DOCSLIB.ORG

Creek Sediments As a Rich Source of Biosafety Level-1 Organisms for Use As Unknowns in an Undergraduate Microbiology Laboratory

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Creek Sediments As a Rich Source of Biosafety Level-1 Organisms for Use As Unknowns in an Undergraduate Microbiology Laboratory Creek Sediments as a Rich Source of BioSafety Level-1 Organisms for Use as Unknowns in an Undergraduate Microbiology Laboratory. Jeffrey D. Newman. Lycoming College, Williamsport, PA. Abstract 2004 & 2005 2006 2007 Table 1. Unknown Organisms Identified by the Spring, ‘04 & ’05 Microbiology Classes Table 2. Unknown Organisms Identified by the Spring, 2006 Microbiology Class Table 3. Unknown Organisms Identified by the Spring, 2007 Microbiology Class Most general Microbiology courses include some type of project in which isolates 16S rRNA 16S 16S 16S 16S BSL species rRNA BSL species rRNA 2004 2005 BSL species % ID rRNA rRNA students must identify an organism that is unknown to them. Often, the identity % ID % ID BSL species % ID BSL species % ID 1 - Arthrobacter nitroguaiacolicus 98 of students’ “unknowns” are known by the instructor, putting pressure on the - Corynebacterium sp. nov. 94 1 Ochrobactrum tritici 99.5 - Arthrobacter bergeri 99 1 Janthinobacterium lividum >99 3 1 Flexibacteriaceae gen nov. sp. nov. ~91 - Gordonia amicalis 98.5 1 Comamonas kersterii 98.5 - Arthrobacter koreensis >97 1 Aeromonas salmonicida 99 student to get the right answer and making the activity more like a test than 1 - Bacillus aquamarinus 97.5 1 Arthrobacter oxydans 99 1 Janthinobacterium lividum 98 - Arthrobacter nitroguaiacolicus 98.5 1 Aeromonas sobria 100 investigative science. In this study, microbes were obtained from creek 2 - Bacillus arvi 99.5-99.8 - Arthrobacter rhombi 99 - Chromobacterium sp. nov. 96 - Arthrobacter sp. bad - Aeromonas sp. bad sediments and used as unknowns in a Microbiology course to test the hypothesis 4 1 Bacillus flexus 97.5-99.3 1 Microbacterium flavescens 98 2 Aeromonas hydrophila 98.5 1 Curtobacterium citreum 98 1 Shewanella putrefaciens 99 2 1 Bacillus licheniformis 99.5-99.8 that this real research experience will engage students and increase the 1 Sanguibacter keddieii 100 1 Buttiauxella agrestis 99 Microbacterium 1 1 - Bacillus muralis 99-100 likelihood that they will continue in Microbiology. 1 Streptomyces avermitis 98.5 1 Buttiauxella izardii 99.3 1 esteraromaticum >97 1 Enterobacter asburiae >97 12 11 1 Bacillus mycoides 97.2-100 - Chryseobacterium sp. nov 94 1 Enterobacter asburiae 99 1 Oerskovia turbata 99 1 Hafnia alvei >98 1 3 - Bacillus odysseyi 98.3-99.0 1 Flavobacterium hibernum 98 1 Serratia fonticola 99 1 Flavobacterium hibernum 98 1,2 Kluyvera cryocrescens 98 Samples were obtained from a variety of sites along the Loyalsock Creek in 6 2 1 Bacillus pumilus 99.3-100 - Flavobacterium sp. nov. 95.3 1,2 Acinetobacter calcoaceticus 97.6 - Flavobacterium sp. nov. 96 1 Pantoea agglomerans 98 5 1 Bacillus subtilis 98.8-100 PA and spread on TSA plates. Isolated colonies were then purified and used as 2 Sphingobacterium faecium 98.8 - Acinetobacter sp. nov. 95 - Flavobacterium sp. nov. 95 1 Pantoea ananatis bad 1 - Bacillus sylvestris 98.8 unknown organisms in a sophomore-junior level Microbiology course. During the - Bacillus arvi 99.3 1 Pseudomonas fragi 99.1 - Sejongia sp. nov. 95 1 Pseudomonas veronii 100 1 1 Paenibacillus amylolyticus 99.5 eight weeks of unknown microbe characterization, students performed Pseudomonas 1 Bacillus flexus >97 1 Pseudomonas fulva >99 1 1,2 Staphylococcus epidermidis 100 1 Bacillus flexus 99 - 98.8 frederiksbergensis - Bacillus muralis >98 1 Pseudomonas jessenii >97 microscopic analysis, biochemical, physiological and antibiotic sensitivity tests 1 2 Staphylococcus haemolyticus 99.5 1 Bacillus licheniformis 97.5 1 Pseudomonas graminis 98.5 - Bacillus sp. nov. 96 - Pseudomonas libanensis >98 and 16S rRNA gene sequence analysis to identify their organisms. During 2004 4 10 1 Serratia fonticola 97.5-100 1 Bacillus pumilus 100 - Pseudomonas kilonensis 99 1 Bacillus pumilis 98.5 - Pseudomonas proteolytica 98 3 1 Serratia grimesii/proteomaculans 99.0-99.5 Exiguobacterium and 2005, when students themselves chose colonies from the spread plates, 1 98.8 - Pseudomonas libanensis 99 1 Bacillus subtilis >97 - Pseudomonas umsongensis 97 1 - Serratia novum 96 oxidotolerans many duplicate unknowns were obtained. Only 23 different species were - Exiguobacterium undae 97 5 1 Serratia plymuthica 99.5-100 1 Paenibacillus cookii 98 - Pseudomonas proteolytica 98.5 identified by the 91 students. Nearly 60% of students had members of the genus 1 Paenibacillus amylolyticus 98 5 2 Yersinia intermedia 97.5-99.8 1 Staphylococcus caprae 99.8 - Pseudomonas sp. bad 2 Staphylococcus pasteuri 99 Bacillus and another 25% had one of four Serratia species. In 2006 and 2007, 1 - Pseudomonas koreensis 99.5 1 Carnobacterium viridans 98.5 1 Pseudomonas syringae bad morphologically distinguishable colonies were chosen from spread plates and 3 - Pseudomonas libanensis 98.5 Bacillus flexus CVB Aeromonas salmonicida MR Bacillus flexus MAM Aeromonas sp. ELP streaked by the instructor to maximize the diversity of unknowns. Of the 89 1 - Pseudomonas mediterranea 99 Bacillus arvi TLF Aeromonas salmonicida ABL Aeromonads Exiguobacterium oxidotolerans CNH Aeromonas sobria DJBH unknown organisms identified in 2006 and 2007, 66 different species were Carnobacterium viridans AJR Aeromonas salmonicida KLK Bacillus subtilis DD Carnobacterium viridans ZRT Shewanella putrefaciens CLH obtained, from 30 genera and 20 families. Nine of these were novel species based Bacillus subtilis SEI Firmicutes Bacillus subtilis JLC Bacillus pumilis JD Shewanella putrefaciens KMF Alteromonads on having <97% sequence identity to type strains, and only 5 were known BSL-2 Bacillus subtilis CI Bacillus licheniformis JAS Enterobacter asburiae BWW Bacillus subtilis SR Bacillus pumilis TCB Kluyvera cryocrescens AMG Bacillus licheniformis BLM organisms. Bacillus licheniformis OJE Staphylococcus caprae AB Hafnia alvei TJC Enterobacteria Bacillus pumilis AS Paenibacillus cookii GMB Pantoea agglomerans AMC Bacillus pumilis LJ Arthrobacter oxydans JNT Pantoea agglomerans BMG Bacillus pumilis ENL Pseudomonas fulva NMG Student learning was assessed using research style lab reports sent to two Bacillus pumilis KAS Arthrobacter rhombi PH Bacillus pumilis EKC Microbacterium flavescens JB Pseudomonas umsongensis DAB other class members for anonymous peer-review and revised before submission Bacillus pumilis JLH Sanguibacter keddieii CTL Actinobacteria Pseudomonas jessenii REB Bacillus pumilis KC Streptomyces avermitis SMC Pseudomonas proteolytica AMW Pseudomonads Bacillus odysseyi AMS for grading. Course evaluation surveys have been very positive. Several students Bacillus odysseyi LLP Corynebacterium sp. nov PH Pseudomonas veronii SLK Bacillus odysseyi ANR Gordonia amicalis JLB Pseudomonas libaniensis KWH have chosen to follow-up on the novel organisms as part of Independent Studies, Bacillus odysseyi RBB Ochrobactrum tritici-grignonense AJF -proteobacteria Janthinobacterium lividum JLB -proteobacteria Bacillus aquamarinus AS Bacillus flexus BLM Honor’s Projects, or the Cell & Molecular Biology Research Methods course and Bacillus arvi BJS Pseudomonas graminis CAK Bacillus arvi PH Pseudomonas graminis SAR Bacillus muralis CAH Bacillus sylvestris MJR Pseudomonas fragi KKB Bacillus subtilis CMD will present their work at the 2007 ASM General Meeting. Bacillus flexus BMF Pseudomonas frederiksbergensis TDM Bacillus pumilis EJU Bacillus flexus NF Pseudomonads Firmicutes Bacillus flexus ARB Pseudomonas kilonensis SKR Bacillus sp. nov. SLS Bacillus flexus JM Firmicutes Pseudomonas proteolytica JMR Staphylococcus pasteuri VJW Bacillus muralis NP Pseudomonas libanensis MPW Exiguobacterium undae SLD Bacillus muralis EP Bacillus mycoides EMH Acinetobacter calcoaceticus TRM Paenibacillus amylolyticus LEB Bacillus mycoides MAZ Acinetobacter sp. nov MAG Moraxellaceae Arthrobacter bergeri MRK Bacillus mycoides EMW Buttiauxella agrestis KAM Arthrobacter bergeri NAW Bacillus mycoides MD Curtobacterium citreum GMT Actino- Bacillus mycoides DPC Buttiauxella izardii SEG Enterobacteria Unknown Microbe Identification Experiment Bacillus mycoides RJF Enterobacter asburiae AMC Microbacterium esteraromaticum JMB Bacillus mycoides DLK Serratia fonticola BRM Oerskovia turbata CJP bacteria Bacillus mycoides EMP Arthrobacter koreensis JWG Bacillus mycoides EW Aeromonas hydrophila JMT Aeromonads Arthrobacter nitroguaiacolicus DVG Project Objectives: Bacillus mycoides SZ Chromobacterium sp. nov JWM Bacillus mycoides EKS Janthinobacterium lividum LAR -proteobacteria Flavobacterium hibernum LES Bacillus mycoides NK Comamonas kersterii DKS Flavobacterium sp. nov. LMK • Engage students in an investigative research experience. Bacillus mycoides EK Flavobacterium hibernum RLF Bacillus mycoides PAK Sphingobacterium faecium CRC Bacteroidetes Bacillus mycoides JAC Sphingobacterium faecium VLVK Flavobacterium sp. nov. AMR • Minimize the risk of working with pathogenic organisms. Bacillus mycoides MB Chryseobacterium sp. nov CTM Sejongia sp. nov. JJC Bacillus mycoides MLH 30.5 Bacillus mycoides ROH Flavobacterium hibernum ECB Bacteroidetes • Integrate lab activities with associated lecture material. Bacillus mycoides CJB Flavobacterium hibernum KJA 30 25 20 15 10 5 0 Bacillus mycoides SMH Flavobacterium sp. nov AEC Nucleotide Substitutions (x100) Staphylococcus haemolyticus EMH 32.8 • DISCOVER NOVEL BACTERIAL SPECIES!!!! Staphylococcus epidermidis EFP Paenibacillus amylolyticus AKS 30 25 20 15 10 5 0 Figure 3. Phylogenetic tree resulting from Clustal W alignment of Arthrobacter nitroguaiacolicus ND Nucleotide Substitutions (x100) Serratia fonticola AP Actinobacteria 2007 unknown microbe 16S
Load more

Recommended publications
  • 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.
    [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]
  • Lactic Acid Bacteria Adjunct Cultures Exert a Mitigation Effect Against
    microorganisms Article Lactic Acid Bacteria Adjunct Cultures Exert a Mitigation Effect against Spoilage Microbiota in Fresh Cheese Daniela Bassi 1,* , Simona Gazzola 1, Eleonora Sattin 2, Fabio Dal Bello 3, Barbara Simionati 4 and Pier Sandro Cocconcelli 1,* 1 Dipartimento di Scienze e Tecnologie Alimentari per una Filiera Agro-Alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; [email protected] 2 BMR Genomics, srl, 35131 Padova, Italy; [email protected] 3 Sacco s.r.l., 22071 Cadorago, Italy; [email protected] 4 EuBiome Srl, 35129 Padova, Italy; [email protected] * Correspondence: [email protected] (D.B.); [email protected] (P.S.C.); Tel.: +39-037-249-9108 (D.B.); +39-052-359-9251 (P.S.C.) Received: 16 July 2020; Accepted: 5 August 2020; Published: 6 August 2020 Abstract: Lactic acid bacteria (LAB) have a strong mitigation potential as adjunct cultures to inhibit undesirable bacteria in fermented foods. In fresh cheese with low salt concentration, spoilage and pathogenic bacteria can affect the shelf life with smear on the surface and packaging blowing. In this work, we studied the spoilage microbiota of an Italian fresh cheese to find tailor-made protective cultures for its shelf life improvement. On 14-tested LAB, three of them, namely Lacticaseibacillus rhamnosus LRH05, Latilactobacillus sakei LSK04, and Carnobacterium maltaromaticum CNB06 were the most effective in inhibiting Gram-negative bacteria. These cultures were assessed by the cultivation-dependent and DNA metabarcoding approach using in vitro experiments and industrial trials. Soft cheese with and without adjunct cultures were prepared and stored at 8 and 14 ◦C until the end of the shelf life in modified atmosphere packaging.
    [Show full text]
  • Influence of Environment and Host Plant Genotype on the Structure And
    Influence of environment and host plant genotype onthe structure and diversity of the Brassica napus seed microbiota Aude Rochefort, Martial Briand, Coralie Marais, Marie-Hélène Wagner, Anne Laperche, Patrick Vallée, Matthieu Barret, Alain Sarniguet To cite this version: Aude Rochefort, Martial Briand, Coralie Marais, Marie-Hélène Wagner, Anne Laperche, et al.. Influ- ence of environment and host plant genotype on the structure and diversity of the Brassica napus seed microbiota. Phytobiomes Journal, APS Publications, 2019, 3 (4), pp.326-336. 10.1094/PBIOMES- 06-19-0031-R. hal-02275205 HAL Id: hal-02275205 https://hal-agrocampus-ouest.archives-ouvertes.fr/hal-02275205 Submitted on 30 Aug 2019 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. Copyright Page 1 of 55 Rochefort et al., Phytobiomes Journal 1 Influence of environment and host plant genotype on the structure and 2 diversity of the Brassica napus seed microbiota 3 4 Authors and affiliations: Aude ROCHEFORT1, Martial BRIAND2, Coralie MARAIS2, Marie- 5 Hélène WAGNER3, Anne LAPERCHE1, Patrick VALLEE1, Matthieu BARRET2, Alain SARNIGUET1* 6 7 1INRA, Agrocampus-Ouest, Université de Rennes 1, UMR 1349 IGEPP (Institute of Genetics, 8 Environment and Plant Protection) – 35653 Le Rheu, France.
    [Show full text]
  • Pseudomonas Versuta Sp. Nov., Isolated from Antarctic Soil
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by NERC Open Research Archive Accepted Manuscript Title: Pseudomonas versuta sp. nov., isolated from Antarctic soil Authors: Wah Seng See-Too, Sergio Salazar, Robson Ee, Peter Convey, Kok-Gan Chan, Alvaro´ Peix PII: S0723-2020(17)30039-5 DOI: http://dx.doi.org/doi:10.1016/j.syapm.2017.03.002 Reference: SYAPM 25827 To appear in: Received date: 12-1-2017 Revised date: 20-3-2017 Accepted date: 24-3-2017 Please cite this article as: Wah Seng See-Too, Sergio Salazar, Robson Ee, Peter Convey, Kok-Gan Chan, Alvaro´ Peix, Pseudomonas versuta sp.nov., isolated from Antarctic soil, Systematic and Applied Microbiologyhttp://dx.doi.org/10.1016/j.syapm.2017.03.002 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Pseudomonas versuta sp. nov., isolated from Antarctic soil Wah Seng See-Too1,2, Sergio Salazar3, Robson Ee1, Peter Convey 2,4, Kok-Gan Chan1,5, Álvaro Peix3,6* 1Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science University of Malaya, 50603 Kuala Lumpur, Malaysia 2National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia 3Instituto de Recursos Naturales y Agrobiología.
    [Show full text]
  • Characterization of Two Unique Cold-Active Lipases Derived from a Novel Deep-Sea Cold Seep Bacterium
    microorganisms Article Characterization of Two Unique Cold-Active Lipases Derived from a Novel Deep-Sea Cold Seep Bacterium Chenchen Guo 1, Rikuan Zheng 2,3,4, Ruining Cai 2,3,4, Chaomin Sun 2,3,4,* and Shimei Wu 1,* 1 College of Life Sciences, Qingdao University, Qingdao 266071, China; [email protected] 2 CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; [email protected] (R.Z.); [email protected] (R.C.) 3 Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China 4 Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China * Correspondence: [email protected] (C.S.); [email protected] (S.W.) Abstract: The deep ocean microbiota has unexplored potential to provide enzymes with unique characteristics. In order to obtain cold-active lipases, bacterial strains isolated from the sediment of the deep-sea cold seep were screened, and a novel strain gcc21 exhibited a high lipase catalytic activity, even at the low temperature of 4 ◦C. The strain gcc21 was identified and proposed to represent a new species of Pseudomonas according to its physiological, biochemical, and genomic characteristics; it was named Pseudomonas marinensis. Two novel encoding genes for cold-active lipases (Lipase 1 and Lipase 2) were identified in the genome of strain gcc21. Genes encoding Lipase 1 and Lipase 2 were respectively cloned and overexpressed in E. coli cells, and corresponding lipases were further purified and characterized. Both Lipase 1 and Lipase 2 showed an optimal catalytic temperature at 4 ◦C, Citation: Guo, C.; Zheng, R.; Cai, R.; which is much lower than those of most reported cold-active lipases, but the activity and stability of Sun, C.; Wu, S.
    [Show full text]
  • Extremophilic Microbes: Diversity and Perspectives
    SPECIAL SECTION: MICROBIAL DIVERSITY Extremophilic microbes: Diversity and perspectives T. Satyanarayana1,*, Chandralata Raghukumar2 and S. Shivaji3 1Department of Microbiology, University of Delhi South Campus, New Delhi 110 021, India 2Biological Oceanography Division, National Institute of Oceanography, Dona Paula, Goa 403 004, India 3Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India Life in extreme environments has been studied inten- A variety of microbes inhabit extreme environments. Extreme is a relative term, which is viewed compared sively focusing attention on the diversity of organisms to what is normal for human beings. Extreme envi- and molecular and regulatory mechanisms involved. The ronments include high temperature, pH, pressure, salt products obtainable from extremophiles such as proteins, concentration, and low temperature, pH, nutrient enzymes (extremozymes) and compatible solutes are of concentration and water availability, and also condi- great interest to biotechnology. This field of research has tions having high levels of radiation, harmful heavy also attracted attention because of its impact on the pos- metals and toxic compounds (organic solvents). Cul- sible existence of life on other planets. ture-dependent and culture-independent (molecular) The progress achieved in research on extremophiles/ methods have been employed for understanding the thermophiles is discussed in international conferences diversity of microbes in these environments. Extensive held every alternate year in different countries. The last global research efforts have revealed the novel diver- conference on extremophiles was held in USA in 2004, sity of extremophilic microbes. These organisms have evolved several structural and chemical adaptations, and that on thermophiles in England in 2003, and the forth- which allow them to survive and grow in extreme en- coming one is due in Australia in 2005.
    [Show full text]
  • Psychrophilic Pseudomonads from Antarctica: Pseudomonas Antarctica Sp
    International Journal of Systematic and Evolutionary Microbiology (2004), 54, 713–719 DOI 10.1099/ijs.0.02827-0 Psychrophilic pseudomonads from Antarctica: Pseudomonas antarctica sp. nov., Pseudomonas meridiana sp. nov. and Pseudomonas proteolytica sp. nov. Gundlapalli S. N. Reddy,1 Genki I. Matsumoto,2 Peter Schumann,3 Erko Stackebrandt3 and Sisinthy Shivaji1 Correspondence 1Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad – 500 007, India Sisinthy Shivaji 2Department of Environmental and Information Science, Otsuma Women’s University, Tamashi, [email protected] Tokyo 206, Japan 3DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig, Germany Thirty-one bacteria that belonged to the genus Pseudomonas were isolated from cyanobacterial mat samples that were collected from various water bodies in Antarctica. All 31 isolates were psychrophilic; they could be divided into three groups, based on their protein profiles. Representative strains of each of the three groups, namely CMS 35T, CMS 38T and CMS 64T, were studied in detail. Based on 16S rRNA gene sequence analysis, it was established that the strains were related closely to the Pseudomonas fluorescens group. Phenotypic and chemotaxonomic characteristics further confirmed their affiliation to this group. The three strains could also be differentiated from each other and the closely related species Pseudomonas orientalis, Pseudomonas brenneri and Pseudomonas migulae, based on phenotypic and chemotaxonomic characteristics and the level of DNA–DNA hybridization. Therefore, it is proposed that strains CMS 35T (=MTCC 4992T=DSM 15318T), CMS 38T (=MTCC 4993T=DSM 15319T) and CMS 64T (=MTCC 4994T=DSM 15321T) should be assigned to novel species of the genus Pseudomonas as Pseudomonas antarctica sp.
    [Show full text]
  • Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Based Identification of the Fish Gut Microbiota
    MATRIX-ASSISTED LASER DESORPTION IONIZATION-TIME OF FLIGHT MASS SPECTROMETRY BASED IDENTIFICATION OF THE FISH GUT MICROBIOTA Miroslava Kačániová1,2*, Margarita Terentjeva3, Alīna Klūga3, Monika Březinová4, Miriam Kádasi Horáková5 Address(es): prof. Ing. Miroslava Kačániová, PhD. 1Department of Microbiology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture, Tr. A. Hlinku 2, SK-94976 Nitra, Slovakia, 2Department of Bioenergy and Food Technology, Faculty of Biology and Agriculture, University of Rzeszow, Zelwerowicza St. 4, PL-35601 Rzeszow, Poland, 3Institute of Food and Environmental Hygiene, Faculty of Veterinary Medicine, Latvia University of Agriculture, K. Helmaņa iela 8, LV-3004, Jelgava, Latvia, 5Department of Landscape Management, Faculty of Agriculture, University of South Bohemia, Studentská 1668, CZ-37005 České Budějovice, Czech Republic, 5Department of Plant Pathology and Mycology, Institute of Forest Ecology, Slovak Academy of Sciences, Akademická 2, SK-94901 Nitra, Slovakia. *Corresponding author: [email protected] doi: 10.15414/jmbfs.2019.9.1.151-155 ARTICLE INFO ABSTRACT Received 11. 3. 2019 The aim of the study was to investigate the composition of intestinal microflora of freshwater fish in Latvia. A total amount of 28 fish Revised 12. 6. 2019 were collected from fishermen (n=20) and retail outlets (n=8), including roach Rutilus rutilus, n=15, crucian carp Carassius carassius, Accepted 12. 6. 2019 n=5, perch Perca fluvialitis, n=5, bream Blicca bjoerkna, n=3. Microbiological testing consisted of the detection of total viable count Published 1. 8. 2019 (TPC), Enterobacteriaceae and coliforms with subsequent identification with MALDI-TOF Biotyper. TPC, coliforms and Enterobacteriaceae counts ranged from 2.7±0.4 to 5.4±0.3, 2.4±1.5 to 3.7±0.7 and 2.00±1.2 to 3.7±2.5 log cfu/g in gut of wild crucian carp and retailed roach, wild perch and retailed roach, and crucian carp and bream, accordingly.
    [Show full text]
  • Spoilage-Associated Psychrotrophic and Psychrophilic Microbiota on Modified Atmosphere Packaged Beef
    TECHNISCHE UNIVERSITÄT MÜNCHEN Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt Lehrstuhl für Technische Mikrobiologie Spoilage-associated psychrotrophic and psychrophilic microbiota on modified atmosphere packaged beef Maik Hilgarth Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigten Dissertation. Vorsitzender: Prof. Dr. Horst-Christian Langowski Prüfer der Dissertation: 1. Prof. Dr. Rudi F. Vogel 2. Prof. Dr. Siegfried Scherer 3. Prof. Dr. Jochen Weiss Die Dissertation wurde am 08.08.2018 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 22.11.2018 angenommen. Spoilage-associated psychrotrophic and psychrophilic microbiota on modified atmosphere packaged beef Maik Hilgarth ‘Everything is everywhere, but, the environment selects’ - Lourens Gerhard Marinus Baas Becking, inspired by Martinus Willem Beijerinck Doctoral thesis Freising, 2018 - This thesis is dedicated to my beloved parents - IV Abbreviations °C degree Celsius (centrigrade) µ micro (10-6) A ampere ANI average nucleotide identity aw water activity B. Brochothrix BHI brain-heart infusion medium BLAST basic local alignment search tool bp base pairs C. Carnobacterium CFC cephalothin-fucidin-cetrimide medium CFU colony forming units contig contiguous consensus
    [Show full text]
  • Assessment of the Microbial Contamination on Pork and Wild Boar Meat by a Culture- Dependent and Independent Approach”
    UNIVERSITÀ DEGLI UNIVERSITEIT GENT STUDI DI NAPOLI “FEDERICO II” PhD Thesis “Assessment of the microbial contamination on pork and wild boar meat by a culture- dependent and independent approach” Candidate Maria Francesca Peruzy Tutor Tutor Prof.ssa Dr. Nicoletta Murru Prof. Dr. Kurt Houf Coordinator Prof. Dr. Giuseppe Cringoli There is a driving force more powerful than steam, electricity and nuclear power: the will Albert Einstein Index 1. Introduction 40 1.1 General overview 43 1.1.1 From the slaughter process to meat production in pork 44 1.1.2 Wild boars: From the field to the table 45 1.2 Microbial contamination and foodborne pathogens of pork carcasses and cuts 47 1.2.1 Spoilage Microbial contamination in pork 47 1.2.2 Pathogens in pork 48 1.2.3 Source of contamination in carcasses and cuts 50 1.2.4 Microbiological parameters and sampling methods according to European legislation 51 1.3 Microbial contamination and foodborne pathogens of wild boar carcasses 54 1.4 The genus Yersinia 57 1.4.1 Yersinia enterocolitica 57 1.4.2 Y. enterocolitica in humans 59 1.4.3 Y. enterocolitica in animals and foods 59 1.5 Cultivation-dependent methods 63 1.5.1 Traditional methods for isolation and identification of bacteria 63 7 Index 1.5.2 Matrix-assisted laser desorption/ionization time-of-flight Mass Spectrometry (MALDI-TOF MS) 64 1.6. Culture-independent techniques as approaches to identifying bacterial communities 68 1.6.1 Illumina Genome Analyzer 70 1.6.2 16s rRNA amplicon sequences 72 1.7 References 74 3.
    [Show full text]
  • Draft Genome Sequence of Pseudomonas Extremaustralis Strain USBA-GBX 515 Isolated from Superparamo Soil Samples in Colombian
    López et al. Standards in Genomic Sciences (2017) 12:78 DOI 10.1186/s40793-017-0292-9 EXTENDED GENOME REPORT Open Access Draft genome sequence of Pseudomonas extremaustralis strain USBA-GBX 515 isolated from Superparamo soil samples in Colombian Andes Gina López1, Carolina Diaz-Cárdenas1, Nicole Shapiro2, Tanja Woyke2, Nikos C. Kyrpides2, J. David Alzate3, Laura N. González3, Silvia Restrepo3 and Sandra Baena1* Abstract Here we present the physiological features of Pseudomonas extremaustralis strain USBA-GBX-515 (CMPUJU 515), isolated from soils in Superparamo ecosystems, > 4000 m.a.s.l, in the northern Andes of South America, as well as the thorough analysis of the draft genome. Strain USBA-GBX-515 is a Gram-negative rod shaped bacterium of 1.0–3. 0 μm × 0.5–1 μm, motile and unable to form spores, it grows aerobically and cells show one single flagellum. Several genetic indices, the phylogenetic analysis of the 16S rRNA gene sequence and the phenotypic characterization confirmed that USBA-GBX-515 is a member of Pseudomonas genus and, the similarity of the 16S rDNA sequence was 100% with P. extremaustralis strain CT14–3T. The draft genome of P. extremaustralis strain USBA-GBX-515 consisted of 6,143,638 Mb with a G + C content of 60.9 mol%. A total of 5665 genes were predicted and of those, 5544 were protein coding genes and 121 were RNA genes. The distribution of genes into COG functional categories showed that most genes were classified in the category of amino acid transport and metabolism (10.5%) followed by transcription (8.4%) and signal transduction mechanisms (7.3%).
    [Show full text]