Complete Genome Sequence of Methanocorpusculum Labreanum Type Strain Z
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Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide
microorganisms Article Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide Kelly J. Hidalgo 1,2,* , Isabel N. Sierra-Garcia 3 , German Zafra 4 and Valéria M. de Oliveira 1 1 Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas–UNICAMP, Av. Alexandre Cazellato 999, 13148-218 Paulínia, Brazil; [email protected] 2 Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato 255, Cidade Universitária, 13083-862 Campinas, Brazil 3 Biology Department & CESAM, University of Aveiro, Aveiro, Portugal, Campus de Santiago, Avenida João Jacinto de Magalhães, 3810-193 Aveiro, Portugal; [email protected] 4 Grupo de Investigación en Bioquímica y Microbiología (GIBIM), Escuela de Microbiología, Universidad Industrial de Santander, Cra 27 calle 9, 680002 Bucaramanga, Colombia; [email protected] * Correspondence: [email protected]; Tel.: +55-19981721510 Abstract: Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to decipher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301.2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 metagenome-assembled genomes (MAGs) of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to archaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied. -
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. -
Development of the Equine Hindgut Microbiome in Semi-Feral and Domestic Conventionally-Managed Foals Meredith K
Tavenner et al. Animal Microbiome (2020) 2:43 Animal Microbiome https://doi.org/10.1186/s42523-020-00060-6 RESEARCH ARTICLE Open Access Development of the equine hindgut microbiome in semi-feral and domestic conventionally-managed foals Meredith K. Tavenner1, Sue M. McDonnell2 and Amy S. Biddle1* Abstract Background: Early development of the gut microbiome is an essential part of neonate health in animals. It is unclear whether the acquisition of gut microbes is different between domesticated animals and their wild counterparts. In this study, fecal samples from ten domestic conventionally managed (DCM) Standardbred and ten semi-feral managed (SFM) Shetland-type pony foals and dams were compared using 16S rRNA sequencing to identify differences in the development of the foal hindgut microbiome related to time and management. Results: Gut microbiome diversity of dams was lower than foals overall and within groups, and foals from both groups at Week 1 had less diverse gut microbiomes than subsequent weeks. The core microbiomes of SFM dams and foals had more taxa overall, and greater numbers of taxa within species groups when compared to DCM dams and foals. The gut microbiomes of SFM foals demonstrated enhanced diversity of key groups: Verrucomicrobia (RFP12), Ruminococcaceae, Fusobacterium spp., and Bacteroides spp., based on age and management. Lactic acid bacteria Lactobacillus spp. and other Lactobacillaceae genera were enriched only in DCM foals, specifically during their second and third week of life. Predicted microbiome functions estimated computationally suggested that SFM foals had higher mean sequence counts for taxa contributing to the digestion of lipids, simple and complex carbohydrates, and protein. -
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. -
Open Dissertation 4-7-09.Pdf
The Pennsylvania State University The Graduate School Department of Civil and Environmental Engineering IMPROVED ANAEROBIC DIGESTER STABILITY TO ORGANIC LOADING RATE SHOCKS WITH THE USE OF AN ENVIRONMENTALLY DERIVED INOCULUM A Dissertation in Environmental Engineering and Biogeochemistry by Lisa Marie Steinberg © 2009 Lisa Marie Steinberg Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2009 The dissertation of Lisa Marie Steinberg was reviewed and approved* by the following: John Regan Associate Professor of Environmental Engineering Dissertation Advisor Chair of Committee Christopher House Associate Professor of Geosciences Bruce Logan Kappe Professor of Environmental Engineering Jenn Macalady Assistant Professor of Geosciences Peggy Johnson Department Head and Professor of Civil Engineering *Signatures are on file in the Graduate School ABSTRACT Anaerobic digestion broadly describes technology that utilizes microorganisms to break down organic matter under anaerobic conditions through the coordinated efforts of several trophic groups of microorganisms. The last step is catalyzed by methanogens which produce primarily methane, carbon dioxide, and water as products of metabolism. Anaerobic digestion occurs naturally in a variety of water-saturated sediments, but is also used to treat waste in constructed reactors. There are a number of advantages to treating waste with anaerobic digestion, but perhaps the greatest is that waste treatment can be coupled to energy generation by the production of a methane-rich biogas. Despite the advantages, anaerobic digestion is severely under-utilized in waste treatment mainly due to the belief that anaerobic digesters are less stable than aerobic treatment processes. Anaerobic digesters are typically operated under warm temperatures and circumneutral pH, with operation outside of these conditions leading to instability and potential reactor failure. -
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. -
Why Co-Digestion for Food Waste and Sewage Sludge?
Drainage Service Department Research & Development Forum Smart City • Innovative Wastewater Management Co-digestion of Food Waste with Sewage Sludge HKU team: Chunxiao WANG, Yubo WANG, Yulin WANG, Tong ZHANG DSD team: Sussana LAI, KK CHEUNG Prof. Tong Zhang Environmental Biotechnology Laboratory The University of Hong Kong 5th December, 2018 Introduction Materials and Method Results and Discussion Conclusion 民以食為天 《漢書》 2 https://newint.org/features/2008/12/01/food-crisis-facts; https://www.youtube.com/watch?v=ExH6kSwoFBw Introduction Materials and Method Results and Discussion Conclusion What is the current situation of food waste around the world? ( Peek , 2014) Nearly about 1.4 billion tonnes food waste (one third of total food production) generated from farmland to meal table annually till 2011 revealed by the United Nations (FAO, 2014). 3584 tonnes food waste generated daily accounting 36% of the municipal solid waste landfilled in Hong Kong (EPD, 2017). Conventionally, food waste was disposed in composting, incineration, landfill and anaerobic digestion (Astals et al., 2014; Wang et al., 2014; Chiu & Lo, 2016; ). AD of food waste became more attractive due to high moisture and organic content in the FW and higher energy recovery potential (Zhang et al., 2007; Astals et al., 2014; Ingrid et al., 2014; Chiu& Lo, 2016). 3 Introduction Materials and Method Results and Discussion Conclusion Why co-digestion for food waste and sewage sludge? From engineering perspective: There are excess capacities in the anaerobic digesters. Food waste could be added and co-digested with sewage sludge to recovery more energy (EPA, 2013; Wang et al., 2015). From technical perspective: Table 1. -
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. -
Nov., Isolated from an Oil-Producing Well
International Journal of Systematic Bacteriology (1998), 48, 821-828 Printed in Great Britain Methanocalculus halotolerans gen. nov., sp. nov., isolated from an oil-producing well Bernard Ollivier,’ Marie-Laure Fardeau,l Jean-Luc Cayol,’ Michel Magot,’ Bharat K. C. Patel,3 Gerard Prensiep and Jean-Louis Garcia’ Author for correspondence: Bernard Ollivier. Tel: + 33 4 91 82 85 76. Fax: + 33 4 91 82 85 70. e-mail : [email protected] 1 Laboratoire ORSTOM de Two irregular coccoid methanogens designated SEBR 4845Tand FRlT were Microbiologie des isolated from an oilfield in Alsace, France. Strain SEBR 4845l (T = type strain) is AnaCrobies, UniversitC de Provence, 13288 Marseille a hydrogenotrophic halotolerant methanogen, which grows optimally at 5 O/O Cedex 9, France NaCl (whr) and tolerates up to 12O/0 NaCI. It does not use methylated * Sanofi Recherche, Groupe compounds and therefore cannot be ascribed to any of the known genera of Elf-Aquitaine, Unit6 de the halophilic methylotrophic methanogens. It differs from hydrogenotrophic Microbiologie, 31 676 members of the orders Methanococcales and Methanomicrobiales in the NaCl La b&ge Cedex, France growth range (0-12% NaCI), which is the widest reported to date for any 3 School of Biomolecular hydrogenotrophic methanogen. 165 rRNA gene sequence analysis indicated and Biomedical Sciences, Griffith University, Nathan that strain SEBR 4845l is a novel isolate for which a new genus is proposed, 41 11, Brisbane, Methanocalculus halotolerans gen. nov., sp. nov. (= OCM 4703 that might be Queensland, Australia indigenous to the oilfield ecosystem. Strain FRlT (= OCM 471) is a moderately 4 Laboratoire de halophilic methanogen which grows optimally at 10% NaCl and tolerates up to Microbiologie, UniversitC 20% NaCI. -
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.