1 Structure and Function of the Methanogenic Microbial Communities in Soils from 1 Flooded Rice and Upland Soybean Fields from S
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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. -
Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide
microorganisms Article Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide Kelly J. Hidalgo 1,2,* , Isabel N. Sierra-Garcia 3 , German Zafra 4 and Valéria M. de Oliveira 1 1 Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas–UNICAMP, Av. Alexandre Cazellato 999, 13148-218 Paulínia, Brazil; [email protected] 2 Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato 255, Cidade Universitária, 13083-862 Campinas, Brazil 3 Biology Department & CESAM, University of Aveiro, Aveiro, Portugal, Campus de Santiago, Avenida João Jacinto de Magalhães, 3810-193 Aveiro, Portugal; [email protected] 4 Grupo de Investigación en Bioquímica y Microbiología (GIBIM), Escuela de Microbiología, Universidad Industrial de Santander, Cra 27 calle 9, 680002 Bucaramanga, Colombia; [email protected] * Correspondence: [email protected]; Tel.: +55-19981721510 Abstract: Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to decipher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301.2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 metagenome-assembled genomes (MAGs) of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to archaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied. -
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. -
Discovery of a Novel Methanogen Prevalent in Thawing Permafrost
ARTICLE Received 11 Jun 2013 | Accepted 7 Jan 2014 | Published 14 Feb 2014 DOI: 10.1038/ncomms4212 Discovery of a novel methanogen prevalent in thawing permafrost Rhiannon Mondav1,*,w, Ben J. Woodcroft1,*, Eun-Hae Kim2, Carmody K. McCalley3,w, Suzanne B. Hodgkins4, Patrick M. Crill5, Jeffrey Chanton4, Gregory B. Hurst6, Nathan C. VerBerkmoes6,w, Scott R. Saleska3, Philip Hugenholtz1, Virginia I. Rich2 & Gene W. Tyson1 Thawing permafrost promotes microbial degradation of cryo-sequestered and new carbon leading to the biogenic production of methane, creating a positive feedback to climate change. Here we determine microbial community composition along a permafrost thaw gradient in northern Sweden. Partially thawed sites were frequently dominated by a single archaeal phylotype, Candidatus ‘Methanoflorens stordalenmirensis’ gen. nov. sp. nov., belonging to the uncultivated lineage ‘Rice Cluster II’ (Candidatus ‘Methanoflorentaceae’ fam. nov.). Metage- nomic sequencing led to the recovery of its near-complete genome, revealing the genes necessary for hydrogenotrophic methanogenesis. These genes are highly expressed and methane carbon isotope data are consistent with hydrogenotrophic production of methane in the partially thawed site. In addition to permafrost wetlands, ‘Methanoflorentaceae’ are widespread in high methane-flux habitats suggesting that this lineage is both prevalent and a major contributor to global methane production. In thawing permafrost, Candidatus ‘M. stordalenmirensis’ appears to be a key mediator of methane-based positive feedback to climate warming. 1 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Queensland, Australia. 2 Department of Soil, Water and Environmental Science, University of Arizona, Tucson, Arizona 85721, USA. 3 Ecology and Evolutionary Biology Department, University of Arizona, Tucson, Arizona 85721, USA. -
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]. -
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. -
Dialogue on the Nomenclature and Classification of Prokaryotes
G Model SYAPM-25929; No. of Pages 10 ARTICLE IN PRESS Systematic and Applied Microbiology xxx (2018) xxx–xxx Contents lists available at ScienceDirect Systematic and Applied Microbiology journal homepage: www.elsevier.de/syapm Dialogue on the nomenclature and classification of prokaryotes a,∗ b Ramon Rosselló-Móra , William B. Whitman a Marine Microbiology Group, IMEDEA (CSIC-UIB), 07190 Esporles, Spain b Department of Microbiology, University of Georgia, Athens, GA 30602, USA a r t i c l e i n f o a b s t r a c t Keywords: The application of next generation sequencing and molecular ecology to the systematics and taxonomy Bacteriological code of prokaryotes offers enormous insights into prokaryotic biology. This discussion explores some major Taxonomy disagreements but also considers the opportunities associated with the nomenclature of the uncultured Nomenclature taxa, the use of genome sequences as type material, the plurality of the nomenclatural code, and the roles Candidatus of an official or computer-assisted taxonomy. Type material © 2018 Elsevier GmbH. All rights reserved. Is naming important when defined here as providing labels Prior to the 1980s, one of the major functions of Bergey’s Manual for biological entities? was to associate the multiple names in current usage with the cor- rect organism. For instance, in the 1948 edition of the Manual, 21 Whitman and 33 names were associated with the common bacterial species now named Escherichia coli and Bacillus subtilis, respectively [5]. When discussing the nomenclature of prokaryotes, we must first This experience illustrates that without a naming system gener- establish the role and importance of naming. -
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. -
Pan-Genome Analysis and Ancestral State Reconstruction Of
www.nature.com/scientificreports OPEN Pan‑genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super‑order Sonam Gaba1,2, Abha Kumari2, Marnix Medema 3 & Rajeev Kaushik1* Halobacteria, a class of Euryarchaeota are extremely halophilic archaea that can adapt to a wide range of salt concentration generally from 10% NaCl to saturated salt concentration of 32% NaCl. It consists of the orders: Halobacteriales, Haloferaciales and Natriabales. Pan‑genome analysis of class Halobacteria was done to explore the core (300) and variable components (Softcore: 998, Cloud:36531, Shell:11784). The core component revealed genes of replication, transcription, translation and repair, whereas the variable component had a major portion of environmental information processing. The pan‑gene matrix was mapped onto the core‑gene tree to fnd the ancestral (44.8%) and derived genes (55.1%) of the Last Common Ancestor of Halobacteria. A High percentage of derived genes along with presence of transformation and conjugation genes indicate the occurrence of horizontal gene transfer during the evolution of Halobacteria. A Core and pan‑gene tree were also constructed to infer a phylogeny which implicated on the new super‑order comprising of Natrialbales and Halobacteriales. Halobacteria1,2 is a class of phylum Euryarchaeota3 consisting of extremely halophilic archaea found till date and contains three orders namely Halobacteriales4,5 Haloferacales5 and Natrialbales5. Tese microorganisms are able to dwell at wide range of salt concentration generally from 10% NaCl to saturated salt concentration of 32% NaCl6. Halobacteria, as the name suggests were once considered a part of a domain "Bacteria" but with the discovery of the third domain "Archaea" by Carl Woese et al.7, it became part of Archaea. -
Extracellular Electron Uptake in Methanosarcinales Is Independent of Multiheme C-Type Cytochromes
University of Southern Denmark Extracellular electron uptake in Methanosarcinales is independent of multiheme c-type cytochromes Yee, Mon Oo; Rotaru, Amelia-Elena Published in: Scientific Reports DOI: 10.1038/s41598-019-57206-z Publication date: 2020 Document version: Final published version Document license: CC BY Citation for pulished version (APA): Yee, M. O., & Rotaru, A-E. (2020). Extracellular electron uptake in Methanosarcinales is independent of multiheme c-type cytochromes. Scientific Reports, 10(1), [372]. https://doi.org/10.1038/s41598-019-57206-z Go to publication entry in University of Southern Denmark's Research Portal Terms of use This work is brought to you by the University of Southern Denmark. Unless otherwise specified it has been shared according to the terms for self-archiving. If no other license is stated, these terms apply: • You may download this work for personal use only. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying this open access version If you believe that this document breaches copyright please contact us providing details and we will investigate your claim. Please direct all enquiries to [email protected] Download date: 10. Oct. 2021 www.nature.com/scientificreports OPEN Extracellular electron uptake in Methanosarcinales is independent of multiheme c-type cytochromes Mon Oo Yee & Amelia-Elena Rotaru* The co-occurrence of Geobacter and Methanosarcinales is often used as a proxy for the manifestation of direct interspecies electron transfer (DIET) in the environment. Here we tested eleven new co- culture combinations between methanogens and electrogens.