Bergey's Manual of Systematic Bacteriology第1版
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The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service. -
Macellibacteroides Fermentans Gen. Nov., Sp. Nov., a Member of the Family Porphyromonadaceae Isolated from an Upflow Anaerobic Filter Treating Abattoir Wastewaters
International Journal of Systematic and Evolutionary Microbiology (2012), 62, 2522–2527 DOI 10.1099/ijs.0.032508-0 Macellibacteroides fermentans gen. nov., sp. nov., a member of the family Porphyromonadaceae isolated from an upflow anaerobic filter treating abattoir wastewaters Linda Jabari,1,2 Hana Gannoun,2 Jean-Luc Cayol,1 Abdeljabbar Hedi,1 Mitsuo Sakamoto,3 Enevold Falsen,4 Moriya Ohkuma,3 Moktar Hamdi,2 Guy Fauque,1 Bernard Ollivier1 and Marie-Laure Fardeau1 Correspondence 1Aix-Marseille Universite´ du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, Case 925, Marie-Laure Fardeau 163 Avenue de Luminy, 13288 Marseille Cedex 9, France [email protected] 2Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Applique´es et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis Cedex, Tunisia 3Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center 2-1 Hirosawa, Wako, Saitama 351-0198, Japan 4CCUG, Culture Collection, Department of Clinical Bacteriology, University of Go¨teborg, 41346 Go¨teborg, Sweden A novel obligately anaerobic, non-spore-forming, rod-shaped mesophilic bacterium, which stained Gram-positive but showed the typical cell wall structure of Gram-negative bacteria, was isolated from an upflow anaerobic filter treating abattoir wastewaters in Tunisia. The strain, designated LIND7HT, grew at 20–45 6C (optimum 35–40 6C) and at pH 5.0–8.5 (optimum pH 6.5–7.5). It did not require NaCl for growth, but was able to grow in the presence of up to 2 % NaCl. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors. -
Robust Taxonomic Classification of Uncharted Microbial Sequences and Bins with CAT and BAT
bioRxiv preprint doi: https://doi.org/10.1101/530188; this version posted January 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT F.A. Bastiaan von Meijenfeldt1,†, Ksenia Arkhipova1,†, Diego D. Cambuy1, Felipe H. Coutinho2,3, Bas E. Dutilh1,2,* 1 Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, The Netherlands. 2 Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands. 3 Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. * To whom correspondence should be addressed. Tel: +31 30 253 4212; Email: [email protected]. † These authors contributed equally to this work. Present Address: [Felipe H. Couthinho], Evolutionary Genomics Group, Departamento de Produccíon y Microbiología, Universidad Miguel Hernández, Campus San Juan, San Juan, Alicante 03550, Spain. ABSTRACT Current-day metagenomics increasingly requires taxonomic classification of long DNA sequences and metagenome-assembled genomes (MAGs) of unknown microorganisms. We show that the standard best-hit approach often leads to classifications that are too specific. We present tools to classify high- quality metagenomic contigs (Contig Annotation Tool, CAT) and MAGs (Bin Annotation Tool, BAT) and thoroughly benchmark them with simulated metagenomic sequences that are classified against a reference database where related sequences are increasingly removed, thereby simulating increasingly unknown queries. We find that the query sequences are correctly classified at low taxonomic ranks if closely related organisms are present in the reference database, while classifications are made higher in the taxonomy when closely related organisms are absent, thus avoiding spurious classification specificity. -
Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis Within the Prevalent Canine Oral Species Porphyromonas Cangingivalis
GBE Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis Ciaran O’Flynn1,*, Oliver Deusch1, Aaron E. Darling2, Jonathan A. Eisen3,4,5, Corrin Wallis1,IanJ.Davis1,and Stephen J. Harris1 1 The WALTHAM Centre for Pet Nutrition, Waltham-on-the-Wolds, United Kingdom Downloaded from 2The ithree Institute, University of Technology Sydney, Ultimo, New South Wales, Australia 3Department of Evolution and Ecology, University of California, Davis 4Department of Medical Microbiology and Immunology, University of California, Davis 5UC Davis Genome Center, University of California, Davis http://gbe.oxfordjournals.org/ *Corresponding author: E-mail: ciaran.ofl[email protected]. Accepted: November 6, 2015 Abstract Porphyromonads play an important role in human periodontal disease and recently have been shown to be highly prevalent in canine mouths. Porphyromonas cangingivalis is the most prevalent canine oral bacterial species in both plaque from healthy gingiva and at University of Technology, Sydney on January 17, 2016 plaque from dogs with early periodontitis. The ability of P. cangingivalis to flourish in the different environmental conditions char- acterized by these two states suggests a degree of metabolic flexibility. To characterize the genes responsible for this, the genomes of 32 isolates (including 18 newly sequenced and assembled) from 18 Porphyromonad species from dogs, humans, and other mammals were compared. Phylogenetic trees inferred using core genes largely matched previous findings; however, comparative genomic analysis identified several genes and pathways relating to heme synthesis that were present in P. cangingivalis but not in other Porphyromonads. Porphyromonas cangingivalis has a complete protoporphyrin IX synthesis pathway potentially allowing it to syn- thesize its own heme unlike pathogenic Porphyromonads such as Porphyromonas gingivalis that acquire heme predominantly from blood. -
Download/Issues/Mining/Reference Guide to Treatment Technologi Es for MIW.Pdf
Removal of Soluble Selenium in the Presence of Nitrate from Coal Mining-Influenced Water by Frank Nkansah - Boadu BSc., Kwame Nkrumah University of Science and Technology, 2003 MASc., The University of British Columbia, 2013 A DISSERTATION SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Chemical and Biological Engineering) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) December 2019 © Frank Nkansah - Boadu, 2019 The following individuals certify that they have read, and recommend to the Faculty of Graduate and Postdoctoral Studies for acceptance, the dissertation entitled: Removal of Soluble Selenium in the Presence of Nitrate from Coal Mining-Influenced Water submitted by Frank Nkansah-Boadu in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Chemical and Biological Engineering Examining Committee: Susan Baldwin, Chemical and Biological Engineering Supervisor Vikramaditya Yadav, Chemical and Biological Engineering Supervisory Committee Member Troy Vassos, Adjunct Professor, Civil Engineering Supervisory Committee Member Anthony Lau, Chemical and Biological Engineering University Examiner Scott Dunbar, Mining Engineering University Examiner ii Abstract Biological treatment to remove dissolved selenium from mining-influenced water (MIW) is inhibited by co-contaminants, especially nitrate. It was hypothesized that selenium reducing microorganisms can be obtained from native mine bacteria at sites affected by MIW due to the selection pressure from elevated selenium concentrations at those sites. Enrichment of these microorganisms and testing of their capacity to remove dissolved selenium from actual coal MIW was the objective of this dissertation. Fifteen sediments were collected from eleven different vegetated or non-vegetated seepage collection ponds and one non-impacted natural wetland. -
Metal Transformation by a Novel Pelosinus Isolate from a Subsurface Environment
INL/JOU-08-14091-Revision-0 Metal Transformation by a Novel Pelosinus Isolate From a Subsurface Environment Allison E. Ray, Peter P. Sheridan, Andrew L. Neal, Yoshiko Fujita, David E. Cummings, Timothy S. Magnuson August 2018 The INL is a U.S. Department of Energy National Laboratory operated by Battelle Energy Alliance INL/JOU-08-14091-Revision-0 Metal Transformation by a Novel Pelosinus Isolate From a Subsurface Environment Allison E. Ray, Peter P. Sheridan, Andrew L. Neal, Yoshiko Fujita, David E. Cummings, Timothy S. Magnuson August 2018 Idaho National Laboratory Idaho Falls, Idaho 83415 http://www.inl.gov Prepared for the U.S. Department of Energy Office of Nuclear Energy Under DOE Idaho Operations Office Contract DE-AC07-05ID14517 fmicb-09-01689 July 25, 2018 Time: 20:42 # 1 ORIGINAL RESEARCH published: xx July 2018 doi: 10.3389/fmicb.2018.01689 1 58 2 59 3 60 4 61 5 62 6 63 7 64 8 65 9 Metal Transformation by a Novel 66 10 67 11 Pelosinus Isolate From a Subsurface 68 12 69 13 Environment 70 14 71 15 Allison E. Ray1,2, Stephanie A. Connon1,3, Andrew L. Neal4†, Yoshiko Fujita2, 72 5 2† 1 16 David E. Cummings , Jani C. Ingram and Timothy S. Magnuson * 73 17 74 1 Department of Biological Sciences, Idaho State University, Pocatello, ID, United States, 2 Bioenergy Technologies, Idaho 18 3 75 Edited by: National Laboratory, Idaho Falls, ID, United States, California Institute of Technology, Pasadena, CA, United States, 19 4 5 76 Pankaj Kumar Arora, Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States, Department of Biology, Point Loma 20 77 Babasaheb Bhimrao Ambedkar Nazarene University, San Diego, CA, United States 21 University, India 78 22 79 Reviewed by: The capability of microorganisms to alter metal speciation offers potential for 23 80 Ramprasad E.V.V., the development of new strategies for immobilization of toxic metals in the 24 University of Hyderabad, India 81 25 Bärbel Ulrike Fösel, environment. -
Electronic Supplementary Information
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2019 Electronic Supplementary Information Microbial community and antibiotic resistance profiles of biomass and effluent are distinctly affected by antibiotic addition to an anaerobic membrane bioreactor Ali Zarei-Baygi*, Moustapha Harb#,*, Phillip Wang*, Lauren Stadler^, and Adam L. Smith*† * Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA 90089, USA # Department of Civil and Environmental Engineering, Lebanese American University, 309 Bassil Building, Byblos, Lebanon ^ Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, Houston, TX 77005, USA †Corresponding author (Adam L. Smith) Phone: +1 213.740.0473 Email: [email protected] Number of pages: 15 Number of figures: 6 Number of tables: 6 S1 Quantification of antibiotics by LC-MS For antibiotics quantification, 10 mL samples were collected for each sampling time point from the influent and effluent of the AnMBR. Both collected samples and standard solutions were filtered through 0.2 µm PTFE syringe filters (Whatman) using 10 mL syringes with Luer lock tips and stored in certified 2 mL amber LC vials (Agilent) at 4 ºC refrigerator for no more than 3 days prior to analysis. Stock solutions of sulfamethoxazole and erythromycin were prepared in HPLC-grade methanol at concentrations of 20 mg/L and stored at -20 ºC. Ampicillin stock solution was prepared in HPLC-grade water at 4 mg/L due to its lack of solubility in methanol and stored at 4 ºC. For each antibiotic, a six-point standard calibration curve was constructed within the appropriate range (i.e., 0.1-30 µg/L to target effluent antibiotics and 30- 400 µg/L to target influent antibiotics). -
UC Berkeley UC Berkeley Electronic Theses and Dissertations
UC Berkeley UC Berkeley Electronic Theses and Dissertations Title Corrinoid Cross-Feeding in the Microbial World Permalink https://escholarship.org/uc/item/2z66b95b Author Dirks, Erica Christine Publication Date 2014 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California Corrinoid Cross-Feeding in the Microbial World By Erica Christine Dirks A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Microbiology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Michiko E. Taga, Chair Professor John D. Coates Professor David Savage Professor Nicole King Fall 2014 Acknowledgements This work would not have been possible without the generous and kind support of many people over the past seven years. To all of my collaborators and mentors I’ve met along the way, especially the members of the Taga lab, a million thanks for all of the advice, discussions, and guidance. Your unselfish willingness to help continues to amaze and inspire me. Working with you has been a true gift. To Shan, I’ve learned so much from you. I wish you every happiness, and I will always think of you as my big sister in science. To Steve, it’s meant so much to me to have you on my side. Your breadth of knowledge astounds me. I hope you never stop telling stories. To Patrick, you are a true friend, and I would have never gotten through without you. To Jerome, together, you know we can defeat the zombie hordes. Thanks for all the car rides! To Mark, for pushing me to go further than I ever imagined I could. -
Acidaminococcus Provencensis Sp. Nov., a New Bacterium Isolated from a Fresh Human Stool Specimen
NEW SPECIES Acidaminococcus provencensis sp. nov., a new bacterium isolated from a fresh human stool specimen T. Takakura1,2, H. Anani3, A. Fadlane2, A. Fontanini2, D. Raoult2,3 and J. Y. Bou Khalil2 1) Hitachi High-Technologies Corporation, Analytical & Medical Solution Business Group, Ibaraki-ken, Japan, 2) Institut Hospitalo-Universitaire Méditerranée- Infection, Marseille, France and 3) Aix-Marseille Université, Institut de Recherche pour le Developpement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France Abstract Acidaminococcus provencensis strain Marseille-P4266T (= CSURP4266T) is a new species isolated from a fresh human stool specimen. © 2019 The Author(s). Published by Elsevier Ltd. Keywords: Acidaminococcus provencensis, Culturomics, Microbiota, New species, Taxonogenomics, TM4000, Stool Original Submission: 17 May 2019; Accepted: 5 June 2019 Article published online: 14 June 2019 imported into MALDI BIOTYPER 3.0 software (Bruker Dal- Corresponding author: J.Y. Bou Khalil, MEPHI, Institut Hospitalo- tonics) and analysed against the main spectra of the bacteria Universitaire Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France. included in two databases (Bruker and the constantly updated E-mail: [email protected] MEPHI databases: https://www.mediterranee-infection.com/ urms-data-base/). The study was validated by the ethics com- mittee of the Institut Fédératif de Recherche IFR48 under number 09-022. Initial growth was obtained after 72 h of Introduction culture in Colombia agar enriched with 5% sheep’s blood (bioMérieux, Marcy l’Etoile, France) in strict anaerobic con- ditions at 37°C. Culturomics is a concept that involves the development of different culture conditions to enlarge our knowledge of the human microbiota through the discovery of previously uncul- Phenotypic characteristics tured bacteria [1–4]. -
Electrochemical Startup Increases 1,3-Propanediol Titers in Mixed-Culture Glycerol Fermentations
G Model PRBI-10464; No. of Pages 10 ARTICLE IN PRESS Process Biochemistry xxx (2015) xxx–xxx Contents lists available at ScienceDirect Process Biochemistry jo urnal homepage: www.elsevier.com/locate/procbio Electrochemical startup increases 1,3-propanediol titers in mixed-culture glycerol fermentations a,∗ a,b a Nikolaos Xafenias , MarySandra Oluchi Anunobi , Valeria Mapelli a Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden b School of Engineering, University of Aberdeen, Aberdeen AB243 UE, United Kingdom a r a t i b s c t l e i n f o r a c t Article history: In this study we investigated the use of electric potential to bioelectrochemically ferment glycerol, a Received 13 May 2015 cheap by-product of biodiesel production, into valuable 1,3-propanediol (1,3-PDO). The 1,3-PDO pro- Received in revised form 7 June 2015 duction rates were increased up to 6 times in electrofermentations, compared to non-electrochemical Accepted 22 June 2015 fermentations, and high concentrations up to 42 g 1,3-PDO/l were achieved in fed-batch mode. Extensive Available online xxx growth of the well-known 1,3-PDO producers Clostridiaceae (55–57%) was observed when an appro- priate potential (−1.1 V vs. SHE) was constantly applied since the start. Potential propionate producers Keywords: (Veillonellaceae) were also among the dominant families (20–21%); however, surprisingly enough, propio- 1,3-Propanediol nate production was not observed. On the contrary, Clostridiaceae were absent, Veillonellaceae dominated Bioelectrochemical systems Bioelectrosynthesis (56–72%), and propionate was produced when electric potential was not sufficient for current produc- Fermentation tion since the beginning. -
Thermanaerovibrio Acidaminovorans Gen
[nternationd Journal ofSystematic Bacterio/ogy (1999), 49,969-974 Printed in Great Britain Phylogenetic relationships of three amino-acid-utilizing anaerobes, Selenomonas acidaminovorans, 'Selenomonas acidaminophila ' and Eubacterium acidaminophilum, as inferred from partial 16s rDNA nucleotide sequences and proposal of Thermanaerovibrio acidaminovorans gen. nov., comb. nov. and Anaeromusa acidaminophila gen. nov., comb. nov. H. Sandra Baena,lr2 Marie-LaureFardeau,' T. S. WOO,^ Bernard Ollivier,l Marc Labat' and Bharat K. C. Pate13 Author for correspondence: Bharat K. C. Patel. Tel: +61 417 726 671. Fax: +61 7 3875 7656. e-mail : [email protected] 1 Laboratoire ORSTOM de 16s rRNA gene sequences of three previously described amino-acid-fermenting Microbiologie des anaerobes, Selenomonas acidaminovorans, 'Selenomonas acidaminophila and AnaBrobies, Universite de Provence, CESB-ESILCase Eubacterium acidaminophilum, were determined. All three were found to 925,163 Avenue de cluster within the Clostridium and related genera of the subphylum of the Luminy, 13288 Marseille Gram-positive bacteria. The thermophile, S. acidaminovorans, formed ap Cedex 9, France individual line of descent and was equidistantly placed between 2 Departamento de Biologia, Dethiosulfovibriopeptidovorans and Anaerobaculum íhermoterrenum Pontificia Universidad Javeriana, PO6 56710, (similarity of 85%), both of which also form single lines of descent. '5. SantaFe de Bogota, acidaminophila ' was related to Clostridium quercicolum, a member of cluster Colombia IX, with a similarity of 90%, whereas E. acidaminophilum was closely related School of Biomolecular to Clostridium litorale (similarity of 96%) as a member of cluster XI. Based on and Biomedical Sciences, the phylogenetic data presented in this report and the phenotypic descriptions Faculty of Science, Griffith University, Brisbane, of these bacteria published previously, it is recommended that S. -
Biodegradation Treatment of Petrochemical Wastewaters
UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA VEGETAL Biodegradation treatment of petrochemical wastewaters Catarina Isabel Nunes Alexandre Dissertação Mestrado em Microbiologia Aplicada Orientadores Doutora Sandra Sanches Professora Doutora Lélia Chambel 2015 Biodegradation treatment of petrochemical wastewaters Catarina Isabel Nunes Alexandre 2015 This thesis was fully performed at the Institute of Experimental and Technologic Biology (IBET) of Instituto de Tecnologia Química e Bioquímica (ITQB) under the direct supervision of Drª Sandra Sanches in the scope of the Master in Applied Microbiology of the Faculty of Sciences of the University of Lisbon. Prof. Drª Lélia Chambel was the internal designated supervisor in the scope of the Master in Applied Microbiology of the Faculty of Sciences of the University of Lisbon. Agradecimentos Gostaria de agradecer a todas as pessoas que estiveram directamente ou indirectamente envolvidas na execução da minha tese de mestrado, pois sem eles a sua realização não teria sido possível. Queria começar por agradecer à Doutora Sandra Sanches, que se demonstrou sempre disponível para esclarecer dúvidas quando precisei, e que fez questão de me ensinar de forma rigorosa e exigente. À Doutora Maria Teresa Crespo, que assim que lhe pedi para me orientar me disse que sim imediatamente, fez questão de me treinar em vários contextos e sempre estimulou o meu envolvimento nas rotinas do laboratório. À Professora Doutora Lélia Chambel, que sempre me esclareceu dúvidas sobre processos burocráticos, me deu conselhos quando eu mais precisei e que me apoiou durante toda a minha tese. Queria também agradecer à Doutora Dulce Brito, que sempre se mostrou disponível para ajudar quando a nossa equipa mais precisava dela, e sempre me ajudou a realizar as tarefas mais básicas do meu trabalho até eu ter ganho a minha autonomia no laboratório.