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Complete Genome Sequence of Methanocorpusculum Labreanum Type Strain Z
Standards in Genomic Sciences (2009) 1: 197-203 DOI:10.4056.sigs.35575 Complete genome sequence of Methanocorpusculum labreanum type strain Z Iain J. Anderson1*, Magdalena Sieprawska-Lupa2, Eugene Goltsman1, Alla Lapidus1, Alex Co- peland1, Tijana Glavina Del Rio1, Hope Tice1, Eileen Dalin1, Kerrie Barry1, Sam Pitluck1, Lo- ren Hauser1,3, Miriam Land1,3, Susan Lucas1, Paul Richardson1, William B. Whitman2, and Nikos C. Kyrpides1 1Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California, USA 2Microbiology Department, University of Georgia, Athens, Georgia, USA 3Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA *Corresponding author: Iain Anderson Keywords: archaea, methanogen, Methanomicrobiales Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicro- biales within the archaeal phylum Euryarchaeota. The type strain Z was isolated from surface sediments of Tar Pit Lake in the La Brea Tar Pits in Los Angeles, California. M. labreanum is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. labreanum type strain Z and its annotation. This is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea. Introduction Methanocorpusculum labreanum is a methanogen the Methanosarcinales are capable of using various belonging to the order Methanomicrobiales within methyl compounds as substrates for methanoge- the archaeal phylum Euryarchaeota. Strain Z is the nesis including acetate, methylamines, and me- type strain of this species. It was isolated from thanol, but Methanomicrobiales are restricted to surface sediments of Tar Pit Lake at the La Brea the same substrates as the Class I methanogens Tar Pits in Los Angeles [1]. -
Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens
microorganisms Article Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens Maryam Rezadehbashi and Susan A. Baldwin * Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, BC V6T 1Z3, Canada; [email protected] * Correspondence: [email protected]; Tel.: +1-604-822-1973 Received: 2 January 2018; Accepted: 17 February 2018; Published: 23 February 2018 Abstract: Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM that grow in these systems and whether they are diverse or restricted to particular phylogenetic or taxonomic groups. A phylogenetic study of four established pilot-scale BCRs on three different mine sites compared the diversity of SRM growing in them. The mine sites were geographically distant from each other, nevertheless the BCRs selected for similar SRM types. Clostridia SRM related to Desulfosporosinus spp. known to be tolerant to high concentrations of copper were members of the core microbial community. Members of the SRM family Desulfobacteraceae were dominant, particularly those related to Desulfatirhabdium butyrativorans. Methanogens were dominant archaea and possibly were present at higher relative abundances than SRM in some BCRs. Both hydrogenotrophic and acetoclastic types were present. There were no strong negative or positive co-occurrence correlations of methanogen and SRM taxa. Knowing which SRM inhabit successfully operating BCRs allows practitioners to target these phylogenetic groups when selecting inoculum for future operations. -
Extensive Microbial Diversity Within the Chicken Gut Microbiome Revealed by Metagenomics and Culture
Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture Rachel Gilroy1, Anuradha Ravi1, Maria Getino2, Isabella Pursley2, Daniel L. Horton2, Nabil-Fareed Alikhan1, Dave Baker1, Karim Gharbi3, Neil Hall3,4, Mick Watson5, Evelien M. Adriaenssens1, Ebenezer Foster-Nyarko1, Sheikh Jarju6, Arss Secka7, Martin Antonio6, Aharon Oren8, Roy R. Chaudhuri9, Roberto La Ragione2, Falk Hildebrand1,3 and Mark J. Pallen1,2,4 1 Quadram Institute Bioscience, Norwich, UK 2 School of Veterinary Medicine, University of Surrey, Guildford, UK 3 Earlham Institute, Norwich Research Park, Norwich, UK 4 University of East Anglia, Norwich, UK 5 Roslin Institute, University of Edinburgh, Edinburgh, UK 6 Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia 7 West Africa Livestock Innovation Centre, Banjul, The Gambia 8 Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Hebrew University of Jerusalem, Jerusalem, Israel 9 Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK ABSTRACT Background: The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. Results: We performed metagenomic sequencing of fifty chicken faecal samples from Submitted 4 December 2020 two breeds and analysed these, alongside all (n = 582) relevant publicly available Accepted 22 January 2021 chicken metagenomes, to cluster over 20 million non-redundant genes and to Published 6 April 2021 construct over 5,500 metagenome-assembled bacterial genomes. -
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. -
An Integrated Study on Microbial Community in Anaerobic Digestion Systems
An Integrated Study on Microbial Community in Anaerobic Digestion Systems DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Yueh-Fen Li Graduate Program in Environmental Science The Ohio State University 2013 Dissertation Committee: Dr. Zhongtang Yu, Advisor Dr. Brian Ahmer Dr. Richard Dick Dr. Olli Tuovinen Copyrighted by Yueh-Fen Li 2013 Abstract Anaerobic digestion (AD) is an attractive microbiological technology for both waste treatment and energy production. Microorganisms are the driving force for the whole transformation process in anaerobic digesters. However, the microbial community underpinning the AD process remains poorly understood, especially with respect to community composition and dynamics in response to variations in feedstocks and operations. The overall objective was to better understand the microbiology driving anaerobic digestion processes by systematically investigating the diversity, composition and succession of microbial communities, both bacterial and archaeal, in anaerobic digesters of different designs, fed different feedstocks, and operated under different conditions. The first two studies focused on propionate-degrading bacteria with an emphasis on syntrophic propionate-oxidizing bacteria. Propionate is one of the most important intermediates and has great influence on AD stability in AD systems because it is inhibitory to methanogens and it can only be metabolized through syntrophic propionate- oxidizing acetogenesis under methanogenic conditions. In the first study (chapter 3), primers specific to the propionate-CoA transferase gene (pct) were designed and used to construct clone libraries, which were sequenced and analyzed to investigate the diversity and distribution of propionate-utilizing bacteria present in the granular and the liquid portions of samples collected from four digesters of different designs, fed different ii feedstocks, and operated at different temperatures. -
Characterizing Bacteria and Methanogens in a Balloon-Type Digester Fed with Dairy Cattle Manure for Anaerobic Mono-Digestion
Pol. J. Environ. Stud. Vol. 28, No. 3 (2019), 1287-1293 DOI: 10.15244/pjoes/76180 ONLINE PUBLICATION DATE: 2018-11-22 Original Research Characterizing Bacteria and Methanogens in a Balloon-Type Digester Fed with Dairy Cattle Manure for Anaerobic Mono-Digestion Christy Manyi-Loh1-3*, Sampson Mamphweli1, Edson Meyer1, Anthony Okoh2, 3 1Fort Hare Institute of Technology, University of Fort Hare, Alice Campus, Alice, Eastern Cape Province, South Africa 2Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice Campus, Alice, Eastern Cape Province, South Africa 3South Africa Medical Research Council Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, Eastern Cape Province, South Africa Received: 14 June 2017 Accepted: 31 July 2017 Abstract In this study, bacteria and methanogens involved in the decomposition of dairy cattle manure have been characterized via cultivation on selective microbiological media by the viable plate count technique. In addition, DNA was extracted from digested samples, and the 16S rRNA gene was amplified using six primer sets specific to bacterial and archaeal domain via PCR. The sequences of the PCR products were determined and compared to similar sequences in the GenBank database using the BLASTN tools to identify the closest relatives. By culture, E. coli, Salmonella, Shigella, and Campylobacter species were identified and belonged to the phylum Proteobacteria. Following, 16S rRNA analysis, Firmicutes (80%) was the most dominant bacterial phylum represented by the predominant order Clostridiales and genus Clostridium. Other members belonged to the phyla Proteobacteria and Spirochaetes. The phylum Euryarchaeota (100%) was the only observed archaeal domain with members that belonged to the dominant class Methanomicrobia and genus Methanocorpusculum. -
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. -
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. -
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 -
Extensive Microbial Diversity Within the Chicken Gut Microbiome Revealed by Metagenomics and Culture
This is a repository copy of Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/173881/ Version: Published Version Article: Gilroy, R., Ravi, A., Getino, M. et al. (17 more authors) (2021) Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture. PeerJ, 9. e10941. ISSN 2167-8359 https://doi.org/10.7717/peerj.10941 Reuse This article is distributed under the terms of the Creative Commons Attribution (CC BY) licence. This licence allows you to distribute, remix, tweak, and build upon the work, even commercially, as long as you credit the authors for the original work. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture Rachel Gilroy1, Anuradha Ravi1, Maria Getino2, Isabella Pursley2, Daniel L. Horton2, Nabil-Fareed Alikhan1, Dave Baker1, Karim Gharbi3, Neil Hall3,4, Mick Watson5, Evelien M. Adriaenssens1, Ebenezer Foster-Nyarko1, Sheikh Jarju6, Arss Secka7, Martin Antonio6, Aharon Oren8, Roy R. Chaudhuri9, Roberto La Ragione2, Falk Hildebrand1,3 and Mark J. -
Application for Approval to Import Into Containment Any New Organism That
ER-AN-02N 10/02 Application for approval to import into FORM 2N containment any new organism that is not genetically modified, under Section 40 of the Page 1 Hazardous Substances and New Organisms Act 1996 FORM NO2N Application for approval to IMPORT INTO CONTAINMENT ANY NEW ORGANISM THAT IS NOT GENETICALLY MODIFIED under section 40 of the Hazardous Substances and New Organisms Act 1996 Application Title: Importation of extremophilic microorganisms from geothermal sites for research purposes Applicant Organisation: Institute of Geological & Nuclear Sciences ERMA Office use only Application Code: Formally received:____/____/____ ERMA NZ Contact: Initial Fee Paid: $ Application Status: ER-AN-02N 10/02 Application for approval to import into FORM 2N containment any new organism that is not genetically modified, under Section 40 of the Page 2 Hazardous Substances and New Organisms Act 1996 IMPORTANT 1. An associated User Guide is available for this form. You should read the User Guide before completing this form. If you need further guidance in completing this form please contact ERMA New Zealand. 2. This application form covers importation into containment of any new organism that is not genetically modified, under section 40 of the Act. 3. If you are making an application to import into containment a genetically modified organism you should complete Form NO2G, instead of this form (Form NO2N). 4. This form, together with form NO2G, replaces all previous versions of Form 2. Older versions should not now be used. You should periodically check with ERMA New Zealand or on the ERMA New Zealand web site for new versions of this form. -
Methanogenic Community Composition in An
Int. Agrophys., 2017, 31, 327-338 doi: 10.1515/intag-2016-0057 Methanogenic community composition in an organic waste mixture in an anaerobic bioreactor** Agata Gryta1, Karolina Oszust1, Małgorzata Brzezińska1, Krzysztof Ziemiński2, Nina Bilińska-Wielgus1, and Magdalena Frąc1* 1Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland 2Institute of Fermentation Technology and Microbiology, Łódź University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland Received October 25, 2016; accepted June 1, 2017 A b s t r a c t. The aim of the study was to elucidate the sub- is microbially mediated engineering with the goals of de- stantial relationship between the compositions of methanogen gradation and stabilisation of organic matter, which results community that assembles in the anaerobic digester mass and in the production of energy-rich composites. This process link it to methane production activity. The results of the meta- involves four sequential steps: hydrolysis, fermentation genomic studies were used to evaluate how the methanogen (acidogenesis), acetogenesis (dehydrogenation) and metha- structure changes during an anaerobic digestion process under various waste retention times (21, 23, 25, 29, 33, 39, 47 and 61 nogenesis (acetoclastic or hydrogenotrophic), all of which days). Phylogenetically coherent populations of methanogens depend on the synergistic interactions of microorganisms were assessed by 16S rRNA gene next-generation sequencing and that form a complex metabolic network. This special pro- terminal restriction fragment length polymorphism fingerprint- cess is catalysed especially by methanogenic Archaea. This ing of a specific molecular marker, the mcrA gene. The results unrepeatable group of microorganisms has the capability to indicated multiple phylogenetically diverse methanogen popu- produce methane from basic substrates, such as CO2, H2, ace- lations associated with the various steps of anaerobic digestion.