Evidence of Active Methanogen Communities in Shallow Sediments
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora
AEM Accepted Manuscript Posted Online 13 March 2015 Appl. Environ. Microbiol. doi:10.1128/AEM.00147-15 Copyright © 2015, American Society for Microbiology. All Rights Reserved. 1 Evidence of active methanogen communities in shallow sediments of the Sonora 2 Margin cold seeps 3 4 Adrien Vigneron#1235, Stéphane L'Haridon23, Anne Godfroy123, Erwan G. Roussel1234, Barry A. 5 Cragg4, R. John Parkes4 and Laurent Toffin123 6 1Ifremer, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, 7 Technopôle Brest Iroise, BP70, Plouzané, France 8 2Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements 9 Extrêmes, UMR6197, Technopôle Brest Iroise, BP70, Plouzané, France 10 3CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, Technopôle 11 Brest Iroise, BP70, Plouzané, France 12 4School of Earth and Ocean Sciences, Cardiff University, Cardiff CF10 3AT, United Kingdom 13 5School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne 14 NE1 7RU, United Kingdom 15 Running Title: Methanogens in the Sonora Margin sediments 16 Keywords: Archaea / methanogenesis / Guaymas Basin / Methanococcoides / 17 Methanogenium 18 Contact of corresponding author: Dr. Adrien Vigneron ; [email protected] ; tel :+33 19 298 224 396 ; fax +33 298 224 557 20 Abstract 21 In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying 22 microbial mats harbor high biogenic methane concentrations, fuelling various microbial 23 communities such as abundant lineages of Anaerobic Methanotrophs (ANME). However 1 24 biodiversity, distribution and metabolism of the microorganisms producing this methane 25 remain poorly understood. In this study, measurements of methanogenesis using 26 radiolabelled dimethylamine, bicarbonate and acetate showed that biogenic methane 27 production in these sediments was mainly dominated by methylotrophic methanogenesis, 28 while the proportion of autotrophic methanogenesis increased with depth. -
Representatives of a Novel Archaeal Phylum Or a Fast-Evolving
Open Access Research2005BrochieretVolume al. 6, Issue 5, Article R42 Nanoarchaea: representatives of a novel archaeal phylum or a comment fast-evolving euryarchaeal lineage related to Thermococcales? Celine Brochier*, Simonetta Gribaldo†, Yvan Zivanovic‡, Fabrice Confalonieri‡ and Patrick Forterre†‡ Addresses: *EA EGEE (Evolution, Génomique, Environnement) Université Aix-Marseille I, Centre Saint-Charles, 3 Place Victor Hugo, 13331 Marseille, Cedex 3, France. †Unite Biologie Moléculaire du Gène chez les Extremophiles, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex ‡ 15, France. Institut de Génétique et Microbiologie, UMR CNRS 8621, Université Paris-Sud, 91405 Orsay, France. reviews Correspondence: Celine Brochier. E-mail: [email protected]. Simonetta Gribaldo. E-mail: [email protected] Published: 14 April 2005 Received: 3 December 2004 Revised: 10 February 2005 Genome Biology 2005, 6:R42 (doi:10.1186/gb-2005-6-5-r42) Accepted: 9 March 2005 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2005/6/5/R42 reports © 2005 Brochier et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Placement<p>Anteins from analysis 25of Nanoarcheumarchaeal of the positiongenomes equitans of suggests Nanoarcheum in the that archaeal N. equitans phylogeny inis likethe lyarchaeal to be the phylogeny representative using aof large a fast-evolving dataset of concatenatedeuryarchaeal ribosomalineage.</p>l pro- deposited research Abstract Background: Cultivable archaeal species are assigned to two phyla - the Crenarchaeota and the Euryarchaeota - by a number of important genetic differences, and this ancient split is strongly supported by phylogenetic analysis. -
Design of Targeted Primers Based on 16S Rrna Sequences in Meta
Zhang et al. BMC Microbiology (2020) 20:25 https://doi.org/10.1186/s12866-020-1707-0 METHODOLOGY ARTICLE Open Access Design of targeted primers based on 16S rRNA sequences in meta-transcriptomic datasets and identification of a novel taxonomic group in the Asgard archaea Ru-Yi Zhang1, Bin Zou1, Yong-Wei Yan1,2, Che Ok Jeon3, Meng Li4, Mingwei Cai4,5 and Zhe-Xue Quan1* Abstract Background: Amplification of small subunit (SSU) rRNA genes with universal primers is a common method used to assess microbial populations in various environmental samples. However, owing to limitations in coverage of these universal primers, some microorganisms remain unidentified. The present study aimed to establish a method for amplifying nearly full-length SSU rRNA gene sequences of previously unidentified prokaryotes, using newly designed targeted primers via primer evaluation in meta-transcriptomic datasets. Methods: Primer binding regions of universal primer 8F/Arch21F for bacteria or archaea were used for primer evaluation of SSU rRNA sequences in meta-transcriptomic datasets. Furthermore, targeted forward primers were designed based on SSU rRNA reads from unclassified groups unmatched with the universal primer 8F/ Arch21F, and these primers were used to amplify nearly full-length special SSU rRNA gene sequences along with universal reverse primer 1492R. Similarity and phylogenetic analysis were used to confirm their novel status. Results: Using this method, we identified unclassified SSU rRNA sequences that were not matched with universal primer 8F and Arch21F. A new group within the Asgard superphylum was amplified by the newly designed specific primer based on these unclassified SSU rRNA sequences by using mudflat samples. -
Presence of Archaea in the Indoor Environment and Their Relationships with Housing Characteristics
Microb Ecol (2016) 72:305–312 DOI 10.1007/s00248-016-0767-z ENVIRONMENTAL MICROBIOLOGY Presence of Archaea in the Indoor Environment and Their Relationships with Housing Characteristics Sepideh Pakpour1,2 & James A. Scott3 & Stuart E. Turvey 4,5 & Jeffrey R. Brook3 & Timothy K. Takaro6 & Malcolm R. Sears7 & John Klironomos1 Received: 3 April 2016 /Accepted: 5 April 2016 /Published online: 20 April 2016 # Springer Science+Business Media New York 2016 Abstract Archaea are widespread and abundant in soils, Based on the results, Archaea are not equally distributed with- oceans, or human and animal gastrointestinal (GI) tracts. in houses, and the areas with greater input of outdoor However, very little is known about the presence of Archaea microbiome and higher traffic and material heterogeneity tend in indoor environments and factors that can regulate their to have a higher abundance of Archaea. Nevertheless, more re- abundances. Using a quantitative PCR approach, and search is needed to better understand causes and consequences of targeting the archaeal and bacterial 16S rRNA genes in floor this microbial group in indoor environments. dust samples, we found that Archaea are a common part of the indoor microbiota, 5.01 ± 0.14 (log 16S rRNA gene copies/g Keywords Archaea . Bacteria . Indoor environment . qPCR . dust, mean ± SE) in bedrooms and 5.58 ± 0.13 in common Building characteristics . Human activities rooms, such as living rooms. Their abundance, however, was lower than bacteria: 9.20 ± 0.32 and 9.17 ± 0.32 in bed- rooms and common rooms, respectively. In addition, by mea- Introduction suring a broad array of environmental factors, we obtained preliminary insights into how the abundance of total archaeal The biology and ecology of the third domain of life, Archaea, 16S rRNA gene copies in indoor environment would be asso- have been studied far less when compared to the other do- ciated with building characteristics and occupants’ activities. -
(12) Patent Application Publication (10) Pub. No.: US 2011/0287504 A1 Mets (43) Pub
US 2011 0287504A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2011/0287504 A1 Mets (43) Pub. Date: Nov. 24, 2011 (54) METHOD AND SYSTEM FOR CONVERTING Publication Classification ELECTRICITY INTO ALTERNATIVE ENERGY RESOURCES (51) Int. Cl. CI2P 5/02 (2006.01) (75) Inventor: Laurens Mets, Chicago, IL (US) (52) U.S. Cl. ........................................................ 435/167 (73) Assignee: THE UNIVERSITY OF CHICAGO, Chicago, IL (US) (57) ABSTRACT (21) Appl. No.: 13/204,398 A method of using electricity to produce methane includes maintaining a culture comprising living methanogenic micro (22) Filed: Aug. 5, 2011 organisms at a temperature above 50° C. in a reactor having a first chamber and a second chamber separated by a proton Related U.S. Application Data permeable barrier, the first chamber comprising a passage between an inlet and an outlet containing at least a porous (63) Continuation of application No. 13/049,775, filed on electrically conductive cathode, the culture, and water, and Mar. 16, 2011, which is a continuation-in-part of appli the second chamber comprising at least an anode. The method cation No. PCT/US 10/40944, filed on Jul. 2, 2010. also includes coupling electricity to the anode and the cath (60) Provisional application No. 61/222,621, filed on Jul. 2, ode, Supplying carbon dioxide to the culture in the first cham 2009, provisional application No. 61/430,071, filed on ber, and collecting methane from the culture at the outlet of Jan. 5, 2011. the first chamber. Patent Application Publication Nov. 24, 2011 Sheet 1 of 12 US 2011/0287504 A1 PRIOR ART O2 H2 CHA -CH -D -O 50 52 -CH CO2 FIG. -
Methanogenic Archaea: Emerging Partners in the Field of Allergic Diseases
Clinical Reviews in Allergy & Immunology (2019) 57:456–466 https://doi.org/10.1007/s12016-019-08766-5 Methanogenic Archaea: Emerging Partners in the Field of Allergic Diseases Youssouf Sereme1,2 & Soraya Mezouar1,2 & Ghiles Grine1,2 & Jean Louis Mege1,2,3 & Michel Drancourt1,2 & Pierre Corbeau4,5,6 & Joana Vitte1,2,3 Published online: 14 September 2019 # Springer Science+Business Media, LLC, part of Springer Nature 2019 Abstract Archaea, which form one of four domains of life alongside Eukarya, Bacteria, and giant viruses, have long been neglected as components of the human microbiota and potential opportunistic infectious pathogens. In this review, we focus on methanogenic Archaea, which rely on hydrogen for their metabolism and growth. On one hand, methanogenic Archaea in the gut are functional associates of the fermentative digestion of dietary fibers, favoring the production of beneficial short-chain fatty acids and likely contributing to the weaning reaction during the neonatal window of opportunity. On the other hand, methanogenic Archaea trigger the activation of innate and adaptive responses and the generation of specific T and B cells in animals and humans. In mouse models, lung hypersensitivity reactions can be induced by inhaled methanogenic Archaea mimicking human professional exposure to organic dust. Changes in methanogenic Archaea of the microbiota are detected in an array of dysimmune conditions comprising inflammatory bowel disease, obesity, malnutrition, anorexia, colorectal cancer, and diverticulosis. At the subcellular level, methanogenic Archaea are activators of the TLR8-dependent NLRP3 inflammasome, modulate the release of antimicrobial peptides and drive the production of proinflammatory, Th-1, Th-2, and Th-17 cytokines. -
Downloaded from the NCBI Website on April to 0.5 M, and 0.5 Ml of Phenol:Chloroform:Isoamyl Alco- 24Th, 2015
Gilmore et al. BMC Genomics (2017) 18:639 DOI 10.1186/s12864-017-4036-4 RESEARCHARTICLE Open Access Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Sean P. Gilmore1, John K. Henske1, Jessica A. Sexton1, Kevin V. Solomon1,6, Susanna Seppälä1,2, Justin I Yoo1, Lauren M. Huyett1, Abe Pressman1, James Z. Cogan3, Veronika Kivenson4, Xuefeng Peng1,4, YerPeng Tan5, David L. Valentine4 and Michelle A. O’Malley1* Abstract Background: The metabolism of archaeal methanogens drives methane release into the environment and is critical to understanding global carbon cycling. Methanogenesis operates at a very low reducing potential compared to other forms of respiration and is therefore critical to many anaerobic environments. Harnessing or altering methanogen metabolism has the potential to mitigate global warming and even be utilized for energy applications. Results: Here, we report draft genome sequences for the isolated methanogens Methanobacterium bryantii, Methanosarcina spelaei, Methanosphaera cuniculi,andMethanocorpusculum parvum. These anaerobic, methane- producing archaea represent a diverse set of isolates, capable of methylotrophic, acetoclastic, and hydrogenotrophic methanogenesis. Assembly and analysis of the genomes allowed for simple and rapid reconstruction of metabolism in the four methanogens. Comparison of the distribution of Clusters of Orthologous Groups (COG) proteins to a sample of genomes from the RefSeq database revealed a trend towards energy conservation in genome composition of all methanogens sequenced. Further analysis of the predicted membrane proteins and transporters distinguished differing energy conservation methods utilized during methanogenesis, such as chemiosmotic coupling in Msar. spelaei and electron bifurcation linked to chemiosmotic coupling in Mbac. bryantii and Msph. cuniculi. Conclusions: Methanogens occupy a unique ecological niche, acting as the terminal electron acceptors in anaerobic environments, and their genomes display a significant shift towards energy conservation. -
Higher-Level Classification of the Archaea: Evolution of Methanogenesis and Methanogens
Archaea 1, 353–363 © 2005 Heron Publishing—Victoria, Canada Higher-level classification of the Archaea: evolution of methanogenesis and methanogens ÉRIC BAPTESTE1,2, CÉLINE BROCHIER3 AND YAN BOUCHER4 1 Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Building, Halifax, NS, B3H 4H7, Canada 2 Corresponding author ([email protected]) 3 EA EGEE (Évolution, Génome, Environnement), Université Aix-Marseille I, Centre Saint-Charles, 13331 Marseille Cedex 3, France 4 Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia Received January 20, 2005; accepted March 29, 2005; published online April 13, 2005 Summary We used a phylogenetic approach to analyze the only one type of biological methane producer, archaeal meth- evolution of methanogenesis and methanogens. We show that anogens. There are five phylogenetically divergent orders 23 vertically transmitted ribosomal proteins do not support the of the domain Archaea (phylum euryarchaeota) that fall un- monophyly of methanogens, and propose instead that there are der the appellation “methanogens” (Garrity 2001): Methano- two distantly related groups of extant archaea that produce bacteriales, Methanopyrales, Methanococcales, Methano- methane, which we have named Class I and Class II. Based on microbiales and Methanosarcinales. All of these orders this finding, we subsequently investigated the uniqueness of contain a wide diversity of taxa that vary greatly in their mor- the origin of methanogenesis by studying both the enzymes of phological and physiological characteristics. However, they methanogenesis and the proteins that synthesize its specific co- all have in common an anaerobic lifestyle and the ability to enzymes. We conclude that hydrogenotrophic methanogenesis produce methane metabolically. -
Taxonomy and Ecology of Methanogens
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Horizon / Pleins textes FEMS Microbiology Reviews 87 (1990) 297-308 297 Pubfished by Elsevier FEMSRE 00180 Taxonomy and ecology of methanogens J.L. Garcia Laboratoire de Microbiologie ORSTOM, Université de Provence, Marseille, France Key words: Methanogens; Archaebacteria; Taxonomy; Ecology 1. INTRODUCTION methane from CO2 using alcohols as hydrogen donors; 2-propanol is oxidized to acetone, and More fhan nine reviews on taxonomy of 2-butanol to 2-butanone. Carbon monoxide may methanogens have been published during the last also be converted into methane; most hydro- decade [l-91, after the discovery of the unique genotrophic species (60%) will also use formate. biochemical and genetic properties of these Some aceticlastic species are incapable of oxidiz- organisms led to the concept of Archaebacteria at ing H,. The aceticlastic species of the genus the end of the seventies. Moreover, important Methanosurcina are the most metabolically diverse economic factors have ,placed these bacteria in the methanogens, whereas the obligate aceticlastic limelight [5], including the need to develop alter- Methanosaeta (Methanothrix) can use only acetate. native forms of energy, xenobiotic pollution con- The taxonomy of the methanogenic bacteria trol, the enhancement of meat yields in the cattle has been extensively revised in the light of new industry, the distinction between biological and information based on comparative studies of 16 S thermocatalytic petroleum generation, and the rRNA oligonucleotide sequences, membrane lipid global distribution of methane in the earth's atmo- composition, and antigenic fingerprinting data. sphere. The phenotypic characteristics often do not pro- vide a sufficient means of distinguishing among taxa or determining the phylogenetic position of a 2. -
Survival of Methanogenic Archaea from Siberian Permafrost Under Simulated Martian Thermal Conditions
Orig Life Evol Biosph DOI 10.1007/s11084-006-9024-7 Survival of Methanogenic Archaea from Siberian Permafrost under Simulated Martian Thermal Conditions Daria Morozova & Diedrich Möhlmann & Dirk Wagner Received: 8 March 2006 / Accepted in revised form: 9 August 2006 # Springer Science + Business Media B.V. 2006 Abstract Methanogenic archaea from Siberian permafrost complementary to the already well-studied methanogens from non-permafrost habitats were exposed to simulated Martian conditions. After 22 days of exposure to thermo-physical conditions at Martian low- and mid- latitudes up to 90% of methanogenic archaea from Siberian permafrost survived in pure cultures as well as in environmental samples. In contrast, only 0.3% –5.8% of reference organisms from non-permafrost habitats survived at these conditions. This suggests that methanogens from terrestrial permafrost seem to be remarkably resistant to Martian conditions. Our data also suggest that in scenario of subsurface lithoautotrophic life on Mars, methanogenic archaea from Siberian permafrost could be used as appropriate candidates for the microbial life on Mars. Keywords methanogenic archaea . permafrost . astrobiology . life on Mars . Mars simulation experiments Introduction Of all the planets explored by spacecrafts in the last four decades, Mars is considered as one of the most similar planets to Earth, even though it is characterized by extreme cold and dry conditions today. This view has been supported by the current ESA mission Mars Express, which identified several different forms of water on Mars and methane in the Martian atmosphere (Formisano 2004). Because of the expected short lifetime of methane, this trace gas could only originate from active volcanism – which was not yet observed on Mars – or from biological sources. -
Methanogenic Microorganisms in Industrial Wastewater Anaerobic Treatment
processes Review Methanogenic Microorganisms in Industrial Wastewater Anaerobic Treatment Monika Vítˇezová 1 , Anna Kohoutová 1, Tomáš Vítˇez 1,2,* , Nikola Hanišáková 1 and Ivan Kushkevych 1,* 1 Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; [email protected] (M.V.); [email protected] (A.K.); [email protected] (N.H.) 2 Department of Agricultural, Food and Environmental Engineering, Faculty of AgriSciences, Mendel University, 61300 Brno, Czech Republic * Correspondence: [email protected] (T.V.); [email protected] (I.K.); Tel.: +420-549-49-7177 (T.V.); +420-549-49-5315 (I.K.) Received: 31 October 2020; Accepted: 24 November 2020; Published: 26 November 2020 Abstract: Over the past decades, anaerobic biotechnology is commonly used for treating high-strength wastewaters from different industries. This biotechnology depends on interactions and co-operation between microorganisms in the anaerobic environment where many pollutants’ transformation to energy-rich biogas occurs. Properties of wastewater vary across industries and significantly affect microbiome composition in the anaerobic reactor. Methanogenic archaea play a crucial role during anaerobic wastewater treatment. The most abundant acetoclastic methanogens in the anaerobic reactors for industrial wastewater treatment are Methanosarcina sp. and Methanotrix sp. Hydrogenotrophic representatives of methanogens presented in the anaerobic reactors are characterized by a wide species diversity. Methanoculleus -
University of Wisconsin System Solid Waste Research Program
UNIVERSITY OF WISCONSIN SYSTEM SOLID WASTE RESEARCH PROGRAM Microbial Diversity and Dynamics during Methane Production from Municipal Solid Waste 2010 Christopher A. Bareither Georgia L. Wolfe Katherine D. McMahon Craig H. Benson University of Wisconsin-Madison Waste Management 33 (2013) 1982–1992 Contents lists available at SciVerse ScienceDirect Waste Management journal homepage: www.elsevier.com/locate/wasman Microbial diversity and dynamics during methane production from municipal solid waste ⇑ Christopher A. Bareither a,b, , Georgia L. Wolfe c, Katherine D. McMahon d, Craig H. Benson e a Civil & Environmental Engineering, Colorado State University, Ft. Collins, CO 80532, USA b Geological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA c Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA d Bacteriology, Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA e Civil & Environmental Engineering, Geological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA article info abstract Article history: The objectives of this study were to characterize development of bacterial and archaeal populations dur- Received 1 October 2012 ing biodegradation of municipal solid waste (MSW) and to link specific methanogens to methane gener- Accepted 14 December 2012 ation. Experiments were conducted in three 0.61-m-diameter by 0.90-m-tall laboratory reactors to Available online 12 January 2013 simulate MSW bioreactor landfills. Pyrosequencing of 16S rRNA genes was used to characterize microbial communities in both leachate and solid waste. Microbial assemblages in effluent leachate were similar Keywords: between reactors during peak methane generation. Specific groups within the Bacteroidetes and Ther- Bioreactor landfill matogae phyla were present in all samples and were particularly abundant during peak methane gener- Methane ation.