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Microbial Community Structure Dynamics in Ohio River Sediments During Reductive Dechlorination of Pcbs
University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS Andres Enrique Nunez University of Kentucky Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Nunez, Andres Enrique, "MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS" (2008). University of Kentucky Doctoral Dissertations. 679. https://uknowledge.uky.edu/gradschool_diss/679 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Andres Enrique Nunez The Graduate School University of Kentucky 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS ABSTRACT OF DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Agriculture at the University of Kentucky By Andres Enrique Nunez Director: Dr. Elisa M. D’Angelo Lexington, KY 2008 Copyright © Andres Enrique Nunez 2008 ABSTRACT OF DISSERTATION MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS The entire stretch of the Ohio River is under fish consumption advisories due to contamination with polychlorinated biphenyls (PCBs). In this study, natural attenuation and biostimulation of PCBs and microbial communities responsible for PCB transformations were investigated in Ohio River sediments. Natural attenuation of PCBs was negligible in sediments, which was likely attributed to low temperature conditions during most of the year, as well as low amounts of available nitrogen, phosphorus, and organic carbon. -
Phylogenetic Analysis Reveals an Ancient Gene Duplication As The
1 Phylogenetic analysis reveals an ancient gene duplication as 2 the origin of the MdtABC efflux pump. 3 4 Kamil Górecki1, Megan M. McEvoy1,2,3 5 1Institute for Society & Genetics, 2Department of MicroBiology, Immunology & Molecular 6 Genetics, and 3Molecular Biology Institute, University of California, Los Angeles, CA 90095, 7 United States of America 8 Corresponding author: [email protected] (M.M.M.) 9 1 10 Abstract 11 The efflux pumps from the Resistance-Nodulation-Division family, RND, are main 12 contributors to intrinsic antibiotic resistance in Gram-negative bacteria. Among this family, the 13 MdtABC pump is unusual by having two inner membrane components. The two components, 14 MdtB and MdtC are homologs, therefore it is evident that the two components arose by gene 15 duplication. In this paper, we describe the results obtained from a phylogenetic analysis of the 16 MdtBC pumps in the context of other RNDs. We show that the individual inner membrane 17 components (MdtB and MdtC) are conserved throughout the Proteobacterial species and that their 18 existence is a result of a single gene duplication. We argue that this gene duplication was an ancient 19 event which occurred before the split of Proteobacteria into Alpha-, Beta- and Gamma- classes. 20 Moreover, we find that the MdtABC pumps and the MexMN pump from Pseudomonas aeruginosa 21 share a close common ancestor, suggesting the MexMN pump arose by another gene duplication 22 event of the original Mdt ancestor. Taken together, these results shed light on the evolution of the 23 RND efflux pumps and demonstrate the ancient origin of the Mdt pumps and suggest that the core 24 bacterial efflux pump repertoires have been generally stable throughout the course of evolution. -
Isolation and Characterization of Achromobacter Sp. CX2 From
Ann Microbiol (2015) 65:1699–1707 DOI 10.1007/s13213-014-1009-6 ORIGINAL ARTICLE Isolation and characterization of Achromobacter sp. CX2 from symbiotic Cytophagales, a non-cellulolytic bacterium showing synergism with cellulolytic microbes by producing β-glucosidase Xiaoyi Chen & Ying Wang & Fan Yang & Yinbo Qu & Xianzhen Li Received: 27 August 2014 /Accepted: 24 November 2014 /Published online: 10 December 2014 # Springer-Verlag Berlin Heidelberg and the University of Milan 2014 Abstract A Gram-negative, obligately aerobic, non- degradation by cellulase (Carpita and Gibeaut 1993). There- cellulolytic bacterium was isolated from the cellulolytic asso- fore, efficient degradation is the result of multiple activities ciation of Cytophagales. It exhibits biochemical properties working synergistically to efficiently solubilize crystalline cel- that are consistent with its classification in the genus lulose (Sánchez et al. 2004;Lietal.2009). Most known Achromobacter. Phylogenetic analysis together with the phe- cellulolytic organisms produce multiple cellulases that act syn- notypic characteristics suggest that the isolate could be a novel ergistically on native cellulose (Wilson 2008)aswellaspro- species of the genus Achromobacter and designated as CX2 (= duce some other proteins that enhance cellulose hydrolysis CGMCC 1.12675=CICC 23807). The strain CX2 is the sym- (Wang et al. 2011a, b). Synergistic cooperation of different biotic microbe of Cytophagales and produces β-glucosidase. enzymes is a prerequisite for the efficient degradation of cellu- The results showed that the non-cellulolytic Achromobacter lose (Jalak et al. 2012). Both Trichoderma reesi and Aspergillus sp. CX2 has synergistic activity with cellulolytic microbes by niger were co-cultured to increase the levels of different enzy- producing β-glucosidase. -
Detection of a Bacterial Group Within the Phylum Chloroflexi And
Microbes Environ. Vol. 21, No. 3, 154–162, 2006 http://wwwsoc.nii.ac.jp/jsme2/ Detection of a Bacterial Group within the Phylum Chloroflexi and Reductive-Dehalogenase-Homologous Genes in Pentachlorobenzene- Dechlorinating Estuarine Sediment from the Arakawa River, Japan KYOSUKE SANTOH1, ATSUSHI KOUZUMA1, RYOKO ISHIZEKI2, KENICHI IWATA1, MINORU SHIMURA3, TOSHIO HAYAKAWA3, TOSHIHIRO HOAKI4, HIDEAKI NOJIRI1, TOSHIO OMORI2, HISAKAZU YAMANE1 and HIROSHI HABE1*† 1 Biotechnology Research Center, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657, Japan 2 Department of Industrial Chemistry, Faculty of Engineering, Shibaura Institute of Technology, Minato-ku, Tokyo 108–8548, Japan 3 Environmental Biotechnology Laboratory, Railway Technical Research Institute, 2–8–38 Hikari-cho, Kokubunji-shi, Tokyo 185–8540, Japan 4 Technology Research Center, Taisei Corporation, 344–1 Nase, Totsuka-ku, Yokohama 245–0051, Japan (Received April 21, 2006—Accepted June 12, 2006) We enriched a pentachlorobenzene (pentaCB)-dechlorinating microbial consortium from an estuarine-sedi- ment sample obtained from the mouth of the Arakawa River. The sediment was incubated together with a mix- ture of four electron donors and pentaCB, and after five months of incubation, the microbial community structure was analyzed. Both DGGE and clone library analyses showed that the most expansive phylogenetic group within the consortium was affiliated with the phylum Chloroflexi, which includes Dehalococcoides-like bacteria. PCR using a degenerate primer set targeting conserved regions in reductive-dehalogenase-homologous (rdh) genes from Dehalococcoides species revealed that DNA fragments (approximately 1.5–1.7 kb) of rdh genes were am- plified from genomic DNA of the consortium. The deduced amino acid sequences of the rdh genes shared sever- al characteristics of reductive dehalogenases. -
Response of Heterotrophic Stream Biofilm Communities to a Gradient of Resources
The following supplement accompanies the article Response of heterotrophic stream biofilm communities to a gradient of resources D. J. Van Horn1,*, R. L. Sinsabaugh1, C. D. Takacs-Vesbach1, K. R. Mitchell1,2, C. N. Dahm1 1Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA 2Present address: Department of Microbiology & Immunology, University of British Columbia Life Sciences Centre, Vancouver BC V6T 1Z3, Canada *Email: [email protected] Aquatic Microbial Ecology 64:149–161 (2011) Table S1. Representative sequences for each OTU, associated GenBank accession numbers, and taxonomic classifications with bootstrap values (in parentheses), generated in mothur using 14956 reference sequences from the SILVA data base Treatment Accession Sequence name SILVA taxonomy classification number Control JF695047 BF8FCONT18Fa04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Cellvibrio(100);unclassified; Control JF695049 BF8FCONT18Fa12.b1 Bacteria(100);Proteobacteria(100);Alphaproteobacteria(100);Rhizobiales(100);Methylocystaceae(100);uncultured(100);unclassified; Control JF695054 BF8FCONT18Fc01.b1 Bacteria(100);Planctomycetes(100);Planctomycetacia(100);Planctomycetales(100);Planctomycetaceae(100);Isosphaera(50);unclassified; Control JF695056 BF8FCONT18Fc04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Xanthomonadales(100);Xanthomonadaceae(100);uncultured(64);unclassified; Control JF695057 BF8FCONT18Fc06.b1 Bacteria(100);Proteobacteria(100);Betaproteobacteria(100);Burkholderiales(100);Comamonadaceae(100);Ideonella(54);unclassified; -
Bacterial Diversity in the Surface Sediments of the Hypoxic Zone Near
ORIGINAL RESEARCH Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea Qi Ye, Ying Wu, Zhuoyi Zhu, Xiaona Wang, Zhongqiao Li & Jing Zhang State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China Keywords Abstract Bacteria, Changjiang Estuary, hypoxia, Miseq Illumina sequencing, sediment Changjiang (Yangtze River) Estuary has experienced severe hypoxia since the 1950s. In order to investigate potential ecological functions of key microorgan- Correspondence isms in relation to hypoxia, we performed 16S rRNA-based Illumina Miseq Qi Ye, East China Normal University, State Key sequencing to explore the bacterial diversity in the surface sediments of the Laboratory of Estuarine and Coastal Research, hypoxic zone near the Changjiang Estuary and in the East China Sea (ECS). 3663 North Zhongshan Road, SKLEC Building, Room 419, Shanghai 200062, China. The results showed that numerous Proteobacteria-affiliated sequences in the sedi- Tel: 86-021-52124974; ments of the inner continental shelf were related to both sulfate-reducing and Fax: 86-021- 62546441; sulfur-oxidizing bacteria, suggesting an active sulfur cycle in this area. Many E-mail: [email protected] sequences retrieved from the hypoxic zone were also related to Planctomycetes from two marine upwelling systems, which may be involved in the initial break- Funding Information down of sulfated heteropolysaccharides. Bacteroidetes, which is expected to degrade This study was funded by the Shanghai Pujiang high-molecular-weight organic matter, was abundant in all the studied stations Talent Program (12PJ1403100), the National except for station A8, which was the deepest and possessed the largest grain Natural Science Foundation of China (41276081), the Key Project of Chinese size. -
Identification of Active Methylotroph Populations in an Acidic Forest Soil
Microbiology (2002), 148, 2331–2342 Printed in Great Britain Identification of active methylotroph populations in an acidic forest soil by stable- isotope probing Stefan Radajewski,1 Gordon Webster,2† David S. Reay,3‡ Samantha A. Morris,1 Philip Ineson,4 David B. Nedwell,3 James I. Prosser2 and J. Colin Murrell1 Author for correspondence: J. Colin Murrell. Tel: j44 24 7652 2553. Fax: j44 24 7652 3568. e-mail: cmurrell!bio.warwick.ac.uk 1 Department of Biological Stable-isotope probing (SIP) is a culture-independent technique that enables Sciences, University of the isolation of DNA from micro-organisms that are actively involved in a Warwick, Coventry CV4 7AL, UK specific metabolic process. In this study, SIP was used to characterize the active methylotroph populations in forest soil (pH 35) microcosms that were exposed 2 Department of Molecular 13 13 13 13 and Cell Biology, to CH3OH or CH4. Distinct C-labelled DNA ( C-DNA) fractions were resolved University of Aberdeen, from total community DNA by CsCl density-gradient centrifugation. Analysis of Institute of Medical 16S rDNA sequences amplified from the 13C-DNA revealed that bacteria related Sciences, Foresterhill, Aberdeen AB25 2ZD, UK to the genera Methylocella, Methylocapsa, Methylocystis and Rhodoblastus had assimilated the 13C-labelled substrates, which suggested that moderately 3 Department of Biological Sciences, University of acidophilic methylotroph populations were active in the microcosms. Essex, Wivenhoe Park, Enrichments targeted towards the active proteobacterial CH3OH utilizers were Colchester, Essex CO4 3SQ, successful, although none of these bacteria were isolated into pure culture. A UK parallel analysis of genes encoding the key enzymes methanol dehydrogenase 4 Department of Biology, and particulate methane monooxygenase reflected the 16S rDNA analysis, but University of York, PO Box 373, YO10 5YW, UK unexpectedly revealed sequences related to the ammonia monooxygenase of ammonia-oxidizing bacteria (AOB) from the β-subclass of the Proteobacteria. -
Microbial Community Response to Heavy and Light Crude Oil in the Great Lakes
Microbial Community Response to Heavy and Light Crude Oil in the Great Lakes Stephen Techtmann 10/24/19 Microbial Sensors Techtmann Lab @ MTU Investigating the applications of environmental microbial communities Hydraulic Fracturing Related Antibiotic Resistance Oil Bioremediation Techtmann Lab @ MTU Overview • Background on oil biodegradation • Microbial response to light and heavy crude oil in the Great Lakes • Machine learning for prediction of contamination in the Great Lakes. Oil Spills Deepwater Horizon Enbridge Line 6B Deepwater Horizon Oil Spill • 4,1000,000 bbl of oil released • Light Sweet Crude oil released • April 20, 2010 • 1101.7 miles of shoreline oiled Atlas and Hazen 2011 Enbridge Line 6B Spill – Marshall MI • 20,082 bbl of oil released • Diluted Bitumen • July 26, 2010 • 70 miles of shoreline oiled https://www.mlive.com/news/kalamazoo/2010/07/state_of_emergency_declared_as.html Oil Transmissions Pipelines in the Great Lakes Region Line 5: • 645 miles from Superior WI to Sarnia Ontario • 540,000 barrels per day • Light crude and natural gas liquids (NGLs) Crude oil Oil types and API Gravity Microbes and Biotechnology (Bioremediation) Low cost input Microbe High value output Decreased Cost Contaminant Increased Efficiency Carbon dioxide or non- toxic daughter products Carbon dioxide Microbial Biomass Petroleum Microbe Daughter Products Water Microbial Ecology and Biotechnology Low cost input Microbe High value output Decreased Cost/Increased Efficiency Complex input Input A Microbe Microbe Output A Input B Microbe Output -
Metagenomic Insights Into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines
Lawrence Berkeley National Laboratory Recent Work Title Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines. Permalink https://escholarship.org/uc/item/9xc5s0v5 Journal Frontiers in microbiology, 7(FEB) ISSN 1664-302X Authors Vavourakis, Charlotte D Ghai, Rohit Rodriguez-Valera, Francisco et al. Publication Date 2016 DOI 10.3389/fmicb.2016.00211 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ORIGINAL RESEARCH published: 25 February 2016 doi: 10.3389/fmicb.2016.00211 Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines Charlotte D. Vavourakis 1, Rohit Ghai 2, 3, Francisco Rodriguez-Valera 2, Dimitry Y. Sorokin 4, 5, Susannah G. Tringe 6, Philip Hugenholtz 7 and Gerard Muyzer 1* 1 Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands, 2 Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain, 3 Department of Aquatic Microbial Ecology, Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Ceskéˇ Budejovice,ˇ Czech Republic, 4 Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia, 5 Department of Biotechnology, Delft University of Technology, Delft, Netherlands, 6 The Department of Energy Joint Genome Institute, Walnut Creek, CA, USA, 7 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration Edited by: of sodium carbonates in the absence of major divalent cations. -
Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz
Alpine soil bacterial community and environmental filters Bahar Shahnavaz To cite this version: Bahar Shahnavaz. Alpine soil bacterial community and environmental filters. Other [q-bio.OT]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00515414 HAL Id: tel-00515414 https://tel.archives-ouvertes.fr/tel-00515414 Submitted on 6 Sep 2010 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. THÈSE Pour l’obtention du titre de l'Université Joseph-Fourier - Grenoble 1 École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Par Bahar SHAHNAVAZ Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean MARTIN Examinateur Dr. Yves JOUANNEAU Président du jury Dr. Roberto GEREMIA Directeur de thèse Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) THÈSE Pour l’obtention du titre de Docteur de l’Université de Grenoble École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Bahar SHAHNAVAZ Directeur : Roberto GEREMIA Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. -
Functional Structure of the Bromeliad Tank Microbiome Is Strongly Shaped by Local Geochemical Conditions
Environmental Microbiology (2017) 19(8), 3132–3151 doi:10.1111/1462-2920.13788 Functional structure of the bromeliad tank microbiome is strongly shaped by local geochemical conditions Stilianos Louca,1,2* Saulo M. S. Jacques,3,4 denitrification steps, ammonification, sulfate respira- Aliny P. F. Pires,3 Juliana S. Leal,3,5 tion, methanogenesis, reductive acetogenesis and 6 1,2,7 Angelica L. Gonzalez, Michael Doebeli and anoxygenic phototrophy. Overall, CO2 reducers domi- Vinicius F. Farjalla3 nated in abundance over sulfate reducers, and 1Biodiversity Research Centre, University of British anoxygenic phototrophs largely outnumbered oxy- Columbia, Vancouver, BC, Canada. genic photoautotrophs. Functional community 2Department of Zoology, University of British Columbia, structure correlated strongly with environmental vari- Vancouver, BC, Canada. ables, between and within a single bromeliad species. 3Department of Ecology, Biology Institute, Universidade Methanogens and reductive acetogens correlated Federal do Rio de Janeiro, Rio de Janeiro, Brazil. with detrital volume and canopy coverage, and exhib- 4Programa de Pos-Graduac ¸ao~ em Ecologia e ited higher relative abundances in N. cruenta.A Evoluc¸ao,~ Universidade Estadual do Rio de Janeiro, Rio comparison of bromeliads to freshwater lake sedi- de Janeiro, Brazil. ments and soil from around the world, revealed stark differences in terms of taxonomic as well as func- 5Programa de Pos-Graduac ¸ao~ em Ecologia, tional microbial community structure. Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil. 6Biology Department & Center for Computational & Introduction Integrative Biology, Rutgers University, Camden, NJ, USA. Bromeliads (fam. Bromeliaceae) are plants found through- 7Department of Mathematics, University of British out the neotropics, with many species having rosette-like Columbia, Vancouver, BC, Canada. -
Full Paper Ilumatobacter Fluminis Gen. Nov., Sp. Nov., a Novel Actinobacterium Isolated from the Sediment of an Estuary
J. Gen. Appl. Microbiol., 55, 201‒205 (2009) Full Paper Ilumatobacter fl uminis gen. nov., sp. nov., a novel actinobacterium isolated from the sediment of an estuary Atsuko Matsumoto,1 Hiroki Kasai,2 Yoshihide Matsuo,2 Satoshi Ōmura,1 Yoshikazu Shizuri,2 and Yōko Takahashi1,* 1 Kitasato Institute for Life Sciences, Kitasato University, Minato-ku, Tokyo 108‒8641, Japan 2 Marine Biotechnology Institute, Kitasato University, Kamaishi, Iwate 026‒0001, Japan (Received December 1, 2008; Accepted February 2, 2009) Bacterial strain YM22-133T was isolated from the sediment of an estuary and grew in media with an artifi cial seawater base. Strain YM22-133T was Gram-positive, aerobic, non-motile and rod shaped. The cell-wall peptidoglycan contained LL-DAP, glycine, alanine and hydroxyglutamate. The predominant menaquinone was MK-9 (H8), with MK-9 (H0), MK-9 (H2), MK-9 (H4) and MK-9 (H6) present as minor menaquinones. The G+C content of the genomic DNA from the strain was 68 mol%. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain is near- est to Acidimicrobium ferrooxidans DSM 10331T. However, the similarity is relatively low (87.1%) and the physiological characteristics are also different: Acidimicrobium ferrooxidans is thermo- tolerant and acidophilic. Therefore, strain YM22-133T can be classifi ed as a novel genus and species, Ilumatobacter fl uminis gen. nov., sp. nov. (type strain YM22-133T =DSM 18936T=MBIC 08263T). Key Words—Acidimicrobium; Actinobacteria; artifi cial sea water; Ilumatobacter fl uminis gen. nov., sp. nov. Introduction isolated as part of this study. Phylogenetic analysis on the basis of 16S rRNA gene sequence analysis showed Recently, bacteria isolated from marine environ- that the strain is most closely related to the genus Aci- ments have attracted attention due to the recognition dimicrobium (Clark and Norris, 1996).