Methanogenic Microorganisms in Industrial Wastewater Anaerobic Treatment
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Diversity of Bacteria and Archaea in the Deep-Sea Low-Temperature Hydrothermal Sulfide Chimney of the Northeastern Pacific Ocean
African Journal of Biotechnology Vol. 11(2), pp. 337-345, 5 January, 2012 Available online at http://www.academicjournals.org/AJB DOI: 10.5897/AJB11.2692 ISSN 1684–5315 © 2012 Academic Journals Full Length Research Paper Diversity of bacteria and archaea in the deep-sea low-temperature hydrothermal sulfide chimney of the Northeastern Pacific Ocean Xia Ding1*, Xiao-Jue Peng1#, Xiao-Tong Peng2 and Huai-Yang Zhou3 1College of Life Sciences and Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330031, China. 2Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China. 3National Key Laboratory of Marine Geology, Tongji University, Shanghai 200092, China. Accepted 4 November, 2011 Our knowledge of the diversity and role of hydrothermal vents microorganisms has considerably expanded over the past decade, while little is known about the diversity of microorganisms in low-temperature hydrothermal sulfide chimney. In this study, denaturing gradient gel electrophoresis (DGGE) and 16S rDNA sequencing were used to examine the abundance and diversity of microorganisms from the exterior to the interior of the deep sea low-temperature hydrothermal sulfide chimney of the Northeastern Pacific Ocean. DGGE profiles revealed that both bacteria and archaea could be examined in all three zones of the chimney wall and the compositions of microbial communities within different zones were vastly different. Overall, for archaea, cell abundance was greatest in the outermost zone of the chimney wall. For bacteria, there was no significant difference in cell abundance among three zones. In addition, phylogenetic analysis revealed that Verrucomicrobia and Deltaproteobacteria were the predominant bacterial members in exterior zone, beta Proteobacteria were the dominant members in middle zone, and Bacillus were the abundant microorganisms in interior zone. -
Complete Genome Sequence of Methanocorpusculum Labreanum Type Strain Z
Standards in Genomic Sciences (2009) 1: 197-203 DOI:10.4056.sigs.35575 Complete genome sequence of Methanocorpusculum labreanum type strain Z Iain J. Anderson1*, Magdalena Sieprawska-Lupa2, Eugene Goltsman1, Alla Lapidus1, Alex Co- peland1, Tijana Glavina Del Rio1, Hope Tice1, Eileen Dalin1, Kerrie Barry1, Sam Pitluck1, Lo- ren Hauser1,3, Miriam Land1,3, Susan Lucas1, Paul Richardson1, William B. Whitman2, and Nikos C. Kyrpides1 1Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California, USA 2Microbiology Department, University of Georgia, Athens, Georgia, USA 3Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA *Corresponding author: Iain Anderson Keywords: archaea, methanogen, Methanomicrobiales Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicro- biales within the archaeal phylum Euryarchaeota. The type strain Z was isolated from surface sediments of Tar Pit Lake in the La Brea Tar Pits in Los Angeles, California. M. labreanum is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. labreanum type strain Z and its annotation. This is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea. Introduction Methanocorpusculum labreanum is a methanogen the Methanosarcinales are capable of using various belonging to the order Methanomicrobiales within methyl compounds as substrates for methanoge- the archaeal phylum Euryarchaeota. Strain Z is the nesis including acetate, methylamines, and me- type strain of this species. It was isolated from thanol, but Methanomicrobiales are restricted to surface sediments of Tar Pit Lake at the La Brea the same substrates as the Class I methanogens Tar Pits in Los Angeles [1]. -
Methanothermus Fervidus Type Strain (V24S)
UC Davis UC Davis Previously Published Works Title Complete genome sequence of Methanothermus fervidus type strain (V24S). Permalink https://escholarship.org/uc/item/9367m39j Journal Standards in genomic sciences, 3(3) ISSN 1944-3277 Authors Anderson, Iain Djao, Olivier Duplex Ngatchou Misra, Monica et al. Publication Date 2010-11-20 DOI 10.4056/sigs.1283367 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2010) 3:315-324 DOI:10.4056/sigs.1283367 Complete genome sequence of Methanothermus fervidus type strain (V24ST) Iain Anderson1, Olivier Duplex Ngatchou Djao2, Monica Misra1,3, Olga Chertkov1,3, Matt Nolan1, Susan Lucas1, Alla Lapidus1, Tijana Glavina Del Rio1, Hope Tice1, Jan-Fang Cheng1, Roxanne Tapia1,3, Cliff Han1,3, Lynne Goodwin1,3, Sam Pitluck1, Konstantinos Liolios1, Natalia Ivanova1, Konstantinos Mavromatis1, Natalia Mikhailova1, Amrita Pati1, Evelyne Brambilla4, Amy Chen5, Krishna Palaniappan5, Miriam Land1,6, Loren Hauser1,6, Yun-Juan Chang1,6, Cynthia D. Jeffries1,6, Johannes Sikorski4, Stefan Spring4, Manfred Rohde2, Konrad Eichinger7, Harald Huber7, Reinhard Wirth7, Markus Göker4, John C. Detter1, Tanja Woyke1, James Bristow1, Jonathan A. Eisen1,8, Victor Markowitz5, Philip Hugenholtz1, Hans-Peter Klenk4, and Nikos C. Kyrpides1* 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 5 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 6 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 7 University of Regensburg, Archaeenzentrum, Regensburg, Germany 8 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Nikos C. -
Review Article: Inhibition of Methanogenic Archaea by Statins As a Targeted Management Strategy for Constipation and Related Disorders
Alimentary Pharmacology and Therapeutics Review article: inhibition of methanogenic archaea by statins as a targeted management strategy for constipation and related disorders K. Gottlieb*, V. Wacher*, J. Sliman* & M. Pimentel† *Synthetic Biologics, Inc., Rockville, SUMMARY MD, USA. † Gastroenterology, Cedars-Sinai Background Medical Center, Los Angeles, CA, USA. Observational studies show a strong association between delayed intestinal transit and the production of methane. Experimental data suggest a direct inhibitory activity of methane on the colonic and ileal smooth muscle and Correspondence to: a possible role for methane as a gasotransmitter. Archaea are the only con- Dr K. Gottlieb, Synthetic Biologics, fi Inc., 9605 Medical Center Drive, rmed biological sources of methane in nature and Methanobrevibacter Rockville, MD 20850, USA. smithii is the predominant methanogen in the human intestine. E-mail: [email protected] Aim To review the biosynthesis and composition of archaeal cell membranes, Publication data archaeal methanogenesis and the mechanism of action of statins in this context. Submitted 8 September 2015 First decision 29 September 2015 Methods Resubmitted 7 October 2015 Narrative review of the literature. Resubmitted 20 October 2015 Accepted 20 October 2015 Results EV Pub Online 11 November 2015 Statins can inhibit archaeal cell membrane biosynthesis without affecting This uncommissioned review article was bacterial numbers as demonstrated in livestock and humans. This opens subject to full peer-review. the possibility of a therapeutic intervention that targets a specific aetiologi- cal factor of constipation while protecting the intestinal microbiome. While it is generally believed that statins inhibit methane production via their effect on cell membrane biosynthesis, mediated by inhibition of the HMG- CoA reductase, there is accumulating evidence for an alternative or addi- tional mechanism of action where statins inhibit methanogenesis directly. -
Regeneration of Unconventional Natural Gas by Methanogens Co
www.nature.com/scientificreports OPEN Regeneration of unconventional natural gas by methanogens co‑existing with sulfate‑reducing prokaryotes in deep shale wells in China Yimeng Zhang1,2,3, Zhisheng Yu1*, Yiming Zhang4 & Hongxun Zhang1 Biogenic methane in shallow shale reservoirs has been proven to contribute to economic recovery of unconventional natural gas. However, whether the microbes inhabiting the deeper shale reservoirs at an average depth of 4.1 km and even co-occurring with sulfate-reducing prokaryote (SRP) have the potential to produce biomethane is still unclear. Stable isotopic technique with culture‑dependent and independent approaches were employed to investigate the microbial and functional diversity related to methanogenic pathways and explore the relationship between SRP and methanogens in the shales in the Sichuan Basin, China. Although stable isotopic ratios of the gas implied a thermogenic origin for methane, the decreased trend of stable carbon and hydrogen isotope value provided clues for increasing microbial activities along with sustained gas production in these wells. These deep shale-gas wells harbored high abundance of methanogens (17.2%) with ability of utilizing various substrates for methanogenesis, which co-existed with SRP (6.7%). All genes required for performing methylotrophic, hydrogenotrophic and acetoclastic methanogenesis were present. Methane production experiments of produced water, with and without additional available substrates for methanogens, further confrmed biomethane production via all three methanogenic pathways. Statistical analysis and incubation tests revealed the partnership between SRP and methanogens under in situ sulfate concentration (~ 9 mg/L). These results suggest that biomethane could be produced with more fexible stimulation strategies for unconventional natural gas recovery even at the higher depths and at the presence of SRP. -
Methane Production on Rock and Soil Substrates by Methanogens: Implications for Life on Mars
Bioastronomy 2007: Molecules, Microbes, and Extraterrestrial Life ASP Conference Series, Vol. 420, 2009 K. J. Meech, J. V. Keane, M. J. Mumma, J. L. Siefert, and D. J. Werthimer, eds. Methane Production on Rock and Soil Substrates by Methanogens: Implications for Life on Mars H. A. Kozup and T. A. Kral 1West Virginia University, WV 26505 2Arkansas Center for Space and Planetary Sciences, University of Arkansas, Fayetteville 72701 Abstract. In order to understand the methanogens as models for possible life on Mars, and some of the factors likely to be important in determining their abundance and distribution, we have measured their ability to produce methane on a few types of inorganic rock and soil substrates. Since organic ma- terials have not been detected in measurable quantities at the surface of Mars, there is no reason to believe that they would exist in the subsurface. Samples of three methanogens (Methanosarcina barkeri, Methanobacterium formicicum, and Methanothermobacter wolfeii) were placed on four substrates (sand, gravel, basalt, and a Mars soil simulant, JSC Mars-1) and methane production mea- sured. Glass beads were used as a control substrate. As in earlier experiments with JSC Mars-1 soil simulant, a crushed volcanic tephra, methane was pro- duced by all three methanogens when placed on the substrates, sand and gravel. None produced methane on basalt in these experiments, a mineral common in Martian soil. While these substrates do not represent the full range of materials likely to be present on the surface of Mars, the present results suggest that while some surface materials on Mars may not support this type of organism, others might. -
Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens
microorganisms Article Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens Maryam Rezadehbashi and Susan A. Baldwin * Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, BC V6T 1Z3, Canada; [email protected] * Correspondence: [email protected]; Tel.: +1-604-822-1973 Received: 2 January 2018; Accepted: 17 February 2018; Published: 23 February 2018 Abstract: Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM that grow in these systems and whether they are diverse or restricted to particular phylogenetic or taxonomic groups. A phylogenetic study of four established pilot-scale BCRs on three different mine sites compared the diversity of SRM growing in them. The mine sites were geographically distant from each other, nevertheless the BCRs selected for similar SRM types. Clostridia SRM related to Desulfosporosinus spp. known to be tolerant to high concentrations of copper were members of the core microbial community. Members of the SRM family Desulfobacteraceae were dominant, particularly those related to Desulfatirhabdium butyrativorans. Methanogens were dominant archaea and possibly were present at higher relative abundances than SRM in some BCRs. Both hydrogenotrophic and acetoclastic types were present. There were no strong negative or positive co-occurrence correlations of methanogen and SRM taxa. Knowing which SRM inhabit successfully operating BCRs allows practitioners to target these phylogenetic groups when selecting inoculum for future operations. -
Application to Develop Low Risk Gmos
NO3P Develop in containment a project of low risk genetically ER-AF-NO3P-3 modified organisms by rapid assessment 12/07 Application title: Identification and characterization of Potential Methane Mitigation Technologies Applicant organisation: AgResearch Ltd Considered by: IBSC ERMA Please clearly identify any confidential information and attach as a separate appendix. Please complete the following before submitting your application: All sections completed Yes Appendices enclosed Yes/NA Confidential information identified and enclosed separately Yes/NA Copies of references attached Yes/NA Application signed and dated Yes Electronic copy of application e-mailed to ERMA New Yes Zealand Signed: Date: 9 May 2011 20 Customhouse Quay Cnr Waring Taylor and Customhouse Quay PO Box 131, Wellington Phone: 04 916 2426 Fax: 04 914 0433 Email: [email protected] Website: www.ermanz.govt.nz Develop in containment a project of low risk genetically modified organisms by rapid assessment 1. An associated User Guide NO3P is available for this form and we strongly advise that you read this User Guide before filling out this application form. If you need guidance in completing this form please contact ERMA New Zealand or your IBSC. 2. This application form only covers the development of low-risk genetically modified organisms that meet Category A and/or B experiments as defined in the HSNO (Low-Risk Genetic Modification) Regulations 2003. 3. If you are making an application that includes not low-risk genetic modification experiments, as described in the HSNO (Low-Risk Genetic Modification) Regulations 2003, then you should complete form NO3O instead. 4. This form replaces all previous versions of Form NO3P. -
Phylogenetics of Archaeal Lipids Amy Kelly 9/27/2006 Outline
Phylogenetics of Archaeal Lipids Amy Kelly 9/27/2006 Outline • Phlogenetics of Archaea • Phlogenetics of archaeal lipids • Papers Phyla • Two? main phyla – Euryarchaeota • Methanogens • Extreme halophiles • Extreme thermophiles • Sulfate-reducing – Crenarchaeota • Extreme thermophiles – Korarchaeota? • Hyperthermophiles • indicated only by environmental DNA sequences – Nanoarchaeum? • N. equitans a fast evolving euryarchaeal lineage, not novel, early diverging archaeal phylum – Ancient archael group? • In deepest brances of Crenarchaea? Euryarchaea? Archaeal Lipids • Methanogens – Di- and tetra-ethers of glycerol and isoprenoid alcohols – Core mostly archaeol or caldarchaeol – Core sometimes sn-2- or Images removed due to sn-3-hydroxyarchaeol or copyright considerations. macrocyclic archaeol –PMI • Halophiles – Similar to methanogens – Exclusively synthesize bacterioruberin • Marine Crenarchaea Depositional Archaeal Lipids Biological Origin Environment Crocetane methanotrophs? methane seeps? methanogens, PMI (2,6,10,15,19-pentamethylicosane) methanotrophs hypersaline, anoxic Squalane hypersaline? C31-C40 head-to-head isoprenoids Smit & Mushegian • “Lost” enzymes of MVA pathway must exist – Phosphomevalonate kinase (PMK) – Diphosphomevalonate decarboxylase – Isopentenyl diphosphate isomerase (IPPI) Kaneda et al. 2001 Rohdich et al. 2001 Boucher et al. • Isoprenoid biosynthesis of archaea evolved through a combination of processes – Co-option of ancestral enzymes – Modification of enzymatic specificity – Orthologous and non-orthologous gene -
Effect of High Cationic Flocculant on Anaerobic Digestion of Municipal Wastewater
University of Louisville ThinkIR: The University of Louisville's Institutional Repository Electronic Theses and Dissertations 5-2017 Effect of high cationic flocculant on anaerobic digestion of municipal wastewater. Prathap D. John University of Louisville Follow this and additional works at: https://ir.library.louisville.edu/etd Part of the Environmental Engineering Commons, and the Other Chemical Engineering Commons Recommended Citation John, Prathap D., "Effect of high cationic flocculant on anaerobic digestion of municipal wastewater." (2017). Electronic Theses and Dissertations. Paper 2815. https://doi.org/10.18297/etd/2815 This Master's Thesis is brought to you for free and open access by ThinkIR: The University of Louisville's Institutional Repository. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of ThinkIR: The University of Louisville's Institutional Repository. This title appears here courtesy of the author, who has retained all other copyrights. For more information, please contact [email protected]. EFFECT OF HIGH CATIONIC FLOCCULANT ON ANAEROBIC DIGESTION OF MUNICIPAL WASTEWATER By Prathap Daniel John B.S, University of Louisville, 2006 A Thesis Submitted to the Faculty of the University of Louisville J.B. Speed School of Engineering as Partial Fulfillment of the Requirements for the Professional Degree MASTER OF ENGINEERING Department of Chemical Engineering March 2017 ii EFFECT OF HIGH CATIONIC FLOCCULANT ON ANAEROBIC DIGESTION OF MUNICIPAL WASTEWATER APPROVAL PAGE Submitted by: __________________________________ Prathap Daniel John A Thesis Approved On ____________________________________ (Date) by the Following Reading and Examination Committee: ___________________________________ Dr. R. Eric Berson, Thesis Director ___________________________________ Dr. James Watters ___________________________________ Dr. Thomas Rockaway ii ACKNOWLEDGEMENTS I would like to thank the Conn Center for Renewable Energy Research and my research advisor Dr. -
FORMATION of HABITABLE WORLDS and FATE of HABITABLE ENVIRONMENTS 6:00 P.M
45th Lunar and Planetary Science Conference (2014) sess726.pdf Thursday, March 20, 2014 [R726] POSTER SESSION: FORMATION OF HABITABLE WORLDS AND FATE OF HABITABLE ENVIRONMENTS 6:00 p.m. Town Center Exhibit Area Johnson T. A. Park A. Hand K. P. POSTER LOCATION #473 The Workman-Reynolds Effect: An Investigation of the Ice-Water Interface of Dilute Salt Solutions [#1672] We report on experiments on the voltage potential that results from rapidly freezing dilute aqueous solutions. These results have application to icy satellites. Taylor A. R. Olsen A. A. Hausrath E. M. POSTER LOCATION #474 Serpentinite Dissolution: An Analog to Mantle-Ocean Interaction on Europa [#1903] Laboratory-based dissolution experiments between serpentinite rock and a variety of acids represent mantle-ocean interaction on the jovian moon, Europa. Hausrath E. M. Adcock C. T. Elwood Madden M. E. Gainey S. R. Olsen A. A. et al. POSTER LOCATION #475 Using Geochemical Kinetics to Interpret Potential Habitability [#2376] Geochemical kinetics can help shed light on factors affecting habitability, including water, release of nutrients, redox, pH, temperature, and ionic strength. Som S. M. Fristad K. E. Hoehler T. M. POSTER LOCATION #476 An Integrative Approach to Assessing Habitability of H2 Metabolisms in Hydrothermal Springs [#2828] We present an ongoing project that surveys H2 from springs sourced in rocks of varying silica content and in parallel investigate habitability numerically. Djordjevic S. Mickol R. L. Kral T. A. POSTER LOCATION #477 Simulating Martian Conditions: Methanogen Survivability During Freeze-Thaw Cycles [#2539] Methanogens are obligate anaerobes that tolerate a wide range of conditions. It is proposed that these Archaea are able to persist in a martian environment. -
Histone Variants in Archaea and the Evolution of Combinatorial Chromatin Complexity
Histone variants in archaea and the evolution of combinatorial chromatin complexity Kathryn M. Stevensa,b, Jacob B. Swadlinga,b, Antoine Hochera,b, Corinna Bangc,d, Simonetta Gribaldoe, Ruth A. Schmitzc, and Tobias Warneckea,b,1 aMolecular Systems Group, Quantitative Biology Section, Medical Research Council London Institute of Medical Sciences, London W12 0NN, United Kingdom; bInstitute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom; cInstitute for General Microbiology, University of Kiel, 24118 Kiel, Germany; dInstitute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany; and eDepartment of Microbiology, Unit “Evolutionary Biology of the Microbial Cell,” Institut Pasteur, 75015 Paris, France Edited by W. Ford Doolittle, Dalhousie University, Halifax, NS, Canada, and approved October 28, 2020 (received for review April 14, 2020) Nucleosomes in eukaryotes act as platforms for the dynamic inte- additional histone dimers can be taggedontothistetramertoyield gration of epigenetic information. Posttranslational modifications oligomers of increasing length that wrap correspondingly more DNA are reversibly added or removed and core histones exchanged for (3, 6–9). Almost all archaeal histones lack tails and PTMs have yet to paralogous variants, in concert with changing demands on tran- be reported. Many archaea do, however, encode multiple histone scription and genome accessibility. Histones are also common in paralogs (8, 10) that can flexibly homo- and heterodimerize in