Distribution of Pseudomonas Species in a Dairy Plant Affected By
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The Ever-Expanding Pseudomonas Genus: Description of 43
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 14 July 2021 doi:10.20944/preprints202107.0335.v1 Article The Ever-Expanding Pseudomonas Genus: Description of 43 New Species and Partition of the Pseudomonas Putida Group Léa Girard1+, Cédric Lood1,2+, Monica Höfte3, Peter Vandamme4, Hassan Rokni-Zadeh5, Vera van Noort1,6, Rob Lavigne2*, René De Mot1,* 1 Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Aren- berg 20, 3001 Leuven, Belgium; [email protected] (L.G.), [email protected] (C.L.), [email protected] (V.v.N.) 2 Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium; [email protected] 3 Department of Plants and Crops, Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium 4 Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; [email protected] 5 Zanjan Pharmaceutical Biotechnology Research Center, Zanjan University of Medical Sciences, 45139-56184 Zanjan, Iran; [email protected] 6 Institute of Biology, Leiden University, Sylviusweg 72, 2333 Leiden, The Netherlands + The authors contributed equally to this work. * Correspondence: [email protected], +3216379524; [email protected] ; Tel.: +3216329681 Abstract: The genus Pseudomonas hosts an extensive genetic diversity and is one of the largest genera among Gram-negative bacteria. Type strains of Pseudomonas are well-known to represent only a small fraction of this diversity and the number of available Pseudomonas genome sequences is increasing rapidly. Consequently, new Pseudomonas species are regularly reported and the number of species within the genus is in constant evolution. -
Università Degli Studi Di Padova Dipartimento Di Biomedicina Comparata Ed Alimentazione
UNIVERSITÀ DEGLI STUDI DI PADOVA DIPARTIMENTO DI BIOMEDICINA COMPARATA ED ALIMENTAZIONE SCUOLA DI DOTTORATO IN SCIENZE VETERINARIE Curriculum Unico Ciclo XXVIII PhD Thesis INTO THE BLUE: Spoilage phenotypes of Pseudomonas fluorescens in food matrices Director of the School: Illustrious Professor Gianfranco Gabai Department of Comparative Biomedicine and Food Science Supervisor: Dr Barbara Cardazzo Department of Comparative Biomedicine and Food Science PhD Student: Andreani Nadia Andrea 1061930 Academic year 2015 To my family of origin and my family that is to be To my beloved uncle Piero Science needs freedom, and freedom presupposes responsibility… (Professor Gerhard Gottschalk, Göttingen, 30th September 2015, ProkaGENOMICS Conference) Table of Contents Table of Contents Table of Contents ..................................................................................................................... VII List of Tables............................................................................................................................. XI List of Illustrations ................................................................................................................ XIII ABSTRACT .............................................................................................................................. XV ESPOSIZIONE RIASSUNTIVA ............................................................................................ XVII ACKNOWLEDGEMENTS .................................................................................................... -
Isolation and Identification of Endophytic Bacteria from Mycorrhizal Tissues of Terrestrial Orchids from Southern Chile
diversity Article Isolation and Identification of Endophytic Bacteria from Mycorrhizal Tissues of Terrestrial Orchids from Southern Chile Héctor Herrera 1 , Tedy Sanhueza 1, AlžbˇetaNovotná 2, Trevor C. Charles 3 and Cesar Arriagada 1,* 1 Laboratorio de Biorremediación, Facultad de Ciencias Agropecuarias y Forestales, Departamento de Ciencias Forestales, Universidad de La Frontera, 4811230 Temuco, Chile; [email protected] (H.H.); [email protected] (T.S.) 2 Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 Ceskˇ é Budˇejovice,Czech Republic; [email protected] 3 Department of Biology, University of Waterloo, University Avenue West, Waterloo, ON N2L 3G1, Canada; [email protected] * Correspondence: [email protected]; Tel.: +56-045-232-5635; Fax: +56-045-234-1467 Received: 24 December 2019; Accepted: 24 January 2020; Published: 30 January 2020 Abstract: Endophytic bacteria are relevant symbionts that contribute to plant growth and development. However, the diversity of bacteria associated with the roots of terrestrial orchids colonizing Andean ecosystems is limited. This study identifies and examines the capabilities of endophytic bacteria associated with peloton-containing roots of six terrestrial orchid species from southern Chile. To achieve our goals, we placed superficially disinfected root fragments harboring pelotons on oatmeal agar (OMA) with no antibiotic addition and cultured them until the bacteria appeared. Subsequently, they were purified and identified using molecular tools and examined for plant growth metabolites production and antifungal activity. In total, 168 bacterial strains were isolated and assigned to 8 OTUs. The orders Pseudomonadales, Burkholderiales, and Xanthomonadales of phylum Proteobacteria were the most frequent. The orders Bacillales and Flavobacteriales of the phylla Firmicutes and Bacteroidetes were also obtained. -
Mitigating Biofouling on Reverse Osmosis Membranes Via Greener Preservatives
Mitigating biofouling on reverse osmosis membranes via greener preservatives by Anna Curtin Biology (BSc), Le Moyne College, 2017 A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of MASTER OF APPLIED SCIENCE in the Department of Civil Engineering, University of Victoria © Anna Curtin, 2020 University of Victoria All rights reserved. This Thesis may not be reproduced in whole or in part, by photocopy or other means, without the permission of the author. Supervisory Committee Mitigating biofouling on reverse osmosis membranes via greener preservatives by Anna Curtin Biology (BSc), Le Moyne College, 2017 Supervisory Committee Heather Buckley, Department of Civil Engineering Supervisor Caetano Dorea, Department of Civil Engineering, Civil Engineering Departmental Member ii Abstract Water scarcity is an issue faced across the globe that is only expected to worsen in the coming years. We are therefore in need of methods for treating non-traditional sources of water. One promising method is desalination of brackish and seawater via reverse osmosis (RO). RO, however, is limited by biofouling, which is the buildup of organisms at the water-membrane interface. Biofouling causes the RO membrane to clog over time, which increases the energy requirement of the system. Eventually, the RO membrane must be treated, which tends to damage the membrane, reducing its lifespan. Additionally, antifoulant chemicals have the potential to create antimicrobial resistance, especially if they remain undegraded in the concentrate water. Finally, the hazard of chemicals used to treat biofouling must be acknowledged because although unlikely, smaller molecules run the risk of passing through the membrane and negatively impacting humans and the environment. -
To Obtain Approval for Projects to Develop Genetically Modified Organisms in Containment
APPLICATION FORM Containment – GMO Project To obtain approval for projects to develop genetically modified organisms in containment Send to Environmental Protection Authority preferably by email ([email protected]) or alternatively by post (Private Bag 63002, Wellington 6140) Payment must accompany final application; see our fees and charges schedule for details. Application Number APP203205 Date 02/10/2017 www.epa.govt.nz 2 Application Form Approval for projects to develop genetically modified organisms in containment Completing this application form 1. This form has been approved under section 42A of the Hazardous Substances and New Organisms (HSNO) Act 1996. It only covers projects for development (production, fermentation or regeneration) of genetically modified organisms in containment. This application form may be used to seek approvals for a range of new organisms, if the organisms are part of a defined project and meet the criteria for low risk modifications. Low risk genetic modification is defined in the HSNO (Low Risk Genetic Modification) Regulations: http://www.legislation.govt.nz/regulation/public/2003/0152/latest/DLM195215.html. 2. If you wish to make an application for another type of approval or for another use (such as an emergency, special emergency or release), a different form will have to be used. All forms are available on our website. 3. It is recommended that you contact an Advisor at the Environmental Protection Authority (EPA) as early in the application process as possible. An Advisor can assist you with any questions you have during the preparation of your application. 4. Unless otherwise indicated, all sections of this form must be completed for the application to be formally received and assessed. -
Aquatic Microbial Ecology 80:15
The following supplement accompanies the article Isolates as models to study bacterial ecophysiology and biogeochemistry Åke Hagström*, Farooq Azam, Carlo Berg, Ulla Li Zweifel *Corresponding author: [email protected] Aquatic Microbial Ecology 80: 15–27 (2017) Supplementary Materials & Methods The bacteria characterized in this study were collected from sites at three different sea areas; the Northern Baltic Sea (63°30’N, 19°48’E), Northwest Mediterranean Sea (43°41'N, 7°19'E) and Southern California Bight (32°53'N, 117°15'W). Seawater was spread onto Zobell agar plates or marine agar plates (DIFCO) and incubated at in situ temperature. Colonies were picked and plate- purified before being frozen in liquid medium with 20% glycerol. The collection represents aerobic heterotrophic bacteria from pelagic waters. Bacteria were grown in media according to their physiological needs of salinity. Isolates from the Baltic Sea were grown on Zobell media (ZoBELL, 1941) (800 ml filtered seawater from the Baltic, 200 ml Milli-Q water, 5g Bacto-peptone, 1g Bacto-yeast extract). Isolates from the Mediterranean Sea and the Southern California Bight were grown on marine agar or marine broth (DIFCO laboratories). The optimal temperature for growth was determined by growing each isolate in 4ml of appropriate media at 5, 10, 15, 20, 25, 30, 35, 40, 45 and 50o C with gentle shaking. Growth was measured by an increase in absorbance at 550nm. Statistical analyses The influence of temperature, geographical origin and taxonomic affiliation on growth rates was assessed by a two-way analysis of variance (ANOVA) in R (http://www.r-project.org/) and the “car” package. -
Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior
bioRxiv preprint doi: https://doi.org/10.1101/499715; this version posted December 19, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1! Introducing THOR, a model microbiome for genetic dissection of community behavior 2! 3! 4! Gabriel L. Lozano1,2, Juan I. Bravo1,2, Manuel F. Garavito Diago1, Hyun Bong Park3,4, Amanda 5! Hurley1, S. Brook Peterson5, Eric V. Stabb6, Jason M. Crawford3,4,7, Nichole A. Broderick8, Jo 6! Handelsman1,2* 7! 8! 9! ¹Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin- 10! Madison 11! 2Department of Molecular, Cellular and Developmental Biology, Yale University 12! 3Department of Chemistry, Yale University 13! 4Chemical Biology Institute, Yale University 14! 5Department of Microbiology, University of Washington 15! 6Department of Microbiology, University of Georgia 16! 7Department of Microbial Pathogenesis, Yale School of Medicine 17! 8Department of Molecular and Cell Biology, University of Connecticut 18! 19! *To whom correspondence should be addressed [email protected] 20! 21! 22! ! 1! bioRxiv preprint doi: https://doi.org/10.1101/499715; this version posted December 19, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 23! ABSTRACT 24! The quest to manipulate microbiomes has intensified, but many microbial communities have 25! proven recalcitrant to sustained change. -
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. -
Draft Genome Sequence of Pseudomonas Moraviensis Strain Devor Implicates Metabolic Versatility and Bioremediation Potential
Genomics Data 9 (2016) 154–159 Contents lists available at ScienceDirect Genomics Data journal homepage: www.elsevier.com/locate/gdata Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential Neil T. Miller a,DannyFullera,M.B.Cougera, Mark Bagazinski a,PhilipBoynea, Robert C. Devor a, Radwa A. Hanafy a, Connie Budd a, Donald P. French b, Wouter D. Hoff a, Noha Youssef a,⁎ a Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States b Department of Integrative Biology, Oklahoma State University, Stillwater, OK, United States article info abstract Article history: Pseudomonas moraviensis is a predominant member of soil environments. We here report on the genomic Received 19 July 2016 analysis of Pseudomonas moraviensis strain Devor that was isolated from a gate at Oklahoma State University, Accepted 2 August 2016 Stillwater, OK, USA. The partial genome of Pseudomonas moraviensis strain Devor consists of 6016489 bp of Available online 4 August 2016 DNA with 5290 protein-coding genes and 66 RNA genes. This is the first detailed analysis of a P. moraviensis genome. Genomic analysis revealed metabolic versatility with genes involved in the metabolism and transport Keywords: of fructose, xylose, mannose and all amino acids with the exception of tryptophan and valine, implying that Pseudomonas moraviensis Draft genome sequence the organism is a versatile heterotroph. The genome of P. moraviensis strain Devor was rich in transporters Detailed analysis and, based on COG analysis, did not cluster closely with P. moraviensis R28-S genome, the only previous report Student Initiated Microbial Discovery (SIMD) of a P. -
Pseudomonas Eucalypticola Sp. Nov., a Producer of Antifungal Agents Isolated from Eucalyptus Dunnii Leaves
www.nature.com/scientificreports OPEN Pseudomonas eucalypticola sp. nov., a producer of antifungal agents isolated from Eucalyptus dunnii leaves Yujing Liu, Zhang Song, Hualong Zeng, Meng Lu, Weiyao Zhu, Xiaoting Wang, Xinkun Lian & Qinghua Zhang* Pseudomonas are ubiquitously occurring microorganisms and are known for their ability to produce antimicrobials. An endophytic bacterial strain NP-1 T, isolated from Eucalyptus dunnii leaves, exhibits antifungal properties against fve tested phytopathogenic fungi. The strain is a Gram-negative rod- shaped bacterium containing a single polar fagellum. It is strictly aerobic, grows at 4–37 °C, 2–5% NaCl, and pH 3–7. The 16S rRNA sequence analysis showed that NP-1 T belongs to the Pseudomonas genus. Phylogenetic analysis based on four concatenated partial genes (16S rDNA, gyrB, rpoB and rpoD) and the phylogenomic tree indicated that NP-1 T belongs to Pseudomonas fuorescens lineage but is distinct from any known Pseudomonas species. The G + C mol % of NP-1 T genome is 63.96, and the diferences between NP-1 T and related species are larger than 1. The digital DNA- DNA hybridization and tetranucleotide signatures are 23.8 and 0.97, which clearly separates strain NP-1 T from its closest neighbours, Pseudomonas coleopterorum and Pseudomonas rhizosphaerae. Its phenotypic and chemotaxonomic features confrmed its diferentiation from related taxa. The results from this polyphasic approach support the classifcation of NP-1 T as a novel species of Pseudomonas, and the name of Pseudomonas eucalypticola is thus proposed for this strain, whose type is NP-1 T (= CCTCC M2018494T = JCM 33572 T). Te genus Pseudomonas belongs to the family Pseudomonadaceae within γ-Proteobacteria and is composed of Gram-negative, aerobic, non-spore forming rod-shaped bacteria that are motile by polar fagella1. -
Comparative Analysis of the Core Proteomes Among The
diversity Article Comparative Analysis of the Core Proteomes among the Pseudomonas Major Evolutionary Groups Reveals Species-Specific Adaptations for Pseudomonas aeruginosa and Pseudomonas chlororaphis Marios Nikolaidis 1, Dimitris Mossialos 2 , Stephen G. Oliver 3 and Grigorios D. Amoutzias 1,* 1 Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece; [email protected] 2 Microbial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece; [email protected] 3 Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK; [email protected] * Correspondence: [email protected]; Tel.: +30-2410-565-289; Fax: +30-2410-565-290 Received: 22 June 2020; Accepted: 22 July 2020; Published: 24 July 2020 Abstract: The Pseudomonas genus includes many species living in diverse environments and hosts. It is important to understand which are the major evolutionary groups and what are the genomic/proteomic components they have in common or are unique. Towards this goal, we analyzed 494 complete Pseudomonas proteomes and identified 297 core-orthologues. The subsequent phylogenomic analysis revealed two well-defined species (Pseudomonas aeruginosa and Pseudomonas chlororaphis) and four wider phylogenetic groups (Pseudomonas fluorescens, Pseudomonas stutzeri, Pseudomonas syringae, Pseudomonas putida) with a sufficient number of proteomes. As expected, the genus-level core proteome was highly enriched for proteins involved in metabolism, translation, and transcription. In addition, between 39–70% of the core proteins in each group had a significant presence in each of all the other groups. Group-specific core proteins were also identified, with P. aeruginosa having the highest number of these and P. -
Supplementary Materials For
Supplementary Materials for Positive interactions are common among culturable bacteria Jared Kehe, Anthony Ortiz, Anthony Kulesa, Jeff Gore, Paul C. Blainey, Jonathan Friedman Correspondence to: [email protected], [email protected] This PDF file includes: Materials and Methods Figs. S1 to S21 Tables S1 to S3 Materials and Methods Strain isolation from soil samples Soil samples (two ~12cm columns of topsoil, ~4cm in diameter) were collected from multiple locations in greater Boston on November 12, 2017 (5.6°C) (specific locations listed in Table S1). Each sample was diluted in PBS within a few hours of collection (5 g soil vortexed in 40 mL PBS). Single strains were first isolated by streaking 70 µL of dilutions of this mixture (10- 1, 10-2, 10-3, and 10-4) on 20 different solid (agar) media [Tryptic Soy Broth (TSB) (Bacto), 1% v/v TSB, Lysogeny Broth (LB) (Bacto), 1% v/v LB, Nutrient Broth (NB) (Bacto), 1% v/v NB, M9 salts (Sigma-Aldrich) + 0.5% w/v glucose, M9 salts + 0.005% w/v glucose, M9 salts + 0.005% w/v glucose + 0.2% w/v casamino acids, M9 salts + 0.005% w/v glucose + 0.002% w/v casamino acids, M9 salts + 0.5% w/v glucose + 0.2% w/v casamino acids at pH = 4 and 5, M9 salts + 0.005% w/v glucose + 0.002% w/v casamino acids at pH = 4 and 5, Actinomycete Isolation Agar (Teknova), Brucella Agar (Teknova), Streptomyces Medium (Teknova), Campylobacter Medium (Teknova), Bordetella Medium (Teknova), and ATCC Medium 1111 (Teknova)].