Microbial Community Structures Differentiated in a Single-Chamber
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Actes Congrès MICROBIOD 1
Actes du congrès international "Biotechnologie microbienne au service du développement" (MICROBIOD) Marrakech, MAROC 02-05 Novembre 2009 "Ce travail est publié avec le soutien du Ministère de l'Education Nationale, de l'Enseignement Supérieur, de la Formation des Cadres et de la Recherche Scientifique et du CNRST". MICROBIONA Edition www.ucam.ac.ma/microbiona 1 1 Mot du Comité d'organisation Cher (e) membre de MICROBIONA Cher(e) Participant(e), Sous le Haut Patronage de sa Majesté le Roi Mohammed VI, l'Association MICROBIONA et la Faculté des Sciences Semlalia, Université Cadi Ayyad, organisent du 02 au 05 Novembre 2009, en collaboration avec la Société Française de Microbiologie, le Pôle de Compétences Eau et Environnement et l'Incubateur Universitaire de Marrakech, le congrès international "Biotechnologie microbienne au service du développement" (MICROBIOD). Cette manifestation scientifique spécialisée permettra la rencontre de chercheurs de renommée internationale dans le domaine de la biotechnologie microbienne. Le congrès MICROBIOD est une opportunité pour les participants de mettre en relief l’importance socio-économique et environnementale de la valorisation et l’application de nouvelles techniques de biotechnologie microbienne dans divers domaines appliquées au développement et la gestion durable des ressources, à savoir l’agriculture, l'alimentation, l'environnement, la santé, l’industrie agro-alimentaire et le traitement et recyclage des eaux et des déchets par voie microbienne. Ce congrès sera également l’occasion pour les enseignants-chercheurs et les étudiants-chercheurs marocains d’actualiser leurs connaissances dans le domaine des biotechnologies microbiennes, qui serviront à l’amélioration de leurs recherches et enseignements. Le congrès MICROBIOD sera également l’occasion pour certains de nos collaborateurs étrangers de contribuer de près à la formation de nos étudiants en biotechnologie microbienne et ceci par la discussion des protocoles de travail, des méthodes d’analyse et des résultats obtenus. -
Metagenomes of Native and Electrode-Enriched Microbial Communities from the Soudan Iron Mine Jonathan P
Metagenomes of native and electrode-enriched microbial communities from the Soudan Iron Mine Jonathan P. Badalamenti and Daniel R. Bond Department of Microbiology and BioTechnology Institute, University of Minnesota - Twin Cities, Saint Paul, Minnesota, USA Twitter: @JonBadalamenti @wanderingbond Summary Approach - compare metagenomes from native and electrode-enriched deep subsurface microbial communities 30 Despite apparent carbon limitation, anoxic deep subsurface brines at the Soudan ) enriched 2 Underground Iron Mine harbor active microbial communities . To characterize these 20 A/cm µ assemblages, we performed shotgun metagenomics of native and enriched samples. enrich ( harvest cells collect inoculate +0.24 V extract 10 Follwing enrichment on poised electrodes and long read sequencing, we recovered Soudan brine electrode 20° C from DNA biodreactors current electrodes from the metagenome the closed, circular genome of a novel Desulfuromonas sp. 0 0 10 20 30 40 filtrate PacBio RS II Illumina HiSeq with remarkable genomic features that were not fully resolved by short read assem- extract time (d) long reads short reads TFF DNA unenriched bly alone. This organism was essentially absent in unenriched Soudan communities, 0.1 µm retentate assembled metagenomes reconstruct long read return de novo complete genome(s) assembly indicating that electrodes are highly selective for putative metal reducers. Native HGAP assembly community metagenomes suggest that carbon cycling is driven by methyl-C me- IDBA_UD 1 hybrid tabolism, in particular methylotrophic methanogenesis. Our results highlight the 3 µm prefilter assembly N4 binning promising potential for long reads in metagenomic surveys of low-diversity environ- borehole N4 binning read trimming and filtering brine de novo ments. -
Electron Transfer Through the Outer Membrane of Geobacter Sulfurreducens a DISSERTATION SUBMITTED to the FACULTY of the UNIVE
Electron transfer through the outer membrane of Geobacter sulfurreducens A DISSERTATION SUBMITTED TO THE FACULTY OF THE UNIVERSITY OF MINNESOTA BY Fernanda Jiménez Otero IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR IN PHILOSOPHY Dr. Daniel R. Bond May, 2018 Fernanda Jiménez Otero, 2018, © Acknowledgements This dissertation and the degree I have gained with it, would not have been possible without the help and support from an invaluable group of people. The training I received from Chi Ho Chan and Caleb Levar continues to be essential in the way I approach scientific endeavors. The quality of genetic studies and rigor in microbiology techniques they taught me is a standard I hope to meet throughout my career. Daniel Bond has been much more than I ever expected from an advisor. I have not only gained scientific knowledge from him, but I will take with me the example of what a great mentor represents. His enthusiasm for science is only rivaled by his commitment to past and present members of his laboratory. I am extremely honored to be able to count myself in that group, and I will do my best to represent him proudly in future endeavors. Throughout these five years, Jeff Gralnick has given me numerous opportunities to explore all aspects of a scientific career. Not only is Chapter 2 a result of his vision, but I feel less intimidated by a career in science as a result of his mentoring and support. The faculty members in my committee- Carrie Wilmot, Brandy Toner, and Larry Wackett, have made sure I am well prepared for i every step through graduate school. -
(Pelobacter) and Methanococcoides Are Responsible for Choline-Dependent Methanogenesis in a Coastal Saltmarsh Sediment
The ISME Journal https://doi.org/10.1038/s41396-018-0269-8 ARTICLE Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment 1 1 1 2 3 1 Eleanor Jameson ● Jason Stephenson ● Helen Jones ● Andrew Millard ● Anne-Kristin Kaster ● Kevin J. Purdy ● 4 5 1 Ruth Airs ● J. Colin Murrell ● Yin Chen Received: 22 January 2018 / Revised: 11 June 2018 / Accepted: 26 July 2018 © The Author(s) 2018. This article is published with open access Abstract Coastal saltmarsh sediments represent an important source of natural methane emissions, much of which originates from quaternary and methylated amines, such as choline and trimethylamine. In this study, we combine DNA stable isotope 13 probing with high throughput sequencing of 16S rRNA genes and C2-choline enriched metagenomes, followed by metagenome data assembly, to identify the key microbes responsible for methanogenesis from choline. Microcosm 13 incubation with C2-choline leads to the formation of trimethylamine and subsequent methane production, suggesting that 1234567890();,: 1234567890();,: choline-dependent methanogenesis is a two-step process involving trimethylamine as the key intermediate. Amplicon sequencing analysis identifies Deltaproteobacteria of the genera Pelobacter as the major choline utilizers. Methanogenic Archaea of the genera Methanococcoides become enriched in choline-amended microcosms, indicating their role in methane formation from trimethylamine. The binning of metagenomic DNA results in the identification of bins classified as Pelobacter and Methanococcoides. Analyses of these bins reveal that Pelobacter have the genetic potential to degrade choline to trimethylamine using the choline-trimethylamine lyase pathway, whereas Methanococcoides are capable of methanogenesis using the pyrrolysine-containing trimethylamine methyltransferase pathway. -
Characterization of the Deltaproteobacteria in Contaminated and Uncontaminated Stream Sediments and Identification of Potential Mercury Methylators
Vol. 66: 271–282, 2012 AQUATIC MICROBIAL ECOLOGY Published online July 9 doi: 10.3354/ame01563 Aquat Microb Ecol Characterization of the Deltaproteobacteria in contaminated and uncontaminated stream sediments and identification of potential mercury methylators Jennifer J. Mosher1,3, Tatiana A. Vishnivetskaya1,4, Dwayne A. Elias1, Mircea Podar1, Scott C. Brooks2, Steven D. Brown1, Craig C. Brandt1, Anthony V. Palumbo1,* 1Biosciences Division, and 2Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA 3Present address: Stroud Water Research Center, Avondale, Pennsylvania 19311, USA 4Present address: Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37998, USA ABSTRACT: Microbial communities were examined in surface stream sediments at 5 conta - minated sites and 1 control site near Oak Ridge, TN, USA, to identify bacteria that could be con- tributing to mercury (Hg) methylation. The phylogenetic composition of the sediment bacterial community was examined over 3 quarterly sampling periods (36 samples) using 16S rRNA gene pyro sequencing. Only 3064 sequences (0.85% of the total community) were identified as Delta - proteobacteria, the only group known to methylate Hg, using the Ribosomal Database Project classifier at the 99% confidence threshold. Constrained ordination techniques indicated statisti- cally significant positive linear correlations between Desulfobulbus spp., Desulfonema spp. and Desulfobacca spp. and methyl-Hg concentrations at the Hg-contaminated sites. In contrast, the distribution of organisms related to Byssovorax spp. was significantly correlated to inorganic car- bon, nitrate and uranium concentrations but not to Hg or methyl-Hg. Overall, the abundance and richness of Deltaproteobacteria sequences were higher in uncontaminated sediments, while the majority of the members present at the contaminated sites were either known potential metal- reducers/methylators or metal tolerant species. -
Mechanisms of Novel Anaerobic Aromatic Degradation Pathways in Geobacter Daltonii
Georgia State University ScholarWorks @ Georgia State University Biology Dissertations Department of Biology Summer 8-12-2014 Benzene and Beyond: Mechanisms of Novel Anaerobic Aromatic Degradation Pathways in Geobacter daltonii Alison Kanak Follow this and additional works at: https://scholarworks.gsu.edu/biology_diss Recommended Citation Kanak, Alison, "Benzene and Beyond: Mechanisms of Novel Anaerobic Aromatic Degradation Pathways in Geobacter daltonii." Dissertation, Georgia State University, 2014. https://scholarworks.gsu.edu/biology_diss/143 This Dissertation is brought to you for free and open access by the Department of Biology at ScholarWorks @ Georgia State University. It has been accepted for inclusion in Biology Dissertations by an authorized administrator of ScholarWorks @ Georgia State University. For more information, please contact [email protected]. BENZENE AND BEYOND: MECHANISMS OF NOVEL ANAEROBIC AROMATIC DEGRADATION PATHWAYS IN GEOBACTER DALTONII by ALISON KANAK Under the Direction of Kuk-Jeong Chin ABSTRACT Petroleum spills causes contamination of drinking water with carcinogenic aromatic compounds including benzene and cresol. Current knowledge of anaerobic benzene and cresol degradation is extremely limited and it makes bioremediation challenging. Geobacter daltonii strain FRC-32 is a metal-reducing bacterium isolated from radionuclides and hydrocarbon- contaminated subsurface sediments. It is notable for its anaerobic oxidation of benzene and its unique ability to metabolize p-, m-, or o-cresol as a sole carbon source. Location of genes involved in aromatic compound degradation and genes unique to G. daltonii were elucidated by genomic analysis using BLAST. Genes predicted to play a role in aromatic degradation cluster into an aromatic island near the start of the genome. Of particular note, G. -
Supplementary Material
Supplementary Material 1 Supplementary Figures and Tables 1.1 Supplementary Figures Deltaproteobacterium PSCGC (2) Deltaproteobacteria Gammaproteobacteria bacterium isolate NP949 Gammaproteobacteria Deltaproteobacteria bacterium spp. (4) Deltaproteobacteria Streptomyces sp. CNQ-509 Actinobacteria candidate division KSB1 bacterium RBG_16_48_16 candidate division KSB1 Dethiobacter alkaliphilus AHT-1 Firmicutes-Clostridia Desulfuromonas sp. DDH-964 Deltaproteobacteria Desulfuromonas spp. (2) Deltaproteobacteria OTU-487 (Deltaproteobacteria bacterium 37-65-8) Spirochaetes bacterium (2) Spirochaetes Methanocella sp. RC-I Methanomicrobia Methanoregula boonei 6A8 Methanomicrobia candidate division OP9 bacterium SCGC AAA255-N14 Atribacteria Methanoregulace aearchaeon JGI M3C4D3-001-G22 Methanomicrobia Methanomicrobia (5) Methanofollis liminatans GKZPZ Methanomicrobia OTU-267 (uncultured microorganism) Candidatus Aminicenantes bacterium RBG_13_59_9 Aminicenantes Methanomassiliicoccus luminyensis B10 Thermoplasmata Anaerolineae bacterium CG_4_9_14_0_8 Chloroflexi Elusimicrobia bacterium GW (2) Elusimicrobia candidate division WOR-3 bacterium SM23_42 Methanomassiliicoccales archaeon RumEn M1 Thermoplasmata OTU-858 (uncultured microorganism) OTU-544 (uncultured bacterium) Theionarchaea archaeon DG-70-1 Theionarchaea Chloroflexi bacterium RIFOXYD12_FULL_57_15 Chloroflexi OTU-201 (uncultured bacterium) OTU-481 (uncultured bacterium) Methanomicrobia (6) Lentisphaerae bacterium (2) Lentisphaerae Fimicutes (5) Bdellovibrionales bacterium GWB1_55_8 Deltaproteobacteria -
Ferrihydrite Associated Organic Matter (OM) Stimulates Reduction by Shewanella Oneidensis MR-1 and a Complex Microbial Consortia Rebecca E
Ferrihydrite associated organic matter (OM) stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortia Rebecca E. Cooper1, Karin Eusterhues2, Carl-Eric Wegner1, Kai Uwe Totsche2, Kirsten Küsel1,3 1Aquatic Geomicrobiology, Friedrich Schiller University, Jena, 07743, Germany 5 2Department of Hydrogeology, Institute of Geosciences, Friedrich Schiller University, Jena, 07743, Germany 3The German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, 07743, Germany Correspondence to: Kirsten Küsel ([email protected]) Abstract. The formation of Fe(III) oxides in natural environments occurs in the presence of natural organic matter (OM), resulting in the formation of OM-mineral complexes that form through adsorption or coprecipitation processes. Thus, 10 microbial Fe(III) reduction in natural environments most often occurs in the presence of OM-mineral complexes rather than pure Fe(III) minerals. This study investigated to what extent the content of adsorbed or coprecipitated OM on ferrihydrite influences the rate of Fe(III) reduction by Shewanella oneidensis MR-1, a model Fe(III)-reducing microorganism, in comparison to a microbial consortium extracted from the acidic, Fe-rich Schlöppnerbrunnen fen. We found that increased OM content led to increased rates of microbial Fe(III) reduction by S. oneidensis MR-1 in contrast to earlier findings with the 15 model organism Geobacter bremensis. Ferrihydrite-OM coprecipitates were reduced slightly faster than ferrihydrites with adsorbed OM. Surprisingly, the complex microbial consortia stimulated by a mixture of electrons donors (lactate, acetate, and glucose) mimics S. oneidensis under the same experimental Fe(III)-reducing conditions suggesting similar mechanisms of electron transfer whether or not the OM is adsorbed or coprecipitated to the mineral surfaces. -
Universitá Di Bologna MICROBIAL ECOLOGY of BIOTECHNOLOGICAL PROCESSES
Alma Mater Studiorum – Universitá di Bologna Dottorato di Ricerca in Scienze Biochimiche e Biotecnologiche Ciclo XXVII Settore Concorsuale 03/D1 Settore Scientifico Disciplinare CHIM/11 MICROBIAL ECOLOGY OF BIOTECHNOLOGICAL PROCESSES Presentata da: Dott.ssa Serena Fraraccio Coordinatore Dottorato Relatore Chiar.mo Prof. Chiar.mo Prof. Fabio Fava Santi Mario Spampinato Correlatori Giulio Zanaroli, Ph.D. Assoc. Prof. Ondřej Uhlík, Ph.D. Esame finale anno 2015 Abstract The investigation of phylogenetic diversity and functionality of complex microbial communities in relation to changes in the environmental conditions represents a major challenge of microbial ecology research. Nowadays, particular attention is paid to microbial communities occurring at environmental sites contaminated by recalcitrant and toxic organic compounds. Extended research has evidenced that such communities evolve some metabolic abilities leading to the partial degradation or complete mineralization of the contaminants. Determination of such biodegradation potential can be the starting point for the development of cost effective biotechnological processes for the bioremediation of contaminated matrices. This work showed how metagenomics-based microbial ecology investigations supported the choice or the development of three different bioremediation strategies. First, PCR-DGGE and PCR-cloning approaches served the molecular characterization of microbial communities enriched through sequential development stages of an aerobic cometabolic process for the treatment of groundwater -
Comparative Metatranscriptomics Reveals Extracellular Electron Transfer Pathways Conferring Microbial Adaptivity to Surface Redox Potential Changes
The ISME Journal (2018) 12:2844–2863 https://doi.org/10.1038/s41396-018-0238-2 ARTICLE Comparative metatranscriptomics reveals extracellular electron transfer pathways conferring microbial adaptivity to surface redox potential changes 1,2 2,3,4,5 2,8 5 2,6,7 Shun’ichi Ishii ● Shino Suzuki ● Aaron Tenney ● Kenneth H. Nealson ● Orianna Bretschger Received: 1 December 2017 / Revised: 12 April 2018 / Accepted: 30 June 2018 / Published online: 26 July 2018 © The Author(s) 2018. This article is published with open access Abstract Some microbes can capture energy through redox reactions with electron flow to solid-phase electron acceptors, such as metal-oxides or poised electrodes, via extracellular electron transfer (EET). While diverse oxide minerals, exhibiting different surface redox potentials, are widely distributed on Earth, little is known about how microbes sense and use the minerals. Here we show electrochemical, metabolic, and transcriptional responses of EET-active microbial communities established on poised electrodes to changes in the surface redox potentials (as electron acceptors) and surrounding substrates (as electron donors). Combination of genome-centric stimulus-induced metatranscriptomics and metabolic pathway investigation revealed 1234567890();,: 1234567890();,: that nine Geobacter/Pelobacter microbes performed EET activity differently according to their preferable surface potentials and substrates. While the Geobacter/Pelobacter microbes coded numerous numbers of multi-heme c-type cytochromes and conductive e-pili, wide variations in gene expression were seen in response to altering surrounding substrates and surface potentials, accelerating EET via poised electrode or limiting EET via an open circuit system. These flexible responses suggest that a wide variety of EET-active microbes utilizing diverse EET mechanisms may work together to provide such EET-active communities with an impressive ability to handle major changes in surface potential and carbon source availability. -
MAPEAMENTO DE GENES Nif PUBLICADOS NO NCBI USANDO CONCEITOS DE MINERAÇÃO DE DADOS E INTELIGÊNCIA ARTIFICIAL
UNIVERSIDADE FEDERAL DO PARANÁ MICHELLY ALVES COUTINHO GEHLEN MAPEAMENTO DE GENES nif PUBLICADOS NO NCBI USANDO CONCEITOS DE MINERAÇÃO DE DADOS E INTELIGÊNCIA ARTIFICIAL CURITIBA 2011 MICHELLY ALVES COUTINHO GEHLEN MAPEAMENTO DE GENES nif PUBLICADOS NO NCBI USANDO CONCEITOS DE MINERAÇÃO DE DADOS E INTELIGÊNCIA ARTIFICIAL Dissertação apresentada ao Curso de Pós- Graduação em Bioinformática da Universidade Federal do Paraná, como requisito parcial para a obtenção do título de Mestre em Bioinformática. Orientador : Roberto Tadeu Raittz, Dr. Co-orientadora : Liu Un Rigo, Dra. CURITIBA 2011 TERMO DE APROVAÇÃO MICHELLY ALVES COUTINHO GEHLEN MAPEAMENTO DE GENES nif PUBLICADOS NO NCBI USANDO CONCEITOS DE MINERAÇÃO DE DADOS E INTELIGÊNCIA ARTIFICIAL Dissertação aprovada como requisito parcial para obtenção do grau de Mestre em Bioinformática, pelo Programa de Pós-Graduação em Bioinformática, Setor de Educação Profissional e Tecnológica, Universidade Federal do Paraná, pela seguinte banca examinadora: Orientador : Prof. Dr. Roberto Tadeu Raittz Co-orientador : Profª. Drª. Liu Un Rigo Prof. Dr. João Artur de Souza Universidade Federal de Santa Catarina Profª. Drª. Maria Berenice Reynaud Steffens Universidade Federal do Paraná Prof. Dr. Roberto Tadeu Raittz Universidade Federal do Paraná Profª. Drª. Liu Un Rigo Universidade Federal do Paraná Curitiba, 17 de fevereiro de 2011. Para Téco, Lucas, Tiago, Pai e Mãe. Amo vocês. AGRADECIMENTOS À Deus, pela oportunidade de crescimento e aprimoramento, de vida e de fé. A Mãezinha do Céu, por ficar sempre do meu lado, me carregando no colo, cada uma das muitas vezes em que eu caí. Ao meu marido, Téco, pelo amor, demonstrado no silêncio do olhar e nos gestos concretos de apoio sempre presentes. -
Ferrihydrite-Associated Organic Matter (OM) Stimulates Reduction by Shewanella Oneidensis MR-1 and a Complex Microbial Consortia
Biogeosciences, 14, 5171–5188, 2017 https://doi.org/10.5194/bg-14-5171-2017 © Author(s) 2017. This work is distributed under the Creative Commons Attribution 4.0 License. Ferrihydrite-associated organic matter (OM) stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortia Rebecca Elizabeth Cooper1, Karin Eusterhues2, Carl-Eric Wegner1, Kai Uwe Totsche2, and Kirsten Küsel1,3 1Aquatic Geomicrobiology, Friedrich Schiller University, 07743 Jena, Germany 2Department of Hydrogeology, Institute of Geosciences, Friedrich Schiller University, 07743 Jena, Germany 3The German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 07743 Leipzig, Germany Correspondence to: Kirsten Küsel ([email protected]) Received: 27 June 2017 – Discussion started: 6 July 2017 Revised: 24 September 2017 – Accepted: 2 October 2017 – Published: 20 November 2017 Abstract. The formation of Fe(III) oxides in natural environ- an electron sink. Instead, OM–mineral complexes favored ments occurs in the presence of natural organic matter (OM), the enrichment of microbes including Desulfobacteria and resulting in the formation of OM–mineral complexes that Pelosinus sp., both of which can utilize lactate and acetate as form through adsorption or coprecipitation processes. Thus, an electron donor under Fe(III)-reducing conditions. In sum- microbial Fe(III) reduction in natural environments most of- mary, this study shows that increasing concentrations of OM ten occurs in the presence of OM–mineral complexes rather in OM–mineral complexes determines microbial Fe(III) re- than pure Fe(III) minerals. This study investigated to what duction rates and shapes the microbial community structure extent does the content of adsorbed or coprecipitated OM on involved in the reductive dissolution of ferrihydrite.