Dynamics of Soil Bacterial Communities in Response to Repeated Application of Manure Containing Sulfadiazine
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Diversity and Taxonomic Novelty of Actinobacteria Isolated from The
Diversity and taxonomic novelty of Actinobacteria isolated from the Atacama Desert and their potential to produce antibiotics Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Christian-Albrechts-Universität zu Kiel Vorgelegt von Alvaro S. Villalobos Kiel 2018 Referent: Prof. Dr. Johannes F. Imhoff Korreferent: Prof. Dr. Ute Hentschel Humeida Tag der mündlichen Prüfung: Zum Druck genehmigt: 03.12.2018 gez. Prof. Dr. Frank Kempken, Dekan Table of contents Summary .......................................................................................................................................... 1 Zusammenfassung ............................................................................................................................ 2 Introduction ...................................................................................................................................... 3 Geological and climatic background of Atacama Desert ............................................................. 3 Microbiology of Atacama Desert ................................................................................................. 5 Natural products from Atacama Desert ........................................................................................ 9 References .................................................................................................................................. 12 Aim of the thesis ........................................................................................................................... -
Microbacterium Flavum Sp. Nov. and Microbacterium Lacus Sp. Nov
Actinomycetologica (2007) 21:53–58 Copyright Ó 2007 The Society for Actinomycetes Japan VOL. 21, NO. 2 Microbacterium flavum sp. nov. and Microbacterium lacus sp. nov., isolated from marine environments. Akiko Kageyama1, Yoko Takahashi1Ã, Yoshihide Matsuo2, Kyoko Adachi2, Hiroaki Kasai2, Yoshikazu Shizuri2 and Satoshi O¯ mura1;3 1Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8642, Japan. 2Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan. 3The Kitasato Institute, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8642, Japan. (Received Feb. 21, 2007 / Accepted Jul. 9, 2007 / Published Sep. 10, 2007) Strains YM18-098T and A5E-52T were both Gram-positive, aerobic, irregular rod-shaped bacteria, with lysine and ornithine as the diagnostic diamino acids of their peptidoglycans, respectively. The acyl type of the peptidoglycan in both cases was N-glycolyl. The major menaquinones were MK-11, -12 and -13. Mycolic acids were not detected. The G+C content of the DNA was 69–70 mol%. Comparative 16S rRNA studies revealed that the isolates belonged to the genus Microbacterium, that YM18-098T was closely related to the species Microbacterium lacticum and Microbacterium schleiferi, and that A5E-52T was closely related to the species Microbacterium aurum, Microbacterium aoyamense, Microbacterium deminutum and Microbacterium pumilum. DNA-DNA relatedness analysis showed that the isolated strains represented two separate genomic species. Based on both phenotypic and genotypic data, the following new species of the genus Microbacterium are proposed: Microbacterium flavum sp. nov. and Microbacterium lacus sp. nov., with the type strains YM18-098T (= MBIC08278T, DSM 18909T) and A5E-52T (= MBIC08279T, DSM 18910T), respectively. -
TECHNISCHE UNIVERSITÄT MÜNCHEN Lehrstuhl Für Mikrobielle Ökologie Analyse Der Bakteriellen Biodiversität Von Boviner Rohmil
TECHNISCHE UNIVERSITÄT MÜNCHEN Lehrstuhl für Mikrobielle Ökologie Analyse der bakteriellen Biodiversität von boviner Rohmilch mittels kultureller und kulturunabhängiger Verfahren Franziska Thekla Breitenwieser Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigten Dissertation. Vorsitzender: Prof. Dr. Ulrich Kulozik Prüfer der Dissertation: 1. Prof. Dr. Siegfried Scherer 2. Prof. Dr. Rudi F. Vogel Die Dissertation wurde am 23.03.2018 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 04.07.2018 angenommen. Inhaltsverzeichnis INHALTSVERZEICHNIS INHALTSVERZEICHNIS ..................................................................................................... I ZUSAMMENFASSUNG ...................................................................................................... V SUMMARY ....................................................................................................................... VII ABBILDUNGSVERZEICHNIS ......................................................................................... IX TABELLENVERZEICHNIS .............................................................................................. XI ABKÜRZUNGSVERZEICHNIS ..................................................................................... XIII 1. -
Tartu Ülikool Loodus- Ja Tehnoloogiateaduskond Molekulaar- Ja Rakubioloogia Instituut Geneetika Õppetool
TARTU ÜLIKOOL LOODUS- JA TEHNOLOOGIATEADUSKOND MOLEKULAAR- JA RAKUBIOLOOGIA INSTITUUT GENEETIKA ÕPPETOOL Elerin Toomik Puidujäätmete komposti mikroobikoosluse kirjeldamine Bakalaureusetöö Juhendaja Anne Menert PhD Signe Viggor PhD TARTU 2015 KASUTATUD LÜHENDID ...................................................................................................... 4 SISSEJUHATUS ........................................................................................................................ 5 KIRJANDUSE ÜLEVAADE ..................................................................................................... 6 1.1 Taimeraku kesta ehitus ..................................................................................................... 6 1.1.1 Lignotselluloosi komponendid ja nende lagundamine .............................................. 7 1.1.1.1 Tselluloos ja selle ensümaatiline lagundamine .................................................. 7 1.1.1.2 Hemitselluloos ja selle ensümaatiline lagundamine ......................................... 10 1.1.1.3 Ligniin ja selle ensümaatiline lagundamine ..................................................... 11 1.1.1.4 Teised taimeraku ühendid ja nende lagundamine ............................................. 16 1.2. PUIDUJÄÄTMETE KOMPOSTIMINE ....................................................................... 19 1.2.1 Kompostimise faasid ............................................................................................... 19 1.2.2 Kompostimisel olulised füüsikalis-keemilised -
Structural and Functional Diversity of the Diazotrophic Community in Xeric Ecosystems: Response to Nitrogen Availability
UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO BIOLOGIA VEGETAL Structural and functional diversity of the diazotrophic community in xeric ecosystems: response to nitrogen availability Carolina Cristiano de Almeida Mestrado em Microbiologia Aplicada Dissertação orientada por: Prof. Cristina Maria Nobre Sobral de Vilhena da Cruz Houghton Prof. Rogério Paulo de Andrade Tenreiro 2019 This Dissertation was fully performed at Plant Soil Ecology at cE3c under the direct co-supervision of Prof. Cristina Maria Nobre Sobral de Vilhena da Cruz Houghton Professor Rogério Paulo de Andrade Tenreiro was the internal supervisor designated in the scope of the Master in Applied Microbiology of the Faculty of Sciences of the University of Lisbon ACKNOWLEDGMENTS This dissertation arose from the collaboration between the Plant Soil Ecology group at cE3c and the Laboratory of Microbiology and Biotechnology at BioISI. This work would not be possible without the assistance and commitment of the individuals involved. First, I would like to express my greatest gratefulness to Professor Cristina Cruz, for the opportunity that was given to me. Thank you for the knowledge shared and for always having an enthusiastic perspective which is contagious. To Professor Rogério Tenreiro, thank you for welcoming me, for always pushing me to see further and for helping me to build more critical thinking. Thank you for all the knowledge shared with me, and for the ideas that help my work to go beyond what I thought was possible. I would also like to thank all members of the PSE group for their contribution, especially to Teresa Dias who has made possible this work with the samples used as well as every soil characteristic. -
A Report of 38 Unrecorded Bacterial Species in Korea, Belonging to the Phylum Actinobacteria
Journal of Species Research 5(2):223-234, 2016 A report of 38 unrecorded bacterial species in Korea, belonging to the phylum Actinobacteria Mi-Sun Kim1, Ji-Hee Lee1, Joo-Won Kang1, Seung-Bum Kim2, Jang-Cheon Cho3, Jung-Hoon Yoon4, Ki-seong Joh5, Chang-Jun Cha6, Wan-Taek Im7, Jin-Woo Bae8, Kwang-Yeop Jahng9, Che-Ok Jeon10 and Chi-Nam Seong1,* 1Department of Biology, Sunchon National University, Suncheon 57922, Korea 2Department of Microbiology, Chungnam National University, Daejeon 34134, Korea 3Department of Biological Sciences, Inha University, Incheon 22212, Korea 4Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon 16419, Korea 5Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Korea 6Department of Biotechnology, Chung-Ang University, Anseong 17546, Korea 7Department of Biotechnology, Hankyong National University, Anseong 17579, Korea 8Department of Biology, Kyung Hee University, Seoul 02447, Korea 9Department of Life Sciences, Chonbuk National University, Jeonju 28644, Korea 10Department of Life Science, Chung-Ang University, Seoul 06974, Korea *Correspondent: [email protected] As a subset work for the collection of indigenous prokaryotic species in Korea, 38 actinobacterial strains were isolated from various environmental samples obtained from plant root, ginseng cultivating soil, mud flat, freshwater and seawater. Each strain showed higher 16S rRNA gene sequence similarity (>99.1%) and formed a robust phylogenetic clade with closest actinobacterial species which were defined and validated with nomenclature, already. There is no official description on these 38 actinobacterial species in Korea. Consequently, unrecorded 37 species of 24 genera in the 12 families belonging to the order Actinomycetales of the phylum Actinobacteria were found in Korea. -
Aproximació a La Diversitat De Microorganismes
APROXIMACIÓ A LA DIVERSITAT DE MICROORGANISMES Estudi fenotípic i genotípic del microbioma de conills salvatges com a via per a introduir-se al món de la Microbiologia 16 DE GENER DE 2016 PSEUDÒNIM: CALAVERA DE FOC Institut ¿?¿?¿? Curs 2016/2017 Departament de Ciències Naturals TUTORA: ¿?¿?¿? Treball de Recerca de Batxillerat Institut ¿?¿?¿? Batxillerat científic APROXIMACIÓ A LA DIVERSITAT DE MICROORGANISMES Estudi fenotípic i genotípic del microbioma de conills salvatges com a via per a introduir-se al món de la Microbiologia Memòria presentada pel Sr. Calavera de Foc com a resultat del seu treball en el camp de la Microbiologia durant la seva estada en el CEAB (Centre d’Estudis Avançats de Blanes) Calavera de foc Centre d’Estudis Avançats de Blanes (CEAB) Blanes, estiu de 2016 “ El sentido de la vida es 5′-3′ ” Dra. Rosa Elena Sarmiento (Ciutat de Mèxic, Mèxic; 28 d’agost de 1966) SUMARI Resum general del treball presentat 1 1. Introducció 2 1.1 Brainstorming i Worrywillie per escollir la temàtica 2 1.2 Contacte amb el CEAB – CSIC 4 1.3 Objectius del treball 5 1.4 Hipòtesi de partida 6 DOCUMENTACIÓ 2. Obtenció d’informació sobre l’àmbit microbiològic 8 2.1 Història de la Microbiologia 9 2.1.1 Introducció 9 2.1.2 Nomenclatura de microorganismes 11 2.1.3 Tipus de microorganismes 11 2.1.4 Organització cel·lular dels organismes 14 2.1.5 Cronologia dels successos en Microbiologia 15 2.1.5.1 Etapa especulativa (des de l’antiguitat fins 1675) 15 2.1.5.2 Etapa de les observacions (de 1675 a mitjan segle XIX) 16 2.1.5.3 Etapa dels cultius (segle XIX – segle XX) 20 2.1.5.4 Etapa de les especialitzacions (des del s. -
UNIVERSITY of NEVADA, RENO Dimensions of Antarctic Microbial
UNIVERSITY OF NEVADA, RENO Dimensions of Antarctic microbial life revealed through microscopic, cultivation-based, molecular phylogenetic and environmental genomic characterization A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biochemistry by Emanuele Kuhn Dr. Alison E. Murray/Dissertation Advisor May, 2014 Copyright by Emanuele Kuhn 2014 All Rights Reserved P age | i Abstract Extreme cold temperatures have shaped Antarctic environments and the life that lives within them. Microorganisms affiliated with the three domains of life - Bacteria, Archaea, and Eukaryote - can be found in Antarctic environments from deep subglacial lakes to dry deserts and from deep oceans to cold and dark winter surface seawaters. This dissertation focused on the investigation of the microbial assemblage in two Antarctic environments: Lake Vida, located in the McMurdo Dry Valleys, and the surface seawater from the Antarctic Peninsula. Lake Vida has a thick (27+ m) ice cover which seals a cryogenic brine reservoir within the lake ice below 16 m. This brine’s environment challenges the conditions for the existence of life. Despite the perceived challenges of aphotic, anoxic and freezing conditions, the brine contained an abundant assemblage (6.13 ± 1.65 × 10 7 cells mL -1) of ultra-small cells 0.192 ± 0.065 μm in diameter and a less abundant assemblage (1.47 ± 0.25 × 10 5 cells mL -1) of microbial cells ranging from > 0.2 to 1.5 μm in length. Scanning electron microscopy provided supporting evidence for cell membranes associated with the ~ 0.2 μm cells and helped discern a second smaller size class of particles (0.084 ± 0.063 μm). -
Ambio Annexe 1
AMBIO ANNEXE 1 Cyanobacteria in cold environments ...................................................................................................... 2 Hidden levels of phylodiversity in Antarctic green algae ...................................................................... 15 Evolution & Biodiversity in the Antarctic .............................................................................................. 25 The limnology and biology of the Dufek Massif, Transantarctic Mountains 82° South ....................... 35 Lowcyanobacterial diversity in biotopes of theTransantarctic Mountains and ShackletonRange (80°82°S),Antarctica .............................................................................................................................. 53 Systematic and Applied Microbiology .................................................................................................. 68 The gyrB gene is a useful phylogeneticmarker for exploring the diversity of Flavobacterium strains isolated from terrestrial and aquatic habitats in Antarctica ................................................................. 77 Heterotrophic bacterial diversity in aquatic microbial mat communities from Antarctica ................. 90 Culturable Diversity of Heterotrophic Bacteria in Forlidas Pond (Pensacola Mountains) and Lundström Lake (Shackleton Range), Antarctica ............................................................................... 102. Evidence for widespread endemism among Antarctic micro-organisms .......................................... -
Genetic Diversity of Actinobacteria Isolated from Lake Magadi Regina
Genetic Diversity of Actinobacteria Isolated from Lake Magadi Regina Chemutai Ronoh A thesis submitted in partial fulfillment for the degree of Master of Science in Genetics in the Jomo Kenyatta University of Agriculture and Technology 2013. DECLARATION This thesis is my original work and has not been presented for a degree in any other University. Signature: --------------------------------------- Date: ------------------------ Regina Chemutai Ronoh. This thesis has been submitted for examination with our approval as university supervisors. Signature: ------------------------------------------ Date: ----------------------- Prof. Hamadi Boga JKUAT, Kenya Signature: ---------------------------------------- Date: -------------------------- Dr. Romano Mwirichia JKUAT, Kenya Signature-------------------------------------- Date: ------------------------- . Dr. Nancy Budambula JKUAT, Kenya ii DEDICATION I dedicate this thesis to my family for their moral support and words of encouragement. iii ACKNOWLEDGEMENTS First and foremost I thank God who makes all things possible. Without Him I cannot accomplish anything. My gratitude goes to my supervisors; Prof. Boga, Dr. Mwirichia and Dr. Budambula, for their academic and technical advice that brought this research work to maturity. I especially thank Prof. Boga for research grant that enabled me to do my project. I also thank the Institute of Biotechnology Research for allowing me to use their laboratory. I thank the Director and all the staff of the institute for assisting whenever possible. I also -
Papier-ARB-Manuscript-Dépot Institutionnel
1 Amoeba-resisting bacteria found in multilamellar bodies secreted by Dictyostelium 2 discoideum: social amoebae can also package bacteria 3 4 Valérie E. Paquet1,2 and Steve J. Charette1,2,3* 5 6 1. Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, 7 Université Laval, Quebec City, QC, Canada 8 2. Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de 9 Québec, Hôpital Laval, Quebec City, QC, Canada 10 3. Département de biochimie, de microbiologie et de bio-informatique, Faculté des 11 sciences et de génie, Université Laval, Quebec City, QC, Canada 12 13 *Corresponding author: 14 Steve J. Charette, 1030 avenue de la medicine, Pavillon Marchand, local 4245, Université 15 Laval, Quebec City, QC, Canada, G1V 0A6, telephone: 1-418-656-2131, ext. 6914, fax: 16 1-418-656-7176, email: [email protected] 17 18 Running title (60 characters with space): Packaging of amoeba-resisting bacteria by D. 19 discoideum 20 21 Keywords (6): Multilamellar bodies; Dictyostelium discoideum; packaged bacteria, 22 amoeba-resisting bacteria, Cupriavidus, Rathayibacter 23 1 24 ABSTRACT 25 Many bacteria can resist phagocytic digestion by various protozoa. Some of these 26 bacteria (all human pathogens) are known to be packaged in multilamellar bodies 27 produced in the phagocytic pathway of the protozoa and that are secreted into the 28 extracellular milieu. Packaged bacteria are protected from harsh conditions, and the 29 packaging process is suspected to promote bacterial persistence in the environment. To 30 date, only a limited number of protozoa, belonging to free-living amoebae and ciliates, 31 have been shown to perform bacteria packaging. -
'Biodeterioration of Limestone: Role of Bacterial Biofilms and Possible Intervention Strategies'
'Biodeterioration of limestone: role of bacterial biofilms and possible intervention strategies' Philip Skipper (12255097) PhD Thesis June / 2018 1 To my wife, Lynda Skipper. Without whom none of this would have been possible. 2 Acknowledgements I would like to thank my supervisor, Doctor Ronald Dixon, for all his support, help, advice and encouragement, and for bravely allowing a slightly late topic change. I would also like to thank Doctor Ross Williams and Henning Schulze, my co-supervisors, for their advice and encouragement. Thanks also go to Michael Shaw for use of his 16S rRNA primers (p. 48, 49) as well as his friendship, to Alice Gillet for her friendship and provision of the surface profilometer work (p. 47, 66 & 67), and of course to the rest of the Microbiology laboratory team. I would also like to thank Doctor Lynda Skipper for her assistance in note taking and taking photographs during the initial sampling (p. 45, 46 & 60) as well as salt and biocide treatment, SEM imaging and EDX testing of the stone blocks for the salting analysis of biocides (p.53 & 163). I would like to thank Mary Webster for allowing me to use the isolates gathered during her Masters project and providing her sampling sheets (p. 45, 61 & Appendix A) and Doctor Alan McNally for PCR amplification and sequencing of the total population genomic DNA isolates for metagenomics and providing the raw data generated by the sequencer (p. 51 & 61). I am grateful to the School of Life Sciences, especially the former Head of School Professor Libby John, for covering the main research costs of this study.