Temperature and Inoculum Origin Influence the Performance of Ex-Situ Biological Hydrogen Methanation
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Methanobrevibacter Cuticularis Sp
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Oct. 1996, p. 3620–3631 Vol. 62, No. 10 0099-2240/96/$04.0010 Copyright q 1996, American Society for Microbiology Physiological Ecology of Methanobrevibacter cuticularis sp. nov. and Methanobrevibacter curvatus sp. nov., Isolated from the Hindgut of the Termite Reticulitermes flavipes JARED R. LEADBETTER AND JOHN A. BREZNAK* Department of Microbiology and Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824-1101 Received 11 January 1996/Accepted 15 July 1996 Two morphologically distinct, H2- and CO2-utilizing methanogens were isolated from gut homogenates of the subterranean termite, Reticulitermes flavipes (Kollar) (Rhinotermitidae). Strain RFM-1 was a short straight rod (0.4 by 1.2 mm), whereas strain RFM-2 was a slightly curved rod (0.34 by 1.6 mm) that possessed polar fibers. Their morphology, gram-positive staining reaction, resistance to cell lysis by chemical agents, and narrow range of utilizable substrates were typical of species belonging to the family Methanobacteriaceae. Analysis of the nearly complete sequences of the small-subunit rRNA-encoding genes confirmed this affiliation and supported their recognition as new species of Methanobrevibacter: M. cuticularis (RFM-1) and M. curvatus (RFM-2). The per cell rates of methanogenesis by strains RFM-1 and RFM-2 in vitro, taken together with their in situ population densities (ca. 106 cells z gut21; equivalent to 109 cells z ml of gut fluid21), could fully account for the rate of methane emission by the live termites. UV epifluorescence and electron microscopy confirmed that RFM-1- and RFM-2-type cells were the dominant methanogens in R. -
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. -
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. -
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 -
Supporting Information
Supporting Information Lozupone et al. 10.1073/pnas.0807339105 SI Methods nococcus, and Eubacterium grouped with members of other Determining the Environmental Distribution of Sequenced Genomes. named genera with high bootstrap support (Fig. 1A). One To obtain information on the lifestyle of the isolate and its reported member of the Bacteroidetes (Bacteroides capillosus) source, we looked at descriptive information from NCBI grouped firmly within the Firmicutes. This taxonomic error was (www.ncbi.nlm.nih.gov/genomes/lproks.cgi) and other related not surprising because gut isolates have often been classified as publications. We also determined which 16S rRNA-based envi- Bacteroides based on an obligate anaerobe, Gram-negative, ronmental surveys of microbial assemblages deposited near- nonsporulating phenotype alone (6, 7). A more recent 16S identical sequences in GenBank. We first downloaded the gbenv rRNA-based analysis of the genus Clostridium defined phylo- files from the NCBI ftp site on December 31, 2007, and used genetically related clusters (4, 5), and these designations were them to create a BLAST database. These files contain GenBank supported in our phylogenetic analysis of the Clostridium species in the HGMI pipeline. We thus designated these Clostridium records for the ENV database, a component of the nonredun- species, along with the species from other named genera that dant nucleotide database (nt) where 16S rRNA environmental cluster with them in bootstrap supported nodes, as being within survey data are deposited. GenBank records for hits with Ͼ98% these clusters. sequence identity over 400 bp to the 16S rRNA sequence of each of the 67 genomes were parsed to get a list of study titles Annotation of GTs and GHs. -
Development of the Equine Hindgut Microbiome in Semi-Feral and Domestic Conventionally-Managed Foals Meredith K
Tavenner et al. Animal Microbiome (2020) 2:43 Animal Microbiome https://doi.org/10.1186/s42523-020-00060-6 RESEARCH ARTICLE Open Access Development of the equine hindgut microbiome in semi-feral and domestic conventionally-managed foals Meredith K. Tavenner1, Sue M. McDonnell2 and Amy S. Biddle1* Abstract Background: Early development of the gut microbiome is an essential part of neonate health in animals. It is unclear whether the acquisition of gut microbes is different between domesticated animals and their wild counterparts. In this study, fecal samples from ten domestic conventionally managed (DCM) Standardbred and ten semi-feral managed (SFM) Shetland-type pony foals and dams were compared using 16S rRNA sequencing to identify differences in the development of the foal hindgut microbiome related to time and management. Results: Gut microbiome diversity of dams was lower than foals overall and within groups, and foals from both groups at Week 1 had less diverse gut microbiomes than subsequent weeks. The core microbiomes of SFM dams and foals had more taxa overall, and greater numbers of taxa within species groups when compared to DCM dams and foals. The gut microbiomes of SFM foals demonstrated enhanced diversity of key groups: Verrucomicrobia (RFP12), Ruminococcaceae, Fusobacterium spp., and Bacteroides spp., based on age and management. Lactic acid bacteria Lactobacillus spp. and other Lactobacillaceae genera were enriched only in DCM foals, specifically during their second and third week of life. Predicted microbiome functions estimated computationally suggested that SFM foals had higher mean sequence counts for taxa contributing to the digestion of lipids, simple and complex carbohydrates, and protein. -
Susceptibility of Archaea to Antimicrobial Agents: Applications to Clinical Microbiology
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector REVIEW 10.1111/j.1469-0691.2012.03913.x Susceptibility of archaea to antimicrobial agents: applications to clinical microbiology S. Khelaifia and M. Drancourt Unite´ de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 6236 IRD 3R198, Me´diterrane´e Infection, Faculte´ de Me´decine, Aix-marseille-Universite´, Marseille, France Abstract We herein review the state of knowledge regarding the in vitro and in vivo susceptibility of archaea to antimicrobial agents, including some new molecules. Indeed, some archaea colonizing the human microbiota have been implicated in diseases such as periodontopathy. Archaea are characterized by their broad-spectrum resistance to antimicrobial agents. In particular, their cell wall lacks peptidoglycan, making them resistant to antimicrobial agents interfering with peptidoglycan biosynthesis. Archaea are, however, susceptible to the pro- tein synthesis inhibitor fusidic acid and imidazole derivatives. Also, squalamine, an antimicrobial agent acting on the cell wall, proved effective against human methanogenic archaea. In vitro susceptibility data could be used to design protocols for the decontamination of complex microbiota and the selective isolation of archaea in anaerobic culture. Keywords: Antimicrobial agent, archaea, methanogenic archaea, microbiota, susceptibility testing Article published online: 23 May 2012 Clin Microbiol Infect 2012; 18: 841–848 Corresponding author: M. Drancourt, Unite´ des Rickettsies, Fa- culte´ de Me´decine, 27, Boulevard Jean Moulin-Cedex 5, France E-mail: [email protected] Methanogenic archaea (herein referred to as methano- Introduction gens) are the sole organisms producing methane from H2 +CO2 [6]. -
Methanobacterium Paludis Sp. Nov. and a Novel Strain of Methanobacterium Lacus Isolated from Northern Peatlands
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by The University of North Carolina at Greensboro Archived version from NCDOCKS Institutional Repository http://libres.uncg.edu/ir/asu/ Methanobacterium Paludis Sp. Nov. And A Novel Strain Of Methanobacterium Lacus Isolated From Northern Peatlands By: Suzanna L. Brauer, Hinsby Cadillo-Quiroz, Noah Goodson, Joseph B. Yavitt & Stephen H. Zinder Abstract Two mesophilic, hydrogenotrophic methanogens, designated strains SWAN1T and AL-21, were isolated from two contrasting peatlands: a near circumneutral temperate minerotrophic fen in New York State, USA, and an acidic boreal poor fen site in Alaska, USA, respectively. Cells of the two strains were rod-shaped, non- motile, stained Gram-negative and resisted lysis with 0.1 % SDS. Cell size was 0.6 1.5–2.8 mm for strain SWAN1T and 0.45–0.85 1.5–35 mm for strain AL-21. The strains used H2/CO2 but not formate or other substrates for methanogenesis, grew optimally around 32–37 6C, and their growth spanned through a slightly low to neutral pH range (4.7–7.1). Strain AL-21 grew optimally closer to neutrality at pH 6.2, whereas strain SWAN1T showed a lower optimal pH at 5.4–5.7. The two strains were sensitive to NaCl with a maximal tolerance at 160 mM for strain SWAN1T and 50 mM for strain AL-21. Na2S was toxic at very low concentrations (0.01–0.8 mM), resulting in growth inhibition above these values. The DNA G+C content of the genomes was 35.7 mol% for strain SWAN1T and 35.8 mol% for strain AL-21. -
METHANOGENS AS MODELS for LIFE on MARS. R. L. Mickol1, W. H. Waddell2, and T
Eighth International Conference on Mars (2014) 1005.pdf METHANOGENS AS MODELS FOR LIFE ON MARS. R. L. Mickol1, W. H. Waddell2, and T. A. Kral1,3, 1Arkansas Center for Space and Planetary Sciences, 202 Old Museum Building, University of Arkansas, Fayetteville, Arkansas, 72701, USA, [[email protected]], 2Dept. of Health, Human Performance, and Recreation, HPER 308, University of Arkansas, Fayetteville, Arkansas, 72701, USA, 3Dept. of Biological Sciences, SCEN 632, University of Arkansas, Fayetteville, Arkansas, 72701, USA. Introduction: The discovery of methane in the Sciences, University of Arkansas, Fayetteville, Arkan- martian atmosphere [1-4] has fueled the study of meth- sas. All four methanogen species were tested in these anogens as ideal candidates for life on Mars. Methano- experiments. Methanogens were grown in their respec- gens are chemoautotrophs from the domain Archaea. tive anaerobic growth media and placed into the cham- These microorganisms utilize hydrogen as an energy ber with a palladium catalyst box to remove residual source and carbon dioxide as a carbon source to pro- oxygen. The chamber was evacuated to a pre- duce methane. Methanogens can be considered ideal determined pressure and filled with 80:20 H2:CO2 gas. candidates for life on Mars because they are anaerobic, This procedure was repeated three times to ensure re- they do not require organic nutrients and are non- moval of the atmosphere. The chamber was then main- photosynthetic, indicating they could exist in sub- tained at the desired pressure (133-143 mbar, 67-72 surface environments. mbar, 33-38 mbar, 6-10 mbar, 7-20 mbar) for the dura- Our lab has studied methanogens as models for life tion of the experiments. -
Brian W. Waters
INVESTIGATION OF 2-OXOACID OXIDOREDUCTASES IN METHANOCOCCUS MARIPALUDIS AND LARGE-SCALE GROWTH OF M. MARIPALUDIS by BRIAN W. WATERS (Under the direction of Dr. William B. Whitman) ABSTRACT With the emergence of Methanococcus maripaludis as a genetic model for methanogens, it becomes imperative to devise inexpensive yet effective ways to grow large numbers of cells for protein studies. Chapter 2 details methods that were used to cut costs of growing M. maripaludis in large scale. Also, large scale growth under different conditions was explored in order to find the conditions that yield the most cells. Chapter 3 details the phylogenetic analysis of 2-oxoacid oxidoreductase (OR) homologs from M. maripaludis. ORs are enzymes that catalyze the oxidative decarboxylation of 2-oxoacids to their acyl-CoA derivatives in many prokaryotes. Also in chapter 3, a specific OR homolog in M. maripaludis, an indolepyruvate oxidoreductase (IOR), was mutagenized, and the mutant was characterized. PCR and Southern hybridization analysis showed gene replacement. A no-growth phenotype on media containing aromatic amino acid derivatives was found. INDEX WORDS: Methanococcus maripaludis, fermentor, 2-oxoacid oxidoreductase, indolepyruvate oxidoreductase INVESTIGATION OF 2-OXOACID OXIDOREDUCTASES IN METHANOCOCCUS MARIPALUDIS AND LARGE-SCALE GROWTH OF M. MARIPALUDIS by BRIAN W. WATERS B.S., The University of Georgia,1999 A Thesis Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirements for the Degree MASTER OF SCIENCE ATHENS, GEORGIA 2002 © 2002 Brian W. Waters All Rights Reserved INVESTIGATION OF 2-OXOACID OXIDOREDUCTASES IN METHANOCOCCUS MARIPALUDIS AND LARGE-SCALE GROWTH OF M. MARIPALUDIS by BRIAN W. -
Methanogens Diversity During Anaerobic Sewage Sludge Stabilization and the Effect of Temperature
processes Article Methanogens Diversity during Anaerobic Sewage Sludge Stabilization and the Effect of Temperature Tomáš Vítˇez 1,2, David Novák 3, Jan Lochman 3,* and Monika Vítˇezová 1,* 1 Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; [email protected] 2 Department of Agricultural, Food and Environmental Engineering, Faculty of AgriSciences, Mendel University, 61300 Brno, Czech Republic 3 Department of Biochemistry, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; [email protected] * Correspondence: [email protected] (J.L.); [email protected] (M.V.); Tel.: +420-549-495-602 (J.L.); Tel.: +420-549-497-177 (M.V.) Received: 29 June 2020; Accepted: 10 July 2020; Published: 12 July 2020 Abstract: Anaerobic sludge stabilization is a commonly used technology. Most fermenters are operated at a mesophilic temperature regime. Modern trends in waste management aim to minimize waste generation. One of the strategies can be achieved by anaerobically stabilizing the sludge by raising the temperature. Higher temperatures will allow faster decomposition of organic matter, shortening the retention time, and increasing biogas production. This work is focused on the description of changes in the community of methanogenic microorganisms at different temperatures during the sludge stabilization. At higher temperatures, biogas contained a higher percentage of methane, however, there was an undesirable accumulation of ammonia in the fermenter. Representatives of the hydrogenotrophic genus Methanoliea were described at all temperatures tested. At temperatures up to 50 ◦C, a significant proportion of methanogens were also formed by acetoclastic representatives of Methanosaeta sp. and acetoclastic representatives of the order Methanosarcinales. -
Can Methanogens Grow in a Perchlorate Environment on Mars? T.A
72nd Annual Meteoritical Society Meeting (2009) 5136.pdf CAN METHANOGENS GROW IN A PERCHLORATE ENVIRONMENT ON MARS? T.A. Kral1,2, T. Goodhart1, K.L. Howe2 and P. Gavin2. 1Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, 2Arkansas Cen- ter for Space and Planetary Sciences, University of Arkansas, Fayetteville, AR 72701. [email protected]. Introduction: We have been studying methanogens as a model for life on Mars for a number of years now. Methanogens are microorganism in the domain Archaea that use carbon diox- ide as a carbon source, molecular hydrogen as an energy source, produce methane as a by-product of metabolism, and have been shown to grow on a Mars soil simulant, JSC Mars-1 (1). The relatively recent discovery of methane in the Martian atmosphere has added relevance to these types of studies (2). In 2008, The Mars Phoenix Lander discovered perchlorate at its landing site in concentrations of approximately 1.0wt% (3). Because of perchlo- rate’s powerful oxidizing property, many believed that the chances for extant life on the planet had decreased. Methods: The research reported here was designed to de- termine if methanogens could grow in the presence of three dif- ferent perchlorate salts. The methanogens tested were Methanothermobacter wolfeii, Methanosarcina barkeri, Metha- nobacterium formicicum and Methanococcus maripaludis. Stan- dard growth media were prepared containing 0, 0.1, 0.5 and 1.0wt% magnesium perchlorate, sodium perchlorate, or potas- sium perchlorate. Organisms were inoculated into their respective media followed by incubation at each organism’s optimal growth temperature. Methane production, commonly used to measure methanogen growth, was measured by gas chromatography of headspace samples.