Actinobacteria As Essential Symbionts in Firebugs and Cotton Stainers
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Corynebacterium Sp.|NML98-0116
1 Limnochorda_pilosa~GCF_001544015.1@NZ_AP014924=Bacteria-Firmicutes-Limnochordia-Limnochordales-Limnochordaceae-Limnochorda-Limnochorda_pilosa 0,9635 Ammonifex_degensii|KC4~GCF_000024605.1@NC_013385=Bacteria-Firmicutes-Clostridia-Thermoanaerobacterales-Thermoanaerobacteraceae-Ammonifex-Ammonifex_degensii 0,985 Symbiobacterium_thermophilum|IAM14863~GCF_000009905.1@NC_006177=Bacteria-Firmicutes-Clostridia-Clostridiales-Symbiobacteriaceae-Symbiobacterium-Symbiobacterium_thermophilum Varibaculum_timonense~GCF_900169515.1@NZ_LT827020=Bacteria-Actinobacteria-Actinobacteria-Actinomycetales-Actinomycetaceae-Varibaculum-Varibaculum_timonense 1 Rubrobacter_aplysinae~GCF_001029505.1@NZ_LEKH01000003=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_aplysinae 0,975 Rubrobacter_xylanophilus|DSM9941~GCF_000014185.1@NC_008148=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_xylanophilus 1 Rubrobacter_radiotolerans~GCF_000661895.1@NZ_CP007514=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_radiotolerans Actinobacteria_bacterium_rbg_16_64_13~GCA_001768675.1@MELN01000053=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_rbg_16_64_13 1 Actinobacteria_bacterium_13_2_20cm_68_14~GCA_001914705.1@MNDB01000040=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_13_2_20cm_68_14 1 0,9803 Thermoleophilum_album~GCF_900108055.1@NZ_FNWJ01000001=Bacteria-Actinobacteria-Thermoleophilia-Thermoleophilales-Thermoleophilaceae-Thermoleophilum-Thermoleophilum_album -
Dissertation Implementing Organic Amendments To
DISSERTATION IMPLEMENTING ORGANIC AMENDMENTS TO ENHANCE MAIZE YIELD, SOIL MOISTURE, AND MICROBIAL NUTRIENT CYCLING IN TEMPERATE AGRICULTURE Submitted by Erika J. Foster Graduate Degree Program in Ecology In partial fulfillment of the requirements For the Degree of Doctor of Philosophy Colorado State University Fort Collins, Colorado Summer 2018 Doctoral Committee: Advisor: M. Francesca Cotrufo Louise Comas Charles Rhoades Matthew D. Wallenstein Copyright by Erika J. Foster 2018 All Rights Reserved i ABSTRACT IMPLEMENTING ORGANIC AMENDMENTS TO ENHANCE MAIZE YIELD, SOIL MOISTURE, AND MICROBIAL NUTRIENT CYCLING IN TEMPERATE AGRICULTURE To sustain agricultural production into the future, management should enhance natural biogeochemical cycling within the soil. Strategies to increase yield while reducing chemical fertilizer inputs and irrigation require robust research and development before widespread implementation. Current innovations in crop production use amendments such as manure and biochar charcoal to increase soil organic matter and improve soil structure, water, and nutrient content. Organic amendments also provide substrate and habitat for soil microorganisms that can play a key role cycling nutrients, improving nutrient availability for crops. Additional plant growth promoting bacteria can be incorporated into the soil as inocula to enhance soil nutrient cycling through mechanisms like phosphorus solubilization. Since microbial inoculation is highly effective under drought conditions, this technique pairs well in agricultural systems using limited irrigation to save water, particularly in semi-arid regions where climate change and population growth exacerbate water scarcity. The research in this dissertation examines synergistic techniques to reduce irrigation inputs, while building soil organic matter, and promoting natural microbial function to increase crop available nutrients. The research was conducted on conventional irrigated maize systems at the Agricultural Research Development and Education Center north of Fort Collins, CO. -
Actinobacteria and the Vitamin Metabolism of Firebugs
Actinobacteria and the Vitamin Metabolism of Firebugs - Characterizing a mutualism's specificity and functional importance - Seit 1558 Dissertation To Fulfill the Requirements for the Degree of „Doctor of Philosophy“ (PhD) Submitted to the Council of the Faculty of Biology and Pharmacy of the Friedrich Schiller University Jena by M.S. Hassan Salem Born on 16.01.1986 in Cairo, Egypt i Das Promotionsgesuch wurde eingereicht und bewilligt am: Gutachter: 1) 2) 3) Das Promotionskolloquium wurde abgelegt am: ii To Nagla and Samy, for ensuring that life’s possibilities remain endless To Aly, for sharing everything* And to Aileen, my beloved HERC2 mutant * Everything except our first Gameboy (circa 1993). For all else, I am profoundly grateful. i ii CONTENTS LIST OF PUBLICATIONS ................................................................................................... 1 CHAPTER 1: SYMBIOSIS AND THE EVOLUTION OF BIOLOGICAL NOVELTY IN INSECTS ............................................................................................................................ 3 1.1 The organism in the age of the holobiont: It, itself, they .................................................. 3 1.2 Adaptive significance of symbiosis .................................................................................. 4 1.3 Symbiont-mediated diversification ................................................................................... 5 1.4 Revisiting Darwin’s mystery of mysteries: The role of symbiosis in species formation 6 1.5 Homeostasis of symbioses -
Microbiome of Odontogenic Abscesses
microorganisms Article Microbiome of Odontogenic Abscesses Sebastian Böttger 1,* , Silke Zechel-Gran 2, Daniel Schmermund 1, Philipp Streckbein 1 , Jan-Falco Wilbrand 1 , Michael Knitschke 1 , Jörn Pons-Kühnemann 3, Torsten Hain 2,4, Markus Weigel 2 , Hans-Peter Howaldt 1, Eugen Domann 4,5 and Sameh Attia 1 1 Department of Oral and Maxillofacial Surgery, Justus-Liebig-University Giessen, University Hospital Giessen and Marburg, Giessen, D-35392 Giessen, Germany; [email protected] (D.S.); [email protected] (P.S.); [email protected] (J.-F.W.); [email protected] (M.K.); [email protected] (H.-P.H.); [email protected] (S.A.) 2 Institute of Medical Microbiology, Justus-Liebig-University Giessen, D-35392 Giessen, Germany; [email protected] (S.Z.-G.); [email protected] (T.H.); [email protected] (M.W.) 3 Institute of Medical Informatics, Justus-Liebig-University Giessen, D-35392 Giessen, Germany; [email protected] 4 German Center for Infection Research (DZIF), Justus-Liebig-University Giessen, Partner Site Giessen-Marburg-Langen, D-35392 Giessen, Germany; [email protected] 5 Institute of Hygiene and Environmental Medicine, Justus-Liebig-University Giessen, D-35392 Giessen, Germany * Correspondence: [email protected]; Tel.: +49-641-98546271 Abstract: Severe odontogenic abscesses are regularly caused by bacteria of the physiological oral Citation: Böttger, S.; Zechel-Gran, S.; microbiome. However, the culture of these bacteria is often prone to errors and sometimes does not Schmermund, D.; Streckbein, P.; result in any bacterial growth. -
Novel Molecular, Structural and Evolutionary Characteristics of the Phosphoketolases from Bifidobacteria and Coriobacteriales
RESEARCH ARTICLE Novel molecular, structural and evolutionary characteristics of the phosphoketolases from bifidobacteria and Coriobacteriales Radhey S. Gupta*, Anish Nanda, Bijendra Khadka Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada * [email protected] a1111111111 a1111111111 a1111111111 Abstract a1111111111 Members from the order Bifidobacteriales, which include many species exhibiting health a1111111111 promoting effects, differ from all other organisms in using a unique pathway for carbohydrate metabolism, known as the ªbifid shuntº, which utilizes the enzyme phosphoketolase (PK) to carry out the phosphorolysis of both fructose-6-phosphate (F6P) and xylulose-5-phosphate (X5P). In contrast to bifidobacteria, the PKs found in other organisms (referred to XPK) are OPEN ACCESS able to metabolize primarily X5P and show very little activity towards F6P. Presently, very lit- Citation: Gupta RS, Nanda A, Khadka B (2017) tle is known about the molecular or biochemical basis of the differences in the two forms of Novel molecular, structural and evolutionary PKs. Comparative analyses of PK sequences from different organisms reported here have characteristics of the phosphoketolases from bifidobacteria and Coriobacteriales. PLoS ONE 12 identified multiple high-specific sequence features in the forms of conserved signature (2): e0172176. doi:10.1371/journal.pone.0172176 inserts and deletions (CSIs) in the PK sequences that clearly distinguish the X5P/F6P phos- Editor: Eugene A. Permyakov, Russian Academy of phoketolases (XFPK) of bifidobacteria from the XPK homologs found in most other organ- Medical Sciences, RUSSIAN FEDERATION isms. Interestingly, most of the molecular signatures that are specific for the XFPK from Received: December 12, 2016 bifidobacteria are also shared by the PK homologs from the Coriobacteriales order of Acti- nobacteria. -
Genome Sequencing and Description of Oerskovia Enterophila Vjag, an Agar- and Cellulose-Degrading Bacterium Vanessa Jag1*† , Anja Poehlein2†, Frank R
Jag et al. Standards in Genomic Sciences (2017) 12:30 DOI 10.1186/s40793-017-0244-4 SHORT GENOME REPORT Open Access Genome sequencing and description of Oerskovia enterophila VJag, an agar- and cellulose-degrading bacterium Vanessa Jag1*† , Anja Poehlein2†, Frank R. Bengelsdorf1, Rolf Daniel2 and Peter Dürre1 Abstract A nonmotile, Gram-positive bacterium that shows an elongated and branching cell shape was isolated from soil samples from the botanical garden of Ulm University, Ulm, Germany. Here, the isolation procedure, identification, genome sequencing and metabolic features of the strain are described. Phylogenetic analysis allowed to identify the isolated strain as Oerskovia enterophila. The genus Oerskovia belongs to the family Cellulomonadaceae within the order Actinomycetales. The length of cells of O. enterophila ranges from 1 μmto15μm, depending on the growth phase. In the exponential growth phase, cells show an elongated and branching shape, whereas cells break up to round or coccoid elements in the stationary growth phase. The 4,535,074 bp long genome consists of 85 contigs with 3918 protein-coding genes and 57 RNA genes. The isolated strain was shown to degrade numerous complex carbon sources such as cellulose, chitin, and starch, which can be found ubiquitously in nature. Moreover, analysis of the genomic sequence revealed the genetic potential to degrade these compounds. Keywords: Oerskovia, Cellulomonadaceae, Cellulose degradation, Soil bacteria, Phylogenetic analysis Introduction from 51% to more than 70% [5–7]. Actinobacteria are Oerskovia enterophila was formerly characterized as widely distributed in terrestrial as well as in aquatic Promicromonospora enterophila by Jàger et al. in 1983 habitats [8, 9]. -
The Diversity of Cultivable Hydrocarbon-Degrading Bacteria Isolated from Crude Oil Contaminated Soil and Sludge from Arzew Refinery in Algeria
THE DIVERSITY OF CULTIVABLE HYDROCARBON-DEGRADING BACTERIA ISOLATED FROM CRUDE OIL CONTAMINATED SOIL AND SLUDGE FROM ARZEW REFINERY IN ALGERIA Sonia SEKKOUR1*, Abdelkader BEKKI1, Zoulikha BOUCHIBA1, Timothy M. Vogel2, Elisabeth NAVARRO2 Address(es): Ing. Sonia SEKKOUR PhD., 1Université Ahmed Benbella, Faculté des sciences de la nature et de la vie, Département de Biotechnologie, Laboratoire de biotechnologie des rhizobiums et amélioration des plantes, 31000 Oran, Algérie. 2Environmental Microbial Genomics Group, Laboratoire Ampère, Centre National de la Recherche Scientifique, UMR5005, Institut National de la Recherche Agronomique, USC1407, Ecole Centrale de Lyon, Université de Lyon, Ecully, France. *Corresponding author: [email protected] doi: 10.15414/jmbfs.2019.9.1.70-77 ARTICLE INFO ABSTRACT Received 27. 3. 2018 The use of autochtonious bacterial strains is a valuable bioremediation strategy for cleaning the environment from hydrocarbon Revised 19. 2. 2019 pollutants. The isolation, selection and identification of hydrocarbon-degrading bacteria is therefore crucial for obtaining the most Accepted 14. 3. 2019 promising strains for decontaminate a specific site. In this study, two different media, a minimal medium supplemented with petroleum Published 1. 8. 2019 and with oil refinery sludge as sole carbon source, were used for the isolation of native hydrocarbon-degrading bacterial strains from crude oil contaminated soils and oil refinery sludges which allowed isolation of fifty-eight strains.The evalution of diversity of twenty- two bacterials isolates reveled a dominance of the phylum Proteobacteria (20/22 strains), with a unique class of Alphaproteobacteria, Regular article the two remaining strains belong to the phylum Actinobacteria. Partial 16S rRNA gene sequencing performed on isolates showed high level of identity with known sequences. -
Promicromonospora Flava Sp. Nov., Isolated from Sediment of the Baltic Sea
International Journal of Systematic and Evolutionary Microbiology (2009), 59, 1599–1602 DOI 10.1099/ijs.0.006197-0 Promicromonospora flava sp. nov., isolated from sediment of the Baltic Sea Yi Jiang,1,2 Jutta Wiese,1 Yan-Ru Cao,2 Li-Hua Xu,2 Johannes F. Imhoff1 and Cheng-Lin Jiang2 Correspondence 1Leibniz-Institut fu¨r Meereswissenschaften, IFM-GEOMAR, Du¨sternbrooker Weg 20, D-24105 Kiel, Cheng-Lin Jiang Germany [email protected] 2Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China Johannes F. Imhoff [email protected] A Gram-positive, non-spore-forming actinomycete, designated strain CC 0387T, was isolated from a sediment sample from the Baltic Sea, Germany. Classification using a polyphasic approach and comparative 16S rRNA gene sequencing showed that strain CC 0387T belonged to the genus Promicromonospora and displayed more than 3 % 16S rRNA gene sequence divergence from all Promicromonospora species with validly published names. Strain CC 0387T did not produce aerial mycelium. Substrate mycelia were yellowish white to pale orange-yellow and fragmented into bacillary or coccoid elements. The cell wall contained lysine and alanine. Whole- cell hydrolysates contained galactose, glucose, rhamnose and ribose. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, an unknown phospholipid and an unknown glycolipid. The predominant menaquinone was MK-9(H4) (86 %). The G+C content of the DNA was 71.87 mol%. Based on morphological, chemotaxonomic, phenotypic and genetic characteristics, strain CC 0387T (5CCTCC AA208024T5DSM 21481T) represents a novel species, for which the name Promicromonospora flava sp. nov. is proposed. The genus Promicromonospora was proposed by bacteria and fungi, after incubation at 28 uC for 21 days. -
Impact of the Interplay Between Bile Acids, Lipids, Intestinal Coriobacteriaceae and Diet on Host Metabolism
Technische Universität München ZIEL – Zentralinstitut für Ernährungs- und Lebensmittelforschung Nachwuchsgruppe Intestinales Mikrobiom Impact of the interplay between bile acids, lipids, intestinal Coriobacteriaceae and diet on host metabolism Sarah Just 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 (Dr. rer. nat.) genehmigten Dissertation. Vorsitzender: Prof. Dr. rer. nat. Siegfried Scherer Prüfer der Dissertation: 1. Prof. Dr. rer. nat. Dirk Haller 2. Prof. Dr. rer. nat. Martin Klingenspor Die Dissertation wurde am 14.02.2017 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 12.06.2017 angenommen. Abstract Abstract The gut microbiome is a highly diverse ecosystem which influences host metabolism via for instance via conversion of bile acids and production of short chain fatty acids. Changes in gut microbiota profiles are associated with metabolic diseases such as obesity, type-2 diabetes, and non-alcoholic fatty liver disease. However, beyond alteration of the ecosystem structure, only a handful of specific bacterial species were shown to influence host metabolism and knowledge about molecular mechanisms by which gut bacteria regulate host metabolism are scant. The family Coriobacteriaceae (phylum Actinobacteria) comprises dominant members of the human gut microbiome and can metabolize cholesterol-derived substrates such as bile acids. Furthermore, their occurrence has been associated with alterations of lipid and cholesterol metabolism. However, consequences for the host are unknown. Hence, the aim of the present study was to characterize the impact of Coriobacteriaceae on lipid, cholesterol, and bile acid metabolism in vivo. -
Quantification of Slackia and Eggerthella Spp. in Human Feces
fmicb-07-00658 May 5, 2016 Time: 16:44 # 1 View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector ORIGINAL RESEARCH published: 09 May 2016 doi: 10.3389/fmicb.2016.00658 Quantification of Slackia and Eggerthella spp. in Human Feces and Adhesion of Representatives Strains to Caco-2 Cells Gyu-Sung Cho1, Felix Ritzmann2, Marie Eckstein2, Melanie Huch2, Karlis Briviba3, Diana Behsnilian4, Horst Neve1 and Charles M. A. P. Franz1* 1 Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany, 2 Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany, 3 Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut, Edited by: Federal Research Institute of Nutrition and Food, Karlsruhe, Germany, 4 Department of Food Technology and Bioprocess Andrea Gomez-Zavaglia, Engineering, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany Center for Research and Development in Food Cryotechnology – Consejo Nacional Eggerthella and Slackia spp. are gut associated bacteria that have been suggested to De Investigaciones Científicas Y play roles in host lipid and xenobiotic metabolism. A quantitative PCR method for the Técnicas, Argentina selective enumeration of bacteria belonging to either the genus Eggerthella or Slackia Reviewed by: was developed in order to establish the numbers of these bacteria occurring in human Paula Carasi, Universidad Nacional de La Plata, feces. The primers developed for selective amplification of these genera were tested first Argentina in conventional PCR to test for their specificity. -
Systematic Research on Actinomycetes Selected According
Systematic Research on Actinomycetes Selected according to Biological Activities Dissertation Submitted in fulfillment of the requirements for the award of the Doctor (Ph.D.) degree of the Math.-Nat. Fakultät of the Christian-Albrechts-Universität in Kiel By MSci. - Biol. Yi Jiang Leibniz-Institut für Meereswissenschaften, IFM-GEOMAR, Marine Mikrobiologie, Düsternbrooker Weg 20, D-24105 Kiel, Germany Supervised by Prof. Dr. Johannes F. Imhoff Kiel 2009 Referent: Prof. Dr. Johannes F. Imhoff Korreferent: ______________________ Tag der mündlichen Prüfung: Kiel, ____________ Zum Druck genehmigt: Kiel, _____________ Summary Content Chapter 1 Introduction 1 Chapter 2 Habitats, Isolation and Identification 24 Chapter 3 Streptomyces hainanensis sp. nov., a new member of the genus Streptomyces 38 Chapter 4 Actinomycetospora chiangmaiensis gen. nov., sp. nov., a new member of the family Pseudonocardiaceae 52 Chapter 5 A new member of the family Micromonosporaceae, Planosporangium flavogriseum gen nov., sp. nov. 67 Chapter 6 Promicromonospora flava sp. nov., isolated from sediment of the Baltic Sea 87 Chapter 7 Discussion 99 Appendix a Resume, Publication list and Patent 115 Appendix b Medium list 122 Appendix c Abbreviations 126 Appendix d Poster (2007 VAAM, Germany) 127 Appendix e List of research strains 128 Acknowledgements 134 Erklärung 136 Summary Actinomycetes (Actinobacteria) are the group of bacteria producing most of the bioactive metabolites. Approx. 100 out of 150 antibiotics used in human therapy and agriculture are produced by actinomycetes. Finding novel leader compounds from actinomycetes is still one of the promising approaches to develop new pharmaceuticals. The aim of this study was to find new species and genera of actinomycetes as the basis for the discovery of new leader compounds for pharmaceuticals. -
Genome-Based Classification of Micromonosporae
www.nature.com/scientificreports OPEN Genome-based classifcation of micromonosporae with a focus on their biotechnological and Received: 14 August 2017 Accepted: 8 November 2017 ecological potential Published: xx xx xxxx Lorena Carro 1, Imen Nouioui1, Vartul Sangal2, Jan P. Meier-Kolthof 3, Martha E. Trujillo4, Maria del Carmen Montero-Calasanz 1, Nevzat Sahin 5, Darren Lee Smith2, Kristi E. Kim6, Paul Peluso6, Shweta Deshpande7, Tanja Woyke 7, Nicole Shapiro7, Nikos C. Kyrpides7, Hans-Peter Klenk1, Markus Göker 3 & Michael Goodfellow1 There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables.