Ice Nucleation Active Bacteria in Precipitation Are Genetically Diverse and Nucleate Ice by Employing Different Mechanisms
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Doctoral Thesis 2016 UNDERSTANDING the AROMATIC HYDROCARBON DEGRADATION POTENTIAL of PSEUDOMONAS STUTZERI
Doctoral Thesis 2016 UNDERSTANDING THE AROMATIC HYDROCARBON DEGRADATION POTENTIAL OF PSEUDOMONAS STUTZERI: A PROTEO-GENOMIC APPROACH Isabel Brunet Galmés Doctoral Thesis 2016 Doctoral Program of “Microbiologia Ambiental i Biotecnologia” UNDERSTANDING THE AROMATIC HYDROCARBON DEGRADATION POTENTIAL OF PSEUDOMONAS STUTZERI: A PROTEO-GENOMIC APPROACH Isabel Brunet Galmés Thesis Supervisor: Dr. Rafael Bosch Thesis Supervisor: Dra. Balbina Nogales Doctor by the Universitat de les Illes Balears A mumpare i a mumare Agraïments Gràcies Rafel i Balbina per dirigir aquesta tesis, que és tant meva com vostre. A en Rafel per l’oportunitat que em vares donar, ja fa 7 anys, d’entrar al laboratori. Així com també per engrescar-me dins el món de la ciència, i ensenyar-me a treballar tant dins com fora del laboratori. I a na Balbina, pels mil consells que m’ha donat aquests anys, per ensenyar-me a ser més meticulosa amb el que faig i per ajudar-me amb tot el que ha pogut. A en Jordi i n’Elena, per acollir-me dins aquest grup de recerca, pels vostres consells i noves idees per continuar aquesta feina. Voldria agrair també a en Toni Bennasar i en Sebastià les crítiques constructives que m’heu anat fent al llarg d’aquests anys, des del projecte final de màster fins ara. Gràcies també a tots els companys de laboratori, a més de companys sou uns grans amics. Sempre estaré agraïda a na Marga, en Toni Busquets i n’Arantxa, pels grans consells que m’heu donat, tant dins com fora del laboratori, i per estar sempre disposats a donar-me una mà. -
Metaproteogenomic Insights Beyond Bacterial Response to Naphthalene
ORIGINAL ARTICLE ISME Journal – Original article Metaproteogenomic insights beyond bacterial response to 5 naphthalene exposure and bio-stimulation María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V. del Pozo, José María Vieites, Martin von Bergen, José Luis R. Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H. Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert and Manuel Ferrer 10 Supporting Online Material includes Text (Supporting Materials and Methods) Tables S1 to S9 Figures S1 to S7 1 SUPPORTING TEXT Supporting Materials and Methods Soil characterisation Soil pH was measured in a suspension of soil and water (1:2.5) with a glass electrode, and 5 electrical conductivity was measured in the same extract (diluted 1:5). Primary soil characteristics were determined using standard techniques, such as dichromate oxidation (organic matter content), the Kjeldahl method (nitrogen content), the Olsen method (phosphorus content) and a Bernard calcimeter (carbonate content). The Bouyoucos Densimetry method was used to establish textural data. Exchangeable cations (Ca, Mg, K and 10 Na) extracted with 1 M NH 4Cl and exchangeable aluminium extracted with 1 M KCl were determined using atomic absorption/emission spectrophotometry with an AA200 PerkinElmer analyser. The effective cation exchange capacity (ECEC) was calculated as the sum of the values of the last two measurements (sum of the exchangeable cations and the exchangeable Al). Analyses were performed immediately after sampling. 15 Hydrocarbon analysis Extraction (5 g of sample N and Nbs) was performed with dichloromethane:acetone (1:1) using a Soxtherm extraction apparatus (Gerhardt GmbH & Co. -
Evaluating the Diversity and Phylogeny of Plant Growth Promoting Bacteria Associated with Wheat (Triticum Aestivum) Growing in Central Zone of India
Int.J.Curr.Microbiol.App.Sci (2014) 3(5): 432-447 ISSN: 2319-7706 Volume 3 Number 5 (2014) pp. 432-447 http://www.ijcmas.com Original Research Article Evaluating the diversity and phylogeny of plant growth promoting bacteria associated with wheat (Triticum aestivum) growing in central zone of India Priyanka Verma1,2, Ajar Nath Yadav1, Sufia Khannam Kazy2, Anil Kumar Saxena1 and Archna Suman1* 1Division of Microbiology, Indian Agricultural Research Institute, New Delhi- 110012, India 2Department of Biotechnology, National Institute of Technology, Durgapur-713209, India *Corresponding author A B S T R A C T The diversity of plant growth promoting bacteria was investigated from wheat growing in different sites in central zone of India. Epiphytic, endophytic and rhizospheric bacteria were isolated using different growth medium. Bacterial diversity was analysed through amplified ribosomal DNA restriction analysis K e y w o r d s (ARDRA) using three restriction enzymes Alu I, Hae III, and Msp I which led to the grouping of 348 isolates into 24-29 clusters at >75% similarity index. 16S Epiphytic; rRNA gene based phylogenetic analysis, revealed that 134 strains belonged to three Endophytic; phyla namely actinobacteria, firmicutes and proteobacteria with 38 distinct species of 17 genera. Bacillus and Pseudomonas were dominant in rhizosphere while Rhizospheric; Methylobacterium were in phyllosphere. Endophytic niche specific bacteria were PGPB; identified as Delftia and Micrococcus. Sampling of different sites showed variation Drought in diversity indices. In vitro plant growth promoting activities of bacteria exposed stress; more than three beneficial traits which may act independently or concurrently. Biocontrol Phosphate solubilization and siderophores production are the predominant traits exhibited by these microbes. -
Response of Heterotrophic Stream Biofilm Communities to a Gradient of Resources
The following supplement accompanies the article Response of heterotrophic stream biofilm communities to a gradient of resources D. J. Van Horn1,*, R. L. Sinsabaugh1, C. D. Takacs-Vesbach1, K. R. Mitchell1,2, C. N. Dahm1 1Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA 2Present address: Department of Microbiology & Immunology, University of British Columbia Life Sciences Centre, Vancouver BC V6T 1Z3, Canada *Email: [email protected] Aquatic Microbial Ecology 64:149–161 (2011) Table S1. Representative sequences for each OTU, associated GenBank accession numbers, and taxonomic classifications with bootstrap values (in parentheses), generated in mothur using 14956 reference sequences from the SILVA data base Treatment Accession Sequence name SILVA taxonomy classification number Control JF695047 BF8FCONT18Fa04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Cellvibrio(100);unclassified; Control JF695049 BF8FCONT18Fa12.b1 Bacteria(100);Proteobacteria(100);Alphaproteobacteria(100);Rhizobiales(100);Methylocystaceae(100);uncultured(100);unclassified; Control JF695054 BF8FCONT18Fc01.b1 Bacteria(100);Planctomycetes(100);Planctomycetacia(100);Planctomycetales(100);Planctomycetaceae(100);Isosphaera(50);unclassified; Control JF695056 BF8FCONT18Fc04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Xanthomonadales(100);Xanthomonadaceae(100);uncultured(64);unclassified; Control JF695057 BF8FCONT18Fc06.b1 Bacteria(100);Proteobacteria(100);Betaproteobacteria(100);Burkholderiales(100);Comamonadaceae(100);Ideonella(54);unclassified; -
Ice Nucleators, Bacterial Cells and Pseudomonas
1 Ice nucleators, bacterial cells and Pseudomonas syringae in 2 precipitation at Jungfraujoch 3 Emiliano Stopelli1, Franz Conen1, Caroline Guilbaud2, Jakob Zopfi3, Christine Alewell1, 4 Cindy E. Morris2 5 1Environmental Geosciences, University of Basel, 4056 Basel, Switzerland 6 2INRA PACA, UR 0407 Plant Pathology Research Unit, 84143 Montfavet, France 7 3Acquatic and Stable Isotope Biogeochemistry, University of Basel, 4056 Basel, Switzerland 8 Correspondence to: Emiliano Stopelli ([email protected]) and Franz Conen ([email protected]) 9 10 Abstract Ice nucleation is a means by which the deposition of an airborne microorganism can be accelerated 11 under favourable meteorological conditions. Analysis of 56 snow samples collected at the high altitude 12 observatory Jungfraujoch (3580 m a.s.l.) revealed an order of magnitude larger dynamic range of ice nucleating 13 particles active at -8 °C (INPs-8) compared to the total number of bacterial cells (of which 60 % was on average 14 alive). This indicates a shorter atmospheric residence time for INPs-8. Furthermore, concentrations of INPs-8 15 decreased much faster, with an increasing fraction of water precipitated from the air mass prior to sampling, than -1 16 the number of total bacterial cells. Nevertheless, at high wind speeds (> 50 km h ) the ratio of INPs-8 to total 17 bacterial cells largely remained in a range between 10-2 to 10-3, independent of prior precipitation, likely because 18 of recent injections of particles in regions upwind. Based on our field observations, we conclude that ice 19 nucleators travel shorter legs of distance with the atmospheric water cycle than the majority of bacterial cells. -
Hydrologic Highways Between Microbial Communities of the Plant Microbiome? John Tolan Van Stan, Cindy E
Precipitation partitioning - Hydrologic highways between microbial communities of the plant microbiome? John Tolan van Stan, Cindy E. Morris, K Aung, Y Kuzyakov, D Magyar, E A Rebollar, M Remus-Emsermann, Stéphane Uroz, Philippe Vandenkoornhuyse To cite this version: John Tolan van Stan, Cindy E. Morris, K Aung, Y Kuzyakov, D Magyar, et al.. Precipitation partitioning - Hydrologic highways between microbial communities of the plant microbiome?. van Stan John Toland; Gutmann Ethan; Friesen Jan. Precipitation partitioning by vegetation, Springer Nature, pp.229-251, 2020, 978-3-030-29701-5. 10.1007/978-3-030-29702-2_14. hal-02389738 HAL Id: hal-02389738 https://hal.archives-ouvertes.fr/hal-02389738 Submitted on 26 Mar 2020 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. Chapter 14. Precipitation partitioning— Hydrologic highways between microbial communities of the plant microbiome? John T. Van Stan II1*, Cindy E. Morris2, Kyaw Aung3, Yakov Kuzyakov4, Donát Magyar5, Eria A. Rebollar6, Mitja Remus-Emsermann7, Stéphane Uroz8, Philippe Vandenkoornhuyse9 -
Pseudomonas Helmanticensis Sp. Nov., Isolated from Forest Soil
International Journal of Systematic and Evolutionary Microbiology (2014), 64, 2338–2345 DOI 10.1099/ijs.0.063560-0 Pseudomonas helmanticensis sp. nov., isolated from forest soil Martha-Helena Ramı´rez-Bahena,1,2 Maria Jose´ Cuesta,1 Jose´ David Flores-Fe´lix,3 Rebeca Mulas,4 Rau´l Rivas,2,3 Joao Castro-Pinto,5 Javier Bran˜as,5 Daniel Mulas,5 Fernando Gonza´lez-Andre´s,4 Encarna Vela´zquez2,3 and A´ lvaro Peix1,2 Correspondence 1Instituto de Recursos Naturales y Agrobiologı´a, IRNASA-CSIC, Salamanca, Spain A´ lvaro Peix 2Unidad Asociada Grupo de Interaccio´n Planta-Microorganismo, [email protected] Universidad de Salamanca-IRNASA (CSIC), Salamanca, Spain 3Departamento de Microbiologı´a y Gene´tica, Universidad de Salamanca, Salamanca, Spain 4Instituto de Medio Ambiente, Recursos Naturales y Biodiversidad, Universidad de Leo´n, Leo´n, Spain 5Fertiberia S. A., Madrid, Spain A bacterial strain, OHA11T, was isolated during the course of a study of phosphate-solubilizing bacteria occurring in a forest soil from Salamanca, Spain. The 16S rRNA gene sequence of strain OHA11T shared 99.1 % similarity with respect to Pseudomonas baetica a390T, and 98.9 % similarity with the type strains of Pseudomonas jessenii, Pseudomonas moorei, Pseudomonas umsongensis, Pseudomonas mohnii and Pseudomonas koreensis. The analysis of housekeeping genes rpoB, rpoD and gyrB confirmed its phylogenetic affiliation to the genus Pseudomonas and showed similarities lower than 95 % in almost all cases with respect to the above species. Cells possessed two polar flagella. The respiratory quinone was Q9. The major fatty acids were C16 : 0, C18 : 1v7c and summed feature 3 (C16 : 1v7c/iso-C15 : 0 2-OH). -
Soybean Resistance Genes Specific for Different Pseudomonas Syringue Avirwlence Genes Are Auelic, Or Closely Linked, at the RPG1 Locus
Copyright 0 1995 by the Genetics Society of America Soybean Resistance Genes Specific for Different Pseudomonas syringue Avirwlence Genes are AUelic, or Closely Linked, at the RPG1 Locus Tom Ashfield,* Noel T. Keen,+ Richard I. Buzzell: and Roger W. Innes* *Department of Biology, Indiana University, Bloomington, Indiana 47405, $Department of Plant Pathology, University of California, Riverside, California 92521, and fAgriculture & Agri-food Canada, Research Station, Harrow, Ontario NOR lG0, Canada Manuscript received July6, 1995 Accepted for publication September 11, 1995 ABSTRACT RPGl and RPMl are disease resistance genes in soybean and Arabidopsis, respectively, that confer resistance to Pseudomonas syringae strains expressing the avirulence gene awB. RPMl has recently been demonstrated to have a second specificity, also conferring resistance to P. syringae strains expressing [email protected] we show that alleles, or closely linked genes, exist at the RPGl locus in soybean that are specific for either awB or awR@ml and thus can distinguish between these two avirulence genes. ESISTANCE displayed by particular plant cultivars genes specific to avirulence genes of both the soybean R to specific races of a pathogen is often mediated pathogen Psgand the tomato pathogen Pst. The inabil- by single dominant resistance genes (R-genes). Typi- ity of Pstto cause disease in any soybean cultivarcan be cally, these R-genes interact with single dominant “avir- explained, atleast in part, by the presence of a battery of ulence” (aw) genes in the pathogen. Such specific in- resistance genes in soybean that correspond to one or teractions between races of pathogens and cultivars of more avirulence genes present in all Pst strains. -
Eosin Methylene Blue Agar for the Isolation, Cultivation and Differentiation of Gram Negative Enteric Bacilli from Clinical and Other Specimens Product Description
FT-A2WQP0 Eosin Methylene Blue Agar For the isolation, cultivation and differentiation of gram negative enteric bacilli from clinical and other specimens Product Description Name : Eosin Methylene Blue Agar Catalog Number : A2WQP0, 500 g Storage: 2-25°C - Once opened keep powdered medium closed to avoid hydration. Directions for use Formula • Bacteriological Peptone 10 • Eosin Y 0.4 • Lactose 5 • Methylene Blue 0.065 • Sucrose 5 • Bacteriological Agar 13.5 • Dipotassium Phosphate 2 Final pH 7.2 ± 0.2 at 25ºC Preparation Suspend 36 grams of medium in one liter of distilled water. Mix well and dissolve by heating with frequent agitation. Boil for one minute until complete dissolution. Sterilize in autoclave at 121ºC for 15 minutes. Cool to 45-50ºC, mix well, avoiding the formation of bubbles and dispense carefully into Petri Dishes. DO NOT OVEARHEAT. The prepared medium should be stored at 8-15°C. The color is tournasol blue. Sterilization reduces the methylene blue, leaving the medium orange in color. The normal purple may be restored by gently mixing. The reduced medium should be shaken to oxidize the methylene blue; otherwise a dark zone from the top extending downwards will gradually appear. The dehydrated medium should be homogeneous, free flowing and purple-rose flocculent precipitate in color. If there are any physical changes, discard the medium. Uses EOSIN METHYLENE BLUE AGAR is a differential medium similar to Levine EMB Agar (Cat. 1050) and is used for the isolation of Enterobacteria. The use of Eosin Y and Methylene Blue enable differentiation between lactose- fermenting and non-fermenting organisms. -
Survival and Ice Nucleation Activity of Pseudomonas Syringae Strains Exposed To
bioRxiv preprint doi: https://doi.org/10.1101/408906; this version posted September 6, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Survival and ice nucleation activity of Pseudomonas syringae strains exposed to 2 simulated high-altitude atmospheric conditions 3 Gabriel Guarany de Araujoa, Fabio Rodriguesb, Fabio Luiz Teixeira Gonçalvesc, Douglas 4 Galanted,* 5 a Interunities Graduate Program in Biotechnology, University of São Paulo, Brazil 6 b Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, 7 Brazil 8 c Department of Atmospheric Sciences, Institute of Astronomy, Geophysics and 9 Atmospheric Sciences, University of São Paulo, Brazil 10 d Brazilian Synchrotron Light Laboratory, Brazilian Center for Research in Energy and 11 Materials, Brazil 12 * Corresponding author. Brazilian Synchrotron Light Laboratory, Av. Giuseppe Máximo 13 Scolfaro, 10000, CEP 13083‐100, Campinas, São Paulo, Brazil, Tel.: +551935175081; Fax: 14 +551935121004. E-mail address: [email protected] 15 Running title: Survival of ice nucleating bacteria on the atmosphere 16 ABSTRACT 17 The epiphytic bacterium Pseudomonas syringae produces the most efficient and 18 well-studied biological ice nuclei (IN) known. Bioaerosols containing these cells have been 19 proposed to influence cloud glaciation, an important process in the initiation of 20 precipitation. The presence of this species has been reported on rain, snow, and cloud water 1 bioRxiv preprint doi: https://doi.org/10.1101/408906; this version posted September 6, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
BEI Resources Product Information Sheet Catalog No. NR-51597 Pseudomonas Aeruginosa, Strain MRSN 23861
Product Information Sheet for NR-51597 Pseudomonas aeruginosa, Strain MRSN P. aeruginosa is a Gram-negative, aerobic, rod-shaped bacterium with unipolar motility that thrives in many diverse 23861 environments including soil, water and certain eukaryotic hosts. It is a key emerging opportunistic pathogen in animals, Catalog No. NR-51597 including humans and plants. While it rarely infects healthy This reagent is the tangible property of the U.S. Government. individuals, P. aeruginosa causes severe acute and chronic nosocomial infections in immunocompromised or catheterized patients, especially in patients with cystic fibrosis, burns, For research use only. Not for human use. cancer or HIV.3-5 Infections of this type are often highly antibiotic resistant, difficult to eradicate and often lead to Contributor: death. The ability of P. aeruginosa to survive on minimal Multidrug-Resistant Organism Repository and Surveillance nutritional requirements, tolerate a variety of physical Network (MRSN), Bacterial Disease Branch, Walter Reed conditions and rapidly develop resistance during the course of Army Institute of Research, Silver Spring, Maryland, USA therapy has allowed it to persist in both community and 5,6 hospital settings. Manufacturer: BEI Resources Material Provided: Each vial contains approximately 0.5 mL of bacterial culture in Product Description: Tryptic Soy broth supplemented with 10% glycerol. Bacteria Classification: Pseudomonadaceae, Pseudomonas Species: Pseudomonas aeruginosa Note: If homogeneity is required for your intended use, please Strain: MRSN 23861 purify prior to initiating work. Original Source: Pseudomonas aeruginosa (P. aeruginosa), strain MRSN 23861 was isolated in 2014 from a human Packaging/Storage: respiratory sample as part of a surveillance program in the NR-51597 was packaged aseptically in cryovials. -
Pseudomonas Syringae Subsp. Savastanoi (Ex Smith) Subsp
INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY, Apr. 1982, p. 146-169 Vol. 32. No. 2 0020-771 3/82/020166-O4$02.OO/O Pseudomonas syringae subsp. savastanoi (ex Smith) subsp. nov., nom. rev., the Bacterium Causing Excrescences on Oleaceae and Neriurn oleander L. J. D. JANSE Department of Bacteriology, Plant Protection Service, 6700 HC, Wageningen, The Netherlands From a study of the so-called bacterial canker of ash, caused by a variant of “Pseudomonas savastanoi” (Smith) Stevens, it became evident that this variant and the variants of “P. savastanoi” which cause olive knot and oleander knot can be distinguished from one another on the basis of their pathogenicity and host range. All isolates of “P. savastanoi” were recently classified by Dye et al. (Plant Pathol. 59:153-168,1980) as members of a single pathovar of P. syringae van Hall. It appears, however, that these isolates differ sufficiently from the other members of P. syringae to justify subspecies rank for them. The following classification and nomenclature are therefore proposed: Pseudomonas syringae subsp. savastanoi (ex Smith) subsp. nov., nom. rev., to include the olive pathogen (pathovar oleae), the ash pathogen (pathovar fraxini), and the oleander pathogen (pathovar nerii). The type strain of P. syringae subsp. savastanoi is ATCC 13522 (= NCPPB 639). “Pseudomonas savastanoi” (Smith 1908) Ste- mended in the International Code of Nomencla- vens 1913 was previously used as the name of ture of Bacteria (8). the bacterium which causes pernicious excres- According to the available data, the present cences on several species of the Oleaceae. classificationand nomenclature of the organisms (Names in quotation marks are not on the Ap- under discussion are inadequate.