Applications and Systematics of Bacillus and Relatives
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Desulfuribacillus Alkaliarsenatis Gen. Nov. Sp. Nov., a Deep-Lineage
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Extremophiles (2012) 16:597–605 DOI 10.1007/s00792-012-0459-7 ORIGINAL PAPER Desulfuribacillus alkaliarsenatis gen. nov. sp. nov., a deep-lineage, obligately anaerobic, dissimilatory sulfur and arsenate-reducing, haloalkaliphilic representative of the order Bacillales from soda lakes D. Y. Sorokin • T. P. Tourova • M. V. Sukhacheva • G. Muyzer Received: 10 February 2012 / Accepted: 3 May 2012 / Published online: 24 May 2012 Ó The Author(s) 2012. This article is published with open access at Springerlink.com Abstract An anaerobic enrichment culture inoculated possible within a pH range from 9 to 10.5 (optimum at pH with a sample of sediments from soda lakes of the Kulunda 10) and a salt concentration at pH 10 from 0.2 to 2 M total Steppe with elemental sulfur as electron acceptor and for- Na? (optimum at 0.6 M). According to the phylogenetic mate as electron donor at pH 10 and moderate salinity analysis, strain AHT28 represents a deep independent inoculated with sediments from soda lakes in Kulunda lineage within the order Bacillales with a maximum of Steppe (Altai, Russia) resulted in the domination of a 90 % 16S rRNA gene similarity to its closest cultured Gram-positive, spore-forming bacterium strain AHT28. representatives. On the basis of its distinct phenotype and The isolate is an obligate anaerobe capable of respiratory phylogeny, the novel haloalkaliphilic anaerobe is suggested growth using elemental sulfur, thiosulfate (incomplete as a new genus and species, Desulfuribacillus alkaliar- T T reduction) and arsenate as electron acceptor with H2, for- senatis (type strain AHT28 = DSM24608 = UNIQEM mate, pyruvate and lactate as electron donor. -
CALIFORNIA STATE UNIVERSITY, NORTHRIDGE Comparative
CALIFORNIA STATE UNIVERSITY, NORTHRIDGE Comparative Genomics and Epigenomics of Sporosarcina ureae A thesis submitted in partial fulfillment of the requirement for the degree of Master of Science in Biology By Andrew Oliver August 2016 The thesis of Andrew Oliver is approved by: _________________________________________ ____________ Sean Murray, Ph.D. Date _________________________________________ ____________ Gilberto Flores, Ph.D. Date _________________________________________ ____________ Kerry Cooper, Ph.D., Chair Date California State University, Northridge ii Acknowledgments First and foremost, a special thanks to my advisor, Dr. Kerry Cooper, for his advice and, above all, his patience. If I can be half the scientist you are someday, I would be thrilled. I would like to also thank everyone in the Cooper lab, especially my colleagues Courtney Sams and Tabitha Bayangnos. It was a privilege to work along side you. More thanks to my committee members, Dr. Gilberto Flores and Dr. Sean Murray. Dr. Flores, you were instrumental in guiding me to ask the right questions regarding bacterial taxonomy. Dr. Murray, your contributions to my graduate studies would make this section run on for pages. I thank you for taking me under your wing from the beginning. Acknowledgement and thanks to the Baresi lab, especially Dr. Larry Baresi and Tania Kurbessoian for their partnership in this research. Also to Bernardine Pregerson for all the work that lays at the foundation of this study. This research would not be what it is without the help of my childhood friend, Matthew Kay. You wrote programs, taught me coding languages, and challenged me to go digging for answers to very difficult questions. -
Fontibacillus Phaseoli Sp. Nov. Isolated from Phaseolus Vulgaris Nodules
Antonie van Leeuwenhoek (2014) 105:23–28 DOI 10.1007/s10482-013-0049-4 ORIGINAL PAPER Fontibacillus phaseoli sp. nov. isolated from Phaseolus vulgaris nodules Jose´ David Flores-Fe´lix • Rebeca Mulas • Martha-Helena Ramı´rez-Bahena • Marı´a Jose´ Cuesta • Rau´l Rivas • Javier Bran˜as • Daniel Mulas • Fernando Gonza´lez-Andre´s • Alvaro Peix • Encarna Vela´zquez Received: 26 July 2013 / Accepted: 3 October 2013 / Published online: 12 October 2013 Ó Springer Science+Business Media Dordrecht 2013 Abstract A bacterial strain, designated BAPVE7BT, Growth was observed to be supported by many carbo- was isolated from root nodules of Phaseolus vulgaris in hydrates and organic acids as carbon source. MK-7 was Spain. Phylogenetic analysis based on its 16S rRNA gene identified as the predominant menaquinone and the major sequence placed the isolate into the genus Fontibacillus fatty acid (43.7 %) as anteiso-C15:0, as occurs in the other with Fontibacillus panacisegetis KCTC 13564T its species of the genus Fontibacillus.StrainBAPVE7BT closest relative with 97.1 % identity. The isolate was displayed a complex lipid profile consisting of diphos- observed to be a Gram-positive, motile and sporulating phatidylglycerol, phosphatidylglycerol, four glycolipids, rod. The catalase test was negative and oxidase was four phospholipids, two lipids, two aminolipids and weak. The strain was found to reduce nitrate to nitrite and an aminophospholipid. Mesodiaminopimelic acid was to produce b-galactosidase but the production of gela- detected in the peptidoglycan. The G?Ccontentwas tinase, caseinase, urease, arginine dehydrolase, ornithine determined to be 45.6 mol% (Tm). Phylogenetic, che- or lysine decarboxylase was negative. -
Thèses Traditionnelles
UNIVERSITÉ D’AIX-MARSEILLE FACULTÉ DE MÉDECINE DE MARSEILLE ECOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTÉ THÈSE Présentée et publiquement soutenue devant LA FACULTÉ DE MÉDECINE DE MARSEILLE Le 23 Novembre 2017 Par El Hadji SECK Étude de la diversité des procaryotes halophiles du tube digestif par approche de culture Pour obtenir le grade de DOCTORAT d’AIX-MARSEILLE UNIVERSITÉ Spécialité : Pathologie Humaine Membres du Jury de la Thèse : Mr le Professeur Jean-Christophe Lagier Président du jury Mr le Professeur Antoine Andremont Rapporteur Mr le Professeur Raymond Ruimy Rapporteur Mr le Professeur Didier Raoult Directeur de thèse Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR 7278 Directeur : Pr. Didier Raoult 1 Avant-propos : Le format de présentation de cette thèse correspond à une recommandation de la spécialité Maladies Infectieuses et Microbiologie, à l’intérieur du Master des Sciences de la Vie et de la Santé qui dépend de l’Ecole Doctorale des Sciences de la Vie de Marseille. Le candidat est amené à respecter des règles qui lui sont imposées et qui comportent un format de thèse utilisé dans le Nord de l’Europe et qui permet un meilleur rangement que les thèses traditionnelles. Par ailleurs, la partie introduction et bibliographie est remplacée par une revue envoyée dans un journal afin de permettre une évaluation extérieure de la qualité de la revue et de permettre à l’étudiant de commencer le plus tôt possible une bibliographie exhaustive sur le domaine de cette thèse. Par ailleurs, la thèse est présentée sur article publié, accepté ou soumis associé d’un bref commentaire donnant le sens général du travail. -
Paenibacillaceae Cover
The Family Paenibacillaceae Strain Catalog and Reference • BGSC • Daniel R. Zeigler, Director The Family Paenibacillaceae Bacillus Genetic Stock Center Catalog of Strains Part 5 Daniel R. Zeigler, Ph.D. BGSC Director © 2013 Daniel R. Zeigler Bacillus Genetic Stock Center 484 West Twelfth Avenue Biological Sciences 556 Columbus OH 43210 USA www.bgsc.org The Bacillus Genetic Stock Center is supported in part by a grant from the National Sciences Foundation, Award Number: DBI-1349029 The author disclaims any conflict of interest. Description or mention of instrumentation, software, or other products in this book does not imply endorsement by the author or by the Ohio State University. Cover: Paenibacillus dendritiformus colony pattern formation. Color added for effect. Image courtesy of Eshel Ben Jacob. TABLE OF CONTENTS Table of Contents .......................................................................................................................................................... 1 Welcome to the Bacillus Genetic Stock Center ............................................................................................................. 2 What is the Bacillus Genetic Stock Center? ............................................................................................................... 2 What kinds of cultures are available from the BGSC? ............................................................................................... 2 What you can do to help the BGSC ........................................................................................................................... -
5868 Pitombo
GCB Bioenergy (2016) 8, 867–879, doi: 10.1111/gcbb.12284 Exploring soil microbial 16S rRNA sequence data to increase carbon yield and nitrogen efficiency of a bioenergy crop 1,2,3 3 1 LEONARDO M. PITOMBO ,JANAINAB.DOCARMO , MATTIAS DE HOLLANDER , RAFFAELLA ROSSETTO4 , MARYEIMY V. LOP E Z 5 , HEITOR CANTARELLA2 and EIKO E. KURAMAE1 1Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO/KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands, 2Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Bar~ao de Itapura 1481, 13020-902 Campinas, SP, Brazil, 3Department of Environmental Sciences, Federal University of S~ao Carlos (UFSCar), Rod. Jo~ao Leme dos Santos Km 110, 18052-780 Sorocaba, SP, Brazil, 4Polo Piracicaba, Ag^encia Paulista de Tecnologia (APTA), Rodovia SP 127 km 30, 13400-970 Piracicaba, SP, Brazil, 5Department of Soil Science, University of S~ao Paulo (ESALQ/USP), Avenida Padua Dias 11, CEP 13418-260 Piracicaba, SP, Brazil Abstract Crop residues returned to the soil are important for the preservation of soil quality, health, and biodiversity, and they increase agriculture sustainability by recycling nutrients. Sugarcane is a bioenergy crop that produces huge amounts of straw (also known as trash) every year. In addition to straw, the ethanol industry also gener- ates large volumes of vinasse, a liquid residue of ethanol production, which is recycled in sugarcane fields as fertilizer. However, both straw and vinasse have an impact on N2O fluxes from the soil. Nitrous oxide is a greenhouse gas that is a primary concern in biofuel sustainability. Because bacteria and archaea are the main drivers of N redox processes in soil, in this study we propose the identification of taxa related with N2O fluxes by combining functional responses (N2O release) and the abundance of these microorganisms in soil. -
Compile.Xlsx
Silva OTU GS1A % PS1B % Taxonomy_Silva_132 otu0001 0 0 2 0.05 Bacteria;Acidobacteria;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un; otu0002 0 0 1 0.02 Bacteria;Acidobacteria;Acidobacteriia;Solibacterales;Solibacteraceae_(Subgroup_3);PAUC26f; otu0003 49 0.82 5 0.12 Bacteria;Acidobacteria;Aminicenantia;Aminicenantales;Aminicenantales_fa;Aminicenantales_ge; otu0004 1 0.02 7 0.17 Bacteria;Acidobacteria;AT-s3-28;AT-s3-28_or;AT-s3-28_fa;AT-s3-28_ge; otu0005 1 0.02 0 0 Bacteria;Acidobacteria;Blastocatellia_(Subgroup_4);Blastocatellales;Blastocatellaceae;Blastocatella; otu0006 0 0 2 0.05 Bacteria;Acidobacteria;Holophagae;Subgroup_7;Subgroup_7_fa;Subgroup_7_ge; otu0007 1 0.02 0 0 Bacteria;Acidobacteria;ODP1230B23.02;ODP1230B23.02_or;ODP1230B23.02_fa;ODP1230B23.02_ge; otu0008 1 0.02 15 0.36 Bacteria;Acidobacteria;Subgroup_17;Subgroup_17_or;Subgroup_17_fa;Subgroup_17_ge; otu0009 9 0.15 41 0.99 Bacteria;Acidobacteria;Subgroup_21;Subgroup_21_or;Subgroup_21_fa;Subgroup_21_ge; otu0010 5 0.08 50 1.21 Bacteria;Acidobacteria;Subgroup_22;Subgroup_22_or;Subgroup_22_fa;Subgroup_22_ge; otu0011 2 0.03 11 0.27 Bacteria;Acidobacteria;Subgroup_26;Subgroup_26_or;Subgroup_26_fa;Subgroup_26_ge; otu0012 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_5;Subgroup_5_or;Subgroup_5_fa;Subgroup_5_ge; otu0013 1 0.02 13 0.32 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_or;Subgroup_6_fa;Subgroup_6_ge; otu0014 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_un;Subgroup_6_un;Subgroup_6_un; otu0015 8 0.13 30 0.73 Bacteria;Acidobacteria;Subgroup_9;Subgroup_9_or;Subgroup_9_fa;Subgroup_9_ge; -
Bacillus Spp
Characterizing the culturable bacteria isolated from imported, ready-to-eat (RTE) foods for their ability to control Listeria monocytogenes by Krishna Sen Gelda A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Master of Science in Food Science Guelph, Ontario, Canada © Krishna Sen Gelda, September 2019 ABSTRACT CHARACTERIZING THE CULTURABLE BACTERIA ISOLATED FROM IMPORTED, READY-TO-EAT (RTE) FOODS FOR THEIR ABILITY TO CONTROL LISTERIA MONOCYTOGENES Krishna Sen Gelda Advisor: University of Guelph, 2019 Dr. Jeff Farber Listeria monocytogenes, an important foodborne pathogen, remains a significant threat to public health. This thesis investigated the culturable microbiota of select imported, RTE foods to see whether the existing bacterial microflora could inactivate, inhibit the growth and/or cause a reduction in the virulence of L. monocytogenes. Among all the foods tested (dried apple slices, cumin seeds, date fruits, fennel seeds, pistachios, pollen, raisins and seaweed), the date fruit microbiota displayed the most promise for harbouring antagonistic properties against L. monocytogenes. Of the 191 isolates recovered from five different date fruits, 36 (19%) produced zones of inhibition against L. monocytogenes that ranged from 0.3 to 5.8 mm. The inhibitory strains were all identified as Bacillus spp. Among those Bacillus spp. that were tested for their ability to inhibit PrfA, all caused a significant reduction in the activation of the PrfA protein (p-value < 0.05). In addition, the anti-Listeria compound(s) produced by B. altitudinis DS11 were found to be proteinaceous in nature, acid and alkali-tolerant and resistant to temperature treatments up to 100oC. -
Department of Microbiology
SRINIVASAN COLLEGE OF ARTS & SCIENCE (Affiliated to Bharathidasan University, Trichy) PERAMBALUR – 621 212. DEPARTMENT OF MICROBIOLOGY Course : M.Sc Year: I Semester: II Course Material on: MICROBIAL PHYSIOLOGY Sub. Code : P16MB21 Prepared by : Ms. R.KIRUTHIGA, M.Sc., M.Phil., PGDHT ASSISTANT PROFESSOR / MB Month & Year : APRIL – 2020 MICROBIAL PHYSIOLOGY Unit I Cell structure and function Bacterial cell wall - Biosynthesis of peptidoglycan - outer membrane, teichoic acid – Exopolysaccharides; cytoplasmic membrane, pili, fimbriae, S-layer. Transport mechanisms – active, passive, facilitated diffusions – uni, sym, antiports. Electron carriers – artificial electron donors – inhibitors – uncouplers – energy bond – phosphorylation. Unit II Microbial growth Bacterial growth - Phases of growth curve – measurement of growth – calculations of growth rate – generation time – synchronous growth – induction of synchronous growth, synchrony index – factors affecting growth – pH, temperature, substrate and osmotic condition. Survival at extreme environments – starvation – adaptative mechanisms in thermophilic, alkalophilic, osmophilic and psychrophilic. Unit III Microbial pigments and photosynthesis Autotrophs - cyanobacteria - photosynthetic bacteria and green algae – heterotrophs – bacteria, fungi, myxotrophs. Brief account of photosynthetic and accessory pigments – chlorophyll – fluorescence, phosphorescence - bacteriochlorophyll – rhodopsin – carotenoids – phycobiliproteins. Unit IV Carbon assimilation Carbohydrates – anabolism – autotrophy – -
Isolation and Diversity of Sediment Bacteria in The
bioRxiv preprint doi: https://doi.org/10.1101/638304; this version posted May 14, 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 4.0 International license. 1 Isolation and Diversity of Sediment Bacteria in the 2 Hypersaline Aiding Lake, China 3 4 Tong-Wei Guan, Yi-Jin Lin, Meng-Ying Ou, Ke-Bao Chen 5 6 7 Institute of Microbiology, Xihua University, Chengdu 610039, P. R. China. 8 9 Author for correspondence: 10 Tong-Wei Guan 11 Tel/Fax: +86 028 87720552 12 E-mail: [email protected] 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 bioRxiv preprint doi: https://doi.org/10.1101/638304; this version posted May 14, 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 4.0 International license. 29 Abstract A total of 343 bacteria from sediment samples of Aiding Lake, China, were isolated using 30 nine different media with 5% or 15% (w/v) NaCl. The number of species and genera of bacteria recovered 31 from the different media significantly varied, indicating the need to optimize the isolation conditions. 32 The results showed an unexpected level of bacterial diversity, with four phyla (Firmicutes, 33 Actinobacteria, Proteobacteria, and Rhodothermaeota), fourteen orders (Actinopolysporales, 34 Alteromonadales, Bacillales, Balneolales, Chromatiales, Glycomycetales, Jiangellales, Micrococcales, 35 Micromonosporales, Oceanospirillales, Pseudonocardiales, Rhizobiales, Streptomycetales, and 36 Streptosporangiales), including 17 families, 41 genera, and 71 species. -
Abstract Tracing Hydrocarbon
ABSTRACT TRACING HYDROCARBON CONTAMINATION THROUGH HYPERALKALINE ENVIRONMENTS IN THE CALUMET REGION OF SOUTHEASTERN CHICAGO Kathryn Quesnell, MS Department of Geology and Environmental Geosciences Northern Illinois University, 2016 Melissa Lenczewski, Director The Calumet region of Southeastern Chicago was once known for industrialization, which left pollution as its legacy. Disposal of slag and other industrial wastes occurred in nearby wetlands in attempt to create areas suitable for future development. The waste creates an unpredictable, heterogeneous geology and a unique hyperalkaline environment. Upgradient to the field site is a former coking facility, where coke, creosote, and coal weather openly on the ground. Hydrocarbons weather into characteristic polycyclic aromatic hydrocarbons (PAHs), which can be used to create a fingerprint and correlate them to their original parent compound. This investigation identified PAHs present in the nearby surface and groundwaters through use of gas chromatography/mass spectrometry (GC/MS), as well as investigated the relationship between the alkaline environment and the organic contamination. PAH ratio analysis suggests that the organic contamination is not mobile in the groundwater, and instead originated from the air. 16S rDNA profiling suggests that some microbial communities are influenced more by pH, and some are influenced more by the hydrocarbon pollution. BIOLOG Ecoplates revealed that most communities have the ability to metabolize ring structures similar to the shape of PAHs. Analysis with bioinformatics using PICRUSt demonstrates that each community has microbes thought to be capable of hydrocarbon utilization. The field site, as well as nearby areas, are targets for habitat remediation and recreational development. In order for these remediation efforts to be successful, it is vital to understand the geochemistry, weathering, microbiology, and distribution of known contaminants. -
Biodiversity of Moderately Halophilic Bacteria in Hypersaline Habitats in Egypt
J. Gen. Appl. Microbiol., 52, 63–72 (2006) Full Paper Biodiversity of moderately halophilic bacteria in hypersaline habitats in Egypt Hanan Ghozlan,* Hisham Deif, Rania Abu Kandil, and Soraya Sabry Department of Botany, Faculty of Science, University of Alexandria, Moharrem Bey, Egypt (Received January 19, 2005; Accepted November 24, 2005) Screening bacteria from different saline environments in Alexandria. Egypt, lead to the isolation of 76 Gram-negative and 14 Gram-positive moderately halophilic bacteria. The isolates were characterized taxonomically for a total of 155 features. These results were analyzed by numerical techniques using simple matching coefficient (SSM) and the clustering was achieved by the un- weighed pair-group method of association (UPGMA). At 75% similarity level the Gram-negative bacteria were clustered in 7 phena in addition to one single isolate, whereas 4 phena repre- sented the Gram-positive. Based on phenotypic characteristics, it is suggested that the Gram- negative bacteria belong to the genera Pseudoalteromonas, Flavobacterium, Chromohalobacter, Halomonas and Salegentibacter, in addition to the non-identified single isolate. The Gram-posi- tive bacteria are proposed to belong to the genera Halobacillus, Salinicoccus, Staphylococcus and Tetragenococcus. This study provides the first publication on the biodiversity of moderately halophilic bacteria in saline environments in Alexandria, Egypt. Key Words——moderate halophiles; numerical taxonomy; saline environments Introduction physiological adaptation to highly saline concentra- tions and their ecology (Martinez-Canovas et al., 2004; Moderately halophilic bacteria are microorganisms Tokunaga et al., 2004; Ventosa et al., 1998a, b). that can grow optimally in media containing between Hypersaline environments in Egypt are neglected 3% and 15% (w/v) salt (Lichfield, 2002).