DOCSLIB.ORG

TECHNISCHE UNIVERSITÄT MÜNCHEN Identification And

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
TECHNISCHE UNIVERSITÄT MÜNCHEN Identification And TECHNISCHE UNIVERSITÄT MÜNCHEN Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt Lehrstuhl für Technische Mikrobiologie Identification and growth dynamics of meat spoilage microbiota in modified atmosphere packaged poultry meat Linda Höll 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. Vorsitzende/-r: Prof Dr. Karl-Heinz Engel Prüfende/-r der Dissertation: 1. Prof. Dr. Rudi F. Vogel 2. Prof. Dr. Horst-Christian Langowski Die Dissertation wurde am 08.02.2018 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 18.05.2018 angenommen. Identification and growth dynamics of meat spoilage microbiota in modified atmosphere packaged poultry meat Linda Höll Doctoral Thesis Freising 2018 Diese Arbeit wurde gefördert durch das Bundeministerium für Wirtschaft und Energie (BMWi) über die Arbeitsgemeinschaft industrieller Forschungsvereinigungen (AiF) und die Industrievereinigung für Lebensmitteltechnologie und Verpackung e. V. (IVLV) im Rahmen des Projektes AiF 17803 N. Teile dieser Arbeit wurden vorab in Fachzeitschriften publiziert. Details dazu sind in Kapitel 9 List of Publications and Student Theses (Seite 163) zu finden. Danksagung Danksagung Besonders möchte ich mich bei meinem Doktorvater Prof. Dr. Rudi F. Vogel bedanken, ohne den diese Arbeit nicht möglich gewesen wäre. Danke für dein entgegengebrachtes Vertrauen, die zahlreichen Diskussionsrunden, die ständige Unterstützung und deine große Geduld. Außerdem möchte ich mich herzlich bei Prof. Dr. Horst-Christian Langowski für die Begutachtung der Arbeit bedanken, sowie bei Prof. Dr. Karl-Heinz Engel für die Übernahme des Prüfungsvorsitzes. Ich danke meinen Projektpartnern Corinna Franke, Bendix Koopmann und Dr. Hannes Petermeier für die vielen fachübergreifenden Diskussionen und die konstruktive Zusammenarbeit. Prof. Dr. Matthias Ehrmann und Prof. Dr. Ludwig Niessen danke ich für die vielen Ratschläge und praktischen Tipps. Ein großes Dankeschön geht außerdem an Dr. Andreas Geißler und Dr. Jürgen Behr, die mich durch den Dschungel der Bioinformatik geleitet haben und ohne deren Zeit und Geduld Teile dieser Arbeit niemals machbar gewesen wären. Ich bedanke mich bei Angela Seppeur für die Unterstützung bei allen Organisationsfragen. Bei Sabine Forster, Maggie Schreiber, Andrea Pape und Monika Engel für die Unterstützung und Hilfe bei allen Fragen, sowie kleinen und großen Missgeschicken im Laboralltag. Ganz besonders möchte ich mich bei den anderen Kollegen vom TMW Lehrstuhl bedanken, mit denen die drei Jahre wie im Flug vergangen sind. Aus einigen wurden in dieser Zeit echte Freunde. Danke für die offenen Arme, die Schultern zum Anlehnen und Ohren zum Zuhören, für die unterhaltsamen Mittagspausen, Ausflüge ins Freisinger Nachtleben, für die kulinarischen Neu-Entdeckungen und die schönen Radtouren und Bergabenteuer. Außerdem möchte ich mich bei den Personen bedanken, die die Freisinger Zeit zu einer unvergesslichen gemacht haben und die mir sehr ans Herz gewachsen sind. Danke Evi und Philipp, ihr seid großartige Freunde geworden und ich hoffe das bleibt noch lange so! Und danke Steffi, der besten Mitbewohnerin der Welt, egal auf welchem Kontinent sie gerade ist. Zuletzt möchte ich mich von ganzem Herzen bei den wichtigsten Menschen in meinem Leben bedanken, Andy und meiner Familie. Für die Liebe, Geborgenheit, Unterstützung, Ehrlichkeit und die unendliche Geduld. Für das Vertrauen und Verständnis und die immer neue Kraft! Und bei meiner unvergesslichen Oma Rosl. Für den unermesslichen „Allgäuer Gwalt“, der einen die höchsten Gipfel im Leben erklimmen lässt. I Index Index Danksagung ........................................................................................................................... I Abbreviations ....................................................................................................................... VI 1 Introduction ........................................................................................................................ 1 1.1. A short history of food preservation ................................................................................ 1 1.2. Food consumption and loss in the 21st century ............................................................... 4 1.3. Ecological niche meat ..................................................................................................... 7 1.3.1. Biochemistry of meat and fat ....................................................................................... 7 1.3.2. Meat spoilage microbiota and their metabolic activities ................................................ 9 1.4. The detection and identification of meat-spoiling bacteria ............................................. 15 2 Hypotheses and Objectives .............................................................................................. 18 3 Material and Methods ....................................................................................................... 19 3.1. MALDI-TOF MS ............................................................................................................ 19 3.1.1. Direct transfer ............................................................................................................ 19 3.1.2. Cell extraction ............................................................................................................ 19 3.1.3. Data processing ......................................................................................................... 20 3.1.4. New entrance to the database ................................................................................... 20 3.1.5. Cluster analysis ......................................................................................................... 20 3.2. Detection and identification of volatile organic compounds by PTR- and HS-SPME GC- MS....................................................................................................................................... 21 3.3. HPLC analysis .............................................................................................................. 23 3.3.1. Analysis of amino acids ............................................................................................. 23 3.3.2. Analysis of organic acids ........................................................................................... 23 3.3.3. Analysis of carbohydrates .......................................................................................... 23 3.4. Spoilage experiments ................................................................................................... 24 3.4.1. Microbial enumeration ............................................................................................... 24 3.4.2. Determination of chemical parameters ...................................................................... 25 3.4.2.1. Determination of the gas composition ..................................................................... 25 3.4.2.2. pH measurement .................................................................................................... 25 II Index 3.4.3. Methods and aims of different spoilage experiments ................................................. 25 3.4.3.1. Establishment of a database for meat borne bacteria ............................................. 25 3.4.3.2. Identification and growth dynamics of the autochthonous microbiota in different atmospheres and storage temperatures .............................................................................. 26 3.4.3.3. Detection of volatile metabolites during (spontaneous) spoilage ............................. 27 3.4.3.4. Detection of volatile metabolites in single strain experiments .................................. 29 3.4.3.5. Sensory evaluation of meat spoilage ...................................................................... 30 3.5. Isolation and characterization of single strains .............................................................. 32 3.5.1. Media and culture conditions of isolated strains ......................................................... 34 3.5.2. Isolation of bacterial DNA .......................................................................................... 34 3.5.3. 16S rDNA sequence analysis .................................................................................... 34 3.5.4. Random-amplified polymorphic DNA (RAPD) PCR ................................................... 36 3.5.5. Antibiotic tests ........................................................................................................... 37 3.6. Genomics ..................................................................................................................... 38 3.6.1. Genomic DNA extraction ........................................................................................... 38 3.6.2. Data analysis ............................................................................................................. 38 3.7. Transcriptomics ............................................................................................................ 40 3.7.1. RNA extraction .........................................................................................................
Load more

Recommended publications
  • Comparative Analysis of the Core Proteomes Among The
    Diversity 2020, 12, 289 1 of 25 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.: +30‐2410‐565289; Fax: +30‐2410‐565290 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.
    [Show full text]
  • Wild Apple-Associated Fungi and Bacteria Compete to Colonize the Larval Gut of an Invasive Wood-Borer Agrilus Mali in Tianshan Forests
    Wild apple-associated fungi and bacteria compete to colonize the larval gut of an invasive wood-borer Agrilus mali in Tianshan forests Tohir Bozorov ( [email protected] ) Xinjiang Institute of Ecology and Geography https://orcid.org/0000-0002-8925-6533 Zokir Toshmatov Plant Genetics Research Unit: Genetique Quantitative et Evolution Le Moulon Gulnaz Kahar Xinjiang Institute of Ecology and Geography Daoyuan Zhang Xinjiang Institute of Ecology and Geography Hua Shao Xinjiang Institute of Ecology and Geography Yusufjon Gafforov Institute of Botany, Academy of Sciences of Uzbekistan Research Keywords: Agrilus mali, larval gut microbiota, Pseudomonas synxantha, invasive insect, wild apple, 16S rRNA and ITS sequencing Posted Date: March 16th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-287915/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/17 Abstract Background: The gut microora of insects plays important roles throughout their lives. Different foods and geographic locations change gut bacterial communities. The invasive wood-borer Agrilus mali causes extensive mortality of wild apple, Malus sieversii, which is considered a progenitor of all cultivated apples, in Tianshan forests. Recent analysis showed that the gut microbiota of larvae collected from Tianshan forests showed rich bacterial diversity but the absence of fungal species. In this study, we explored the antagonistic ability of gut bacteria to address this absence of fungi in the larval gut. Results: The results demonstrated that gut bacteria were able to selectively inhibit wild apple tree-associated fungi. However, Pseudomonas synxantha showed strong antagonistic ability, producing antifungal compounds. Using different analytical methods, such as column chromatography, mass spectrometry, HPLC and NMR, an antifungal compound, phenazine-1-carboxylic acid (PCA), was identied.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 7476,532 B2 Schneider Et Al
    USOO7476532B2 (12) United States Patent (10) Patent No.: US 7476,532 B2 Schneider et al. (45) Date of Patent: Jan. 13, 2009 (54) MANNITOL INDUCED PROMOTER Makrides, S.C., "Strategies for achieving high-level expression of SYSTEMIS IN BACTERAL, HOST CELLS genes in Escherichia coli,” Microbiol. Rev. 60(3):512-538 (Sep. 1996). (75) Inventors: J. Carrie Schneider, San Diego, CA Sánchez-Romero, J., and De Lorenzo, V., "Genetic engineering of nonpathogenic Pseudomonas strains as biocatalysts for industrial (US); Bettina Rosner, San Diego, CA and environmental process.” in Manual of Industrial Microbiology (US) and Biotechnology, Demain, A, and Davies, J., eds. (ASM Press, Washington, D.C., 1999), pp. 460-474. (73) Assignee: Dow Global Technologies Inc., Schneider J.C., et al., “Auxotrophic markers pyrF and proC can Midland, MI (US) replace antibiotic markers on protein production plasmids in high cell-density Pseudomonas fluorescens fermentation.” Biotechnol. (*) Notice: Subject to any disclaimer, the term of this Prog., 21(2):343-8 (Mar.-Apr. 2005). patent is extended or adjusted under 35 Schweizer, H.P.. "Vectors to express foreign genes and techniques to U.S.C. 154(b) by 0 days. monitor gene expression in Pseudomonads. Curr: Opin. Biotechnol., 12(5):439-445 (Oct. 2001). (21) Appl. No.: 11/447,553 Slater, R., and Williams, R. “The expression of foreign DNA in bacteria.” in Molecular Biology and Biotechnology, Walker, J., and (22) Filed: Jun. 6, 2006 Rapley, R., eds. (The Royal Society of Chemistry, Cambridge, UK, 2000), pp. 125-154. (65) Prior Publication Data Stevens, R.C., “Design of high-throughput methods of protein pro duction for structural biology.” Structure, 8(9):R177-R185 (Sep.
    [Show full text]
  • 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.
    [Show full text]
  • Characterisation of Pseudomonas Spp. Isolated from Foods
    07.QXD 9-03-2007 15:08 Pagina 39 Annals of Microbiology, 57 (1) 39-47 (2007) Characterisation of Pseudomonas spp. isolated from foods Laura FRANZETTI*, Mauro SCARPELLINI Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, sezione Microbiologia Agraria Alimentare Ecologica, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy Received 30 June 2006 / Accepted 27 December 2006 Abstract - Putative Pseudomonas spp. (102 isolates) from different foods were first characterised by API 20NE and then tested for some enzymatic activities (lipase and lecithinase production, starch hydrolysis and proteolytic activity). However subsequent molecular tests did not always confirm the results obtained, thus highlighting the limits of API 20NE. Instead RFLP ITS1 and the sequencing of 16S rRNA gene grouped the isolates into 6 clusters: Pseudomonas fluorescens (cluster I), Pseudomonas fragi (cluster II and V) Pseudomonas migulae (cluster III), Pseudomonas aeruginosa (cluster IV) and Pseudomonas chicorii (cluster VI). The pectinolytic activity was typical of species isolated from vegetable products, especially Pseudomonas fluorescens. Instead Pseudomonas fragi, predominantly isolated from meat was characterised by proteolytic and lipolytic activities. Key words: Pseudomonas fluorescens, enzymatic activity, ITS1. INTRODUCTION the most frequently found species, however the species dis- tribution within the food ecosystem remains relatively The genus Pseudomonas is the most heterogeneous and unknown (Arnaut-Rollier et al., 1999). The principal micro- ecologically significant group of known bacteria, and bial population of many vegetables in the field consists of includes Gram-negative motile aerobic rods that are wide- species of the genus Pseudomonas, especially the fluores- spread throughout nature and characterised by elevated cent forms.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 7,618,799 B2 Coleman Et Al
    US007618799B2 (12) United States Patent (10) Patent No.: US 7,618,799 B2 Coleman et al. (45) Date of Patent: Nov. 17, 2009 (54) BACTERIAL LEADER SEQUENCES FOR NCBI Report for Accession No.YP 346180, Direct Submission on INCREASED EXPRESSION Aug. 8, 2005. Huber, D., “Use of Thioredoxin as a Reporter to Identify a Subset of Escherichia coli Signal Sequences That Promote Signal Recognition (75) Inventors: Russell J. Coleman, San Diego, CA Particle-Dependent Translocation.” Journal of Bacteriology, 2005, (US); Diane Retallack, Poway, CA pp. 2983-2991, vol. 187 (9). (US); Jane C. Schneider, San Diego, Miot, M. and Betton, J., “Protein Quality Control in the Bacterial CA (US); Thomas M. Ramseier, Periplasm.” Microbial Cell Factories, 2004, pp. 1-13. Newton, MA (US); Charles D. Ma, Q., et al., “Protein Secretion Systems of Pseudomonas Hershberger, Poway, CA (US); Stacey aeruginosa and Pfluorescens.” Biochim. Biophys. Acta, Apr. 1, 2003, Lee, San Diego, CA (US): Sol M. pp. 223-233, vol. 1611, No. 1-2. Resnick, Encinitas, CA (US) Retallack, D.M., et al..."Transport of Heterologous Proteins to the Periplasmic Space of Pseudomonas fluorescens Using a Variety of (73) Assignee: Dow Global Technologies Inc, Midland, Native Signal Sequences, ’’ Biotechnol Lett, Oct. 2007, pp. 1483 MI (US) 1491, vol. 29, No. 10. Urban, A., et al., “DsbA and DsbC Affect Extracellular Enzyme Formation in Pseudomonas aeruginosa. J. Bacteriol. Jan. 2001, pp. (*) Notice: Subject to any disclaimer, the term of this 587-596, vol. 183, No. 2. patent is extended or adjusted under 35 Wang, H., et al., “High-level Expression of Human TFF3 in U.S.C.
    [Show full text]
  • Bacterial Diversity from Benthic Mats of Antarctic Lakes As a Source of New Bioactive Metabolites
    Marine Genomics 2 (2009) 33–41 Contents lists available at ScienceDirect Marine Genomics journal homepage: www.elsevier.com/locate/margen Bacterial diversity from benthic mats of Antarctic lakes as a source of new bioactive metabolites Jose Luis Rojas a, Jesús Martín a,1, José Rubén Tormo a,1, Francisca Vicente a,1,MaraBrunatib,2, Ismaela Ciciliato b,3, Daniele Losi b,4, Stefanie Van Trappen c, Joris Mergaert c, Jean Swings c, Flavia Marinelli d, Olga Genilloud a,⁎,1 a CIBE, Merck Research Laboratories, Merck Sharp and Dohme de España S.A., Josefa Valcárcel 38, E-28027 Madrid, Spain b Vicuron Pharmaceuticals (formerly Biosearch Italia S.p.A), Via R. Lepetit 34, 21040 Gerenzano, Varese, Italy c Laboratorium voor Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium d DBSM, University of Insubria, J.H. Dunant 3, 21100 Varese, Italy article info abstract Article history: During the MICROMAT project, the bacterial diversity of microbial mats growing in the benthic environment Received 23 September 2008 of Antarctic lakes was accessed for the discovery of novel antibiotics. In all, 723 Antarctic heterotrophic Received in revised form 22 January 2009 bacteria belonging to novel and/or endemic taxa in the α-, β- and γ-subclasses of the Proteobacteria, the Accepted 2 March 2009 Bacteroidetes branch, and of the high and low percentage G+C Gram-positives, were isolated, cultivated in different media and at different temperatures, and then screened for the production of antimicrobial Keywords: activities. A total of 6348 extracts were prepared by solid phase extraction of the culture broths or by biomass Antarctic lakes Microbial mats solvent extraction.
    [Show full text]
  • Control of Phytopathogenic Microorganisms with Pseudomonas Sp. and Substances and Compositions Derived Therefrom
    (19) TZZ Z_Z_T (11) EP 2 820 140 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: A01N 63/02 (2006.01) A01N 37/06 (2006.01) 10.01.2018 Bulletin 2018/02 A01N 37/36 (2006.01) A01N 43/08 (2006.01) C12P 1/04 (2006.01) (21) Application number: 13754767.5 (86) International application number: (22) Date of filing: 27.02.2013 PCT/US2013/028112 (87) International publication number: WO 2013/130680 (06.09.2013 Gazette 2013/36) (54) CONTROL OF PHYTOPATHOGENIC MICROORGANISMS WITH PSEUDOMONAS SP. AND SUBSTANCES AND COMPOSITIONS DERIVED THEREFROM BEKÄMPFUNG VON PHYTOPATHOGENEN MIKROORGANISMEN MIT PSEUDOMONAS SP. SOWIE DARAUS HERGESTELLTE SUBSTANZEN UND ZUSAMMENSETZUNGEN RÉGULATION DE MICRO-ORGANISMES PHYTOPATHOGÈNES PAR PSEUDOMONAS SP. ET DES SUBSTANCES ET DES COMPOSITIONS OBTENUES À PARTIR DE CELLE-CI (84) Designated Contracting States: • O. COUILLEROT ET AL: "Pseudomonas AL AT BE BG CH CY CZ DE DK EE ES FI FR GB fluorescens and closely-related fluorescent GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO pseudomonads as biocontrol agents of PL PT RO RS SE SI SK SM TR soil-borne phytopathogens", LETTERS IN APPLIED MICROBIOLOGY, vol. 48, no. 5, 1 May (30) Priority: 28.02.2012 US 201261604507 P 2009 (2009-05-01), pages 505-512, XP55202836, 30.07.2012 US 201261670624 P ISSN: 0266-8254, DOI: 10.1111/j.1472-765X.2009.02566.x (43) Date of publication of application: • GUANPENG GAO ET AL: "Effect of Biocontrol 07.01.2015 Bulletin 2015/02 Agent Pseudomonas fluorescens 2P24 on Soil Fungal Community in Cucumber Rhizosphere (73) Proprietor: Marrone Bio Innovations, Inc.
    [Show full text]
  • Chromatic Bacteria – a Broad Host-Range Plasmid and Chromosomal Insertion Toolbox for Fluorescent Protein Expression in Bacteria
    bioRxiv preprint doi: https://doi.org/10.1101/402172; this version posted September 7, 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. Chromatic bacteria – A broad host-range plasmid and chromosomal insertion toolbox for fluorescent protein expression in bacteria Rudolf O. Schlechter1,2, Hyunwoo Jun1#, Michał Bernach1,2#, Simisola Oso1, Erica Boyd1, Dian A. Muñoz-Lintz1, Renwick C. J. Dobson1,2,3, Daniela M. Remus1,2,4, and Mitja N. P. Remus-Emsermann1,2* 1School of Biological Sciences, University of Canterbury, Christchurch, New Zealand. 2Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand. 3Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia. 4Protein Science & Engineering, Callaghan Innovation, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand. # Both authors contributed equally to this work * Correspondence: Mitja N. P. Remus-Emsermann [email protected] Keywords: fluorophore, fluorescent labelling, tagging, Tn5, Tn7, transposon bioRxiv preprint doi: https://doi.org/10.1101/402172; this version posted September 7, 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. Abstract Differential fluorescent labelling of bacteria has become instrumental for many aspects of microbiological research, such as the study of biofilm formation, bacterial individuality, evolution, and bacterial behaviour in complex environments.
    [Show full text]
  • ORIGINAL ARTICLE Metaproteogenomic Insights Beyond Bacterial Response to Naphthalene Exposure and Bio-Stimulation
    The ISME Journal (2013) 7, 122–136 & 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13 www.nature.com/ismej ORIGINAL ARTICLE Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation Marı´a-Eugenia Guazzaroni1,9,11, Florian-Alexander Herbst2,9,Iva´nLores3,9, Javier Tamames4,9, Ana Isabel Pela´ez3, Nieves Lo´pez-Corte´s1, Marı´a Alcaide1, Mercedes V Del Pozo1, Jose´ Marı´a Vieites1, Martin von Bergen2,5, Jose´ Luis R Gallego6, Rafael Bargiela1, Arantxa Lo´pez-Lo´pez7, Dietmar H Pieper8, Ramo´n Rossello´-Mo´ra7, Jesu´ sSa´nchez3,10, Jana Seifert2,10 and Manuel Ferrer1,10 1Department of Biocatalysis, Institute of Catalysis, CSIC, Madrid, Spain; 2Department of Proteomics, UFZ-Helmholtz-Zentrum fu¨r Umweltforschung GmbH, Leipzig, Germany; 3A´rea de Microbiologı´a, IUBA, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain; 4CSIC, Centro Nacional de Biotecnologı´a, Madrid, Spain; 5Department of Metabolomics, UFZ-Helmholtz-Zentrum fu¨r Umweltforschung GmbH, Leipzig, Germany; 6IUBA, A´rea de Prospeccio´n e Investigacio´n Minera, Universidad de Oviedo, Mieres, Spain; 7IMEDEA (CSIC-UIB), Esporles, Spain and 8Helmholtz Zentrum fu¨r Infektionsforschung–HZI, Braunschweig, Germany Microbial metabolism in aromatic-contaminated environments has important ecological implications, and obtaining a complete understanding of this process remains a relevant goal. To understand the roles of biodiversity and aromatic-mediated genetic and metabolic rearrangements, we conducted ‘OMIC’ investigations in an anthropogenically influenced and polyaromatic hydrocarbon (PAH)-contaminated soil with (Nbs) or without (N) bio-stimulation with calcium ammonia nitrate, NH4NO3 and KH2PO4 and the commercial surfactant Iveysol, plus two naphthalene-enriched communities derived from both soils (CN2 and CN1, respectively).
    [Show full text]
  • A Glimpse of the Diversity of Complex Polysaccharide-Degrading Culturable Bacteria from Kongsfjorden, Arctic Ocean
    Ann Microbiol (2017) 67:203–214 DOI 10.1007/s13213-016-1252-0 ORIGINAL ARTICLE A glimpse of the diversity of complex polysaccharide-degrading culturable bacteria from Kongsfjorden, Arctic Ocean Anand Jain1 & Kottekkatu Padinchati Krishnan1 Received: 8 September 2016 /Accepted: 22 December 2016 /Published online: 12 January 2017 # Springer-Verlag Berlin Heidelberg and the University of Milan 2017 Abstract Cold-adapted, complex polysaccharide-degrading within the bacterial genera indicates a role in regulating carbon/ marine bacteria have important implications in biogeochemical carbohydrate turnover in the Kongsfjorden, especially by reduc- processes and biotechnological applications. Bacteria capable of ing recalcitrance. degrading complex polysaccharide substrates, mainly starch, have been isolated from various cold environments, such as sea Keywords Bacteria . Diversity . Culturable . ice, glaciers, subglacial lakes, and marine sediments. However, Polysaccharides . Cold active enzymes . Kongsfjorden the total diversity of polysaccharide-degrading culturable bacteria in Kongsfjorden, Arctic Ocean, remains unexplored. In the study reported here, we tested 215 cold-adapted heterotrophic bacterial Introduction cultures (incubated at 4 and 20 °C, respectively) isolated from Kongsfjorden, for the production of cold-active extracellular Kongsfjorden is an open glacial fjord located on the west coast polysaccharide-degrading enzymes, including amylase, of Spitsbergen, an island in the Svalbard archipelago, situated pectinase, alginase, xylanase, and carboxymethyl (CM)-cellu- in the Arctic Ocean between mainland Norway and the North lase. Our results show that 52 and 41% of the bacterial isolates Pole (79°N, 12°E). It has been identified as a key European tested positive for extracellular enzyme activities at 4 and 20 °C, site for Arctic biodiversity monitoring (Hop et al.
    [Show full text]
  • Ice Nucleation Active Bacteria in Precipitation Are Genetically Diverse and Nucleate Ice by Employing Different Mechanisms
    The ISME Journal (2017) 11, 2740–2753 © 2017 International Society for Microbial Ecology All rights reserved 1751-7362/17 www.nature.com/ismej ORIGINAL ARTICLE Ice nucleation active bacteria in precipitation are genetically diverse and nucleate ice by employing different mechanisms KC Failor1, DG Schmale III1, BA Vinatzer1,4 and CL Monteil1,2,3,4 1Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA; 2CNRS/CEA/Aix-Marseille Université, UMR7265 Institut de biosciences et biotechnologies, Laboratoire de Bioénergétique Cellulaire, Saint-Paul-lès-Durance, France and 3INRA, UR0407 Pathologie Végétale, Montfavet cedex, France A growing body of circumstantial evidence suggests that ice nucleation active (Ice+) bacteria contribute to the initiation of precipitation by heterologous freezing of super-cooled water in clouds. However, little is known about the concentration of Ice+ bacteria in precipitation, their genetic and phenotypic diversity, and their relationship to air mass trajectories and precipitation chemistry. In this study, 23 precipitation events were collected over 15 months in Virginia, USA. Air mass trajectories and water chemistry were determined and 33 134 isolates were screened for ice nucleation activity (INA) at − 8 °C. Of 1144 isolates that tested positive during initial screening, 593 had confirmed INA at − 8 °C in repeated tests. Concentrations of Ice+ strains in precipitation were found to range from 0 to 13 219 colony forming units per liter, with a mean of 384 ± 147. Most Ice+ bacteria were identified as members of known and unknown Ice+ species in the Pseudomonadaceae, Enterobacteriaceae and Xanthomonadaceae families, which nucleate ice employing the well-characterized membrane-bound INA protein.
    [Show full text]