Effects of Ph and Microbial Composition on Odour in Food Waste
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EXPERIMENTAL STUDIES on FERMENTATIVE FIRMICUTES from ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, and THEIR GEOCHEMICAL IMPACTS By
EXPERIMENTAL STUDIES ON FERMENTATIVE FIRMICUTES FROM ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, AND THEIR GEOCHEMICAL IMPACTS By JESSICA KEE EUN CHOI A dissertation submitted to the School of Graduate Studies Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Microbial Biology Written under the direction of Nathan Yee And approved by _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ New Brunswick, New Jersey October 2017 ABSTRACT OF THE DISSERTATION Experimental studies on fermentative Firmicutes from anoxic environments: isolation, evolution and their geochemical impacts by JESSICA KEE EUN CHOI Dissertation director: Nathan Yee Fermentative microorganisms from the bacterial phylum Firmicutes are quite ubiquitous in subsurface environments and play an important biogeochemical role. For instance, fermenters have the ability to take complex molecules and break them into simpler compounds that serve as growth substrates for other organisms. The research presented here focuses on two groups of fermentative Firmicutes, one from the genus Clostridium and the other from the class Negativicutes. Clostridium species are well-known fermenters. Laboratory studies done so far have also displayed the capability to reduce Fe(III), yet the mechanism of this activity has not been investigated -
Bacillus Massiliogorillae Sp. Nov
Standards in Genomic Sciences (2013) 9:93-105 DOI:10.4056/sigs.4388124 Non-contiguous finished genome sequence and description of Bacillus massiliogorillae sp. nov. Mamadou Bhoye Keita1, Seydina M. Diene1, Catherine Robert1, Didier Raoult1,2, Pierre- Edouard Fournier1, and Fadi Bittar1* 1URMITE, Aix-Marseille Université, Faculté de Médecine, Marseille, France 2King Fahad Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia *Correspondence: Fadi Bittar ([email protected]) Keywords: Bacillus massiliogorillae, genome, culturomics, taxonogenomics Strain G2T sp. nov. is the type strain of B. massiliogorillae, a proposed new species within the genus Bacillus. This strain, whose genome is described here, was isolated in France from the fecal sample of a wild western lowland gorilla from Cameroon. B. massiliogorillae is a facul- tative anaerobic, Gram-variable, rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,431,633 bp long genome (1 chromosome but no plasmid) contains 5,179 protein-coding and 98 RNA genes, including 91 tRNA genes. Introduction Strain G2T (= CSUR P206 = DSM 26159) is the type Here we present a summary classification and a strain of B. massiliogorillae sp. nov. This bacterium set of features for B. massiliogorillae sp. nov. strain is a Gram-variable, facultatively anaerobic, indole- G2T together with the description of the complete negative bacillus having rounded-ends. It was iso- genome sequence and annotation. These charac- lated from the stool sample of Gorilla gorilla goril- teristics support the circumscription of the spe- la as part of a “culturomics” study aiming at culti- cies B. -
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ARTICLE Isolation and identification of halophilic and halotolerant bacteria from the sediments of the Qeshm Island mangrove forest Pegah Javid,1 Hassan Zadabbas Shahabadi,2 Homeyra Amirkhani,3 Narges Amrollahi Biuki,1,4* Mohammad Sharif Ranjbar1 1Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar ‘Abbas; 2Department of Marine Biology, Faculty of Marine Sciences, Chabahar Maritime University, Chabahar; 3Microbiology Department; Food, Drug and Standard Bureau of Qeshm Free Zone, Qeshm Island; 4Department of Modern Technology, Mangrove Forest Research Center, University of Hormozgan, Bandar ‘Abbas, Iran ABSTRACT Due to specific environmental and ecological conditions, mangrove forests are known as marine transitional zones between sea and land, and, as such, they host organisms with high ecological plasticity. The mangrove forests of Qeshm Island (Iran) are relatively pristine habitats and represent an ideal target for investigating patterns of either aquatic or benthic biodiversity. To provide insights on microbial diversity in this area, nineteen halophilic and halotolerant bacteria were isolated from the sediments in 2017 during low tide. The extracted bacterial strains were studied morphologically by streaking, initial observation of colonies and bacterial staining, and characterized using a battery of biochemical tests including KOH, MR, VP, urease, TSI, S/I/M, Mac, LIA, ODC, ADH, oxidase, catalase, and tryptophan deaminase. The optimum growth of halophilic bacteria was observed in salt concentrations from 5 to 20% NaCl, whereas the extreme halophilic Gram-positive strain grew in salt concentration of up to 30% NaCl. Molecular analyses were also carried out on four halophilic strains and one extreme halophilic gram-positive bacteria. -
Potencialidades Del Género Bacillus En La Promoción Del Crecimiento Vegetal Y El Control Biológico De Hongos Fitopatógenos Revista CENIC
Revista CENIC. Ciencias Biológicas ISSN: 0253-5688 [email protected] Centro Nacional de Investigaciones Científicas Cuba Tejera-Hernández, Berto; Rojas-Badía, Marcia M.; Heydrich-Pérez, Mayra Potencialidades del género Bacillus en la promoción del crecimiento vegetal y el control biológico de hongos fitopatógenos Revista CENIC. Ciencias Biológicas, vol. 42, núm. 3, septiembre-diciembre, 2011, pp. 131-138 Centro Nacional de Investigaciones Científicas Ciudad de La Habana, Cuba Disponible en: http://www.redalyc.org/articulo.oa?id=181222321004 Cómo citar el artículo Número completo Sistema de Información Científica Más información del artículo Red de Revistas Científicas de América Latina, el Caribe, España y Portugal Página de la revista en redalyc.org Proyecto académico sin fines de lucro, desarrollado bajo la iniciativa de acceso abierto Revista CENIC Ciencias Biológicas, Vol. 42, No. 3, pp. 131-138, septiembre-diciembre, 2011. Potencialidades del género Bacillus en la promoción del crecimiento vegetal y el control biológico de hongos fitopatógenos Berto Tejera-Hernández, Marcia M. Rojas-Badía y Mayra Heydrich-Pérez. Departamento de Microbiología y Virología, Facultad de Biología, Universidad de la Habana. Calle 25 No. 455 entre calles J e I, El Vedado, La Habana, Cuba. Recibido: 22 de noviembre de 2010 Aceptado: 7 de abril de 2011 Palabras clave: Bacillus, interacción planta-microorganismo, promoción del crecimiento vegetal, control biológico. Key words: Bacillus, plant-microbe interaction, plant growth promotion, biological control. RESUMEN. El presente trabajo es una revisión sobre el género Bacillus. Este género se encuentra ampliamente distribui- do en diversos ambientes como agua y suelo debido a su amplia versatilidad metabólica y la presencia de una estructura de resistencia: la endospora. -
Bacillus Subtilis Spores and Their Global Transcriptional Response During Spore Germination
Characterization of different types of radiation- and pressure-induced DNA damage in Bacillus subtilis spores and their global transcriptional response during spore germination Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Ralf Möller aus Suhl / Deutschland Characterization of different types of radiation- and pressure-induced DNA damage in Bacillus subtilis spores and their global transcriptional response during spore germination Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Ralf Möller aus Suhl 1. Referent: Prof. Dr. Dieter Jahn 2. Referent: Prof. Dr. Erko Stackebrandt eingereicht am: 26.09.2007 mündliche Prüfung (Disputation) am: 18.12.2007 Druckjahr 2008 Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Fakultät für Lebenswissenschaften, vertreten durch den Mentor der Arbeit, in folgenden Beiträgen vorab veröffentlicht: PUBLIKATIONEN Moeller, R., G. Horneck, R. Facius, and E. Stackebrandt. 2005. Role of pigmentation in protecting Bacillus sp. endospores against environmental UV radiation. FEMS Microbiol. Ecol. 51:231-236. Moeller, R., G. Horneck, P. Rettberg, H.-J. Mollenkopf, E. Stackebrandt, and W. L. Nicholson. 2006. A method for extracting RNA from dormant and germinating Bacillus subtilis strain 168 endospores. Curr. Microbiol. 53:227-231. Moeller, R., G. Horneck, U. Pogoda de la Vega, P. Rettberg, E. Stackebrandt, G. Reitz, R. -
The Influence of O2 Avaiability on the Growth of Fe(Iii) Reducing Bacteria in Coal Mine-Derived Acid Mine Drainage
THE INFLUENCE OF O2 AVAIABILITY ON THE GROWTH OF FE(III) REDUCING BACTERIA IN COAL MINE-DERIVED ACID MINE DRAINAGE A Thesis Presented to The Graduate Faculty of the University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Zachary Santangelo August, 2019 THE INFLUENCE OF O2 AVAIABILITY ON THE GROWTH OF FE(III) REDUCING BACTERIA IN COAL MINE-DERIVED ACID MINE DRAINAGE Zachary Santangelo Thesis Approved: Accepted: __________________________ __________________________ Advisor Interim Dean of the College Dr. John Senko Dr. Linda M. Subich __________________________ __________________________ Faculty Reader Dean of the Graduate School Dr. Teresa Cutright Dr. Chand Midha __________________________ __________________________ Faculty Reader Date Dr. Linda R. Barrett __________________________ Department Chair Dr. David N. Steer II ACKNOWLEDGEMENTS First, I would like to thank my advisor, Dr. John Senko, for pushing me and making me think about everything from every point of view. His research and ideas helped me think critically about research I never even considered. Dr. Senko constantly helped me become the best writer I could possibly be. I will always appreciate that in my work in the future. The members of my committee: Dr. Teresa Cutright and Dr. Linda Barrett, I offer my sincerest gratitude. I had a couple classes with Dr. Cutright, both of which I repeatedly thought back to when approaching my own research. She helped me not just think about problems, but truly understand what was happening. Dr. Barrett, I sincerely thank for her time in helping me move forward with my thesis, and making sure I knew what I was trying to explain properly. -
Characterization and Description of Heat-Tolerant Bacillus Species
Characterization and Descriptionof Heat-tolerant Bacillus species Isolated from Spacecraft Assembly Facility Kasthuri Venkateswaran,'? Masataka Satomi2, Shirley Chung', RogerKern', and Robert Koukol' 1 Planetary Protection Technologies, Jet Propulsion Laboratory, National Aeronautics and Space Administration, Pasadena, CA 91109, USA 2National Research Institute of Fisheries Science, Food Processing Division,2-12-4 Fukuura, Kanazawa-ku, Yokohama-City, Kanagawa236-8648, Japan. Author for correspondence: Kasthuri Venkateswaran ?Present address and Mailing address: Planetary Protection Technologies, Jet Propulsion Laboratory, National Aeronautics and Space Administration, 4800 Oak Grove Dr.,Pasadena, CA 91109, USA Tel: (818) 393-1481; Fax: (818) 393-4176 E-mail: [email protected] Forward contamination of samples with cells or biomarkers from Earth would seriously compromise interpretation of results of a Space sample return mission. In ongoinginvestigations to map andarchive the microbial footprints in various componentsof spacecraft and itsaccessories, wehave examined the microbial populations of the Jet Propulsion Laboratory, Spacecraft Assembly Facility (SAF). We have exposed witness plates that are made up of spacecraft materials and or painted with spacecraft qualified paints for -7 to 9 months. In the initial studies reported here, we have examined the total cultivable aerobic heterotrophs,and heat- tolerant (8OoC for 15-min.) spore-formers. The resultsshowed that the witness plates coated with spacecraft qualified paints attracted more dust particles than the non- coated stainless steel witness plates. Among four paints tested, witness plates coated withNS43G (an off-white conductivepaint [silicate binder]) accumulated the highest number of particles, hence attracted more cultivable microbes and spore- formers. The microbiologicalexamination revealed that the SAF High Bay-1 harbors mainly Gram-positive microbes and mostly spore-forming Bacillus species. -
Dissimilatory Iron-Reducing and Endosporulating Bacteria
DISSIMILATORY IRON-REDUCING AND ENDOSPORULATING BACTERIA by ROB UCHE ONYENWOKE (Under the Direction of Juergen Wiegel) ABSTRACT This dissertation represents a diversified study of the biochemical, physiological, and genetic traits of members of the low G+C subdivision of the Gram-type positive bacteria, also known as the ‘Firmicutes’. The phylum ‘Firmicutes’ contains a diverse array of taxa that are not easily separated into coherent phylogenetic groups by any one physiological trait, such as endospore-formation or dissimilatory iron reduction. This dissertation considers numerous contemporary, and highly convergent in providing breadth and scope of the subject matter, methods of study. The principle aim was to examine the lineage ‘Firmicutes’ by a) a genomic study of the occurrence or absence of endosporulation genes in numerous members of the lineage, b) classic biochemical studies of the enzymes responsible for biotic iron reduction, and c) culture-dependent studies and isolations of various ‘Firmicutes’ to both identify new iron- reducers and better resolve the taxonomy of the lineage. The work with endosporulation genes has shown there might not be a distinct set of “endosporulation-specific” genes. This raises several new questions about this exceptionally complex process. The work described here on “ferric reductases” suggests there are enzymes capable of iron reduction that also have additional activities. The isolation of novel bacteria presented here have added to the diversity of the ‘Firmicutes’ but have also added to the -
Phylogenetic Relationships Between Bacillus Species and Related Genera Inferred from 16S Rdna Sequences
Brazilian Journal of Microbiology (2009) 40: 505-521 ISSN 1517-8382 PHYLOGENETIC RELATIONSHIPS BETWEEN BACILLUS SPECIES AND RELATED GENERA INFERRED FROM 16S RDNA SEQUENCES Wei Wang; Mi Sun * Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China Submitted: July 14, 2008; Returned to authors for corrections: October 06, 2008; Approved: May 04, 2009. ABSTRACT Neighbor-joining, maximum-parsimony, minimum-evolution, maximum-likelihood and Bayesian trees constructed based on 16S rDNA sequences of 181 type strains of Bacillus species and related taxa manifested nine phylogenetic groups. The phylogenetic analysis showed that Bacillus was not a monophyletic group. B. subtilis was in Group 1. Group 4, 6 and 8 respectively consisted of thermophiles, halophilic or halotolerant bacilli and alkaliphilic bacilli. Group 2, 4 and 8 consisting of Bacillus species and related genera demonstrated that the current taxonomic system did not agree well with the 16S rDNA evolutionary tree s. The position of Caryophanaceae and Planococcaceae in Group 2 suggested that they might be transferred into Bacillaceae, and the heterogeneity of Group 2 implied that some Bacillus species in it might belong to several new genera. Group 9 was mainly comprised of the genera (excluding Bacillus ) of Bacillaceae, so some Bacillus species in Group 9: B. salarius , B. qingdaonensis and B. thermcloacae might not belong to Bacillus . Four Bacillus species, B. schlegelii , B. tusciae , B. edaphicus and B. mucilaginosus were clearly placed outside the nine groups. Keywords: Bacillus phylogeny; Bayesian inference; Evolutionary trees; 16S rDNA INTRODUCTION established before 2000. Bacillus has long been regarded as a In recent years, numerous new species of genus Bacillus phylogenetic heterogeneous group (1). -
Characterization of Bacillus Strains of Marine Origin
INTERNATL MICROBIOL (1999) 2:267–271 267 © Springer-Verlag Ibérica 1999 RESEARCH ARTICLE Elena P. Ivanova1,2 · Mikhail V. Vysotskii2 · Vasilii I. Svetashev2 · Characterization of Bacillus strains Olga I. Nedashkovskaya1 · Natalia M. Gorshkova1 · Valery V. of marine origin Mikhailov1 · Noboru Yumoto3 · Yasushi Shigeri3 · Takahisa Taguchi3 · Susumu Yoshikawa3 1Pacific Institute of Bio-organic Chemistry, Summary A total of twenty aerobic endospore-forming bacilli, isolated from marine Far-Eastern Branch of the Russian Academy invertebrates and sea water of different areas of the Pacific Ocean, were taxonomically of Sciences, Vladivostok, Russia 2Institute of Marine Biology, Far-Eastern Branch characterized. Most of the bacilli (11 strains) of marine origin belonged to the species of the Russian Academy of Sciences, Bacillus subtilis, according to their phenotypic characteristics, antibiotic susceptibility Vladivostok, Russia profiles, and fatty acids patterns. A group of four alkaliphilic strains formed a separate 3Osaka National Research Institute, AIST, Ikeda, Osaka, Japan cluster that was tentatively classified as B. horti. One isolate, KMM 1717, associated with a sponge from the Coral Sea was identified as B. pumilus. Two strains, Bacillus Received 25 February 1999 KMM 1916 and KMM 1918, showed antibiotic sensitivity profiles similar to B. Accepted 15 September 1999 licheniformis, but they had a distinct fatty acid composition and peculiar phenotypic traits. The taxonomic affiliation of KMM 1810 and KMM 1763 remained unclear Correspondence to: Elena P. Ivanova. Pacific Institute of Bio-organic since their fatty acid composition and antibiotic sensitivity patterns were not resembled Chemistry. Far Eastern Branch of the Russian with none of these obtained for Bacillus strains. Academy of Sciences. -
Saline Systems Biomed Central
Saline Systems BioMed Central Research Open Access Diversity of Bacillus-like organisms isolated from deep-sea hypersaline anoxic sediments Andrea M Sass1,2, Boyd A McKew1, Henrik Sass3, Jörg Fichtel4, Kenneth N Timmis1,5,6 and Terry J McGenity*1 Address: 1Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK, 2School of Biosciences, Cardiff University, Cardiff CF10 3YE, UK, 3School of Earth Ocean & Planetary Science, Cardiff University, Cardiff CF10 3YE, UK, 4Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26111 Oldenburg, Germany, 5Helmholtz Center for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany and 6Institute for Microbiology, Technical University Braunschweig, Germany Email: Andrea M Sass - [email protected]; Boyd A McKew - [email protected]; Henrik Sass - [email protected]; Jörg Fichtel - [email protected]; Kenneth N Timmis - [email protected]; Terry J McGenity* - [email protected] * Corresponding author Published: 9 June 2008 Received: 1 February 2008 Accepted: 9 June 2008 Saline Systems 2008, 4:8 doi:10.1186/1746-1448-4-8 This article is available from: http://www.salinesystems.org/content/4/1/8 © 2008 Sass et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The deep-sea, hypersaline anoxic brine lakes in the Mediterranean are among the most extreme environments on earth, and in one of them, the MgCl2-rich Discovery basin, the presence of active microbes is equivocal. -
Reducing Microorganisms in Rice Paddy Soil: Enrichment Cultures with Different Short-Chain Fatty Acids As Electron Donors
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications in the Biological Sciences Papers in the Biological Sciences 2011 Phylogenetic diversity of Fe(III)-reducing microorganisms in rice paddy soil: Enrichment cultures with different short-chain fatty acids as electron donors Huijuan Li Chinese Academy of Sciences, Xiamen, [email protected] Jingjing Peng Chinese Academy of Sciences, Xiamen Karrie A. Weber University of Nebraska-Lincoln, [email protected] Yongguan Zhu Chinese Academy of Sciences, Xiamen, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/bioscifacpub Part of the Life Sciences Commons Li, Huijuan; Peng, Jingjing; Weber, Karrie A.; and Zhu, Yongguan, "Phylogenetic diversity of Fe(III)-reducing microorganisms in rice paddy soil: Enrichment cultures with different short-chain fatty acids as electron donors" (2011). Faculty Publications in the Biological Sciences. 199. https://digitalcommons.unl.edu/bioscifacpub/199 This Article is brought to you for free and open access by the Papers in the Biological Sciences at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications in the Biological Sciences by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Published in Journal of Soils and Sediments 11 (2011), pp. 1234–1242; doi: 10.1007/s11368-011-0371-2 Copyright © 2011 Springer-Verlag. Used by permission. Submitted March 1, 2011; accepted April 20, 2011; published online May 11, 2011 Phylogenetic diversity of Fe(III)-reducing microorganisms in rice paddy soil: Enrichment cultures with different short-chain fatty acids as electron donors Huijuan Li,1, 2 Jingjing Peng,1, 2 Karrie A.