Characteristics of Bacterial Community in Fog Water at Mt. Tai
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Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas Sp
microorganisms Article Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas sp. AAP5 Karel Kopejtka 1 , Yonghui Zeng 1,2, David Kaftan 1,3 , Vadim Selyanin 1, Zdenko Gardian 3,4 , Jürgen Tomasch 5,† , Ruben Sommaruga 6 and Michal Koblížek 1,* 1 Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 81 Tˇreboˇn,Czech Republic; [email protected] (K.K.); [email protected] (Y.Z.); [email protected] (D.K.); [email protected] (V.S.) 2 Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark 3 Faculty of Science, University of South Bohemia, 370 05 Ceskˇ é Budˇejovice,Czech Republic; [email protected] 4 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 Ceskˇ é Budˇejovice,Czech Republic 5 Research Group Microbial Communication, Technical University of Braunschweig, 38106 Braunschweig, Germany; [email protected] 6 Laboratory of Aquatic Photobiology and Plankton Ecology, Department of Ecology, University of Innsbruck, 6020 Innsbruck, Austria; [email protected] * Correspondence: [email protected] † Present Address: Department of Molecular Bacteriology, Helmholtz-Centre for Infection Research, 38106 Braunschweig, Germany. Abstract: An aerobic, yellow-pigmented, bacteriochlorophyll a-producing strain, designated AAP5 Citation: Kopejtka, K.; Zeng, Y.; (=DSM 111157=CCUG 74776), was isolated from the alpine lake Gossenköllesee located in the Ty- Kaftan, D.; Selyanin, V.; Gardian, Z.; rolean Alps, Austria. Here, we report its description and polyphasic characterization. Phylogenetic Tomasch, J.; Sommaruga, R.; Koblížek, analysis of the 16S rRNA gene showed that strain AAP5 belongs to the bacterial genus Sphingomonas M. Characterization of the Aerobic and has the highest pairwise 16S rRNA gene sequence similarity with Sphingomonas glacialis (98.3%), Anoxygenic Phototrophic Bacterium Sphingomonas psychrolutea (96.8%), and Sphingomonas melonis (96.5%). -
Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations
fmicb-09-02879 December 1, 2018 Time: 14:0 # 1 ORIGINAL RESEARCH published: 04 December 2018 doi: 10.3389/fmicb.2018.02879 Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations Klervi Crenn, Delphine Duffieux and Christian Jeanthon* CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community- level methods and culture-based or natural diatom populations. Although bacterial assemblages attached to individual diatoms represents tight associations little is known on their makeup or interactions. Here, we examined the epibiotic bacteria of 436 Thalassiosira and 329 Chaetoceros single cells isolated from natural samples and Edited by: collection cultures, regarded here as short- and long-term associations, respectively. Matthias Wietz, Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning- Alfred Wegener Institut, Germany sequencing of 16S rRNA genes obtained from whole-genome amplification products. Reviewed by: The prevalence of epibiotic bacteria was higher in cultures and dependent of the host Lydia Jeanne Baker, Cornell University, United States species. Culture approaches demonstrated that both diatoms carry distinct bacterial Bryndan Paige Durham, communities in short- and long-term associations. Bacterial epibonts, commonly University of Washington, United States associated with phytoplankton, were repeatedly isolated from cells of diatom collection *Correspondence: cultures but were not recovered from environmental cells. -
Genome Sequence of the Lotus Spp. Microsymbiont Mesorhizobium Loti
Kelly et al. Standards in Genomic Sciences 2014, 9:7 http://www.standardsingenomics.com/content/9/1/7 SHORT GENOME REPORT Open Access Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain NZP2037 Simon Kelly1, John Sullivan1, Clive Ronson1, Rui Tian2, Lambert Bräu3, Karen Davenport4, Hajnalka Daligault4, Tracy Erkkila4, Lynne Goodwin4, Wei Gu4, Christine Munk4, Hazuki Teshima4, Yan Xu4, Patrick Chain4, Tanja Woyke5, Konstantinos Liolios5, Amrita Pati5, Konstantinos Mavromatis6, Victor Markowitz6, Natalia Ivanova5, Nikos Kyrpides5,7 and Wayne Reeve2* Abstract Mesorhizobium loti strain NZP2037 was isolated in 1961 in Palmerston North, New Zealand from a Lotus divaricatus root nodule. Compared to most other M. loti strains, it has a broad host range and is one of very few M. loti strains able to form effective nodules on the agriculturally important legume Lotus pedunculatus. NZP2037 is an aerobic, Gram negative, non-spore-forming rod. This report reveals that the genome of M. loti strain NZP2037 does not harbor any plasmids and contains a single scaffold of size 7,462,792 bp which encodes 7,318 protein-coding genes and 70 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. Keywords: Root-nodule bacteria, Nitrogen fixation, Symbiosis, Alphaproteobacteria Introduction whether the polysaccharide is necessary for nodulation Mesorhizobium loti strain NZP2037 (ICMP1326) was of L. pedunculatus has not been established. isolated in 1961 from a root nodule off a Lotus divarica- Nodulation and nitrogen fixation genes in Mesorhizo- tus plant growing near Palmerston North airport, New bium loti strains are encoded on the chromosome on Zealand [1]. -
Reclassification of Agrobacterium Ferrugineum LMG 128 As Hoeflea
International Journal of Systematic and Evolutionary Microbiology (2005), 55, 1163–1166 DOI 10.1099/ijs.0.63291-0 Reclassification of Agrobacterium ferrugineum LMG 128 as Hoeflea marina gen. nov., sp. nov. Alvaro Peix,1 Rau´l Rivas,2 Martha E. Trujillo,2 Marc Vancanneyt,3 Encarna Vela´zquez2 and Anne Willems3 Correspondence 1Departamento de Produccio´n Vegetal, Instituto de Recursos Naturales y Agrobiologı´a, Encarna Vela´zquez IRNA-CSIC, Spain [email protected] 2Departamento de Microbiologı´a y Gene´tica, Lab. 209, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain 3Laboratory of Microbiology, Dept Biochemistry, Physiology and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium Members of the species Agrobacterium ferrugineum were isolated from marine environments. The type strain of this species (=LMG 22047T=ATCC 25652T) was recently reclassified in the new genus Pseudorhodobacter, in the order ‘Rhodobacterales’ of the class ‘Alphaproteobacteria’. Strain LMG 128 (=ATCC 25654) was also initially classified as belonging to the species Agrobacterium ferrugineum; however, the nearly complete 16S rRNA gene sequence of this strain indicated that it does not belong within the genus Agrobacterium or within the genus Pseudorhodobacter. The closest related organism, with 95?5 % 16S rRNA gene similarity, was Aquamicrobium defluvii from the family ‘Phyllobacteriaceae’ in the order ‘Rhizobiales’. The remaining genera from this order had 16S rRNA gene sequence similarities that were lower than 95?1 % with respect to strain LMG 128. These phylogenetic distances suggested that strain LMG 128 belonged to a different genus. The major fatty acid present in strain LMG 128 was mono-unsaturated straight chain 18 : 1v7c. -
Revised Taxonomy of the Family Rhizobiaceae, and Phylogeny of Mesorhizobia Nodulating Glycyrrhiza Spp
Division of Microbiology and Biotechnology Department of Food and Environmental Sciences University of Helsinki Finland Revised taxonomy of the family Rhizobiaceae, and phylogeny of mesorhizobia nodulating Glycyrrhiza spp. Seyed Abdollah Mousavi Academic Dissertation To be presented, with the permission of the Faculty of Agriculture and Forestry of the University of Helsinki, for public examination in lecture hall 3, Viikki building B, Latokartanonkaari 7, on the 20th of May 2016, at 12 o’clock noon. Helsinki 2016 Supervisor: Professor Kristina Lindström Department of Environmental Sciences University of Helsinki, Finland Pre-examiners: Professor Jaakko Hyvönen Department of Biosciences University of Helsinki, Finland Associate Professor Chang Fu Tian State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University, China Opponent: Professor J. Peter W. Young Department of Biology University of York, England Cover photo by Kristina Lindström Dissertationes Schola Doctoralis Scientiae Circumiectalis, Alimentariae, Biologicae ISSN 2342-5423 (print) ISSN 2342-5431 (online) ISBN 978-951-51-2111-0 (paperback) ISBN 978-951-51-2112-7 (PDF) Electronic version available at http://ethesis.helsinki.fi/ Unigrafia Helsinki 2016 2 ABSTRACT Studies of the taxonomy of bacteria were initiated in the last quarter of the 19th century when bacteria were classified in six genera placed in four tribes based on their morphological appearance. Since then the taxonomy of bacteria has been revolutionized several times. At present, 30 phyla belong to the domain “Bacteria”, which includes over 9600 species. Unlike many eukaryotes, bacteria lack complex morphological characters and practically phylogenetically informative fossils. It is partly due to these reasons that bacterial taxonomy is complicated. -
Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg -
The Differential Interaction of Brucella and Ochrobactrum with Innate
The differential interaction of Brucella and ochrobactrum with innate immunity reveals traits related to the evolution of stealthy pathogens Elías Barquero-Calvo, Raquel Conde-Alvarez, Carlos Chacón-Díaz, Lucía Quesada-Lobo, Anna Martirosyan, Caterina Guzmán-Verri, Maite Iriarte, Mateja Mancek-Keber, Roman Jerala, Jean Pierre Gorvel, et al. To cite this version: Elías Barquero-Calvo, Raquel Conde-Alvarez, Carlos Chacón-Díaz, Lucía Quesada-Lobo, Anna Mar- tirosyan, et al.. The differential interaction of Brucella and ochrobactrum with innate immunity reveals traits related to the evolution of stealthy pathogens. PLoS ONE, Public Library of Science, 2009, 4 (6), pp.e5893. 10.1371/journal.pone.0005893. hal-00431866 HAL Id: hal-00431866 https://hal.archives-ouvertes.fr/hal-00431866 Submitted on 27 Sep 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License The Differential Interaction of Brucella and Ochrobactrum with Innate Immunity Reveals Traits Related to the Evolution of Stealthy -
Intramammary Infections with Coagulase-Negative Staphylococcus Species
Printing of this thesis was financially supported by Printed by University Press, Zelzate ISBN number: 9789058642738 INTRAMAMMARY INFECTIONS WITH COAGULASE-NEGATIVE STAPHYLOCOCCUS SPECIES IN BOVINES - MOLECULAR DIAGNOSTICS AND EPIDEMIOLOGY - KARLIEN SUPRÉ 2011 PROMOTORS/PROMOTOREN Prof. dr. Sarne De Vliegher Faculteit Diergeneeskunde, UGent Prof. dr. Ruth N. Zadoks Royal (Dick) School of Veterinary Studies, University of Edinburgh; Moredun Research Institute, Penicuik, Schotland Prof. dr. Freddy Haesebrouck Faculteit Diergeneeskunde, UGent MEMBERS OF THE EXAMINATION COMMITTEE/LEDEN VAN DE EXAMENCOMMISSIE Prof. dr. dr. h. c. Aart de Kruif Voorzitter van de examencommissie Prof. dr. Mario Vaneechoutte Faculteit Geneeskunde en Gezondheidswetenschappen, UGent Dr. Margo Baele Directie Onderzoeksaangelegenheden, UGent Dr. Lic. Luc De Meulemeester MCC-Vlaanderen, Lier Prof. dr. Geert Opsomer Faculteit Diergeneeskunde, UGent Prof. dr. Marc Heyndrickx Instituut voor Landbouw en Visserijonderzoek (ILVO), Melle Dr. Suvi Taponen University of Helsinki, Finland Prof. dr. Ynte H. Schukken Cornell University, Ithaca, USA INTRAMAMMARY INFECTIONS WITH COAGULASE-NEGATIVE STAPHYLOCOCCUS SPECIES IN BOVINES - MOLECULAR DIAGNOSTICS AND EPIDEMIOLOGY - KARLIEN SUPRÉ Department of Reproduction, Obstetrics, and Herd Health Faculty of Veterinary Medicine, Ghent University Dissertation submitted in the fulfillment of the requirements for the degree of Doctor in Veterinary Sciences, Faculty of Veterinary Medicine, Ghent University INTRAMAMMAIRE INFECTIES MET COAGULASE-NEGATIEVE -
(12) Patent Application Publication (10) Pub. No.: US 2005/0289672 A1 Jefferson (43) Pub
US 2005O289672A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2005/0289672 A1 Jefferson (43) Pub. Date: Dec. 29, 2005 (54) BIOLOGICAL GENE TRANSFER SYSTEM Publication Classification FOR EUKARYOTC CELLS (75) Inventor: Richard A. Jefferson, Canberra (AU) (51) Int. Cl. ............................. A01H 1700; C12N 15/82 (52) U.S. Cl. .............................................................. 800,294 Correspondence Address: CAROL NOTTENBURG 81432ND AVE 5 SEATTLE, WA 98144 (US) (57) ABSTRACT (73) Assignee: CAMBIA Appl. No.: 10/954,147 This invention relates generally to technologies for the (21) transfer of nucleic acids molecules to eukaryotic cells. In Filed: Sep. 28, 2004 particular non-pathogenic Species of bacteria that interact (22) with plant cells are used to transfer nucleic acid Sequences. Related U.S. Application Data The bacteria for transforming plants usually contain binary vectors, Such as a plasmid with a Vir region of a Tiplasmid (60) Provisional application No. 60/583,426, filed on Jun. and a plasmid with a T region containing a DNA sequence 28, 2004. of interest. pEHA105 244981 bp M3REW M13Fw f1 origin accA W pEHA105::pWBE58 (Km, Ap) moaa. Patent Application Publication Dec. 29, 2005 Sheet 1 of 24 US 2005/0289672 A1 FIGURE 1A CLASS ALPHAPROTEOBACTERIA ORDER Rhizobiales family Rhizobiaceae bgenus Rhizobium (includes former Agrobacterium) bgenus Chelatobacter bgenus Sinorhizobium Dunclassified Rhizobiaceae family Bartonellaceae bgenus Bartonella Dunclassified Bartonellaceae family Brucellaceae -
Characteristics of Bacterial Community in Cloud Water at Mt. Tai: Similarity and Disparity Under Polluted and Non-Polluted Cloud Episodes
Characteristics of bacterial community in cloud water at Mt. Tai: similarity and disparity under polluted and non-polluted cloud episodes Min Wei 1, Caihong Xu1, Jianmin Chen1,2,*, Chao Zhu1, Jiarong Li1, Ganglin Lv 1 5 1 Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji’nan 250100, China 2 Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP), Fudan Tyndall Centre, Department of Environmental Science & Engineering, Fudan University, Shanghai 200433, China 10 Correspondence to: JM.Chen ([email protected]) Abstract: Bacteria are widely distributed in atmospheric aerosols and are indispensable components of clouds, playing an important role in the atmospheric hydrological cycle. However, limited information is 15 available about the bacterial community structure and function, especially for the increasing air pollution in the North China Plain. Here, we present a comprehensive characterization of bacterial community composition, function, variation and environmental influence for cloud water collected at Mt. Tai from 24 Jul to 23 Aug 2014. Using Miseq 16S rRNA gene sequencing, the highly diverse bacterial community in cloud water and the predominant phyla of Proteobacteria, Bacteroidetes, 20 Cyanobacteria and Firmicutes were investigated. Bacteria that survive at low temperature, radiation, and poor nutrient conditions were found in cloud water, suggesting adaptation to an extreme environment. The bacterial gene functions predicted from the 16S rRNA gene using -
Characterization of Bacterial Communities Associated
www.nature.com/scientificreports OPEN Characterization of bacterial communities associated with blood‑fed and starved tropical bed bugs, Cimex hemipterus (F.) (Hemiptera): a high throughput metabarcoding analysis Li Lim & Abdul Hafz Ab Majid* With the development of new metagenomic techniques, the microbial community structure of common bed bugs, Cimex lectularius, is well‑studied, while information regarding the constituents of the bacterial communities associated with tropical bed bugs, Cimex hemipterus, is lacking. In this study, the bacteria communities in the blood‑fed and starved tropical bed bugs were analysed and characterized by amplifying the v3‑v4 hypervariable region of the 16S rRNA gene region, followed by MiSeq Illumina sequencing. Across all samples, Proteobacteria made up more than 99% of the microbial community. An alpha‑proteobacterium Wolbachia and gamma‑proteobacterium, including Dickeya chrysanthemi and Pseudomonas, were the dominant OTUs at the genus level. Although the dominant OTUs of bacterial communities of blood‑fed and starved bed bugs were the same, bacterial genera present in lower numbers were varied. The bacteria load in starved bed bugs was also higher than blood‑fed bed bugs. Cimex hemipterus Fabricus (Hemiptera), also known as tropical bed bugs, is an obligate blood-feeding insect throughout their entire developmental cycle, has made a recent resurgence probably due to increased worldwide travel, climate change, and resistance to insecticides1–3. Distribution of tropical bed bugs is inclined to tropical regions, and infestation usually occurs in human dwellings such as dormitories and hotels 1,2. Bed bugs are a nuisance pest to humans as people that are bitten by this insect may experience allergic reactions, iron defciency, and secondary bacterial infection from bite sores4,5. -
Molecular Diversity and Multifarious Plant Growth
Environment Health Techniques 44 Priyanka Verma et al. Research Paper Molecular diversity and multifarious plant growth promoting attributes of Bacilli associated with wheat (Triticum aestivum L.) rhizosphere from six diverse agro-ecological zones of India Priyanka Verma1,2, Ajar Nath Yadav1, Kazy Sufia Khannam2, Sanjay Kumar3, Anil Kumar Saxena1 and Archna Suman1 1 Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India 2 Department of Biotechnology, National Institute of Technology, Durgapur, India 3 Division of Genetics, Indian Agricultural Research Institute, New Delhi, India The diversity of culturable Bacilli was investigated in six wheat cultivating agro-ecological zones of India viz: northern hills, north western plains, north eastern plains, central, peninsular, and southern hills. These agro-ecological regions are based on the climatic conditions such as pH, salinity, drought, and temperature. A total of 395 Bacilli were isolated by heat enrichment and different growth media. Amplified ribosomal DNA restriction analysis using three restriction enzymes AluI, MspI, and HaeIII led to the clustering of these isolates into 19–27 clusters in the different zones at >70% similarity index, adding up to 137 groups. Phylogenetic analysis based on 16S rRNA gene sequencing led to the identification of 55 distinct Bacilli that could be grouped in five families, Bacillaceae (68%), Paenibacillaceae (15%), Planococcaceae (8%), Staphylococcaceae (7%), and Bacillales incertae sedis (2%), which included eight genera namely Bacillus, Exiguobacterium, Lysinibacillus, Paenibacillus, Planococcus, Planomicrobium, Sporosarcina, andStaphylococcus. All 395 isolated Bacilli were screened for their plant growth promoting attributes, which included direct-plant growth promoting (solubilization of phosphorus, potassium, and zinc; production of phytohormones; 1-aminocyclopropane-1-carboxylate deaminase activity and nitrogen fixation), and indirect-plant growth promotion (antagonistic, production of lytic enzymes, siderophore, hydrogen cyanide, and ammonia).