DOCSLIB.ORG

Characterization of Methanogenic Archaea Communities in Biogas Reactors by Quantitative PCR

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Characterization of Methanogenic Archaea Communities in Biogas Reactors by Quantitative PCR Characterization of methanogenic Archaea communities in biogas reactors by quantitative PCR vorgelegt von Ingo Bergmann aus Parchtitz auf Rügen Von der Fakultät III - Prozesswissenschaften der Technischen Universität Berlin zur Erlangung des akademischen Grades Doktor der Naturwissenschaften Dr. rer. nat. genehmigte Dissertation Promotionsausschuss: Vorsitzender: Prof. Dr.-Ing. Sven-Uwe Geißen Berichter: Prof. Dr. rer. nat. Ulrich Szewzyk Berichter: PD Dr. tech. Elisabeth Grohmann Berichter: Dr. rer. nat. Michael Klocke Tag der wissenschaftlichen Aussprache: 19.09.2011 Berlin 2012 D-83 Zwei Dinge sind zu unserer Arbeit nötig: Unermüdliche Ausdauer und die Bereitschaft, etwas, in das man viel Zeit und Arbeit gesteckt hat, wieder wegzuwerfen… Albert Einstein TABLE OF CONTENTS Table of contents 1. Abbreviations .................................................................................... 6 2. Abstract ........................................................................................... 10 3. Zusammenfassung ......................................................................... 12 4. Introduction ..................................................................................... 14 4.1 The politics .................................................................................................. 14 4.2 The practice ................................................................................................. 16 4.3 The process ................................................................................................. 17 4.3.1 The four-stage pathway of anaerobic degradation of organic material to biogas ........................................................................................................... 17 4.3.2 Methanogenesis .................................................................................. 19 4.4 The producers ............................................................................................. 20 4.5 The technique ............................................................................................. 23 4.5.1 The basics of Q-PCR applications ....................................................... 24 4.5.2 Fluorescent probes and dyes ............................................................... 27 4.5.3 Application of Q-PCR in environmental microbiology .......................... 30 4.5.4 Factors for a successful Q-PCR run .................................................... 31 4.5.5 The target genes .................................................................................. 33 4.6 The aims ...................................................................................................... 35 5. Materials and Methods .................................................................... 37 5.1 Model biogas reactors ................................................................................ 37 5.1.1 System 1 .............................................................................................. 37 5.1.2 System 2 .............................................................................................. 37 5.1.3 System 3 .............................................................................................. 38 5.1.4 System 4 .............................................................................................. 38 5.2 Agricultural biogas plants .......................................................................... 42 5.3 Physical and chemical analyses of the biogas and the reactor content 44 5.3.1 Determination of the pH value ............................................................. 44 5.3.2 Calculation of the gas composition ...................................................... 44 5.3.3 Determination of the acid composition ................................................. 44 3 TABLE OF CONTENTS 5.4 DNA-based analysis of the archaeal community structure ..................... 45 5.4.1 Used strains ......................................................................................... 45 5.4.2 DNA extraction and purification ........................................................... 45 5.4.3 DNA quantification ............................................................................... 48 5.4.4 Analysis of the DNA purity ................................................................... 49 5.4.5 Quantitative real-time PCR (Q-PCR) ................................................... 49 6. Results ............................................................................................. 65 6.1 Establishment and application of a Q-PCR assay for the detection of methanogenic Archaea in biogas plants by the use of the 16S rRNA gene 65 6.1.1 Optimization of the PCR conditions of the group-specific 16S rRNA gene assays for quantitative real-time PCR .................................................. 65 6.1.2 Influence of DNA isolation on Q-PCR-based quantification of methanogenic Archaea in biogas fermenters ................................................ 67 6.1.3 Accuracy of the real-time PCR assays and influence of PCR interfering substances on Q-PCR-based quantification of methanogenic Archaea in biogas fermenters ......................................................................................... 75 6.1.4 Application of the 16S rRNA gene real-time PCR assays for analyzing the composition and development of the methanogenic Archaea in meso- and thermophilic biogas reactors ......................................................................... 84 6.2 Development of group-specific primer sets for the detection of methanogenic Archaea in biogas plants by the use of the metabolic mcrA gene ....................................................................................................... 107 7. Discussion ..................................................................................... 123 7.1 Evaluation and optimization of the PCR conditions for amplifying the 16S rRNA gene by using the real-time PCR assay of Yu et al. (2005a) ...... 123 7.2 Design and testing of group-specific Q-PCR primers based on the mcrA gene for the quantification of methanogenic communities .............. 125 7.3 The influence of different DNA isolation methods on the quantification of methanogenic Archaea in biogas reactors by real-time PCR................. 127 7.4 Influences of PCR interfering substances on Q-PCR-based quantification of methanogens in biogas reactors ...................................... 131 4 TABLE OF CONTENTS 7.5 Determination of methanogenic Archaea abundances in semi-continuous fermentation and acidification by overloading in a short-run experiment ...................................................................................... 136 7.6 Methanogenic population dynamics in semi-continuous fermentation and acidification by overloading under mesophilic and thermophilic conditions in a long-run experiment ............................................................. 139 7.7 Determination of the methanogenic community in biogas reactors with different substrates for anaerobic digestion under mesophilic and thermophilic conditions ................................................................................. 143 7.8 Determination of the methanogenic Archaea in agricultural biogas plants ............................................................................................................... 145 8. Outlook .......................................................................................... 148 References ......................................................................................... 149 List of figures .................................................................................... 168 List of tables ...................................................................................... 171 Publication list .................................................................................. 174 Funding .............................................................................................. 178 Acknowledgments ............................................................................ 179 Appendix............................................................................................ 182 5 ABBREVIATIONS 1. Abbreviations A Adenine ABI Applied Biosystems Instruments AF Anaerobic filter approx. Approximately ARC Archaea BA Biogas plant BAC Bacteria BB Brandenburg bp Base pair C Cytosine Carrez I Potassium hexacyanoferrate(II)-3-hydrate Carrez II Zinc sulphate-7-hydrate cf. Confer CSTR Continuously stirred tank reactor CT Threshold cycle number CTAB Cetyl trimethyl ammonium bromide DGGE Denaturing gradient gel electrophoresis DNA Deoxyribonucleic acid dNTP Deoxynucleoside triphosphate DOM Dry organic matter dsDNA Double-stranded deoxyribonucleic acid e.g. Exempli gratia (for example) EDTA Ethylenediaminotetraacetic acid et al. Et alii (and others) F primer Forward primer FAM 6-Carboxyfluoroscein Fig. Figure FISH Fluorescence in-situ hybridization FNR Fachagentur Nachwachsende Rohstoffe e.V. FR Hydrolysis reactor FRET Fluorescence resonance energy transfer 6 ABBREVIATIONS g Gravitational acceleration G Guanidine GC Gas chromatography gDNA genomic deoxyribonucleic acid IPTG Isopropyl β-D-1-thiogalactopyranoside JOE 2,7-Dimethoxy-4,5-dichloro-6-carboxyfluorescein LB Lysogeny broth LOD Limit of detection LOQ Limit of quantification Mb. Methanobacterium Mbb. Methanobrevibacter Mbp Mega base pair MBT Methanobacteriales Mbt. Methanothermobacter Mc. Methanococcus MCC Methanococcales
Load more

Recommended publications
  • (Gid ) Genes Coding for Putative Trna:M5u-54 Methyltransferases in 355 Bacterial and Archaeal Complete Genomes
    Table S1. Taxonomic distribution of the trmA and trmFO (gid ) genes coding for putative tRNA:m5U-54 methyltransferases in 355 bacterial and archaeal complete genomes. Asterisks indicate the presence and the number of putative genes found. Genomes Taxonomic position TrmA Gid Archaea Crenarchaea Aeropyrum pernix_K1 Crenarchaeota; Thermoprotei; Desulfurococcales; Desulfurococcaceae Cenarchaeum symbiosum Crenarchaeota; Thermoprotei; Cenarchaeales; Cenarchaeaceae Pyrobaculum aerophilum_str_IM2 Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae Sulfolobus acidocaldarius_DSM_639 Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus solfataricus Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus tokodaii Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Euryarchaea Archaeoglobus fulgidus Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae Haloarcula marismortui_ATCC_43049 Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Halobacterium sp Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Haloquadratum walsbyi Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloquadra Methanobacterium thermoautotrophicum Euryarchaeota; Methanobacteria; Methanobacteriales; Methanobacteriaceae Methanococcoides burtonii_DSM_6242 Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae Methanococcus jannaschii Euryarchaeota; Methanococci; Methanococcales; Methanococcaceae Methanococcus maripaludis_S2 Euryarchaeota; Methanococci;
    [Show full text]
  • Microbial Extracellular Electron Transfer and Its Relevance to Iron Corrosion
    bs_bs_banner Minireview Microbial extracellular electron transfer and its relevance to iron corrosion Souichiro Kato1,2,3* acetogenic bacteria and nitrate-reducing bacteria. 1Bioproduction Research Institute, National Institute of Abilities of EET and EMIC are now regarded as micro- Advanced Industrial Science and Technology (AIST), bial traits more widespread among diverse microbial 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, clades than was thought previously. In this review, Hokkaido 062-8517,Japan. basic understandings of microbial EET and recent 2Research Center for Advanced Science and progresses in the EMIC research are introduced. Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan. 3Division of Applied Bioscience, Graduate School of Introduction Agriculture, Hokkaido University, Kita-9 Nishi-9,Kita-ku, Acquisition of energy is an indispensable activity for all Sapporo, Hokkaido 060-8589, Japan. living organisms. Most organisms, including human beings, conserve energy through respiration, with Summary organic compounds and oxygen gas as the electron donor and acceptor respectively. In contrast, many Extracellular electron transfer (EET) is a microbial microorganisms have the ability to utilize diverse inor- metabolism that enables efficient electron transfer ganic compounds as the substrates for respiration. Fur- between microbial cells and extracellular solid materi- thermore, some particular microorganisms have the als. Microorganisms harbouring EET abilities have ability to acquire energy through transferring electrons to received considerable attention for their various or from extracellular solid compounds. This microbial biotechnological applications, including bioleaching metabolism is specifically termed as ‘extracellular elec- and bioelectrochemical systems. On the other hand, tron transfer (EET)’ (Gralnick and Newman, 2007; Rich- recent research revealed that microbial EET poten- ter et al., 2012).
    [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]
  • Tour Pages by Clicking This Link
    STATION 1 (Welcome) WELCOME TO THE CBEC TINY THINGS TOUR (STATION 1) This tour is designed to acquaint CBEC visitors with the amazingly diverse array of organisms here that are not typically noticed, mainly because they’re too small to be seen without either very careful observation or the aid of a magnifier (either a handheld device or a microscope). The tour will discuss representatives of the six kingdoms of living things (Bacteria, Archaea, Fungi, Plants, Protists, and Animals), as well as viruses. In addition to brief discussions of the particular organisms themselves, we’ll consider the role that these organisms play in their immediate environment, their effect on the larger biosphere, and their ability to teach us about the past and the future. Taking the Tour: To take the tour, visitors may use the Tiny Things Tour map, where the 14 stations are indicated with red numbers. The map should be used in conjunction with the printable list of stations. The list has the GPS coordinates for each station, along with QR codes that provide links to the web pages that describe each station. The GPS coordinates, as well as a simple description of each location are included on each station’s web page. If visitors haven’t brought along a mobile device (to view the web pages), they can print a copy of the tour pages by clicking this link. A guided version of the Tiny Things Tour is scheduled on a regular basis. Check the CBEC schedule for upcoming guided tours. Each web page includes a photo of the representative organism, it’s common name and scientific name, a description of the station location (including its GPS location), and a description of the organism and its environment.
    [Show full text]
  • 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.
    [Show full text]
  • Partial Purification and Characterization of F₄₂₀- Dependent NADP Reductase from Methanobrevibacter Smithii Strain DE1
    Portland State University PDXScholar Dissertations and Theses Dissertations and Theses 1985 Partial purification and characterization of F₄₂₀- dependent NADP reductase from Methanobrevibacter smithii strain DE1 Scott D. Sheridan Portland State University Follow this and additional works at: https://pdxscholar.library.pdx.edu/open_access_etds Part of the Biology Commons, and the Enzymes and Coenzymes Commons Let us know how access to this document benefits ou.y Recommended Citation Sheridan, Scott D., "Partial purification and characterization of F₄₂₀-dependent NADP reductase from Methanobrevibacter smithii strain DE1" (1985). Dissertations and Theses. Paper 3523. https://doi.org/10.15760/etd.5407 This Thesis is brought to you for free and open access. It has been accepted for inclusion in Dissertations and Theses by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. AN ABSTRACT OF THE THESIS OF Scott D, Sheridan for the Master of Science in Biology presented July 26, 1985. Title: Partial Purification and Characterization of F -dependent 420 NADP Reductase from Methanobrevibacter smithii strain DEl APPROVED BY MEMBERS OF THE THESIS COMMITTEE: L. D. Eirich, Chairman P: L. O'Neill D. Barnum, Graduate Office Representative The F -dependent NADP reductase of Methanobrevibacter 420 smithii has been partially purified employing a combination of affinity chromatography with Blue Sepharose (Cl-6B) and molecular sieve chromatography with Sephacryl S-200, The enzyme, which re- 2 quires reduced F420 as an electron donor, has been purified over 145 fold with a recovery of 6%. A molecular weight of 120,00 for the native enzyme was determined by Sephacryl S-200 chromatography.
    [Show full text]
  • Coexistance of Acetogens, Methanogens and Sulfate Reducing Bacteria in Enrichments from Trunk River
    Coexistance of acetogens, methanogens and sulfate reducing bacteria in enrichments from Trunk River María Consuelo Gazitúa Center for Genomics and Bioinformatics University Mayor - Chile [email protected] Introduction In the absence of oxygen, chemotrophic growth depends on alternative electron acceptors such as nitrate, iron, manganese, sulfate and CO2. In the presence of sulfate, such as in seawater, sulfate reduction is highly favorable, coupling the reduction of sulfate with the oxidation of H2 or simple organic compounds. In the absence of sulfate, methanogenic archaea are able to cleave acetate, producing CO2 and CH4, as well as reduce or disproportionate C1 compounds such as CO2, CO, formate and methanol, using H2 and formate as the main electron donor. Homoacetogenic bacteria use C-1 compounds as electron acceptors, catalyzing the reduction of two CO2 molecules to acetate. This is a highly variable group of strictly anaerobic bacteria, able to grow on a variety of substrates. In most anaerobic environments, hydrogen is present as an intermediate for which sulfate reducing bacteria (SRB), hydrogenotrophic methanogens and homoacetogens will compete. Under standard conditions, sulfate reduction and methanogenesis are thermodynamically more favorable than homoacetogenesis. However, Weijma et al. (2002) reported that when H2/CO2 is added as the sole substrate in sludge bioreactores, heterotrophic SRB and homoacetogens can coexist, suggesting the SRB growth depends on the growth kinetics of the homoacetogens. During the isolation of chemolithotrophic microorganisms during the course, specifically for SRB, homoacetogens and methanogens, the enrichment for SRB showed the coexistence of these three groups, based on measurements of methane, hydrogen sulfide and acetate. Some of the organisms growing in the enrichment formed aggregates, where the presence of methanogens could be inferred based on the blue autofluorescence, after excitation with AF430 (Doddema and Vogels 1978).
    [Show full text]
  • Methanogenesis and Methane Oxidation in Wetlands. Implications in the Global Carbon Cycle
    TORRES OK 09 11/11/05 5:39 PM Page 327 Hidrobiológica 15 (3): 327-349 ARTÍCULO DE REVISIÓN Diciembre 2005 Methanogenesis and methane oxidation in wetlands. Implications in the global carbon cycle Metanogénesis y metano-oxidación en humedales. Implicaciones en el ciclo del carbono global Rocio Torres-Alvarado1, Florina Ramírez-Vives2, Francisco José Fernández 2 e Irene Barriga-Sosa1 1Departamento de Hidrobiología y 2Departamento de Biotecnología. Universidad Autónoma Metropolitana-Iztapalapa (UAM-I). Av. San Rafael Atlixco # 186.Col. Vicentina. A. P. 55 535. Ciudad de México. 09430, México. Torres-Alvarado R., F. Ramírez-Vives, F. J. Fernández e I. Barriga-Sosa. 2005. Methanogenesis and Methane Oxidation in Wetlands. Implications in the Global Carbon Cycle. Hidrobiológica 15 (3): 327-349. ABSTRACT Wetlands are important ecosystems on the Earth. They are distinguished by the presence of water, saturated anoxic soils, and different kinds of vegetation adapted to this conditions. Organic matter in these environments is mineralized mainly in the sediments throughout anaerobic processes where sulfate reduction is one of the most important terminal stages of anaerobic decomposition in coastal wetlands, whereas methanogenesis is important in freshwater wetlands. In this environments, methane, a greenhouse gas, is produced as a result of the activity of a large and diverse group of methanogenic bacteria (Domain Archaea). The generated methane can be diffused to the atmosphere or can be oxidized by several microorganisms under aerobic and anaerobic conditions, such microorganisms intercept and consume this gas diminishing its emission to the atmosphere. The production and consumption of methane in wetlands involve complex physiological processes of plants and microorganisms, which are regulated by climatic and edaphic factors, mainly soil temperature and water table level.
    [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]
  • 2019 Badel Environmental Micro
    The global distribution and evolutionary history of the pT26-2 archaeal plasmid family Catherine Badel, Gaël Erauso, Annika Gomez, Ryan Catchpole, M. Gonnet, Jacques Oberto, Patrick Forterre, Violette da Cunha To cite this version: Catherine Badel, Gaël Erauso, Annika Gomez, Ryan Catchpole, M. Gonnet, et al.. The global distri- bution and evolutionary history of the pT26-2 archaeal plasmid family. Environmental Microbiology, Society for Applied Microbiology and Wiley-Blackwell, 2019, 21 (12), 10.1111/1462-2920.14800. hal- 02292276v2 HAL Id: hal-02292276 https://hal.archives-ouvertes.fr/hal-02292276v2 Submitted on 9 Nov 2020 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. Distributed under a Creative Commons Attribution - NonCommercial - ShareAlike| 4.0 International License Environmental Microbiology (2019) 00(00), 00–00 doi:10.1111/1462-2920.14800 The global distribution and evolutionary history of the pT26-2 archaeal plasmid family Catherine Badel,1 Gaël Erauso,2,3 Annika L. Gomez,4 conserved even in integrated plasmids that have Ryan Catchpole,1 Mathieu Gonnet,2 Jacques Oberto,1 lost replication genes and/or replication origins Patrick Forterre1,4* and Violette Da Cunha 1,4** suggesting that they may be beneficial for their 1Institute for Integrative Biology of the Cell (I2BC), CEA, hosts.
    [Show full text]
  • 1Ki9 Lichtarge Lab 2006
    Pages 1–7 1ki9 Evolutionary trace report by report maker July 15, 2010 4.3.1 Alistat 6 4.3.2 CE 6 4.3.3 DSSP 6 4.3.4 HSSP 6 4.3.5 LaTex 6 4.3.6 Muscle 6 4.3.7 Pymol 6 4.4 Note about ET Viewer 6 4.5 Citing this work 6 4.6 About report maker 7 4.7 Attachments 7 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1ki9): Title: Adenylate kinase from methanococcus thermolithotrophicus Compound: Mol id: 1; molecule: adenylate kinase; chain: a, b, c; synonym: atp-amp transphosphorylase; ec: 2.7.4.3; engineered: yes Organism, scientific name: Methanococcus Thermolithotrophicus; 1ki9 contains a single unique chain 1ki9A (191 residues long) and its homologues 1ki9C and 1ki9B. CONTENTS 2 CHAIN 1KI9A 2.1 P43410 overview 1 Introduction 1 From SwissProt, id P43410, 92% identical to 1ki9A: 2 Chain 1ki9A 1 Description: Adenylate kinase (EC 2.7.4.3) (ATP-AMP transphos- 2.1 P43410 overview 1 phorylase). 2.2 Multiple sequence alignment for 1ki9A 1 Organism, scientific name: Methanococcus thermolithotrophicus. 2.3 Residue ranking in 1ki9A 1 Taxonomy: Archaea; Euryarchaeota; Methanococci; Methanococca- 2.4 Top ranking residues in 1ki9A and their position on les; Methanococcaceae; Methanothermococcus. the structure 2 Catalytic activity: ATP + AMP = 2 ADP. 2.4.1 Clustering of residues at 25% coverage. 2 Biophysicochemical properties: 2.4.2 Overlap with known functional surfaces at Temperature dependence: Active from 60 to 80 degrees Celsius; 25% coverage. 2 Subunit: Monomer (Probable). 2.4.3 Possible novel functional surfaces at 25% Subcellular location: Cytoplasmic.
    [Show full text]