but to date is the first example of an obligate As(V)-respirer that is also an obligate chemo-autotroph, gaining its energy via the oxidation of sulfide to sulfate (Hoeft et al., 2004). Strain SLAS-1, isolated from salt-saturated Searles Lake is a member of the Halananerobiales, and can either grow as a heterotroph (lactate e-donor) or chemo- autotroph (sulfide e-donor) while respiring As(V). The fact that it can achieve this feat at salt-saturation (~ 340 g/L) makes it a true extremophile (Oremland et. al., 2005). Finally, strain PHS-1 isolated from a hot spring on Paoha island in Mono Lake is the first example of a photosynthetic bacterium of the gamma- proteobacteria able to link its growth to As(III)-dependent anoxygenic photosynthesis (Kulp et al., 2008). These novel microbes give us new insights into the evolution of arsenic-based metabolism and their role in the biogeochemical cycling of this toxic element. Hoeft, S.E., et

  17. 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.

  18. Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions.

    Science.gov (United States)

    Hubalek, Valerie; Buck, Moritz; Tan, BoonFei; Foght, Julia; Wendeberg, Annelie; Berry, David; Bertilsson, Stefan; Eiler, Alexander

    2017-01-01

    Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH 4 and CO 2 . Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methanogenic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes encode the capacity for fermentation of alkanes facilitated by energy conservation linked to H 2 metabolism. Instead, the presence of inferred lifestyles based on scavenging anabolic products and intermediate fermentation products derived from detrital biomass was a common feature. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H 2 -producing and syntrophic alkane degrader-methanogen partnership. Compared to previous work, our report points to a higher order of complexity in microbial consortia engaged in anaerobic hydrocarbon transformation. IMPORTANCE Microbial interactions between Archaea and Bacteria mediate many important chemical transformations in the biosphere from degrading abundant polymers to synthesis of toxic compounds. Two of the most pressing issues in microbial interactions are how consortia are established and how we can modulate these microbial communities to express desirable functions. Here, we propose that public goods (i.e., metabolites of high energy demand in biosynthesis) facilitate energy conservation for life under energy-limited conditions and determine the assembly and function of the consortia. Our report suggests that an

  19. 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.

  20. Vertical distribution of archaeal communities associated with anaerobic degradation of pentabromodiphenyl ether (BDE-99) in river-based groundwater recharge with reclaimed water.

    Science.gov (United States)

    Yan, Yulin; Ma, Mengsi; Liu, Xiang; Ma, Weifang; Li, Yangyao

    2018-02-01

    When groundwater is recharged with reclaimed water, the presence of trace amounts of biorefractory pentabromodiphenyl ether (PBDE, specifically BDE-99) might cause potential groundwater pollution. A laboratory-scale column was designed to investigate the distribution of the community of archaea in this scenario and the associated anaerobic degradation of BDE-99. The concentration of BDE-99 decreased significantly as soil depth increased, and fluorescence in situ hybridization (FISH) analysis suggested that archaea exerted significant effects on the biodegradation of PBDE. Through 454 pyrosequencing of 16s rRNA genes, we found that the distribution and structure of the archaeal community associated with anaerobic degradation of BDE-99 in the river-based aquifer media changed significantly between different soil depths. The primary debrominated metabolites varied with changes in the vertically distributed archaeal community. The archaea in the surface layer were dominated by Methanomethylovorans, and the middle layer was mainly composed of Nitrososphaera. Nitrosopumilus and Nitrososphaera were equally abundant in the bottom layer. In addition, Methanomethylovorans abundance depended on the depth of soil, and the relative abundance of Nitrosopumilus increased with increasing depth, which was associated with the oxidation-reduction potential and the content of intermediate metabolites. We propose that Nitrososphaera and Nitrosopumilus might be the key archaeal taxa mediating the biodegradation of BDE-99.

  1. Understanding DNA Repair in Hyperthermophilic Archaea: Persistent Gaps and Other Reasons to Focus on the Fork

    Directory of Open Access Journals (Sweden)

    Dennis W. Grogan

    2015-01-01

    Full Text Available Although hyperthermophilic archaea arguably have a great need for efficient DNA repair, they lack members of several DNA repair protein families broadly conserved among bacteria and eukaryotes. Conversely, the putative DNA repair genes that do occur in these archaea often do not generate the expected phenotype when deleted. The prospect that hyperthermophilic archaea have some unique strategies for coping with DNA damage and replication errors has intellectual and technological appeal, but resolving this question will require alternative coping mechanisms to be proposed and tested experimentally. This review evaluates a combination of four enigmatic properties that distinguishes the hyperthermophilic archaea from all other organisms: DNA polymerase stalling at dU, apparent lack of conventional NER, lack of MutSL homologs, and apparent essentiality of homologous recombination proteins. Hypothetical damage-coping strategies that could explain this set of properties may provide new starting points for efforts to define how archaea differ from conventional models of DNA repair and replication fidelity.

  2. Addition of granular activated carbon and trace elements to favor volatile fatty acid consumption during anaerobic digestion of food waste.

    Science.gov (United States)

    Capson-Tojo, Gabriel; Moscoviz, Roman; Ruiz, Diane; Santa-Catalina, Gaëlle; Trably, Eric; Rouez, Maxime; Crest, Marion; Steyer, Jean-Philippe; Bernet, Nicolas; Delgenès, Jean-Philippe; Escudié, Renaud

    2018-07-01

    The effect of supplementing granular activated carbon and trace elements on the anaerobic digestion performance of consecutive batch reactors treating food waste was investigated. The results from the first batch suggest that addition of activated carbon favored biomass acclimation, improving acetic acid consumption and enhancing methane production. Adding trace elements allowed a faster consumption of propionic acid. A second batch proved that a synergy existed when activated carbon and trace elements were supplemented simultaneously. The degradation kinetics of propionate oxidation were particularly improved, reducing significantly the batch duration and improving the average methane productivities. Addition of activated carbon favored the growth of archaea and syntrophic bacteria, suggesting that interactions between these microorganisms were enhanced. Interestingly, microbial analyses showed that hydrogenotrophic methanogens were predominant. This study shows for the first time that addition of granular activated carbon and trace elements may be a feasible solution to stabilize food waste anaerobic digestion. Copyright © 2018 Elsevier Ltd. All rights reserved.

  3. Implementing Livestock Anaerobic Digestion Projects

    Science.gov (United States)

    Page provides information to help make an informed decision about installing an anaerobic digester. Is it a good match for a farm’s organic waste, project financing, development guidelines and permit requirements?

  4. Anaerobic bacteria that dechlorinate perchloroethene.

    Science.gov (United States)

    Fathepure, B Z; Nengu, J P; Boyd, S A

    1987-01-01

    In this study, we identified specific cultures of anaerobic bacteria that dechlorinate perchlorethene (PCE). The bacteria that significantly dechlorinated PCE were strain DCB-1, an obligate anaerobe previously shown to dechlorinate chlorobenzoate, and two strains of Methanosarcina. The rate of PCE dechlorination by DCB-1 compared favorably with reported rates of trichloroethene bio-oxidation by methanotrophs. Even higher PCE dechlorination rates were achieved when DCB-1 was grown in a methanogenic consortium. PMID:3426224

  5. 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.

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

    International Nuclear Information System (INIS)

    Zhu, Liang; Jin, Jie; Lin, Haizhuan; Gao, Kaituo; Xu, Xiangyang

    2015-01-01

    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 −3 d −1 and 6.0–70.0 g m −3 d −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 2 /CH 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

  7. PENGOLAHAN LIMBAH CAIR INDUSTRI FARMASI FORMULASI DENGAN METODE ANAEROB-AEROB DAN ANAEROB-KOAGULASI

    OpenAIRE

    Farida Crisnaningtyas; Hanny Vistanty

    2016-01-01

    Studi ini membahas mengenai pengolahan limbah cair industri farmasi dalam skala laboratorium dengan menggunakan konsep anaerob-kimia-fisika dan anaerob-aerob. Proses anaerob dilakukan dengan menggunakan reaktor Upflow Anaerobic Sludge Bed reactor (UASBr) pada kisaran OLR (Organic Loading Rate) 0,5 – 2 kg COD/m3hari, yang didahului dengan proses aklimatisasi menggunakan substrat gula. Proses anaerob mampu memberikan efisiensi penurunan COD hingga 74%. Keluaran dari proses anaerob diolah lebih ...

  8. Taxonomic study of extreme halophilic archaea isolated from the "Salar de Atacama", Chile.

    Science.gov (United States)

    Lizama, C; Monteoliva-Sánchez, M; Prado, B; Ramos-Cormenzana, A; Weckesser, J; Campos, V

    2001-11-01

    A large number of halophilic bacteria were isolated in 1984-1992 from the Atacama Saltern (North of Chile). For this study 82 strains of extreme halophilic archaea were selected. The characterization was performed by using the phenotypic characters including morphological, physiological, biochemical, nutritional and antimicrobial susceptibility test. The results, together with those from reference strains, were subjected to numerical analysis, using the Simple Matching (S(SM)) coefficient and clustered by the unweighted pair group method of association (UPGMA). Fifteen phena were obtained at an 70% similarity level. The results obtained reveal a high diversity among the halophilic archaea isolated. Representative strains from the phena were chosen to determine their DNA base composition and the percentage of DNA-DNA similarity compared to reference strains. The 16S rRNA studies showed that some of these strains constitutes a new taxa of extreme halophilic archaea.

  9. Base excision repair in Archaea: back to the future in DNA repair.

    Science.gov (United States)

    Grasso, Stefano; Tell, Gianluca

    2014-09-01

    Together with Bacteria and Eukarya, Archaea represents one of the three domain of life. In contrast with the morphological difference existing between Archaea and Eukarya, these two domains are closely related. Phylogenetic analyses confirm this evolutionary relationship showing that most of the proteins involved in DNA transcription and replication are highly conserved. On the contrary, information is scanty about DNA repair pathways and their mechanisms. In the present review the most important proteins involved in base excision repair, namely glycosylases, AP lyases, AP endonucleases, polymerases, sliding clamps, flap endonucleases, and ligases, will be discussed and compared with bacterial and eukaryotic ones. Finally, possible applications and future perspectives derived from studies on Archaea and their repair pathways, will be taken into account. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. 'Methane oxidation on supported gold catalysts'

    DEFF Research Database (Denmark)

    Walther, Guido

    2008-01-01

    steady-state activity measurements were performed to obtain the reaction rates for CO and H2 oxidation. These reactions were studied on three different gold particle sizes using either O2 or N2O as oxidation agents. Using particle size distributions obtained from TEM analysis, it was found that the CO......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...... the energy stored in the molecule available, is a major research challenge. In this PhD thesis, CH4 oxidation on nanoparticular gold is studied both experimentally and theoretically. In the course of this PhD project, CH4 oxidation was experimentally found more likely to form CO2 and H2O than other low index...

  11. 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...

  12. Methane oxidation in presence of sulfur dioxide

    International Nuclear Information System (INIS)

    Mantashyan, A.A.; Avetisyan, A.M.; Makaryan, E.M.; Wang, H.

    2006-01-01

    The emission of sulfurous gases including SO 2 from stationary power generation remains to be a serious environmental and ecological problem. Sulfurous gases are almost entirely produced from the combustion of sulfur-containing fuels. While fuel desulfurization and flue gas scrubbing is a viable solution, in the developing countries it remains to be an economical challenge to implement these SO x reduction technologies. The oxidation of methane in presence of sulfurous gas (SO 2 ) addition was studied experimentally. Te experiments were conducted in a static reactor at temperature of 728-786 K, and for mixture of C 4 /O 2 ≡ 1/2 at a pressure of 117 Torr with varying amount of SO 2 addition. It was observed that SO 2 addition accelerated the oxidation process, reduced the induction period and increased the extent of methane consumption. At the relatively short resident time (less than 50 sec) SO 3 was detected, but at longer residence time SO 3 was reduced spontaneously to SO 2

  13. Performance and methanogenic community of rotating disk reactor packed with polyurethane during thermophilic anaerobic digestion

    International Nuclear Information System (INIS)

    Yang, Yingnan; Tsukahara, Kenichiro; Sawayama, Shigeki

    2007-01-01

    A newly developed anaerobic rotating disk reactor (ARDR) packed with polyurethane was used in continuous mode for organic waste removal under thermophilic (55 o C) anaerobic conditions. This paper reports the effects of the rotational speed on the methanogenic performance and community in an ARDR supplied with acetic acid synthetic wastewater as the organic substrate. The best performance was obtained from the ARDR with the rotational speed (ω) of 30 rpm. The average removal of dissolved organic carbon was 98.5%, and the methane production rate was 393 ml/l-reactor/day at an organic loading rate of 2.69 g/l-reactor/day. Under these operational conditions, the reactor had a greater biomass retention capacity and better reactor performance than those at other rotational speeds (0, 5 and 60 rpm). The results of 16S rRNA phylogenetic analysis indicated that the major methanogens in the reactor belonged to the genus Methanosarcina spp. The results of real-time polymerase chain reaction (PCR) analysis suggested that the cell density of methanogenic archaea immobilized on the polyurethane foam disk could be concentrated more than 2000 times relative to those in the original thermophilic sludge. Scanning electron microphotographs showed that there were more immobilized microbes at ω of 30 rpm than 60 rpm. A rotational speed on the outer layer of the disk of 6.6 m/min could be appropriate for anaerobic digestion using the polyurethane ARDR

  14. Etude de la réplication de l'ADN chez les Archaea

    OpenAIRE

    Berthon , Jonathan

    2008-01-01

    Thèse réalisée entre France et Japon (boursier JSPS); Cellular organisms belong to one of the three domains of life: Archaea, Bacteria, and Eucarya. Archaea are unicellular organisms with a bacterial phenotype, yet they exhibit many eucaryotic features at the molecular level. In particular, archaeal DNA replication machinery is a homologous and simplified version of that in eucaryotes. In this work, I have studied archaeal DNA replication with both in vitro and in silico approaches.First, I h...

  15. 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

    molecular fossils indicates that these archaea were living chemoautotrophically. Their massive expansion may have been a response to the strong stratification of the ocean during this anoxic event. Indeed, the sedimentary record of archaeal membrane lipids suggests that this anoxic event marks a time......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 archaeal...

  16. Distribution of Metabolically Active Prokaryotes (Archaea and Bacteria) throughout the Profiles of Chernozem and Brown Semidesert Soil

    Science.gov (United States)

    Semenov, M. V.; Manucharova, N. A.; Stepanov, A. L.

    2016-02-01

    The distribution of metabolically active cells of archaea and bacteria in the profiles of typical chernozems (Voronezh oblast) and brown semidesert soils (Astrakhan oblast) of natural and agricultural ecosystems was studied using the method of fluorescent in situ hybridization (FISH). The studied soils differed sharply in the microbial biomass and in the numbers of metabolically active cells of archaea and bacteria. The number of active bacterial cells was 3.5-7.0 times greater than that of archaea. In the arable chernozem, the numbers of active cells of archaea and bacteria were 2.6 and 1.5 times, respectively, lower than those in the chernozem under the shelterbelt. The agricultural use of the brown semidesert soil had little effect on the abundances of bacteria and archaea. The soil organic carbon content was the major factor controlling the numbers of metabolically active cells of both domains. However, the dependence of the abundance of bacteria on the organic matter content was more pronounced. The decrease in the organic carbon and total nitrogen contents down the soil profiles was accompanied by the decrease in the bacteria: archaea ratio attesting to a better adaptation of archaea to the permanent deficiency of carbon and nitrogen. The bacteria: archaea ratio can serve as an ecotrophic indicator of the state of soil microbial communities.

  17. 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

  18. Microbial and nutritional regulation of high-solids anaerobic mono-digestion of fruit and vegetable wastes.

    Science.gov (United States)

    Mu, Hui; Li, Yan; Zhao, Yuxiao; Zhang, Xiaodong; Hua, Dongliang; Xu, Haipeng; Jin, Fuqiang

    2018-02-01

    The anaerobic digestion of single fruit and vegetable wastes (FVW) can be easily interrupted by rapid acidogenesis and inhibition of methanogen, and the digestion system tends to be particularly unstable at high solid content. In this study, the anaerobic digestion of FVW in batch experiments under mesophilic condition at a high solid concentration of 10% was successfully conducted to overcome the acidogenesis problem through several modifications. Firstly, compared with the conventional anaerobic sludge (CAS), the acclimated anaerobic granular sludge (AGS) was found to be a better inoculum due to its higher Archaea abundance. Secondly, waste activated sludge (WAS) was chosen to co-digest with FVW, because WAS had abundant proteins that could generate intermediate ammonium. The ammonium could neutralize the accumulated volatile fatty acids (VFAs) and prevent the pH value of the digestion system from rapidly decreasing. Co-digestion of FVW and WAS with TS ratio of 60:40 gave the highest biogas yield of 562 mL/g-VS and the highest methane yield of 362 mL/g-VS. Key parameters in the digestion process, including VFAs concentration, pH, enzyme activity, and microbial activity, were also examined.

  19. 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.

  20. 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.

  1. Instrumentation in anaerobic treatment - research and practice

    NARCIS (Netherlands)

    Spanjers, H.; Lier, van J.B.

    2006-01-01

    High rate anaerobic treatment reactors are able to uncouple solids and liquid retention time, resulting in high biomass concentrations. Principal advantages of anaerobic treatment include: energy efficiency, low biomass yield, low nutrient requirement and high volumetric organic loadings. In order

  2. 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.

  3. Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence?

    NARCIS (Netherlands)

    Ozuolmez, D.; Na, H.; Lever, M.A.; Kjeldsen, K.U.; Jørgensen, B.B.; Plugge, C.M.

    2015-01-01

    Acetate is a major product of fermentation processes and an important substrate for sulfate reducing bacteria and methanogenic archaea. Most studies on acetate catabolism by sulfate reducers and methanogens have used pure cultures. Less is known about acetate conversion by mixed pure cultures and

  4. Evaluation of biodecolorization of the textile azo dye by halophilic archaea

    Directory of Open Access Journals (Sweden)

    Masoomeh Selseleh Hassan-Kiadehi

    2017-09-01

    Discussion and conclusion: In conclusion, our results indicate that halophilic archaea have very high potential to decolorize azo dyes. Regarding high amounts of salts in textile wastewaters, using such microorganisms which can tolerate the harsh environment in order to decolorize azo dyes, could be a new approach in this field.

  5. Bacteria and Archaea in acidic environments and a key to morphological identification

    Science.gov (United States)

    Robbins, E.I.

    2000-01-01

    Natural and anthropogenic acidic environments are dominated by bacteria and Archaea. As many as 86 genera or species have been identified or isolated from pH morphological characteristics, habitat information and a key for light microscope identification for the non-microbiologist.

  6. Diversity of archaea and bacteria in a biogas reactor fed with ...

    African Journals Online (AJOL)

    Diversity of archaea and bacteria in a biogas reactor fed with Pennisetum sinese ... AFRICAN JOURNALS ONLINE (AJOL) · Journals · Advanced Search · USING ... rumen microbial community in a biogas reactor by 16S rRNA gene analysis, ...

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

    NARCIS (Netherlands)

    Jähme, Michael; Slotboom, Dirk Jan

    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

  8. Detection of methanogenic archaea in seawater particles and the digestive tract of a marine fish species

    NARCIS (Netherlands)

    van der Maarel, MJEC; Sprenger, W; Haanstra, R; Forney, LJ

    1999-01-01

    A methanogen-specific nested PCR approach was used to detect methanogenic archaea in seawater particles of the North Sea and the feces and the digestive tract of flounder (Platichthys flesus), a fish found in the North Sea. A number of 16S rDNA sequences with 97.6-99.5% similarity to

  9. Contributions of ammonia-oxidizing archaea and bacteria to nitrification in Oregon forest soils

    Science.gov (United States)

    Xinda Lu; Peter J. Bottomley; David D. Myrold

    2015-01-01

    Ammonia oxidation, the first step of nitrification, is mediated by both ammonia-oxidizing archaea (AOA) and bacteria (AOB); however, the relative contributions of AOA and AOB to soil nitrification are not well understood. In this study we used 1-octyne to discriminate between AOA-and AOB-supported nitrifi-cation determined both in soil-water slurries and in unsaturated...

  10. Bipyrimidine Signatures as a Photoprotective Genome Strategy in G + C-rich Halophilic Archaea.

    Science.gov (United States)

    Jones, Daniel L; Baxter, Bonnie K

    2016-09-02

    Halophilic archaea experience high levels of ultraviolet (UV) light in their environments and demonstrate resistance to UV irradiation. DNA repair systems and carotenoids provide UV protection but do not account for the high resistance observed. Herein, we consider genomic signatures as an additional photoprotective strategy. The predominant forms of UV-induced DNA damage are cyclobutane pyrimidine dimers, most notoriously thymine dimers (T^Ts), which form at adjacent Ts. We tested whether the high G + C content seen in halophilic archaea serves a photoprotective function through limiting T nucleotides, and thus T^T lesions. However, this speculation overlooks the other bipyrimidine sequences, all of which capable of forming photolesions to varying degrees. Therefore, we designed a program to determine the frequencies of the four bipyrimidine pairs (5' to 3': TT, TC, CT, and CC) within genomes of halophilic archaea and four other randomized sample groups for comparison. The outputs for each sampled genome were weighted by the intrinsic photoreactivities of each dinucleotide pair. Statistical methods were employed to investigate intergroup differences. Our findings indicate that the UV-resistance seen in halophilic archaea can be attributed in part to a genomic strategy: high G + C content and the resulting bipyrimidine signature reduces the genomic photoreactivity.

  11. DNA Repair and Photoprotection: Mechanisms of Overcoming Environmental Ultraviolet Radiation Exposure in Halophilic Archaea.

    Science.gov (United States)

    Jones, Daniel L; Baxter, Bonnie K

    2017-01-01

    Halophilic archaea push the limits of life at several extremes. In particular, they are noted for their biochemical strategies in dealing with osmotic stress, low water activity and cycles of desiccation in their hypersaline environments. Another feature common to their habitats is intense ultraviolet (UV) radiation, which is a challenge that microorganisms must overcome. The consequences of high UV exposure include DNA lesions arising directly from bond rearrangement of adjacent bipyrimidines, or indirectly from oxidative damage, which may ultimately result in mutation and cell death. As such, these microorganisms have evolved a number of strategies to navigate the threat of DNA damage, which we differentiate into two categories: DNA repair and photoprotection. Photoprotection encompasses damage avoidance strategies that serve as a "first line of defense," and in halophilic archaea include pigmentation by carotenoids, mechanisms of oxidative damage avoidance, polyploidy, and genomic signatures that make DNA less susceptible to photodamage. Photolesions that do arise are addressed by a number of DNA repair mechanisms that halophilic archaea efficiently utilize, which include photoreactivation, nucleotide excision repair, base excision repair, and homologous recombination. This review seeks to place DNA damage, repair, and photoprotection in the context of halophilic archaea and the solar radiation of their hypersaline environments. We also provide new insight into the breadth of strategies and how they may work together to produce remarkable UV-resistance for these microorganisms.

  12. Survival of Halophilic Archaea in the Stratosphere as a Mars Analog: A Transcriptomic Approach

    Science.gov (United States)

    DasSarma, S.; DasSarma, P.; Laye, V.; Harvey, J.; Reid, C.; Shultz, J.; Yarborough, A.; Lamb, A.; Koske-Phillips, A.; Herbst, A.; Molina, F.; Grah, O.; Phillips, T.

    2016-05-01

    On Earth, halophilic Archaea tolerate multiple extreme conditions similar to those on Mars. In order to study their survival, we launched live cultures into Earth’s stratosphere on helium balloons. The effects on survival and transcriptomes were interrogated in the lab.

  13. Ion permeability of the cytoplasmic membrane limits the maximum growth temperature of bacteria and archaea

    NARCIS (Netherlands)

    van de Vossenberg, J.L C M; Ubbink-Kok, T.; Elferink, M.G.L.; Driessen, A.J.M.; Konings, W.N

    1995-01-01

    Protons and sodium ions are the most commonly used coupling ions in energy transduction in bacteria and archaea. At their growth temperature, the permeability of the cytoplasmic membrane of thermophilic bacteria to protons is high compared with that of sodium ions. In some thermophiles, sodium is

  14. The cell membrane plays a crucial role in survival of bacteria and archaea in extreme environments

    NARCIS (Netherlands)

    Konings, Wil N.; Albers, Sonja-Verena; Koning, Sonja; Driessen, Arnold J.M.

    2002-01-01

    The cytoplasmic membrane of bacteria and archaea determine to a large extent the composition of the cytoplasm. Since the ion and in particular the proton and/or the sodium ion electrochemical gradients across the membranes are crucial for the bioenergetic conditions of these microorganisms,

  15. Differential antibiotic sensitivity determined by the large ribosomal subunit in thermophilic archaea.

    OpenAIRE

    Ruggero, D; Londei, P

    1996-01-01

    Hybrid ribosomes obtained by mixing the ribosomal subunits of the extremely thermophilic archaea Sulfolobus solfataricus and Desulfurococcus mobilis were tested for their sensitivity to selected antibiotics. It is shown that structural differences in the large ribosomal subunits determine qualitatively and quantitatively the patterns of response to alpha-sarcin and paromomycin in these species.

  16. Association of marine archaea with the digestive tracts of two marine fish species

    NARCIS (Netherlands)

    Maarel, Marc J.E.C. van der; Artz, Rebekka R.E.; Haanstra, Rene; Forney, Larry J.

    Recent studies have shown that archaea which were always thought to live under strict anoxic or extreme environmental conditions are also present in cold, oxygenated seawater, soils, the digestive tract of a holothurian deep-sea-deposit feeder, and a marine sponge, In this study we show, by using

  17. 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

  18. ARCPHdb: A comprehensive protein database for SF1 and SF2 helicase from archaea.

    Science.gov (United States)

    Moukhtar, Mirna; Chaar, Wafi; Abdel-Razzak, Ziad; Khalil, Mohamad; Taha, Samir; Chamieh, Hala

    2017-01-01

    Superfamily 1 and Superfamily 2 helicases, two of the largest helicase protein families, play vital roles in many biological processes including replication, transcription and translation. Study of helicase proteins in the model microorganisms of archaea have largely contributed to the understanding of their function, architecture and assembly. Based on a large phylogenomics approach, we have identified and classified all SF1 and SF2 protein families in ninety five sequenced archaea genomes. Here we developed an online webserver linked to a specialized protein database named ARCPHdb to provide access for SF1 and SF2 helicase families from archaea. ARCPHdb was implemented using MySQL relational database. Web interfaces were developed using Netbeans. Data were stored according to UniProt accession numbers, NCBI Ref Seq ID, PDB IDs and Entrez Databases. A user-friendly interactive web interface has been developed to browse, search and download archaeal helicase protein sequences, their available 3D structure models, and related documentation available in the literature provided by ARCPHdb. The database provides direct links to matching external databases. The ARCPHdb is the first online database to compile all protein information on SF1 and SF2 helicase from archaea in one platform. This database provides essential resource information for all researchers interested in the field. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Substrate and nutrient limitation of ammonia-oxidizing bacteria and archaea in temperate forest soil

    Science.gov (United States)

    J.S. Norman; J.E. Barrett

    2014-01-01

    Ammonia-oxidizing microbes control the rate-limiting step of nitrification, a critical ecosystem process, which affects retention and mobility of nitrogen in soil ecosystems. This study investigated substrate (NH4þ) and nutrient (K and P) limitation of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in temperate forest soils at Coweeta Hydrologic...

  20. Bacteria, not archaea, restore nitrification in a zinc-contaminated soil

    NARCIS (Netherlands)

    Mertens, J.; Broos, K.; Wakelin, S.A.; Kowalchuk, G.A.; Springael, D.; Smolders, E.

    2009-01-01

    Biological ammonia oxidation had long been thought to be mediated solely by discrete clades of - and -proteobacteria (ammonia-oxidizing bacteria; AOB). However, ammonia-oxidizing Crenarchaeota (ammonia-oxidizing archaea; AOA) have recently been identified and proposed to be the dominant agents of

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

    Czech Academy of Sciences Publication Activity Database

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

    2014-01-01

    Roč. 9, č. 7 (2014), e102659 E-ISSN 1932-6203 R&D Projects: GA ČR GA526/09/1570 Institutional support: RVO:60077344 Keywords : methane production * methanogenic Archaea * digestive tracts of millipedes Subject RIV: EG - Zoology Impact factor: 3.234, year: 2014

  2. DNA Repair and Photoprotection: Mechanisms of Overcoming Environmental Ultraviolet Radiation Exposure in Halophilic Archaea

    Directory of Open Access Journals (Sweden)

    Daniel L. Jones

    2017-09-01

    Full Text Available Halophilic archaea push the limits of life at several extremes. In particular, they are noted for their biochemical strategies in dealing with osmotic stress, low water activity and cycles of desiccation in their hypersaline environments. Another feature common to their habitats is intense ultraviolet (UV radiation, which is a challenge that microorganisms must overcome. The consequences of high UV exposure include DNA lesions arising directly from bond rearrangement of adjacent bipyrimidines, or indirectly from oxidative damage, which may ultimately result in mutation and cell death. As such, these microorganisms have evolved a number of strategies to navigate the threat of DNA damage, which we differentiate into two categories: DNA repair and photoprotection. Photoprotection encompasses damage avoidance strategies that serve as a “first line of defense,” and in halophilic archaea include pigmentation by carotenoids, mechanisms of oxidative damage avoidance, polyploidy, and genomic signatures that make DNA less susceptible to photodamage. Photolesions that do arise are addressed by a number of DNA repair mechanisms that halophilic archaea efficiently utilize, which include photoreactivation, nucleotide excision repair, base excision repair, and homologous recombination. This review seeks to place DNA damage, repair, and photoprotection in the context of halophilic archaea and the solar radiation of their hypersaline environments. We also provide new insight into the breadth of strategies and how they may work together to produce remarkable UV-resistance for these microorganisms.

  3. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

    OpenAIRE

    Wolf Yuri I; Novichkov Pavel S; Sorokin Alexander V; Makarova Kira S; Koonin Eugene V

    2007-01-01

    Abstract Background An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). Rapid accumulation of genome sequences creates opportunities for refining COGs ...

  4. 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

  5. Molecular genetic studies on obligate anaerobic bacteria

    International Nuclear Information System (INIS)

    Woods, D.R.

    1982-01-01

    Molecular genetic studies on obligate anaerobic bacteria have lagged behind similar studies in aerobes. However, the current interest in biotechnology, the involvement of anaerobes in disease and the emergence of antibioticresistant strains have focused attention on the genetics of anaerobes. This article reviews molecular genetic studies in Bacteroides spp., Clostridium spp. and methanogens. Certain genetic systems in some anaerobes differ from those in aerobes and illustrate the genetic diversity among bacteria

  6. Kinetics and modeling of anaerobic digestion process

    DEFF Research Database (Denmark)

    Gavala, Hariklia N.; Angelidaki, Irini; Ahring, Birgitte Kiær

    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...

  7. 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 (oxygen...

  8. Viscosity evolution of anaerobic granular sludge

    NARCIS (Netherlands)

    Pevere, A.; Guibaud, G.; Hullebusch, van E.D.; Lens, P.N.L.; Baudu, M.

    2006-01-01

    The evolution of the apparent viscosity at steady shear rate of sieved anaerobic granular sludge (20¿315 ¿m diameter) sampled from different full-scale anaerobic reactors was recorded using rotation tests. The ¿limit viscosity¿ of sieved anaerobic granular sludge was determined from the apparent

  9. The phenomenon of granulation of anaerobic sludge

    NARCIS (Netherlands)

    Hulshoff Pol, L.

    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

  10. 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.

  11. Detection of putatively thermophilic anaerobic methanotrophs in diffuse hydrothermal vent fluids.

    Science.gov (United States)

    Merkel, Alexander Y; Huber, Julie A; Chernyh, Nikolay A; Bonch-Osmolovskaya, Elizaveta A; Lebedinsky, Alexander V

    2013-02-01

    The anaerobic oxidation of methane (AOM) is carried out by a globally distributed group of uncultivated Euryarchaeota, the anaerobic methanotrophic arachaea (ANME). In this work, we used G+C analysis of 16S rRNA genes to identify a putatively thermophilic ANME group and applied newly designed primers to study its distribution in low-temperature diffuse vent fluids from deep-sea hydrothermal vents. We found that the G+C content of the 16S rRNA genes (P(GC)) is significantly higher in the ANME-1GBa group than in other ANME groups. Based on the positive correlation between the P(GC) and optimal growth temperatures (T(opt)) of archaea, we hypothesize that the ANME-1GBa group is adapted to thrive at high temperatures. We designed specific 16S rRNA gene-targeted primers for the ANME-1 cluster to detect all phylogenetic groups within this cluster, including the deeply branching ANME-1GBa group. The primers were successfully tested both in silico and in experiments with sediment samples where ANME-1 phylotypes had previously been detected. The primers were further used to screen for the ANME-1 microorganisms in diffuse vent fluid samples from deep-sea hydrothermal vents in the Pacific Ocean, and sequences belonging to the ANME-1 cluster were detected in four individual vents. Phylotypes belonging to the ANME-1GBa group dominated in clone libraries from three of these vents. Our findings provide evidence of existence of a putatively extremely thermophilic group of methanotrophic archaea that occur in geographically and geologically distinct marine hydrothermal habitats.

  12. Oxygen Effects in Anaerobic Digestion

    Directory of Open Access Journals (Sweden)

    Deshai Botheju

    2009-10-01

    Full Text Available Interaction of free oxygen in bio-gasification is a sparsely studied area, apart from the common argument of oxygen being toxic and inhibitory for anaerobic micro-cultures. Some studies have, however, revealed increased solubilisation of organic matter in the presence of some free oxygen in anaerobic digestion. This article analyses these counterbalancing phenomena with a mathematical modelling approach using the widely accepted biochemical model ADM 1. Aerobic oxidation of soluble carbon and inhibition of obligatory anaerobic organisms are modelled using standard saturation type kinetics. Biomass dependent first order hydrolysis kinetics is used to relate the increased hydrolysis rate with oxygen induced increase in biomass growth. The amended model, ADM 1-Ox (oxygen, has 25 state variables and 22 biochemical processes, presented in matrix form. The computer aided simulation tool AQUASIM 2.1 is used to simulate the developed model. Simulation predictions are evaluated against experimental data obtained using a laboratory batch test array comprising miniature anaerobic bio-reactors of 100 ml total volume each, operated under different initial air headspaces giving rise to the different oxygen loading conditions. The reactors were initially fed with a glucose solution and incubated at 35 Celsius, for 563 hours. Under the oxygen load conditions of 22, 44 and 88 mg/L, the ADM1-Ox model simulations predicted the experimental methane potentials quite adequately. Both the experimental data and the simulations suggest a linear reduction of methane potential with respect to the increase in oxygen load within this range.

  13. 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...

  14. Inhibition of Anaerobic Biological Treatment: A Review

    Science.gov (United States)

    Hou, Li; Ji, Dandan; Zang, Lihua

    2018-01-01

    Anaerobic digestion is a method for treating living and industrial wastewater by anaerobic degradation of organic compounds, which can produce biogas (carbon dioxide and methane mixture) and microbial biomass. And biogas as a renewable resource, can replace the use of ore fuel. In the process of anaerobic digestion, the problems of low methane yield and unstable reaction process are often encountered, which limits the widespread use of this technology. Various inhibitors are the main limiting factors for anaerobic digestion. In this paper, the main factors limiting anaerobic digestion are reviewed, and the latest research progress is introduced.

  15. Anaerobic bacteria as producers of antibiotics.

    Science.gov (United States)

    Behnken, Swantje; Hertweck, Christian

    2012-10-01

    Anaerobic bacteria are the oldest terrestrial creatures. They occur ubiquitously in soil and in the intestine of higher organisms and play a major role in human health, ecology, and industry. However, until lately no antibiotic or any other secondary metabolite has been known from anaerobes. Mining the genome sequences of Clostridium spp. has revealed a high prevalence of putative biosynthesis genes (PKS and NRPS), and only recently the first antibiotic from the anaerobic world, closthioamide, has been isolated from the cellulose degrading bacterium Clostridium cellulolyticum. The successful genetic induction of antibiotic biosynthesis in an anaerobe encourages further investigations of obligate anaerobes to tap their hidden biosynthetic potential.

  16. 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.

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

    Science.gov (United States)

    Montoya, Lilia; Lozada-Chávez, Irma; Amils, Ricardo; Rodriguez, Nuria; Marín, Irma

    2011-01-01

    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. PMID:21915180

  18. Methane-yielding microbial communities processing lactate-rich substrates: a piece of the anaerobic digestion puzzle.

    Science.gov (United States)

    Detman, Anna; Mielecki, Damian; Pleśniak, Łukasz; Bucha, Michał; Janiga, Marek; Matyasik, Irena; Chojnacka, Aleksandra; Jędrysek, Mariusz-Orion; Błaszczyk, Mieczysław K; Sikora, Anna

    2018-01-01

    Anaerobic digestion, whose final products are methane and carbon dioxide, ensures energy flow and circulation of matter in ecosystems. This naturally occurring process is used for the production of renewable energy from biomass. Lactate, a common product of acidic fermentation, is a key intermediate in anaerobic digestion of biomass in the environment and biogas plants. Effective utilization of lactate has been observed in many experimental approaches used to study anaerobic digestion. Interestingly, anaerobic lactate oxidation and lactate oxidizers as a physiological group in methane-yielding microbial communities have not received enough attention in the context of the acetogenic step of anaerobic digestion. This study focuses on metabolic transformation of lactate during the acetogenic and methanogenic steps of anaerobic digestion in methane-yielding bioreactors. Methane-yielding microbial communities instead of pure cultures of acetate producers were used to process artificial lactate-rich media to methane and carbon dioxide in up-flow anaerobic sludge blanket reactors. The media imitated the mixture of acidic products found in anaerobic environments/digesters where lactate fermentation dominates in acidogenesis. Effective utilization of lactate and biogas production was observed. 16S rRNA profiling was used to examine the selected methane-yielding communities. Among Archaea present in the bioreactors, the order Methanosarcinales predominated. The acetoclastic pathway of methane formation was further confirmed by analysis of the stable carbon isotope composition of methane and carbon dioxide. The domain Bacteria was represented by Bacteroidetes , Firmicutes , Proteobacteria , Synergistetes , Actinobacteria , Spirochaetes , Tenericutes , Caldithrix , Verrucomicrobia , Thermotogae , Chloroflexi , Nitrospirae, and Cyanobacteria. Available genome sequences of species and/or genera identified in the microbial communities were searched for genes encoding the lactate

  19. [Current clinical significance of anaerobic bacteremia].

    Science.gov (United States)

    Jirsa, Roman; Marešová, Veronika; Brož, Zdeněk

    2010-10-01

    to estimate tje current clinical significance of anaerobic bacteremia in a group of Czech hospitals. this retrospective analysis comprised 8 444 anaerobic blood cultures in patients admitted to four Czech hospitals between 2004 and 2007. in 16 patients, blood cultures yielded significant anaerobic bacteria. Thus, anaerobic bacteremia accounted for less than 2 % of clinically significant bacteremia. Four patients (18 %) died but none of the deaths could be clearly attributable to anaerobic bacteria in the bloodstream. The most common comorbidities predisposing to anaerobic bacteremia and the most frequent sources of infection were similar to those reported by other authors. The majority of anaerobic bacteremia cases were due to gram-negative bacteria, followed by Clostridium perfringens and, surprisingly, Eubacterium spp. (particularly Eubacterium lentum). anaerobic bacteremia remains rare. The comparison of our data with those by other authors suggests that (despite the reported high mortality) the actual clinical significance of anaerobic bacteremia is rather controversial and that the anaerobic bacteremia might not correspond to more serious pathogenic role of the anaerobic bacteria as the source of infection.

  20. The utility of anaerobic blood culture in detecting facultative anaerobic bacteremia in children.

    Science.gov (United States)

    Shoji, Kensuke; Komuro, Hisako; Watanabe, Yasushi; Miyairi, Isao

    2013-08-01

    Routine anaerobic blood culture is not recommended in children because obligate anaerobic bacteremia is rare in the pediatric population. However, a number of facultative anaerobic bacteria can cause community and hospital acquired infections in children and the utility of anaerobic blood culture for detection of these organisms is still unclear. We conducted a retrospective analysis of all blood culture samples (n = 24,356) at a children's hospital in Japan from October 2009 to June 2012. Among the samples that had paired aerobic and anaerobic blood cultures, 717 samples were considered clinically significant with 418 (58%) organisms detected from both aerobic and anaerobic cultures, 167 (23%) detected only from aerobic culture and 132 (18%) detected only from anaerobic culture. While most facultative anaerobes were detectable by aerobic culture, over 25% of Enterobacteriaceae and 15% of Staphylococcus sp. were detected from anaerobic cultures bottles only, suggesting its potential role in selected settings. Copyright © 2013 Elsevier Inc. All rights reserved.

  1. Approaching the sequential and three-dimensional organization of Archaea, Bacteria and Eukarya genomes. Dynamic Organization of Nuclear Function

    NARCIS (Netherlands)

    T.A. Knoch (Tobias); M. Göker (Markus); R. Lohner (Rudolf); J. Langowski (Jörg)

    2002-01-01

    textabstractThe largely unresolved sequential organization, i.e. the relations within DNA sequences, and its connection to the three-dimensional organization of genomes was investigated by correlation analyses of completely sequenced chromosomes from Viroids, Archaea, Bacteria, Arabidopsis

  2. Chromatin structure and dynamics in hot environments: architectural proteins and DNA topoisomerases of thermophilic archaea.

    Science.gov (United States)

    Visone, Valeria; Vettone, Antonella; Serpe, Mario; Valenti, Anna; Perugino, Giuseppe; Rossi, Mosè; Ciaramella, Maria

    2014-09-25

    In all organisms of the three living domains (Bacteria, Archaea, Eucarya) chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair). Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C), chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.

  3. Chromatin Structure and Dynamics in Hot Environments: Architectural Proteins and DNA Topoisomerases of Thermophilic Archaea

    Directory of Open Access Journals (Sweden)

    Valeria Visone

    2014-09-01

    Full Text Available In all organisms of the three living domains (Bacteria, Archaea, Eucarya chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair. Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C, chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.

  4. 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.

  5. Clinical features of anaerobic orthopaedic infections.

    Science.gov (United States)

    Lebowitz, Dan; Kressmann, Benjamin; Gjoni, Shpresa; Zenelaj, Besa; Grosgurin, Olivier; Marti, Christophe; Zingg, Matthieu; Uçkay, Ilker

    2017-02-01

    Some patient populations and types of orthopaedic surgery could be at particular risk for anaerobic infections. In this retrospective cohort study of operated adult patients with infections from 2004 to 2014, we assessed obligate anaerobes and considered first clinical infection episodes. Anaerobes, isolated from intra-operative samples, were identified in 2.4% of 2740 surgical procedures, of which half (33/65; 51%) were anaerobic monomicrobial infections. Propionibacterium acnes, a penicillin and vancomycin susceptible pathogen, was the predominantly isolated anaerobe. By multivariate analysis, the presence of fracture fixation plates was the variable most strongly associated with anaerobic infection (odds ratio: 2.1, 95% CI: 1.3-3.5). Anaerobes were also associated with spondylodesis and polymicrobial infections. In contrast, it revealed less likely in native bone or prosthetic joint infections and was not related to prior antibiotic use. In conclusion, obligate anaerobes in our case series of orthopaedic infections were rare, and mostly encountered in infections related to trauma with open-fracture fixation devices rather than clean surgical site infection. Anaerobes were often co-pathogens, and cultures most frequently recovered P. acnes. These observations thus do not support changes in current practices such as broader anaerobe coverage for perioperative prophylaxis.

  6. Diversity and abundance of ammonia oxidizing archaea in tropical compost systems

    OpenAIRE

    de Gannes, Vidya; Eudoxie, Gaius; Dyer, David H.; Hickey, William J.

    2012-01-01

    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 p...

  7. DNA Repair and Photoprotection: Mechanisms of Overcoming Environmental Ultraviolet Radiation Exposure in Halophilic Archaea

    OpenAIRE

    Daniel L. Jones; Bonnie K. Baxter

    2017-01-01

    Halophilic archaea push the limits of life at several extremes. In particular, they are noted for their biochemical strategies in dealing with osmotic stress, low water activity and cycles of desiccation in their hypersaline environments. Another feature common to their habitats is intense ultraviolet (UV) radiation, which is a challenge that microorganisms must overcome. The consequences of high UV exposure include DNA lesions arising directly from bond rearrangement of adjacent bipyrimidine...

  8. Table 1. Details of Archaea considered for this study. P hylum Name ...

    Indian Academy of Sciences (India)

    User

    Table 1. Details of Archaea considered for this study. P hylum. Name. Genome G+. C. %. *. G enome. S ize. *. Gene count. *. Max growth temp. (oC). Optimum growth temp (oC). Generation time, tg. (min). ttR. NA. #. dtR. NA. #. Source. †. 1. C renarchaeota. Aeropyrum pernix K1. 56.31 1669696 1752 100 90-95. 200. 42. 42.

  9. Genetic diversity of archaea in deep-sea hydrothermal vent environments.

    OpenAIRE

    Takai, K; Horikoshi, K

    1999-01-01

    Molecular phylogenetic analysis of naturally occurring archaeal communities in deep-sea hydrothermal vent environments was carried out by PCR-mediated small subunit rRNA gene (SSU rDNA) sequencing. As determined through partial sequencing of rDNA clones amplified with archaea-specific primers, the archaeal populations in deep-sea hydrothermal vent environments showed a great genetic diversity, and most members of these populations appeared to be uncultivated and unidentified organisms. In the...

  10. Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

    Science.gov (United States)

    Esser, Dominik; Rauch, Bernadette

    2014-01-01

    SUMMARY The metabolism of Archaea, the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya. However, this metabolic complexity in Archaea is accompanied by the absence of many “classical” pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of “new,” unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea. In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya. Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented. PMID:24600042

  11. Contribution of Ruminal Fungi, Archaea, Protozoa, and Bacteria to the Methane Suppression Caused by Oilseed Supplemented Diets

    OpenAIRE

    Wang, Shaopu; Giller, Katrin; Kreuzer, Michael; Ulbrich, Susanne E.; Braun, Ueli; Schwarm, Angela

    2017-01-01

    Dietary lipids can suppress methane emission from ruminants, but effects are variable. Especially the role of bacteria, archaea, fungi and protozoa in mediating the lipid effects is unclear. In the present in vitro study, archaea, fungi and protozoa were selectively inhibited by specific agents. This was fully or almost fully successful for fungi and protozoa as well as archaeal activity as determined by the methyl-coenzyme M reductase alpha subunit gene. Five different microbial treatments w...

  12. 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 simulated...... earlier by Vavilin and Angelidaki (2005) were used to modernize a kinetic scheme and to obtain the corresponding kinetic coefficients. In the new models, hydrolytic microorganisms were included using Contois kinetics for the hydrolysis/acidogenesis degradation of municipal solid waste (MSW). Monod...... kinetics was applied for description of methanogenesis. Both hydrolytic and methanogenic microorganisms were assumed to be inhibited by high volatile fatty acids (VFA) concentration. According to the new distributed models, the mixing level reduction expressed by increasing dimensionless Peclet number may...

  13. 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. PMID:25028969

  14. Seryl-tRNA Synthetases from Methanogenic Archaea: Suppression of Bacterial Amber Mutation and Heterologous Toxicity

    Directory of Open Access Journals (Sweden)

    Drasko Boko

    2010-01-01

    Full Text Available Methanogenic archaea possess unusual seryl-tRNA synthetases (SerRS, evolutionarily distinct from the SerRSs found in other archaea, eucaryotes and bacteria. Our recent X-ray structural analysis of Methanosarcina barkeri SerRS revealed an idiosyncratic N-terminal domain and catalytic zinc ion in the active site. To shed further light on substrate discrimination by methanogenic-type SerRS, we set up to explore in vivo the interaction of methanogenic-type SerRSs with their cognate tRNAs in Escherichia coli or Saccharomyces cerevisiae. The expression of various methanogenic-type SerRSs was toxic for E. coli, resulting in the synthesis of erroneous proteins, as revealed by β-galactosidase stability assay. Although SerRSs from methanogenic archaea recognize tRNAsSer from all three domains of life in vitro, the toxicity presumably precluded the complementation of endogenous SerRS function in both, E. coli and S. cerevisiae. However, despite the observed toxicity, coexpression of methanogenic-type SerRS with its cognate tRNA suppressed bacterial amber mutation.

  15. Human age and skin physiology shape diversity and abundance of Archaea on skin.

    Science.gov (United States)

    Moissl-Eichinger, Christine; Probst, Alexander J; Birarda, Giovanni; Auerbach, Anna; Koskinen, Kaisa; Wolf, Peter; Holman, Hoi-Ying N

    2017-06-22

    The human skin microbiome acts as an important barrier protecting our body from pathogens and other environmental influences. Recent investigations have provided evidence that Archaea are a constant but highly variable component of the human skin microbiome, yet factors that determine their abundance changes are unknown. Here, we tested the hypothesis that the abundance of archaea on human skin is influenced by human age and skin physiology by quantitative PCR of 51 different skin samples taken from human subjects of various age. Our results reveal that archaea are more abundant in human subjects either older than 60 years or younger than 12 years as compared to middle-aged human subjects. These results, together with results obtained from spectroscopy analysis, allowed us gain first insights into a potential link of lower sebum levels and lipid content and thus reduced skin moisture with an increase in archaeal signatures. Amplicon sequencing of selected samples revealed the prevalence of specific eury- and mainly thaumarchaeal taxa, represented by a core archaeome of the human skin.

  16. In Vitro Antioxidant, Antihemolytic, and Anticancer Activity of the Carotenoids from Halophilic Archaea.

    Science.gov (United States)

    Hou, Jing; Cui, Heng-Lin

    2018-03-01

    Halophilic archaea represent a promising natural source of carotenoids. However, little information is available about the biological effects of carotenoids from halophilic archaea. In this study, the carotenoids produced by seven halophilic archaeal strains Halogeometricum rufum, Halogeometricum limi, Haladaptatus litoreus, Haloplanus vescus, Halopelagius inordinatus, Halogranum rubrum, and Haloferax volcanii were identified by ultraviolet/visible spectroscopy, thin-layer chromatography, and high-performance liquid chromatography-tandem mass spectrometry. The C 50 carotenoids bacterioruberin and its derivatives monoanhydrobacterioruberin and bisanhydrobacterioruberin were found to be the predominant carotenoids. The antioxidant capacities of the carotenoids from these strains were significantly higher than β-carotene as determined by 1,1-diphenyl-2-picrylhydrazyl radical scavenging assay. The antihemolytic activities of these carotenoid extracts against H 2 O 2 -induced hemolysis in mouse erythrocytes were 3.9-6.3 times higher than β-carotene. A dose-dependent in vitro antiproliferative activity against HepG2 cells was observed for the extract from Hgm. limi, while that from Hpn. vescus exhibited a relatively high activity in a dose-independent manner. These results suggested that halophilic archaea could be considered as an alternative source of natural carotenoids with high antioxidant, antihemolytic, and anticancer activity.

  17. Transcription-coupled repair of UV damage in the halophilic archaea.

    Science.gov (United States)

    Stantial, Nicole; Dumpe, Jarrod; Pietrosimone, Kathryn; Baltazar, Felicia; Crowley, David J

    2016-05-01

    Transcription-coupled repair (TCR) is a subpathway of nucleotide excision repair (NER) in which excision repair proteins are targeted to RNA polymerase-arresting lesions located in the transcribed strand of active genes. TCR has been documented in a variety of bacterial and eukaryotic organisms but has yet to be observed in the Archaea. We used Halobacterium sp. NRC-1 and Haloferax volcanii to determine if TCR occurs in the halophilic archaea. Following UV irradiation of exponentially growing cultures, we quantified the rate of repair of cyclobutane pyrimidine dimers in the two strands of the rpoB2B1A1A2 and the trpDFEG operons of Halobacterium sp. NRC-1 and the pts operon of H. volcanii through the use of a Southern blot assay and strand-specific probes. TCR was observed in all three operons and was dependent on the NER gene uvrA in Halobacterium sp. NRC-1, but not in H. volcanii. The halophilic archaea likely employ a novel mechanism for TCR in which an as yet unknown coupling factor recognizes the arrested archaeal RNA polymerase complex and recruits certain NER proteins to complete the process. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Respiratory quinones in Archaea: phylogenetic distribution and application as biomarkers in the marine environment.

    Science.gov (United States)

    Elling, Felix J; Becker, Kevin W; Könneke, Martin; Schröder, Jan M; Kellermann, Matthias Y; Thomm, Michael; Hinrichs, Kai-Uwe

    2016-02-01

    The distribution of respiratory quinone electron carriers among cultivated organisms provides clues on both the taxonomy of their producers and the redox processes these are mediating. Our study of the quinone inventories of 25 archaeal species belonging to the phyla Eury-, Cren- and Thaumarchaeota facilitates their use as chemotaxonomic markers for ecologically important archaeal clades. Saturated and monounsaturated menaquinones with six isoprenoid units forming the alkyl chain may serve as chemotaxonomic markers for Thaumarchaeota. Other diagnostic biomarkers are thiophene-bearing quinones for Sulfolobales and methanophenazines as functional quinone analogues of the Methanosarcinales. The ubiquity of saturated menaquinones in the Archaea in comparison to Bacteria suggests that these compounds may represent an ancestral and diagnostic feature of the Archaea. Overlap between quinone compositions of distinct thermophilic and halophilic archaea and bacteria may indicate lateral gene transfer. The biomarker potential of thaumarchaeal quinones was exemplarily demonstrated on a water column profile of the Black Sea. Both, thaumarchaeal quinones and membrane lipids showed similar distributions with maxima at the chemocline. Quinone distributions indicate that Thaumarchaeota dominate respiratory activity at a narrow interval in the chemocline, while they contribute only 9% to the microbial biomass at this depth, as determined by membrane lipid analysis. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

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

    Science.gov (United States)

    Verhaart, Marcel R A; Bielen, Abraham A M; van der Oost, John; Stams, Alfons J M; Kengen, Servé 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 promising is this respect. In addition to the high polysaccharide-hydrolysing capacities of many of these organisms, an important advantage is their ability to use most of the reducing equivalents (e.g. NADH, reduced ferredoxin) formed during glycolysis for the production of hydrogen, enabling H2/hexose ratios of between 3.0 and 4.0. So, despite the fact that the hydrogen-yielding reactions, especially the one from NADH, are thermodynamically unfavourable, high hydrogen yields are obtained. In this review we focus on three different mechanisms that are employed by a few model organisms, viz. Caldicellulosiruptor saccharolyticus and Thermoanaerobacter tengcongensis, Thermotoga maritima, and Pyrococcus furiosus, to efficiently produce hydrogen. In addition, recent developments to improve hydrogen production by hyperthermophilic and extremely thermophilic bacteria and archaea are discussed.

  20. Genetic diversity of archaea in deep-sea hydrothermal vent environments.

    Science.gov (United States)

    Takai, K; Horikoshi, K

    1999-08-01

    Molecular phylogenetic analysis of naturally occurring archaeal communities in deep-sea hydrothermal vent environments was carried out by PCR-mediated small subunit rRNA gene (SSU rDNA) sequencing. As determined through partial sequencing of rDNA clones amplified with archaea-specific primers, the archaeal populations in deep-sea hydrothermal vent environments showed a great genetic diversity, and most members of these populations appeared to be uncultivated and unidentified organisms. In the phylogenetic analysis, a number of rDNA sequences obtained from deep-sea hydrothermal vents were placed in deep lineages of the crenarchaeotic phylum prior to the divergence of cultivated thermophilic members of the crenarchaeota or between thermophilic members of the euryarchaeota and members of the methanogen-halophile clade. Whole cell in situ hybridization analysis suggested that some microorganisms of novel phylotypes predicted by molecular phylogenetic analysis were likely present in deep-sea hydrothermal vent environments. These findings expand our view of the genetic diversity of archaea in deep-sea hydrothermal vent environments and of the phylogenetic organization of archaea.

  1. RNA degradation in Archaea and Gram-negative bacteria different from Escherichia coli.

    Science.gov (United States)

    Evguenieva-Hackenberg, Elena; Klug, Gabriele

    2009-01-01

    Exoribonucleolytic and endoribonucleolytic activities are important for controlled degradation of RNA and contribute to the regulation of gene expression at the posttranscriptional level by influencing the half-lives of specific messenger RNAs. The RNA half-lives are determined by the characteristics of the RNA substrates and by the availability and the properties of the involved proteins-ribonucleases and assisting polypeptides. Much is known about RNA degradation in Eukarya and Bacteria, but there is limited information about RNA-degrading enzymes and RNA destabilizing or stabilizing elements in the domain of the Archaea. The recent progress in the understanding of the structure and function of the archaeal exosome, a protein complex with RNA-degrading and RNA-tailing capabilities, has given some first insights into the mechanisms of RNA degradation in the third domain of life and into the evolution of RNA-degrading enzymes. Moreover, other archaeal RNases with degrading potential have been described and a new mechanism for protection of the 5'-end of RNA in Archaea was discovered. Here, we summarize the current knowledge on RNA degradation in the Archaea. Additionally, RNA degradation mechanisms in Rhodobacter capsulatus and Pseudomonas syringae are compared to those in the major model organism for Gram-negatives, Escherichia coli, which dominates our view on RNA degradation in Bacteria.

  2. 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.

  3. The growing tree of Archaea: new perspectives on their diversity, evolution and ecology.

    Science.gov (United States)

    Adam, Panagiotis S; Borrel, Guillaume; Brochier-Armanet, Céline; Gribaldo, Simonetta

    2017-11-01

    The Archaea occupy a key position in the Tree of Life, and are a major fraction of microbial diversity. Abundant in soils, ocean sediments and the water column, they have crucial roles in processes mediating global carbon and nutrient fluxes. Moreover, they represent an important component of the human microbiome, where their role in health and disease is still unclear. The development of culture-independent sequencing techniques has provided unprecedented access to genomic data from a large number of so far inaccessible archaeal lineages. This is revolutionizing our view of the diversity and metabolic potential of the Archaea in a wide variety of environments, an important step toward understanding their ecological role. The archaeal tree is being rapidly filled up with new branches constituting phyla, classes and orders, generating novel challenges for high-rank systematics, and providing key information for dissecting the origin of this domain, the evolutionary trajectories that have shaped its current diversity, and its relationships with Bacteria and Eukarya. The present picture is that of a huge diversity of the Archaea, which we are only starting to explore.

  4. Anaerobic thermophilic culture-system

    Energy Technology Data Exchange (ETDEWEB)

    Ljungdahl, L G; Wiegel, J K.W.

    1981-04-14

    A mixed culture system of Thermoanaerobacter ethanolicus and Clostridium thermocellum is employed for anaerobic, thermophilic ethanol fermentation of cellulose. By cellulase action, monosaccharides are formed which inhibit the growth of C. thermocellum, but are fermented by T. ethanolicus. Thus, at a regulated pH-value of 7.5, this mixed culture system of micro organisms results in a cellulose fermentation with a considerably higher ethanol yield.

  5. Endocarditis caused by anaerobic bacteria.

    Science.gov (United States)

    Kestler, M; Muñoz, P; Marín, M; Goenaga, M A; Idígoras Viedma, P; de Alarcón, A; Lepe, J A; Sousa Regueiro, D; Bravo-Ferrer, J M; Pajarón, M; Costas, C; García-López, M V; Hidalgo-Tenorio, C; Moreno, M; Bouza, E

    2017-10-01

    Infective endocarditis (IE) caused by anaerobic bacteria is a rare and poorly characterized disease. Most data reported in the literature are from case reports [1-3]. Therefore, we assessed the situation of anaerobic IE (AIE) in Spain using the database of the Spanish Collaboration on Endocarditis (GAMES). We performed a prospective study from 2008 to 2016 in 26 Spanish centers. We included 2491 consecutive cases of definite IE (Duke criteria). Anaerobic bacteria caused 22 cases (0.9%) of definite IE. Median age was 66 years (IQR, 56-73), and 19 (86.4%) patients were men. Most patients (14 [63.6%]) had prosthetic valve IE and all episodes were left-sided: aortic valves, 12 (54.5%); and mitral valves, 8 (36.4%). The most common pathogens were Propionibacterium acnes (14 [63.6%]), Lactobacillus spp (3 [13.63%]), and Clostridium spp. (2 [9.0%]), and the infection was mainly odontogenic. Fifteen of the 22 patients (68.2%) underwent cardiac surgery. Mortality was 18.2% during admission and 5.5% after 1 year of follow-up. When patients with AIE were compared with the rest of the cohort, we found that although those with AIE had a similar age and Charlson comorbidity index, they were more likely to have community-acquired IE (86.4% vs. 60.9%, p = 0.01), have undergone cardiac surgery (68.2% vs 48.7% p = 0.06), and have had lower mortality rates during admission (18.2% vs. 27.3%). IE due to anaerobic bacteria is an uncommon disease that affects mainly prosthetic valves and frequently requires surgery. Otherwise, there are no major differences between AIE and IE caused by other microorganisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. 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.

  7. Anaerobic digestion of food waste - Effect of recirculation and temperature on performance and microbiology.

    Science.gov (United States)

    Zamanzadeh, Mirzaman; Hagen, Live H; Svensson, Kine; Linjordet, Roar; Horn, Svein J

    2016-06-01

    Recirculation of digestate was investigated as a strategy to dilute the food waste before feeding to anaerobic digesters, and its effects on microbial community structure and performance were studied. Two anaerobic digesters with digestate recirculation were operated at 37 °C (MD + R) and 55 °C (TD + R) and compared to two additional digesters without digestate recirculation operated at the same temperatures (MD and TD). The MD + R digester demonstrated quite stable and similar performance to the MD digester in terms of the methane yield (around 480 mL CH4 per gVSadded). In both MD and MD + R Methanosaeta was the dominant archaea. However, the bacterial community structure was significantly different in the two digesters. Firmicutes dominated in the MD + R, while Chloroflexi was the dominant phylum in the MD. Regarding the thermophilic digesters, the TD + R showed the lowest methane yield (401 mL CH4 per gVSadded) and accumulation of VFAs. In contrast to the mesophilic digesters, the microbial communities in the thermophilic digesters were rather similar, consisting mainly of the phyla Firmicutes, Thermotoga, Synergistetes and the hydrogenotrophic methanogen Methanothermobacter. The impact of ammonia inhibition was different depending on the digesters configurations and operating temperatures. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Efficacies of Various Anaerobic Starter Seeds for Biogas Production from Different Types of Wastewater

    Directory of Open Access Journals (Sweden)

    Pawinee Chaiprasert

    2017-01-01

    Full Text Available Various anaerobic starter seeds from different sources were investigated for their efficacies in treatment of different types of wastewater. Six combinations of starter seeds and wastewaters were selected out of 25 combination batch experiments and operated in semicontinuous reactors. It was noticed that the efficacies of various anaerobic starter seeds for biogas production from different types of wastewater in terms of reactor performance and stability were depended on wastewater characteristics and F/M ratio affecting microbial community and their microbial activities. However, exogenous starter seed can be used across different types of wastewater with or without acclimatization. Four reactors reached the targeted OLR of 2 kg COD/m3·d with high performance and stability except for concentrated rubber wastewater (RBw, even using high active starter seeds of cassava starch (CSs and palm oil (POs. The toxic compounds in RBw such as ammonia and sulfate might also adversely affect methanogenic activity in CSsRBw and POsRBw reactors. DGGE analysis showed that propionate utilizers, Smithella propionica strain LYP and Syntrophus sp., were detected in all samples. For Archaea domain, methylotrophic, hydrogenotrophic, and acetoclastic methanogens were also detected. Syntrophic relationships were assumed between propionate utilizers and methanogens as acetate/H2 producers and utilizers, respectively.

  9. A portable anaerobic microbioreactor reveals optimum growth conditions for the methanogen Methanosaeta concilii.

    Science.gov (United States)

    Steinhaus, Benjamin; Garcia, Marcelo L; Shen, Amy Q; Angenent, Largus T

    2007-03-01

    Conventional studies of the optimum growth conditions for methanogens (methane-producing, obligate anaerobic archaea) are typically conducted with serum bottles or bioreactors. The use of microfluidics to culture methanogens allows direct microscopic observations of the time-integrated response of growth. Here, we developed a microbioreactor (microBR) with approximately 1-microl microchannels to study some optimum growth conditions for the methanogen Methanosaeta concilii. The microBR is contained in an anaerobic chamber specifically designed to place it directly onto an inverted light microscope stage while maintaining a N2-CO2 environment. The methanogen was cultured for months inside microchannels of different widths. Channel width was manipulated to create various fluid velocities, allowing the direct study of the behavior and responses of M. concilii to various shear stresses and revealing an optimum shear level of approximately 20 to 35 microPa. Gradients in a single microchannel were then used to find an optimum pH level of 7.6 and an optimum total NH4-N concentration of less than 1,100 mg/liter (<47 mg/liter as free NH3-N) for M. concilii under conditions of the previously determined ideal shear stress and pH and at a temperature of 35 degrees C.

  10. Electron acceptors for anaerobic oxidation of methane drive microbial community structure and diversity in mud volcanoes.

    Science.gov (United States)

    Ren, Ge; Ma, Anzhou; Zhang, Yanfen; Deng, Ye; Zheng, Guodong; Zhuang, Xuliang; Zhuang, Guoqiang; Fortin, Danielle

    2018-04-06

    Mud volcanoes (MVs) emit globally significant quantities of methane into the atmosphere, however, methane cycling in such environments is not yet fully understood, as the roles of microbes and their associated biogeochemical processes have been largely overlooked. Here, we used data from high-throughput sequencing of microbial 16S rRNA gene amplicons from six MVs in the Junggar Basin in northwest China to quantify patterns of diversity and characterize the community structure of archaea and bacteria. We found anaerobic methanotrophs and diverse sulfate- and iron-reducing microbes in all of the samples, and the diversity of both archaeal and bacterial communities was strongly linked to the concentrations of sulfate, iron and nitrate, which could act as electron acceptors in anaerobic oxidation of methane (AOM). The impacts of sulfate/iron/nitrate on AOM in the MVs were verified by microcosm experiments. Further, two representative MVs were selected to explore the microbial interactions based on phylogenetic molecular ecological networks. The sites showed distinct network structures, key species and microbial interactions, with more complex and numerous linkages between methane-cycling microbes and their partners being observed in the iron/sulfate-rich MV. These findings suggest that electron acceptors are important factors driving the structure of microbial communities in these methane-rich environments. © 2018 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  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

  12. 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 for these ......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...

  13. In situ identification of the synthrophic protein fermentative Coprothermobacter spp. involved in the thermophilic anaerobic digestion process.

    Science.gov (United States)

    Gagliano, Maria Cristina; Braguglia, Camilla Maria; Rossetti, Simona

    2014-09-01

    Thermophilic bacteria have recently attracted great attention because of their potential application in improving different biochemical processes such as anaerobic digestion of various substrates, wastewater treatment or hydrogen production. In this study we report on the design of a specific 16S rRNA-targeted oligonucleotide probe for detecting members of Coprothermobacter genus characterized by a strong protease activity to degrade proteins and peptides. The newly designed CTH485 probe and helper probes hCTH429 and hCTH439 were optimized for use in fluorescence in situ hybridization (FISH) on thermophilic anaerobic sludge samples. In situ probing revealed that thermo-adaptive mechanisms shaping the 16S rRNA gene may affect the identification of thermophilic microorganisms. The novel developed FISH probe extends the possibility to study the widespread thermophilic syntrophic interaction of Coprothermobacter spp. with hydrogenotrophic methanogenic archaea, whose establishment is a great benefit for the whole anaerobic system. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  14. Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge

    Directory of Open Access Journals (Sweden)

    Simon J. McIlroy

    2017-06-01

    Full Text Available Anaerobic digestion for biogas production is reliant on the tightly coupled synergistic activities of complex microbial consortia. Members of the uncultured A6 phylotype, within the phylum Chloroflexi, are among the most abundant genus-level-taxa of mesophilic anaerobic digester systems treating primary and surplus sludge from wastewater treatment plants, yet are known only by their 16S rRNA gene sequence. This study applied metagenomics to obtain a complete circular genome (2.57 Mbp from a representative of the A6 taxon. Preliminary annotation of the genome indicates these organisms to be anaerobic chemoorganoheterotrophs with a fermentative metabolism. Given their observed abundance, they are likely important primary fermenters in digester systems. Application of fluorescence in situ hybridisation probes designed in this study revealed their morphology to be short filaments present within the flocs. The A6 were sometimes co-located with the filamentous Archaea Methanosaeta spp. suggesting potential undetermined synergistic relationships. Based on its genome sequence and morphology we propose the species name Brevefilum fermentans gen. nov. sp. nov.

  15. Effects of chlortetracycline, Cu and their combination on the performance and microbial community dynamics in swine manure anaerobic digestion.

    Science.gov (United States)

    Wang, Rui; Zhang, Junya; Liu, Jibao; Yu, Dawei; Zhong, Hui; Wang, Yawei; Chen, Meixue; Tong, Juan; Wei, Yuansong

    2018-05-01

    Swine manure was typical for the combined pollution of heavy metals and antibiotics. The effects of widely used veterinary antibiotic chlortetracycline (CTC), Cu and their combination on swine manure anaerobic digestion performance and microbial community have never been investigated. Thus, four 2L anaerobic digestion reactors were established including reactor A (control), B (CTC spiked by 0.5g/kg dry weight, dw), C (Cu spiked by 5g/kg dw) and D (combination of CTC, 0.5g/kg dw, and Cu, 5g/kg dw), and dynamics of bacterial and archaeal community structure was investigated using high throughput sequencing method. Results showed that addition of CTC and Cu separately could increase the total biogas production by 21.6% and 15.8%, respectively, while combination of CTC and Cu severely inhibited anaerobic digestion (by 30.3%). Furthermore, corresponding to different stages and reactors, four kinds of microbes including bacteria and archaea were described in detail, and the effects of CTC, Cu and their combination mainly occurred at hydrolysis and acidification phases. The addition of Cu alone changed the dynamics of archaeal community significantly. It was genus Methanomassiliicoccus that dominated at the active methane production for A, B and D, while it was genus Methanobrevibacter and Methanoculleus for C. Copyright © 2017. Published by Elsevier B.V.

  16. Physiology, anaerobes, and the origin of mitosing cells 50 years on.

    Science.gov (United States)

    Martin, William F

    2017-12-07

    Endosymbiotic theory posits that some organelles or structures of eukaryotic cells stem from free-living prokaryotes that became endosymbionts within a host cell. Endosymbiosis has a long and turbulent history of controversy and debate going back over 100 years. The 1967 paper by Lynn Sagan (later Lynn Margulis) forced a reluctant field to take endosymbiotic theory seriously and to incorporate it into the fabric of evolutionary thinking. Margulis envisaged three cellular partners associating in series at eukaryotic origin: the host (an engulfing bacterium), the mitochondrion (a respiring bacterium), and the flagellum (a spirochaete), with lineages descended from that flagellated eukaryote subsequently acquiring plastids from cyanobacteria, but on multiple different occasions in her 1967 account. Today, the endosymbiotic origin of mitochondria and plastids (each single events, the data now say) is uncontested textbook knowledge. The host has been more elusive, recent findings identifying it as a member of the archaea, not as a sister group of the archaea. Margulis's proposal for a spirochaete origin of flagellae was abandoned by everyone except her, because no data ever came around to support the idea. Her 1967 proposal that mitochondria and plastids arose from different endosymbionts was novel. The paper presented an appealing narrative that linked the origin of mitochondria with oxygen in Earth history: cyanobacteria make oxygen, oxygen starts accumulating in the atmosphere about 2.4 billion years ago, oxygen begets oxygen-respiring bacteria that become mitochondria via symbiosis, followed by later (numerous) multiple, independent symbioses involving cyanobacteria that brought photosynthesis to eukaryotes. With the focus on oxygen, Margulis's account of eukaryote origin was however unprepared to accommodate the discovery of mitochondria in eukaryotic anaerobes. Today's oxygen narrative has it that the oceans were anoxic up until about 580 million years ago, while

  17. 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...... regarding the treatment of xenobiotics is shown with the focus on the UASB reactor, but the applicability of other reactor designs for treatment of hazardous waste is also included. Bioaugmentation has proved to be a viable technique to enhance a specific activity in anaerobic reactors and recent research...

  18. Physiologically anaerobic microorganisms of the deep subsurface

    Energy Technology Data Exchange (ETDEWEB)

    Stevens, S.E. Jr.; Chung, K.T.

    1991-06-01

    This study seeks to determine numbers, diversity, and morphology of anaerobic microorganisms in 15 samples of subsurface material from the Idaho National Engineering Laboratory, in 18 samples from the Hanford Reservation and in 1 rock sample from the Nevada Test Site; set up long term experiments on the chemical activities of anaerobic microorganisms based on these same samples; work to improve methods for the micro-scale determination of in situ anaerobic microbial activity;and to begin to isolate anaerobes from these samples into axenic culture with identification of the axenic isolates.

  19. Comparison of various microbial inocula for the efficient anaerobic digestion of Laminaria hyperborea.

    Science.gov (United States)

    Sutherland, Alastair D; Varela, Joao C

    2014-01-23

    The hydrolysis of seaweed polysaccharides is the rate limiting step in anaerobic digestion (AD) of seaweeds. Seven different microbial inocula and a mixture of these (inoculum 8) were therefore compared in triplicate, each grown over four weeks in static culture for the ability to degrade Laminaria hyperborea seaweed and produce methane through AD. All the inocula could degrade L. hyperborea and produce methane to some extent. However, an inoculum of slurry from a human sewage anaerobic digester, one of rumen contents from seaweed-eating North Ronaldsay sheep and inoculum 8 used most seaweed volatile solids (VS) (means ranged between 59 and 68% used), suggesting that these each had efficient seaweed polysaccharide digesting bacteria. The human sewage inoculum, an inoculum of anaerobic marine mud mixed with rotting seaweed and inoculum 8 all developed to give higher volumes of methane (means between 41 and 62.5 ml g-1 of seaweed VS by week four) ,compared to other inocula (means between 3.5 and 27.5 ml g-1 VS). Inoculum 8 also gave the highest acetate production (6.5 mmol g-1 VS) in a single-stage fermenter AD system and produced most methane (8.4 mL mmol acetate-1) in phase II of a two-stage AD system. Overall inoculum 8 was found to be the most efficient inoculum for AD of seaweed. The study therefore showed that selection and inclusion of efficient polysaccharide hydrolysing bacteria and methanogenic archaea in an inoculum offer increased methane productivity in AD of L. hyperborea. This inoculum will now being tested in larger scale (10L) continuously stirred reactors optimised for feed rate and retention time to determine maximum methane production under single-stage and two-stage AD systems.

  20. Evaluating the effects of activated carbon on methane generation and the fate of antibiotic resistant genes and class I integrons during anaerobic digestion of solid organic wastes.

    Science.gov (United States)

    Zhang, Jingxin; Mao, Feijian; Loh, Kai-Chee; Gin, Karina Yew-Hoong; Dai, Yanjun; Tong, Yen Wah

    2018-02-01

    The effects of activated carbon (AC) on methane production and the fate of antibiotic resistance genes (ARGs) were evaluated through comparing the anaerobic digestion performance and transformation of ARGs among anaerobic mono-digestion of food waste, co-digestion of food waste and chicken manure, and co-digestion of food waste and waste activated sludge. Results showed that adding AC in anaerobic digesters improved methane yield by at least double through the enrichment of bacteria and archaea. Conventional digestion process showed ability in removing certain types of ARGs, such as tetA, tetX, sul1, sul2, cmlA, floR, and intl1. Supplementing AC in anaerobic digester enhanced the removal of most of the ARGs in mono-digestion of food waste. The effects tended to be minimal in co-digestion of co-substrates such as chicken manure and waste activated sludge, both of which contain a certain amount of antibiotics. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. ANAEROBIC BIODEGRADATION OF A BIODEGRADABLE MATERIAL UNDER ANAEROBIC - THERMOPHILIC DIGESTION

    Directory of Open Access Journals (Sweden)

    RICARDO CAMACHO-MUÑOZ

    2014-12-01

    Full Text Available This paper dertermined the anaerobic biodegradation of a polymer obtained by extrusion process of native cassava starch, polylactic acid and polycaprolactone. Initially a thermophilic - methanogenic inoculum was prepared from urban solid waste. The gas final methane concentration and medium’s pH reached values of 59,6% and 7,89 respectively. The assay assembly was carried out according ASTM D5511 standard. The biodegradation percent of used materials after 15 day of digestion were: 77,49%, 61,27%, 0,31% for cellulose, sample and polyethylene respectively. Due cellulose showed biodegradation levels higher than 70% it’s deduced that the inoculum conditions were appropriate. A biodegradation level of 61,27%, 59,35% of methane concentration in sample’s evolved gas and a medium’s finale pH of 7,71 in sample’s vessels, reveal the extruded polymer´s capacity to be anaerobically degraded under thermophilic- high solid concentration conditions.

  2. Activity, Microenvironments, and Community Structure of Aerobic and Anaerobic Ammonium Oxidizing Prokaryotes in Estuarine Sediment (Randers Fjord, DK)

    DEFF Research Database (Denmark)

    Schramm, Andreas; Revsbech, Niels Peter; Dalsgaard, Tage

    2006-01-01

    ACTIVITY, MICROENVIRONMENTS, AND COMMUNITY STRUCTURE OF AEROBIC AND ANAEROBIC AMMONIUM OXIDIZING PROKARYOTES IN ESTUARINE SEDIMENT (RANDERS FJORD, DK) A. Schramm 1, N.P. Revsbech 1, T. Dalsgaard 2, E. Piña-Ochoa 3, J. de la Torré 4, D.A. Stahl 4, N. Risgaard-Petersen 2 1 Department of Biological...... conversion of ammonium with nitrite to N2, is increasingly recognized as link in the aquatic nitrogen cycle. However, factors regulating the occurrence and activity of anammox bacteria are still poorly understood. Besides the influence of abiotic factors, anammox might be controlled by either aerobic ammonia...... oxidizing bacteria and archaea (AOB and AOA) or nitrate-reducing/denitrifying bacteria via their supply of nitrite. Along the Randers Fjord estuary (Denmark), gradients of salinity, nutrients, and organic loading can be observed, and anammox has been detected previously at some sites. The aim of this study...

  3. Method for anaerobic fermentation and biogas production

    DEFF Research Database (Denmark)

    2013-01-01

    The present invention relates to a method for biomass processing, anaerobic fermentation of the processed biomass, and the production biogas. In particular, the invention relates to a system and method for generating biogas from anaerobic fermentation of processed organic material that comprises...

  4. Integrated anaerobic and aerobic treatment of sewage

    NARCIS (Netherlands)

    Wang, K.

    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-)

  5. Anaerobic exercise - Induced changes in serum mineral ...

    African Journals Online (AJOL)

    Anaerobic exercise, a non 02 – dependent energy metabolism leads to transient metabolic changes, which are corrected gradually by homestatic mechanism. We investigated in eight male subjects, the effects of anaerobic exercise after a day sedentary activity on serum mineral concentration. There was significant ...

  6. 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

  7. Boosting biomethane yield and production rate with graphene: The potential of direct interspecies electron transfer in anaerobic digestion.

    Science.gov (United States)

    Lin, Richen; Cheng, Jun; Zhang, Jiabei; Zhou, Junhu; Cen, Kefa; Murphy, Jerry D

    2017-09-01

    Interspecies electron transfer between bacteria and archaea plays a vital role in enhancing energy efficiency of anaerobic digestion (AD). Conductive carbon materials (i.e. graphene nanomaterial and activated charcoal) were assessed to enhance AD of ethanol (a key intermediate product after acidogenesis of algae). The addition of graphene (1.0g/L) resulted in the highest biomethane yield (695.0±9.1mL/g) and production rate (95.7±7.6mL/g/d), corresponding to an enhancement of 25.0% in biomethane yield and 19.5% in production rate. The ethanol degradation constant was accordingly improved by 29.1% in the presence of graphene. Microbial analyses revealed that electrogenic bacteria of Geobacter and Pseudomonas along with archaea Methanobacterium and Methanospirillum might participate in direct interspecies electron transfer (DIET). Theoretical calculations provided evidence that graphene-based DIET can sustained a much higher electron transfer flux than conventional hydrogen transfer. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts in a sulfidic marine habitat.

    Science.gov (United States)

    Muller, Félix; Brissac, Terry; Le Bris, Nadine; Felbeck, Horst; Gros, Olivier

    2010-08-01

    Archaea may be involved in global energy cycles, and are known for their ability to interact with eukaryotic species (sponges, corals and ascidians) or as archaeal-bacterial consortia. The recently proposed phylum Thaumarchaeota may represent the deepest branching lineage in the archaeal phylogeny emerging before the divergence between Euryarchaeota and Crenarchaeota. Here we report the first characterization of two marine thaumarchaeal species from shallow waters that consist of multiple giant cells. One species is coated with sulfur-oxidizing γ-Proteobacteria. These new uncultured thaumarchaeal species are able to live in the sulfide-rich environments of a tropical mangrove swamp, either on living tissues such as roots or on various kinds of materials such as stones, sunken woods, etc. These archaea and archaea/bacteria associations have been studied using light microscopy, transmission electron microscopy and scanning electron microscopy. Species identification of archaeons and the putative bacterial symbiont have been assessed by 16S small subunit ribosomal RNA analysis. The sulfur-oxidizing ability of the bacteria has been assessed by genetic investigation on alpha-subunit of the adenosine-5'-phosphosulfate reductase/oxidase's (AprA). Species identifications have been confirmed by fluorescence in situ hybridization using specific probes designed in this study. In this article, we describe two new giant archaeal species that form the biggest archaeal filaments ever observed. One of these species is covered by a specific biofilm of sulfur-oxidizing γ-Proteobacteria. This study highlights an unexpected morphological and genetic diversity of the phylum Thaumarchaeota. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

  9. Stoichiometric and kinetic analysis of extreme halophilic Archaea on various substrates in a corrosion resistant bioreactor.

    Science.gov (United States)

    Lorantfy, Bettina; Seyer, Bernhard; Herwig, Christoph

    2014-01-25

    Extreme halophilic Archaea are extremophile species which can thrive in hypersaline environments of up to 3-5 M sodium chloride concentration. Although their ecology and physiology are widely identified on the microbiological level, little emphasis has been laid on quantitative bioprocess development with extreme halophiles. The goal of this study was to establish, on the one hand, a methodological basis for quantitative bioprocess analysis of extreme halophilic Archaea with an extreme halophilic strain as an example. Firstly, as a novel usage, a corrosion resistant bioreactor setup for extreme halophiles has been implemented. Then, paying special attention to total bioprocess quantification approaches, an indirect method for biomass quantification using on-line process signals was introduced. Subsequently, robust quantitative data evaluation methods for halophiles could be developed, providing defined and controlled cultivation conditions in the bioreactor and therefore obtaining suitable quality of on-line as well as off-line datasets. On the other hand, new physiological results of extreme halophiles in bioreactor have also been obtained based on the quantitative methodological tools. For the first time, quantitative data on stoichiometry and kinetics were collected and evaluated on different carbon sources. The results on various substrates were interpreted, with proposed metabolic mechanisms, by linking to the reported primary carbon metabolism of extreme halophilic Archaea. Moreover, results of chemostat cultures demonstrated that extreme halophilic organisms show Monod-kinetics on different sole carbon sources. A diauxic growth pattern was described on a mixture of substrates in batch cultivations. In addition, the methodologies presented here enable one to characterize the utilized strain Haloferax mediterranei (HFX) as a potential new host organism. Thus, this study offers a strong methodological basis as well as a fundamental physiological assessment for

  10. 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.

  11. Computational Exploration of Putative LuxR Solos in Archaea and Their Functional Implications in Quorum Sensing

    Science.gov (United States)

    Rajput, Akanksha; Kumar, Manoj

    2017-01-01

    LuxR solos are unexplored in Archaea, despite their vital role in the bacterial regulatory network. They assist bacteria in perceiving acyl homoserine lactones (AHLs) and/or non-AHLs signaling molecules for establishing intraspecies, interspecies, and interkingdom communication. In this study, we explored the potential LuxR solos of Archaea from InterPro v62.0 meta-database employing taxonomic, probable function, distribution, and evolutionary aspects to decipher their role in quorum sensing (QS). Our bioinformatics analyses showed that putative LuxR solos of Archaea shared few conserved domains with bacterial LuxR despite having less similarity within proteins. Functional characterization revealed their ability to bind various AHLs and/or non-AHLs signaling molecules that involve in QS cascades alike bacteria. Further, the phylogenetic study indicates that Archaeal LuxR solos (with less substitution per site) evolved divergently from bacteria and share distant homology along with instances of horizontal gene transfer. Moreover, Archaea possessing putative LuxR solos, exhibit the correlation between taxonomy and ecological niche despite being the inhabitant of diverse habitats like halophilic, thermophilic, barophilic, methanogenic, and chemolithotrophic. Therefore, this study would shed light in deciphering the role of the putative LuxR solos of Archaea to adapt varied habitats via multilevel communication with other organisms using QS. PMID:28515720

  12. Computational Exploration of Putative LuxR Solos in Archaea and Their Functional Implications in Quorum Sensing

    Directory of Open Access Journals (Sweden)

    Akanksha Rajput

    2017-05-01

    Full Text Available LuxR solos are unexplored in Archaea, despite their vital role in the bacterial regulatory network. They assist bacteria in perceiving acyl homoserine lactones (AHLs and/or non-AHLs signaling molecules for establishing intraspecies, interspecies, and interkingdom communication. In this study, we explored the potential LuxR solos of Archaea from InterPro v62.0 meta-database employing taxonomic, probable function, distribution, and evolutionary aspects to decipher their role in quorum sensing (QS. Our bioinformatics analyses showed that putative LuxR solos of Archaea shared few conserved domains with bacterial LuxR despite having less similarity within proteins. Functional characterization revealed their ability to bind various AHLs and/or non-AHLs signaling molecules that involve in QS cascades alike bacteria. Further, the phylogenetic study indicates that Archaeal LuxR solos (with less substitution per site evolved divergently from bacteria and share distant homology along with instances of horizontal gene transfer. Moreover, Archaea possessing putative LuxR solos, exhibit the correlation between taxonomy and ecological niche despite being the inhabitant of diverse habitats like halophilic, thermophilic, barophilic, methanogenic, and chemolithotrophic. Therefore, this study would shed light in deciphering the role of the putative LuxR solos of Archaea to adapt varied habitats via multilevel communication with other organisms using QS.

  13. Archaea como componentes da microbiota endofítica de frutos do cafeeiro

    OpenAIRE

    Oliveira, Marcelo Nagem Valério de

    2009-01-01

    Este é o primeiro estudo de diversidade genética da comunidade de Archaea associada a frutos de café (Coffea arabica L.). Ele foi realizado em amostras de frutos no estádio cereja das cultivares Bourbon Amarelo, Bourbon Vermelho, Catuaí Amarelo, Catuaí Vermelho e Catucaí Vermelho, em diferentes altitudes. A diversidade de arqueas presentes durante a secagem natural de grãos despolpados em terreiro revestido com cimento também foi estudada. A adição de proteases durante a etapa de lise celular...

  14. Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment.

    Science.gov (United States)

    Wurzbacher, Christian; Fuchs, Andrea; Attermeyer, Katrin; Frindte, Katharina; Grossart, Hans-Peter; Hupfer, Michael; Casper, Peter; Monaghan, Michael T

    2017-04-08

    Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments. We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to 137 Cs dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota. Community β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO 2 and CH 4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions. By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and

  15. Uncovering Mechanisms for Repair and Protection in Cold Environments Through Studies of Cold Adapted Archaea

    Science.gov (United States)

    2009-12-18

    Cpn60) subunits is more abundant during growth at 4°C compared to 23°C. Consistent with this, cold shock studies in thermophilic archaea, and...helicases (Mbur_0245, Mbur_1950): These enzymes may be responsible for unwinding secondary structures in messenger RNA, and a role in cold adaptation in M...limiting step, it is unsurprising that these enzymes showed higher abundance at 4ºC. ParA protein (Mbur_2141): ParA ATPases are a ubiquitous

  16. 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.

  17. Reverse-transcriptional gene expression of anammox and ammonia-oxidizing archaea and bacteria in soybean and rice paddy soils of Northeast China.

    Science.gov (United States)

    Wang, Jing; Dong, Hailiang; Wang, Weidong; Gu, Ji-Dong

    2014-03-01

    The relative gene expression of hydrazine oxidoreductase encoding gene (hzo) for anaerobic ammonium oxidizing bacteria (anammox) and ammonia monooxygenase encoding gene (amoA) for both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in Sanjiang Plain soybean and rice paddy soils of Northeast China was investigated by using real-time reverse-transcriptional quantitative PCR. Metabolically active populations of anammox, AOA, and AOB in rice paddy soils were evident by the presence and successful quantification of hzo mRNA and amoA mRNA genes. The expression ratio of amoA gene for both AOA and AOB varied between soybean soils and different rice paddy soils while the expression of hzo gene for anammox was detectable only in rice paddy soils by showing a diverse relative expression ratio in each soil sample. Gene expression of both archaeal and bacterial amoA genes in rice paddy soils differed among the three sampling depths, but that of hzo was not. Both archaeal and bacterial amoA genes showed an increase trend of expression level with continuation of rice paddy cultivation, but the low expression ratio of hzo gene indicated a relatively small contribution of anammox in overall removal of inorganic nitrogen through N2 even under anoxic and high nitrogen input in agriculture. Bacterial amoA gene from two soybean fields and three rice paddy fields were also analyzed for community composition by denaturing gradient gel electrophoresis fingerprint. Community shift was observed between soybean and paddy fields and within each of them. The consistent occurrence of three bands 5, 6, and 7 in all samples showed their high adaptability for both arid cultivation and continuous rice paddy cultivation. Our data suggest that AOA and AOB are playing a more important role in nitrogen transformation in agricultural soils in oxic or anoxic environment and anammox bacteria may also contribute but in a less extent to N transformation in these agricultural soils

  18. Community Structure of Denitrifiers, Bacteria, and Archaea along Redox Gradients in Pacific Northwest Marine Sediments by Terminal Restriction Fragment Length Polymorphism Analysis of Amplified Nitrite Reductase (nirS) and 16S rRNA Genes

    Science.gov (United States)

    Braker, Gesche; Ayala-del-Río, Héctor L.; Devol, Allan H.; Fesefeldt, Andreas; Tiedje, James M.

    2001-01-01

    Steep vertical gradients of oxidants (O2 and NO3−) in Puget Sound and Washington continental margin sediments indicate that aerobic respiration and denitrification occur within the top few millimeters to centimeters. To systematically explore the underlying communities of denitrifiers, Bacteria, and Archaea along redox gradients at distant geographic locations, nitrite reductase (nirS) genes and bacterial and archaeal 16S rRNA genes (rDNAs) were PCR amplified and analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis. The suitablility of T-RFLP analysis for investigating communities of nirS-containing denitrifiers was established by the correspondence of dominant terminal restriction fragments (T-RFs) of nirS to computer-simulated T-RFs of nirS clones. These clones belonged to clusters II, III, and IV from the same cores and were analyzed in a previous study (G. Braker, J. Zhou, L. Wu, A. H. Devol, and J. M. Tiedje, Appl. Environ. Microbiol. 66:2096–2104, 2000). T-RFLP analysis of nirS and bacterial rDNA revealed a high level of functional and phylogenetic diversity, whereas the level of diversity of Archaea was lower. A comparison of T-RFLPs based on the presence or absence of T-RFs and correspondence analysis based on the frequencies and heights of T-RFs allowed us to group sediment samples according to the sampling location and thus clearly distinguish Puget Sound and the Washington margin populations. However, changes in community structure within sediment core sections during the transition from aerobic to anaerobic conditions were minor. Thus, within the top layers of marine sediments, redox gradients seem to result from the differential metabolic activities of populations of similar communities, probably through mixing by marine invertebrates rather than from the development of distinct communities. PMID:11282647

  19. Meta-Analysis of Quantification Methods Shows that Archaea and Bacteria Have Similar Abundances in the Subseafloor

    Science.gov (United States)

    May, Megan K.; Kevorkian, Richard T.; Steen, Andrew D.

    2013-01-01

    There is no universally accepted method to quantify bacteria and archaea in seawater and marine sediments, and different methods have produced conflicting results with the same samples. To identify best practices, we compiled data from 65 studies, plus our own measurements, in which bacteria and archaea were quantified with fluorescent in situ hybridization (FISH), catalyzed reporter deposition FISH (CARD-FISH), polyribonucleotide FISH, or quantitative PCR (qPCR). To estimate efficiency, we defined “yield” to be the sum of bacteria and archaea counted by these techniques divided by the total number of cells. In seawater, the yield was high (median, 71%) and was similar for FISH, CARD-FISH, and polyribonucleotide FISH. In sediments, only measurements by CARD-FISH in which archaeal cells were permeabilized with proteinase K showed high yields (median, 84%). Therefore, the majority of cells in both environments appear to be alive, since they contain intact ribosomes. In sediments, the sum of bacterial and archaeal 16S rRNA gene qPCR counts was not closely related to cell counts, even after accounting for variations in copy numbers per genome. However, qPCR measurements were precise relative to other qPCR measurements made on the same samples. qPCR is therefore a reliable relative quantification method. Inconsistent results for the relative abundance of bacteria versus archaea in deep subsurface sediments were resolved by the removal of CARD-FISH measurements in which lysozyme was used to permeabilize archaeal cells and qPCR measurements which used ARCH516 as an archaeal primer or TaqMan probe. Data from best-practice methods showed that archaea and bacteria decreased as the depth in seawater and marine sediments increased, although archaea decreased more slowly. PMID:24096423

  20. 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.