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Methanosaeta Pelagica" Sp
Aceticlastic and NaCl-Requiring Methanogen "Methanosaeta pelagica" sp. nov., Isolated from Marine Tidal Flat Title Sediment Author(s) Mori, Koji; Iino, Takao; Suzuki, Ken-Ichiro; Yamaguchi, Kaoru; Kamagata, Yoichi Applied and Environmental Microbiology, 78(9), 3416-3423 Citation https://doi.org/10.1128/AEM.07484-11 Issue Date 2012-05 Doc URL http://hdl.handle.net/2115/50384 Rights © 2012 by the American Society for Microbiology Type article (author version) File Information AEM78-9_3416-3423.pdf Instructions for use Hokkaido University Collection of Scholarly and Academic Papers : HUSCAP Mori et al. Title 2 Aceticlastic and NaCl-requiring methanogen “Methanosaeta pelagica” sp. nov., isolated from marine tidal flat sediment. 4 Authors 6 Koji Mori,1 Takao Iino,2 Ken-ichiro Suzuki,1 Kaoru Yamaguchi1 & Yoichi Kamagata3 1NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 8 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan 2Japan Collection of Microorganisms, RIKEN BioResource Center, 2-1 Hirosawa, Wako, Saitama 10 351-0198, Japan 3Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology 12 (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 400-8511, Japan 14 Corresponding author Koji Mori 16 NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan 18 Tel, +81-438-20-5763; Fax, +81-438-52-2329; E-mail, [email protected] 20 Running title Marine aceticlastic methanogen, Methanosaeta pelagica 22 1 Mori et al. 2 ABSTRACT Acetate is a key compound for anaerobic organic matter degradation, and so far, two genera, 4 Methanosaeta and Methanosarcina, are only contributors for acetate degradation among methanogens. -
Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae -
MIAMI UNIVERSITY the Graduate School Certificate for Approving The
MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Qiuyuan Huang Candidate for the Degree: Doctor of Philosophy _______________________________________ Hailiang Dong, Director ________________________________________ Yildirim Dilek, Reader ________________________________________ Jonathan Levy, Reader ______________________________________ Chuanlun Zhang, External examiner ______________________________________ Annette Bollmann, Graduate School Representative ABSTRACT GEOMICROBIAL INVESTIGATIONS ON EXTREME ENVIRONMENTS: LINKING GEOCHEMISTRY TO MICROBIAL ECOLOGY IN TERRESTRIAL HOT SPRINGS AND SALINE LAKES by Qiuyuan Huang Terrestrial hot springs and saline lakes represent two extreme environments for microbial life and constitute an important part of global ecosystems that affect the biogeochemical cycling of life-essential elements. Despite the advances in our understanding of microbial ecology in the past decade, important questions remain regarding the link between microbial diversity and geochemical factors under these extreme conditions. This dissertation first investigates a series of hot springs with wide ranges of temperature (26-92oC) and pH (3.72-8.2) from the Tibetan Plateau in China and the Philippines. Within each region, microbial diversity and geochemical conditions were studied using an integrated approach with 16S rRNA molecular phylogeny and a suite of geochemical analyses. In Tibetan springs, the microbial community was dominated by archaeal phylum Thaumarchaeota -
Insights Into Archaeal Evolution and Symbiosis from the Genomes of a Nanoarchaeon and Its Inferred Crenarchaeal Host from Obsidian Pool, Yellowstone National Park
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Microbiology Publications and Other Works Microbiology 4-22-2013 Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar University of Tennessee - Knoxville, [email protected] Kira S. Makarova National Institutes of Health David E. Graham University of Tennessee - Knoxville, [email protected] Yuri I. Wolf National Institutes of Health Eugene V. Koonin National Institutes of Health See next page for additional authors Follow this and additional works at: https://trace.tennessee.edu/utk_micrpubs Part of the Microbiology Commons Recommended Citation Biology Direct 2013, 8:9 doi:10.1186/1745-6150-8-9 This Article is brought to you for free and open access by the Microbiology at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Microbiology Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Authors Mircea Podar, Kira S. Makarova, David E. Graham, Yuri I. Wolf, Eugene V. Koonin, and Anna-Louise Reysenbach This article is available at TRACE: Tennessee Research and Creative Exchange: https://trace.tennessee.edu/ utk_micrpubs/44 Podar et al. Biology Direct 2013, 8:9 http://www.biology-direct.com/content/8/1/9 RESEARCH Open Access Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park Mircea Podar1,2*, Kira S Makarova3, David E Graham1,2, Yuri I Wolf3, Eugene V Koonin3 and Anna-Louise Reysenbach4 Abstract Background: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. -
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. -
UNIVERSITY of CALIFORNIA RIVERSIDE Microbial
UNIVERSITY OF CALIFORNIA RIVERSIDE Microbial Diversity Studies in Sediments of Perennially Ice-covered Lakes, McMurdo Dry Valleys, Antarctica A Dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philososphy in Microbiology by Chao Tang December 2009 Dissertation Committee: Dr. Brian Lanoil, Chairperson Dr. James Borneman Dr. David Crowley Copyright by Chao Tang 2009 The Dissertation of Chao Tang is approved: Committee Chairperson University of California, Riverside Acknowledgments There are numerous people who have provided me with help and inspiration during my studies here at UC Riverside. First and foremost, I would like to express my sincere appreciation for my advisor, Dr. Brian Lanoil, for giving me a great opportunity to study Antarctica microbiology, challenging and guiding me in pursuit of science. I would also like to acknowledge the past and present members of the Lanoil and Stein groups for the stimulating scientific discussions, help with experiments and encouragement in persevering through difficult times. I would like to thank Dr. David Crowley and Dr. James Borneman on my dissertation committee for their support and advice. I’d also like to thank our collaborators in the McMurdo Dry Valleys Microbial Observatory program, Dr. Michael Madigan from Southern Illinois University and Dr. Vladimir Samarkin from University of Georgia, Athens, for bringing field equipments, joint sampling efforts, and sharing their knowledge and insights for my research. I appreciate the Long Term Ecological Research limnology team led by Dr. John Priscu of Montana State University for help with fieldwork and their friendship. I am very grateful to my parents for their love, support, understanding and patience over the years. -
(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. -
Unexpected Competitiveness of Methanosaetapopulations At
Unexpected competitiveness of Methanosaetapopulations at elevated acetate concentrations in methanogenic treatment of animal wastewater Authors Authors and affiliations Si Chen Huicai Cheng Jiang Liu Terry C. Hazen Vicki Huang Qiang He o o o o o o o o o 1. 1. 2. 2. 3. 3. 4. 4. 5. 5. Environmental biotechnology First Online: 17 November 2016 2 Shares 354Downloads 3 Citations Abstract Acetoclastic methanogenesis is a key metabolic process in anaerobic digestion, a technology with broad applications in biogas production and waste treatment. Acetoclastic methanogenesis is known to be performed by two archaeal genera, Methanosaeta and Methanosarcina. The conventional model posits that Methanosaeta populations are more competitive at low acetate levels (<1 mM) than Methanosarcina and vice versa at higher acetate concentrations. While this model is supported by an extensive body of studies, reports of inconsistency have grown that Methanosaeta were observed to outnumber Methanosarcina at elevated acetate levels. In this study, monitoring of anaerobic digesters treating animal wastewater unexpectedly identified Methanosaeta as the dominant acetoclastic methanogen population at both low and high acetate levels during organic overloading. The surprising competitiveness of Methanosaeta at elevated acetate was further supported by the enrichment of Methanosaetawith high concentrations of acetate (20 mM). The dominance of Methanosaeta in the methanogen community could be reproduced in anaerobic digesters with the direct addition of acetate to above 20 mM, again supporting the competitiveness of Methanosaeta over Methanosarcina at elevated acetate levels. This study for the first time systematically demonstrated that the dominance of Methanosaeta populations in anaerobic digestion could be linked to the competitiveness of Methanosaeta at elevated acetate concentrations. -
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. -
Diversity of Methane-Cycling Microorganisms in Soils and Their Relation to Oxygen
Diversity of Methane-cycling Microorganisms in Soils and Their Relation to Oxygen Claudia Knief* Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany. *Correspondence: [email protected] htps://doi.org/10.21775/cimb.033.023 Abstract Introduction Microorganisms are important players in the Methane cycling microorganisms are of interest global methane cycle. Anaerobic methanogenic for microbiologists since more than a century. archaea are largely responsible for methane pro- Research on these microorganisms was initially duction, while aerobic methanotrophic bacteria, largely driven by the curiosity to understand their as well as anaerobic methanotrophic bacteria particular physiology that leads to the production and archaea, are involved in methane oxidation. or consumption of methane. While this interest is In anoxic wetland soils, methanogens produce still a driver, the importance of methane as green- methane, while methanotrophs act as a flter house gas has become another important factor, and reduce methane emissions. In the predomi- promoting further research on methanogenic and nantly oxic upland soils, aerobic methanotrophs methanotrophic microorganisms. Tis leads to a oxidize atmospheric methane. Tis review gives continuously beter understanding of their physi- an overview of the diversity of methanogenic ology and ecology, and it becomes evident that and methanotrophic microorganisms, highlights the processes of microbial methane production recent discoveries and provides information and consumption are mediated by more com- concerning their occurrence in soils. Recent plex functional guilds than initially thought. Te fndings indicate that the methanogenic and improved understanding is not only due to the con- methanotrophic lifestyles are more widespread stantly increasing diversity of methanogenic and in microorganisms than previously thought, and methanotrophic microorganisms (e.g. -
Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes
GBE Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes Dennifier Costa Brandao~ Cruz1, Lenon Lima Santana1, Alexandre Siqueira Guedes2, Jorge Teodoro de Souza3,*, and Phellippe Arthur Santos Marbach1,* 1CCAAB, Biological Sciences, Recoˆ ncavo da Bahia Federal University, Cruz das Almas, Bahia, Brazil 2Agronomy School, Federal University of Goias, Goiania,^ Goias, Brazil 3 Department of Phytopathology, Federal University of Lavras, Minas Gerais, Brazil Downloaded from https://academic.oup.com/gbe/article/11/4/1235/5345563 by guest on 27 September 2021 *Corresponding authors: E-mails: [email protected]fla.br; [email protected]. Accepted: February 16, 2019 Abstract The last two steps of the purine biosynthetic pathway may be catalyzed by different enzymes in prokaryotes. The genes that encode these enzymes include homologs of purH, purP, purO and those encoding the AICARFT and IMPCH domains of PurH, here named purV and purJ, respectively. In Bacteria, these reactions are mainly catalyzed by the domains AICARFT and IMPCH of PurH. In Archaea, these reactions may be carried out by PurH and also by PurP and PurO, both considered signatures of this domain and analogous to the AICARFT and IMPCH domains of PurH, respectively. These genes were searched for in 1,403 completely sequenced prokaryotic genomes publicly available. Our analyses revealed taxonomic patterns for the distribution of these genes and anticorrelations in their occurrence. The analyses of bacterial genomes revealed the existence of genes coding for PurV, PurJ, and PurO, which may no longer be considered signatures of the domain Archaea. Although highly divergent, the PurOs of Archaea and Bacteria show a high level of conservation in the amino acids of the active sites of the protein, allowing us to infer that these enzymes are analogs. -
Microbial Community Analysis of the University of Wisconsin Oshkosh Dry Biodigester
UNIVERSITY OF WISCONSIN SYSTEM SOLID WASTE RESEARCH PROGRAM Student Project Report Microbial Community Analysis of the University of Wisconsin Oshkosh Dry Biodigester May 2015 Student Investigator: Jessi Zimmerman Advisor: Dr. Eric Matson University of Wisconsin-Oshkosh 1 Abstract In natural environments, heterotrophic bacteria and methanogenic Archaea assist in the degradation of organic waste, which results in the production of a mixture of carbon dioxide and methane gas, together known as biogas. In the UW-Oshkosh dry anaerobic biodigester, these same naturally occurring microbial processes are utilized to benefit the University and surrounding community. Organic waste produced by local farms, grocery stores, and residential households are collected and delivered to the biodigester facility rather than being added to landfills. These waste products serve as the feedstock for biogas production. The combustible biogas is captured and used as fuel for a combined heat and power generator, which meets about 10% of the campus electricity demand and helps to heat the digester and other nearby campus facilities. The process reduces the University’s operating costs while diverting some forms of municipal waste away from landfills and provides a cleaner alternative to fossil fuels. The composition of the incoming feedstock is closely monitored as are the physicochemical conditions such as temperature, pH and hydration. These are measured at the beginning and throughout the cycle, because they can influence methane output. What is not measured (and not currently known) is how the growth of microbial species changes throughout the course of the digestion cycle. In particular, changes that may occur in methanogenic species richness and relative abundance are likely to influence biogas quality and output.