DOCSLIB.ORG

Hydrogen-Limited Growth of Hyperthermophilic Methanogens at Deep-Sea Hydrothermal Vents

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Hydrogen-Limited Growth of Hyperthermophilic Methanogens at Deep-Sea Hydrothermal Vents Hydrogen-limited growth of hyperthermophilic methanogens at deep-sea hydrothermal vents Helene C. Ver Eeckea, David A. Butterfieldb, Julie A. Huberc, Marvin D. Lilleyd, Eric J. Olsond, Kevin K. Roeb, Leigh J. Evanse, Alexandr Y. Merkelf, Holly V. Cantinc, and James F. Holdena,1 aDepartment of Microbiology, University of Massachusetts, Amherst, MA 01003; bJoint Institute for the Study of the Atmosphere and Ocean and dSchool of Oceanography, University of Washington, Seattle, WA 98195; cJosephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543; eCooperative Institute for Marine Resources Studies, Oregon State University, Newport, OR 97365; and fWinogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved June 29, 2012 (received for review April 21, 2012) Microbial productivity at hydrothermal vents is among the highest Deep-sea hydrothermal vents are among the most productive found anywhere in the deep ocean, but constraints on microbial regions within igneous ocean crust and provide a starting point growth and metabolism at vents are lacking. We used a combina- for modeling subseafloor microbial processes associated with tion of cultivation, molecular, and geochemical tools to verify pure hydrothermal circulation in basalt. Thermophilic and hyperther- culture H2 threshold measurements for hyperthermophilic metha- mophilic methanogens belonging to the order Methanococcales nogenesis in low-temperature hydrothermal fluids from Axial Vol- are commonly found autotrophs in vent environments (14–21). fi cano and Endeavour Segment in the northeastern Paci c Ocean. These organisms anaerobically convert H2 and CO2 into biomass, Two Methanocaldococcus strains from Axial and Methanocaldo- CH4 and H2O. Limited data suggest that the abundances of coccus jannaschii showed similar Monod growth kinetics when methanogens and the extent of methanogenic fluid chemistry al- grown in a bioreactor at varying H2 concentrations. Their H2 teration are elevated in ultramafic vent sites, where serpentini- μ – half-saturation value was 66 M, and growth ceased below 17 zation leads to high H concentrations (16, 19–21), and at volcanic μ 2 23 MH2, 10-fold lower than previously predicted. By comparison, eruption sites, where posteruption H is also more abundant (14, fl 2 measured H2 and CH4 concentrations in uids suggest that there – fl fi Methanocaldococcus 22 25). In contrast, methanogen abundances and uid alterations was generally suf cient H2 for growth at are often low to undetectable in other midocean ridge and vol- Axial but not at Endeavour. Fluids from one vent at Axial (Marker canic arc hydrothermal systems, where H concentrations are also 113) had anomalously high CH concentrations and contained 2 4 relatively low (20, 26–29). This pattern of H -limited methano- various thermal classes of methanogens based on cultivation 2 genesis generally fits those predicted in bioenergetic models (11, and mcrA/mrtA analyses. At Endeavour, methanogens were largely undetectable in fluid samples based on cultivation and 13), but the temperature-dependent maintenance energy data molecular screens, although abundances of hyperthermophilic het- used for these models lack data for methanogenesis and all other erotrophs were relatively high. Where present, Methanocaldococ- anaerobic metabolisms above 65 °C (30). Without empirically cus genes were the predominant mcrA/mrtA sequences recovered determined growth kinetic constraints, H2 availability cannot be fi and comprised ∼0.2–6% of the total archaeal community. Field shown de nitively to be a key factor driving methanogen abun- and coculture data suggest that H2 limitation may be partly ame- dance and distribution at thermophilic growth temperatures in liorated by H2 syntrophy with hyperthermophilic heterotrophs. vent systems. The purposes of this study were to define the Monod growth These data support our estimated H2 threshold for hyperthermo- philic methanogenesis at vents and highlight the need for coupled kinetics on H2 and minimum H2 concentrations required for laboratory and field measurements to constrain microbial distribu- the growth of Methanocaldococcus jannaschii and two Meth- tion and biogeochemical impacts in the deep sea. anocaldococcus species isolated from deep-sea hydrothermal vents at Axial Volcano, strains JH146 and JH123. Sequencing t is estimated that perhaps a third [56–90 petagrams (Pg)] of and quantitative PCR (qPCR) analysis were used to determine fi Ithe Earth’s total bacterial and archaeal carbon (106–333 Pg) the diversity and abundance of methanogen-speci c methyl exists within marine subsurface sediments (1–3). These global coenzyme M reductase (mcrA) genes in low-temperature vent estimates do not include microbial carbon in igneous ocean fluids from Axial Volcano and nearby Endeavour Segment. The crust, wherein an additional 200 Pg of carbon has been proposed abundances of thermophilic and hyperthermophilic metha- to exist primarily within its porous extrusive layer (layer 2A), nogens and hyperthermophilic heterotrophs were determined where hydrothermal fluids circulate through basalt as old as 65 using culture-dependent techniques from the same fluids. Fi- Ma (4). Therefore, microbes in marine sediments and ocean nally, these data were correlated with fluid geochemistry from crust have the potential to have a significant impact on bio- the two sites, as well as with methanogen abundance and geo- geochemical fluxes and carbon cycles in the deep ocean. Meth- chemical data from vent sites worldwide, to link our predictions anogenesis and sulfate reduction are often the predominant of high-temperature methanogenesis with in situ measurements. anaerobic microbial processes in many deep subsurface marine sediments, especially near continental margins (5, 6), and methanogens and sulfate reducers are also frequently found in Author contributions: H.C.V., D.A.B., J.A.H., and J.F.H. designed research; H.C.V., D.A.B., J.A.H., deep subsurface terrestrial basalts (7–9). However, models of E.J.O., K.K.R., L.J.E., A.Y.M., H.V.C., and J.F.H. performed research; H.C.V., D.A.B., J.A.H., the rates and constraints of various aerobic and anaerobic M.D.L., and J.F.H. analyzed data; and H.C.V., D.A.B., J.A.H., and J.F.H. wrote the paper. biogeochemical processes in deep subsurface environments, The authors declare no conflict of interest. especially within hard rock, are nascent because of these envi- This article is a PNAS Direct Submission. ronments being difficult to access. This has generated interest Freely available online through the PNAS open access option. in quantitatively modeling habitability and biogeochemical Data deposition: The sequences reported in this paper have been deposited in the Gen- processes within the deep subsurface using bioenergetic pre- Bank database (accession nos. HQ635140–HQ635763). dictions of microbial metabolism, based on the supply of geo- 1To whom correspondence should be addressed. E-mail: [email protected]. chemical energy and the metabolic energy demand of the This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. organisms (10–13). 1073/pnas.1206632109/-/DCSupplemental. 13674–13679 | PNAS | August 21, 2012 | vol. 109 | no. 34 www.pnas.org/cgi/doi/10.1073/pnas.1206632109 Downloaded by guest on September 24, 2021 Results and Discussion decreasing H2 concentrations (Fig. 1 and Fig. S1). The minimum Growth Kinetics and H Limitation of Methanocaldococcus spp. Three H2 concentration for the growth of M. jannaschii was between 17 2 μ μ hyperthermophilic Methanocaldococcus species were grown in M and 23 M (Fig. 1A), whereas the minimum concentration B a gas flow-controlled bioreactor at either 82 °C or 70 °C to de- for strains JH146 (Fig. 1 ) and JH123 (Fig. S1) was between 10 μM and 17 μM. Statistically, there was no difference in the termine the effect of H2 concentration on growth. Two of the fi H2-dependent Monod growth kinetic parameters, namely, the organisms (JH146 and JH123) had been puri ed from low- growth rate half-saturation constant (K ) and maximum growth fl s temperature hydrothermal uids collected at Axial Volcano in rate (μmax), for the three organisms (Fig. 1C). The Ks for the 2008. The third organism was the commercially available M. pooled data for all three strains was 66 μM. The effect of hy- jannaschii DSM 2661 strain. All three organisms had longer drostatic pressure on our minimum H2 and Ks estimates was not doubling times and lower maximum cell concentrations with tested. Pressure has a very minor effect on values of standard molal Gibbs energy (ΔGr°) for reactions occurring in the aqueous phase (11, 31). Growth rates and hydrogenase activities of M. jannaschii increased modestly with pressure (32–34). However, A it is not known whether pressure significantly affects the organ- ) 10 ism’saffinity for aqueous H2, and this is area for future research. 7 In comparison, the H2 Ks values for the mesophilic metha- 8 nogens Methanospirillum hungatei and Methanobacterium bryantii, , × 10 each grown at 37 °C, were 6.6 μM and 18 μM, respectively (35, -1 36), and the minimum H2 threshold for M. bryantii was 2.4 μM 6 (36). Therefore, the generally higher demand for H2 by Meth- ls (ml anocaldococcus spp. may be a reflection of higher growth energy 4 requirements for hydrogenotrophic methanogens at hyper- thermophilic temperatures, as previously predicted (11). The minimum H2 threshold for methanogenesis at 82 °C in this study 2 was more than 10-fold lower than had been predicted (11), but this reflects the need to refine the parameters used to predict maintenance energies for hyperthermophiles in bioenergetics Number of CellNumber 0 0 2 4 6 8 10 12 14 models through experimentation. For example, increasing the SCIENCES activation energy (E ) in the Hoehler model (11) from 69.4 to ENVIRONMENTAL − a Time (h) 80 kJ mol 1 decreases cellular maintenance energies at 82 °C B more than 36-fold, which would predict a lower minimum H 10 2 ) threshold for the organisms.
Load more

Recommended publications
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Adaptations of Methanococcus Maripaludis to Its Unique Lifestyle
    ADAPTATIONS OF METHANOCOCCUS MARIPALUDIS TO ITS UNIQUE LIFESTYLE by YUCHEN LIU (Under the Direction of William B. Whitman) ABSTRACT Methanococcus maripaludis is an obligate anaerobic, methane-producing archaeon. In addition to the unique methanogenesis pathway, unconventional biochemistry is present in this organism in adaptation to its unique lifestyle. The Sac10b homolog in M. maripaludis, Mma10b, is not abundant and constitutes only ~ 0.01% of the total cellular protein. It binds to DNA with sequence-specificity. Disruption of mma10b resulted in poor growth of the mutant in minimal medium. These results suggested that the physiological role of Mma10b in the mesophilic methanococci is greatly diverged from the homologs in thermophiles, which are highly abundant and associate with DNA without sequence-specificity. M. maripaludis synthesizes lysine through the DapL pathway, which uses diaminopimelate aminotransferase (DapL) to catalyze the direct transfer of an amino group from L-glutamate to L-tetrahydrodipicolinate (THDPA), forming LL-diaminopimelate (LL-DAP). This is different from the conventional acylation pathway in many bacteria that convert THDPA to LL-DAP in three steps: succinylation or acetylation, transamination, and desuccinylation or deacetylation. The DapL pathway eliminates the expense of using succinyl-CoA or acetyl-CoA and may represent a thriftier mode for lysine biosynthesis. Methanogens synthesize cysteine primarily on tRNACys via the two-step SepRS/SepCysS pathway. In the first step, tRNACys is aminoacylated with O-phosphoserine (Sep) by O- phosphoseryl-tRNA synthetase (SepRS). In the second step, the Sep moiety on Sep-tRNACys is converted to cysteine with a sulfur source to form Cys-tRNACys by Sep-tRNA:Cys-tRNA synthase (SepCysS).
    [Show full text]
  • Hyperthermophilic Methanogenic Archaea Act As High-Pressure CH4 Cell Factories
    ARTICLE https://doi.org/10.1038/s42003-021-01828-5 OPEN Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories Lisa-Maria Mauerhofer1, Sara Zwirtmayr2, Patricia Pappenreiter2, Sébastien Bernacchi 3, Arne H. Seifert3, Barbara Reischl1,3, Tilman Schmider1, Ruth-Sophie Taubner 1,2, Christian Paulik 2 & ✉ Simon K.-M. R. Rittmann 1 Bioprocesses converting carbon dioxide with molecular hydrogen to methane (CH4) are currently being developed to enable a transition to a renewable energy production system. In this study, we present a comprehensive physiological and biotechnological examination of 80 methanogenic archaea (methanogens) quantifying growth and CH4 production kinetics at 1234567890():,; hyperbaric pressures up to 50 bar with regard to media, macro-, and micro-nutrient supply, specific genomic features, and cell envelope architecture. Our analysis aimed to system- atically prioritize high-pressure and high-performance methanogens. We found that the hyperthermophilic methanococci Methanotorris igneus and Methanocaldococcoccus jannaschii are high-pressure CH4 cell factories. Furthermore, our analysis revealed that high- performance methanogens are covered with an S-layer, and that they harbour the amino acid motif Tyrα444 Glyα445 Tyrα446 in the alpha subunit of the methyl-coenzyme M reduc- tase. Thus, high-pressure biological CH4 production in pure culture could provide a purpo- seful route for the transition to a carbon-neutral bioenergy sector. 1 Archaea Physiology & Biotechnology Group, Department Functional and Evolutionary Ecology, Universität Wien, Wien, Austria. 2 Institute for Chemical ✉ Technology of Organic Materials, Johannes Kepler Universität Linz, Linz, Austria. 3 Krajete GmbH, Linz, Austria. email: [email protected] COMMUNICATIONS BIOLOGY | (2021) 4:289 | https://doi.org/10.1038/s42003-021-01828-5 | www.nature.com/commsbio 1 ARTICLE COMMUNICATIONS BIOLOGY | https://doi.org/10.1038/s42003-021-01828-5 26 ethane (CH4) is an energy carrier of worldwide growth and CH4 production .
    [Show full text]
  • Widespread Distribution of Archaeal Reverse Gyrase in Thermophilic Bacteria Suggests a Complex History of Vertical Inheritance and Lateral Gene Transfers
    Archaea 2, 83–93 © 2006 Heron Publishing—Victoria, Canada Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers CÉLINE BROCHIER-ARMANET1,3 and PATRICK FORTERRE2,4 1 EA 3781 EGEE (Evolution Génome Environnement), Université de Provence Aix-Marseille I, Centre Saint-Charles, 3 Place Victor Hugo 13331, Marseille Cedex 3, France 2 Institut de Génétique et Microbiologie, UMR CNRS 8621, Université Paris-Sud, 91405 Orsay, France 3 Corresponding author ([email protected]) 4 Unité Biologie Moléculaire du Gène chez les Extremophiles, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France Received September 21, 2005; accepted May 26, 2006; published online August 18, 2006 Summary Reverse gyrase, an enzyme of uncertain funtion, Introduction is present in all hyperthermophilic archaea and bacteria. Previ- Reverse gyrase, an enzyme first discovered in the hyper- ous phylogenetic studies have suggested that the gene for re- thermophilic archaeon Sulfolobus acidocaldarius, is formed verse gyrase has an archaeal origin and was transferred later- by the combination of an N-terminal helicase module and a ally (LGT) to the ancestors of the two bacterial hyperther- C-terminal topoisomerase module (see Declais et al. 2000 for mophilic phyla, Thermotogales and Aquificales. Here, we per- a review). Comparative genomic analysis performed 4 years formed an in-depth analysis of the evolutionary history of ago showed that reverse gyrase was at that time the only pro- reverse gyrase in light of genomic progress. We found genes tein specific for hyperthermophiles (i.e., present in all hyper- coding for reverse gyrase in the genomes of several ther- thermophiles and absent in all non-hyperthermophiles) (For- mophilic bacteria that belong to phyla other than Aquificales and Thermotogales.
    [Show full text]
  • Systematic Bacteriology Second Edition
    BERGEY'S MANUAL® OF Systematic Bacteriology Second Edition Volume One The Archaea and the Deeply Branching and Phototrophic Bacteria Springer New York Berlin Heidelberg Barcelona HongKong London Milan Paris Singapore Tokyo BERGEY'S MANUAL® OF Systematic Bacteriology Second Edition Volume One The Archaea and the Deeply Branching and Phototrophic Bacteria David R. Boone Richard W. Castenholz EDITORS, VOLUME ONE George M. Garrity EDITOR-IN-CHIEF EDITORIAL BOARD James T. Staley, Chairman, David R. Boone, Vice Chairman, Don J. Brenner, Richard W. Castenholz, George M. Garrity, Michael Goodfellow, Noel R. Krieg, Fred A. Rainey, Karl-Heinz Schleifer WITH CONTRIBUTIONS FROM 105 COLLEAGUES Springer George M. Garrity Department of Microbiology and Molecular Genetics Bergey's Manual Trust Michigan State University East Lansing, MI 48824-1101 USA Library of Congress Cataloging-in-Publication Data Bergey's manual of systematic bacteriology / David R. Boone, Richard W. Castenholz, editors, volume 1 ; George M. Garrity, editor-in-chief.-2nd ed. p.cm. Includes bibliographical references and index. Contents: v.I. The archaea and the deeply branching and phototrophic bacteria. ISBN 0-387-98771-1 (alk. paper) 1. Bacteria-Classification. I. Title: Systematic bacteriology. II. Boone, David R. III. Castenholz, Richard W. IV. Garrity, George M. QR81.B462001 579.3'01 '2-dc21 2001020400 With 330 illustrations The following proprietary names of products are used in this volume: Casamino@ acids; Vector NTI®; XLI0-Gold®; Gelrite®; Tryptone@l; Phytagel@; bio-Trypcasew; Trypticasev; Oxoid® purified agar. Printed on acid-free paper. First edition published 1984-1989 by Bergey's Manual Trust and Williams & Wilkins, Baltimore. © 2001 Bergey's Manual Trust All rights reserved.
    [Show full text]
  • Phylogenetic- and Genome-Derived Insight Into the Evolution of N-Glycosylation in Archaea ⇑ Lina Kaminski A, Mor N
    Molecular Phylogenetics and Evolution 68 (2013) 327–339 Contents lists available at SciVerse ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Phylogenetic- and genome-derived insight into the evolution of N-glycosylation in Archaea ⇑ Lina Kaminski a, Mor N. Lurie-Weinberger b, Thorsten Allers c, Uri Gophna b, Jerry Eichler a, a Department of Life Sciences, Ben Gurion University, Beersheva 84105, Israel b Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel c School of Biology, University of Nottingham, Nottingham NG7 2UH, UK article info abstract Article history: N-glycosylation, the covalent attachment of oligosaccharides to target protein Asn residues, is a post- Received 25 January 2013 translational modification that occurs in all three domains of life. In Archaea, the N-linked glycans that Revised 23 March 2013 decorate experimentally characterized glycoproteins reveal a diversity in composition and content Accepted 26 March 2013 unequaled by their bacterial or eukaryal counterparts. At the same time, relatively little is known of Available online 6 April 2013 archaeal N-glycosylation pathways outside of a handful of model strains. To gain insight into the distri- bution and evolutionary history of the archaeal version of this universal protein-processing event, 168 Keywords: archaeal genome sequences were scanned for the presence of aglB, encoding the known archaeal oli- Archaea gosaccharyltransferase, an enzyme key to N-glycosylation. Such analysis predicts the presence of AglB N-glycosylation Oligosaccharyltransferase in 166 species, with some species seemingly containing multiple versions of the protein. Phylogenetic analysis reveals that the events leading to aglB duplication occurred at various points during archaeal evolution.
    [Show full text]
  • Quantitative Detection of Culturable Methanogenic Archaea Abundance in Anaerobic Treatment Systems Using the Sequence-Specific Rrna Cleavage Method
    The ISME Journal (2009) 3, 522–535 & 2009 International Society for Microbial Ecology All rights reserved 1751-7362/09 $32.00 www.nature.com/ismej ORIGINAL ARTICLE Quantitative detection of culturable methanogenic archaea abundance in anaerobic treatment systems using the sequence-specific rRNA cleavage method Takashi Narihiro1, Takeshi Terada1, Akiko Ohashi1, Jer-Horng Wu2,4, Wen-Tso Liu2,5, Nobuo Araki3, Yoichi Kamagata1,6, Kazunori Nakamura1 and Yuji Sekiguchi1 1Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan; 2Division of Environmental Science and Engineering, National University of Singapore, Singapore and 3Department of Civil Engineering, Nagaoka National College of Technology, Nagaoka, Japan A method based on sequence-specific cleavage of rRNA with ribonuclease H was used to detect almost all known cultivable methanogens in anaerobic biological treatment systems. To do so, a total of 40 scissor probes in different phylogeny specificities were designed or modified from previous studies, optimized for their specificities under digestion conditions with 32 methanogenic reference strains, and then applied to detect methanogens in sludge samples taken from 6 different anaerobic treatment processes. Among these processes, known aceticlastic and hydrogenotrophic groups of methanogens from the families Methanosarcinaceae, Methanosaetaceae, Methanobacter- iaceae, Methanothermaceae and Methanocaldococcaceae could be successfully detected and
    [Show full text]
  • Interactions Between Anaerobic Fungi and Methanogens in the Rumen and Their Biotechnological Potential in Biogas Production from Lignocellulosic Materials
    microorganisms Review Interactions between Anaerobic Fungi and Methanogens in the Rumen and Their Biotechnological Potential in Biogas Production from Lignocellulosic Materials Yuqi Li 1 , Zhenxiang Meng 1, Yao Xu 1, Qicheng Shi 1, Yuping Ma 1, Min Aung 1,2, Yanfen Cheng 1,* and Weiyun Zhu 1 1 Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; [email protected] (Y.L.); [email protected] (Z.M.); [email protected] (Y.X.); [email protected] (Q.S.); [email protected] (Y.M.); [email protected] (M.A.); [email protected] (W.Z.) 2 Department of Animal Nutrition, University of Veterinary Science, Nay Pyi Taw 15013, Myanmar * Correspondence: [email protected]; Tel.: +86-25-84395523 Abstract: Anaerobic fungi in the digestive tract of herbivores are one of the critical types of fiber- degrading microorganisms present in the rumen. They degrade lignocellulosic materials using unique rhizoid structures and a diverse range of fiber-degrading enzymes, producing metabolic products such as H2/CO2, formate, lactate, acetate, and ethanol. Methanogens in the rumen utilize some of these products (e.g., H2 and formate) to produce methane. An investigation of the interac- tions between anaerobic fungi and methanogens is helpful as it provides valuable insight into the microbial interactions within the rumen. During the last few decades, research has demonstrated that anaerobic fungi stimulate the growth of methanogens and maintain methanogenic diversity. Meanwhile, methanogens increase the fiber-degrading capability of anaerobic fungi and stimulate Citation: Li, Y.; Meng, Z.; Xu, Y.; Shi, metabolic pathways in the fungal hydrogenosome.
    [Show full text]
  • Insights Into Dynamics of Mobile Genetic Elements in Hyperthermophilic Environments from Five New Thermococcus Plasmids
    Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new thermococcus plasmids. Mart Krupovic, Mathieu Gonnet, Wajdi Ben Hania, Patrick Forterre, Gaël Erauso To cite this version: Mart Krupovic, Mathieu Gonnet, Wajdi Ben Hania, Patrick Forterre, Gaël Erauso. Insights into dy- namics of mobile genetic elements in hyperthermophilic environments from five new thermococcus plas- mids.. PLoS ONE, Public Library of Science, 2013, 8 (1), pp.e49044. 10.1371/journal.pone.0049044. hal-00748527 HAL Id: hal-00748527 https://hal.archives-ouvertes.fr/hal-00748527 Submitted on 29 Jan 2013 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Insights into Dynamics of Mobile Genetic Elements in Hyperthermophilic Environments from Five New Thermococcus Plasmids Mart Krupovic1, Mathieu Gonnet2, Wajdi Ben Hania3, Patrick Forterre1,4, Gae¨l Erauso2,3* 1 Unite´ Biologie Mole´culaire du Ge`ne chez les Extreˆmophiles, De´partement de Microbiologie, Institut Pasteur, Paris, France, 2 Laboratoire de Microbiologie des Environnements Extreˆmes, UMR6197 CNRS-IFREMER-Universite´ de Bretagne Occidentale, Plouzane´, France, 3 Equipe Microbiologie Environnementale et Biotechnologie, Mediterranean Institute of Oceanography (MIO), UMR CNRS 7294/IRD 235, Marseille France, 4 Laboratoire de Biologie Mole´culaire du Ge`ne chez les Extreˆmophiles Institut de Ge´ne´tique et Microbiologie, CNRS-UMR 8621, Universite´ Paris-Sud 11, Orsay, France Abstract Mobilome of hyperthermophilic archaea dwelling in deep-sea hydrothermal vents is poorly characterized.
    [Show full text]
  • From Metagenomics to Bioproducts
    Utah State University DigitalCommons@USU All Graduate Theses and Dissertations Graduate Studies 8-2013 Utilizing Municipal and Industrial Wastes for the Production of Bioproducts: from Metagenomics to Bioproducts Joshua T. Ellis Utah State University Follow this and additional works at: https://digitalcommons.usu.edu/etd Part of the Biomedical Engineering and Bioengineering Commons Recommended Citation Ellis, Joshua T., "Utilizing Municipal and Industrial Wastes for the Production of Bioproducts: from Metagenomics to Bioproducts" (2013). All Graduate Theses and Dissertations. 1702. https://digitalcommons.usu.edu/etd/1702 This Dissertation is brought to you for free and open access by the Graduate Studies at DigitalCommons@USU. It has been accepted for inclusion in All Graduate Theses and Dissertations by an authorized administrator of DigitalCommons@USU. For more information, please contact [email protected]. UTILIZING MUNICIPAL AND INDUSTRIAL WASTES FOR THE PRODUCTION OF BIOPRODUCTS: FROM METAGENOMICS TO BIOPRODUCTS by Joshua Todd Ellis A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biological Engineering Approved: Charles D. Miller, PhD Ronald C. Sims, PhD Committee Co-Chairman Committee Co-Chairman H. Scott Hinton, Dean of the Issa Hamud, MS, PE College of Engineering Committee Member Committee Member Jon Takemoto, PhD Mark McLellan, PhD Committee Member Vice President for Research and Dean of the School of Graduate Studies UTAH STATE UNIVERISTY Logan, Utah 2013 ii Copyright © Joshua Todd Ellis 2013 All Rights Reserved iii ABSTRACT Utilizing Municipal and Industrial Wastes for the Production of Bioproducts: from Metagenomics to Bioproducts by Joshua T. Ellis, Doctor of Philosophy Utah State University, 2013 Major Professors: Dr.
    [Show full text]