Isolation and Characterization of Bacteria Resistant to Metallic Copper Surfaces
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Statement on the Update of the List of QPS-Recommended
Downloaded from orbit.dtu.dk on: Sep 27, 2021 EFSA BIOHAZ Panel (EFSA Panel on Biological Hazards), 2014. Statement on the update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 1: Suitability of taxonomic units notified to EFSA until October 2014 EFSA Publication Link to article, DOI: 10.2903/j.efsa.2014.3938 Publication date: 2014 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): EFSA Publication (2014). EFSA BIOHAZ Panel (EFSA Panel on Biological Hazards), 2014. Statement on the update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 1: Suitability of taxonomic units notified to EFSA until October 2014. Europen Food Safety Authority. the EFSA Journal Vol. 12(12) No. 3938 https://doi.org/10.2903/j.efsa.2014.3938 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. -
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. -
Diverse Bacterial Communities Are Recruited on Spores of Different
1 Diverse bacterial communities are recruited on spores of different 2 arbuscular mycorrhizal fungal isolates 3 Monica Agnolucci*, Fabio Battini, Caterina Cristani, Manuela Giovannetti 4 Department of Agriculture, Food and Environment, University of Pisa, Via del 5 Borghetto 80, 56124 Pisa, Italy 6 7 RUNNING HEAD: Diverse bacterial communities recruited on AMF spores 8 *Corresponding author: M. Agnolucci, Department of Agriculture, Food and 9 Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy 10 Phone: +39.0502216647, Fax: +39.0502220606, e-mail address: 11 [email protected] 12 13 Abstract 14 Arbuscular mycorrhizal fungi (AMF) establish mutualistic symbioses with the roots of 15 most food crops, playing a key role in soil fertility and plant nutrition and health. The 16 beneficial activity of AMF may be positively affected by bacterial communities living 17 associated with mycorrhizal roots, spores and extraradical hyphae. Here we investigated 18 the diversity of bacterial communities associated with the spores of six AMF isolates, 19 belonging to different genera and species and maintained for several generations in pot- 20 cultures with the same host plant, under the same environmental conditions and with the 21 same soil. The occurrence of large bacterial communities intimately associated with 22 spores of the AMF isolates was revealed by PCR-DGGE analysis and sequencing of 1 23 DGGE bands. Cluster and canonical correspondence analysis showed that the six AMF 24 isolates displayed diverse bacterial community profiles unrelated with their taxonomic 25 position, suggesting that each AMF isolate recruits on its spores a different microbiota. 26 The 48 sequenced fragments were affiliated with Actinomycetales, Bacillales, 27 Pseudomonadales, Burkholderiales, Rhizobiales and with Mollicutes related 28 endobacteria (Mre). -
Communautés Microbiennes De La Baie De Raisin : Incidence Des Facteurs Biotiques Et Abiotiques Guilherme Marques Martins
Communautés microbiennes de la baie de raisin : Incidence des facteurs biotiques et abiotiques Guilherme Marques Martins To cite this version: Guilherme Marques Martins. Communautés microbiennes de la baie de raisin : Incidence des facteurs biotiques et abiotiques : Incidence des facteurs biotiques et abiotiques. Sciences du Vivant [q-bio]. Université de Bordeaux Ségalen (Bordeaux 2), 2012. Français. tel-02802218 HAL Id: tel-02802218 https://hal.inrae.fr/tel-02802218 Submitted on 5 Jun 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. Année 2012 Thèse n°1924 THÈSE pour le DOCTORAT DE L’UNIVERSITÉ BORDEAUX 2 Ecole doctorale Mention : Sciences, Technologie, Santé Option : Œnologie Présentée et soutenue publiquement Le 3 juillet 2012 Par Guilherme MARTINS Né le 7/10/81 à Coimbra, Portugal Communautés microbiennes de la baie de raisin Incidence des facteurs biotiques et abiotiques Membres du Jury Mr. P. REY, Professeur à Bordeaux Sciences Agro Président Mr. R. DURAN, Professeur à l’Université de Pau et des Pays de l'Adour Rapporteur Mme M.C. MONTEL, Directrice de recherche à l’INRA de Clermont-Ferrand Rapporteur Mr. S. COMPANT, Maître de conférences à l’Université de Toulouse Examinateur Mme A. -
Complete Genome Sequence and Function Gene Identify of Prometryne-Degrading Strain Pseudomonas Sp
microorganisms Article Complete Genome Sequence and Function Gene Identify of Prometryne-Degrading Strain Pseudomonas sp. DY-1 Dong Liang 1,† , Changyixin Xiao 1,† , Fuping Song 2, Haitao Li 1 , Rongmei Liu 1,* and Jiguo Gao 1,* 1 College of Life Science, Northeast Agricultural University, Harbin 150038, China; [email protected] (D.L.); [email protected] (C.X.); [email protected] (H.L.) 2 State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; [email protected] * Correspondence: [email protected] (R.L.); [email protected] (J.G.); Tel.: +86-133-5999-0992 (J.G.) † These authors contributed equally to this work. Abstract: The genus Pseudomonas is widely recognized for its potential for environmental reme- diation and plant growth promotion. Pseudomonas sp. DY-1 was isolated from the agricultural soil contaminated five years by prometryne, it manifested an outstanding prometryne degradation efficiency and an untapped potential for plant resistance improvement. Thus, it is meaningful to comprehend the genetic background for strain DY-1. The whole genome sequence of this strain revealed a series of environment adaptive and plant beneficial genes which involved in environmen- tal stress response, heavy metal or metalloid resistance, nitrate dissimilatory reduction, riboflavin synthesis, and iron acquisition. Detailed analyses presented the potential of strain DY-1 for degrad- ing various organic compounds via a homogenized pathway or the protocatechuate and catechol branches of the β-ketoadipate pathway. In addition, heterologous expression, and high efficiency Citation: Liang, D.; Xiao, C.; Song, F.; liquid chromatography (HPLC) confirmed that prometryne could be oxidized by a Baeyer-Villiger Li, H.; Liu, R.; Gao, J. -
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. -
Optimized Analysis of the Lung Allograft Microbiota from Bronchoalveolar Lavage Fluid
Optimized Analysis of the Lung Allograft Microbiota from Bronchoalveolar Lavage Fluid by Janice Evana Prescod A thesis submitted in conformity with the requirements for the degree of Master of Science Department of Laboratory of Medicine and Pathobiology University of Toronto © Copyright by Janice Evana Prescod 2018 Optimized Analysis of the Lung Allograft Microbiota from Bronchoalveolar Lavage Fluid Janice Prescod Master of Science Department of Laboratory of Medicine and Pathobiology University of Toronto 2018 Abstract Introduction: Use of bronchoalveolar lavage fluid (BALF) for analysis of the allograft microbiota in lung transplant recipients (LTR) by culture-independent analysis poses specific challenges due to its highly variable bacterial density. Approach: We developed a methodology to analyze low- density BALF using a serially diluted mock community and BALF from uninfected LTR. Methods/Results: A mock microbial community was used to establish the properties of true- positive taxa and contaminants in BALF. Contaminants had an inverse relationship with input bacterial density. Concentrating samples increased the bacterial density and the ratio of community taxa (signal) to contaminants (noise), whereas DNase treatment decreased density and signal:noise. Systematic removal of contaminants had an important impact on microbiota-inflammation correlations in BALF. Conclusions: There is an inverse relationship between microbial density and the proportion of contaminants within microbial communities across the density range of BALF. This study has implications for the analysis and interpretation of BALF microbiota. ii Acknowledgments To my supervisor, Dr. Bryan Coburn, I am eternally grateful for the opportunity you have given me by accepting me as your graduate student. Over the past two years working with you has been both rewarding and at times very challenging. -
Doctor of Philosophy
BIOPROSPECTS OF RHIZOSPHERE BACTERIA ASSOCIATED WITH COASTAL SAND DUNE VEGETATION, IPOMOEA PES-CAPRAE AND SPINIFEX LITTOREUS Thesis submitted to the GOA UNIVERSITY for the award of the degree of DOCTOR OF PHILOSOPHY In MICROBIOLOGY by Aureen Remedios Lemos Godinho, M. Sc., M. Phil. '.,---* V ,...-' '—"•-..,„, So 1\ .14 G.* 7 •.. , , `1, A. , , . r ......----- ..... Under the guidance of Li t. ri Dr.(Mrs.) Saroj Bhosle I *7sil Reader & Head - ------" ,4 Department of Microbiology ( CZ P‘,/;:41. Goa University, Goa AUGUST 2007 Certificate This is to certify that Ms. Aureen Remedios Lemos Godinho has worked on the thesis entitled "Bioprospects of rhizosphere bacteria associated with coastal sand dune vegetation, Ipomoea pes-caprae and Spinifex littoreus" under my supervision and guidance. This thesis, being submitted to the Goa University, Taleigao Plateau, Goa, for the award of the degree of Doctor of Philosophy in Microbiology, is an original record of the work carried out by the candidate herself and has not been submitted for the award of any other degree or diploma of this or any other University in India or abroad. Dr. (Mrs.) Saroj Bhosle RESEARCH GUIDE, Reader & Head, Department of Microbiology, \/ ,■ 1 Uct fre Goa University, Goa-403206 9 K Texaftc( e. eS Declaration I hereby state that this thesis for the PhD degree in Microbiology on "Bioprospects of rhizosphere bacteria associated with coastal sand dune vegetation, Ipomoea pes-caprae and Spinifex littoreus" is my original contribution and that the thesis and any part of it have not been previously submitted for the award of any degree/diploma of any University or Institute. -
Microbial Community and Biogeochemical Characteristics in Reclaimed Soils at Pt Bukit Asam Coal Mine, South Sumatra, Indonesia
MICROBIAL COMMUNITY AND BIOGEOCHEMICAL CHARACTERISTICS IN RECLAIMED SOILS AT PT BUKIT ASAM COAL MINE, SOUTH SUMATRA, INDONESIA A thesis presented to the faculty of the Graduate School of Western Carolina University in partial fulfillment of the requirements for the degree of Master of Science in Biology By Kyle Bryce Corcoran Co-Directors: Dr. Jerry R. Miller, Dr. John P. Gannon Department of Geosciences and Natural Resources Committee Members: Dr. Sean P. O’Connell, Department of Biology Dr. Thomas H. Martin, Department of Biology March 2018 ACKNOWLEDGEMENTS I would like to express my sincere gratitude to my thesis co-advisors, Dr. Jerry Miller and Dr. JP Gannon for their dedication, and encouragement throughout my graduate school experience. If it weren’t for the many hours spent helping me build the framework of this project, and critiquing my work, I would have never built the confidence that I have now. I would also like to thank all of my committee members: Dr. Sean P. O’Connell, Dr. Thomas H. Martin for the time you took to teach me new techniques regarding microbial and statistical analyses. In addition, thank you so much Micky Aja, Amar Amay, and Adi Arti Elettaria for accompanying me during my stay in Indonesia. I truly appreciate the friendships I have built with you all throughout this time and will never forget how much you all helped me throughout this experience. Trip Krenz, you have watched over me and seen me grow over the last several years. Thank you for always telling me to hold my head high and to look at the positive things that were meant to come my way. -
Metagenomic Characterization of Bacterial Communities on Ready-To-Eat Vegetables and Effects of Household Washing on Their Diversity and Composition
pathogens Article Metagenomic Characterization of Bacterial Communities on Ready-to-Eat Vegetables and Effects of Household Washing on their Diversity and Composition Soultana Tatsika 1,2, Katerina Karamanoli 3, Hera Karayanni 4 and Savvas Genitsaris 1,* 1 School of Economics, Business Administration and Legal Studies, International Hellenic University, 57001 Thermi, Greece; [email protected] 2 Hellenic Food Safety Authority (EFET), 57001 Pylaia, Greece 3 School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; [email protected] 4 Department of Biological Applications and Technology, University of Ioannina, 45100 Ioannina, Greece; [email protected] * Correspondence: [email protected] Received: 8 February 2019; Accepted: 15 March 2019; Published: 19 March 2019 Abstract: Ready-to-eat (RTE) leafy salad vegetables are considered foods that can be consumed immediately at the point of sale without further treatment. The aim of the study was to investigate the bacterial community composition of RTE salads at the point of consumption and the changes in bacterial diversity and composition associated with different household washing treatments. The bacterial microbiomes of rocket and spinach leaves were examined by means of 16S rRNA gene high-throughput sequencing. Overall, 886 Operational Taxonomic Units (OTUs) were detected in the salads’ leaves. Proteobacteria was the most diverse high-level taxonomic group followed by Bacteroidetes and Firmicutes. Although they were processed at the same production facilities, rocket showed different bacterial community composition than spinach salads, mainly attributed to the different contributions of Proteobacteria and Bacteroidetes to the total OTU number. The tested household decontamination treatments proved inefficient in changing the bacterial community composition in both RTE salads. -
Massilia Umbonata Sp. Nov., Able to Accumulate Poly-B-Hydroxybutyrate, Isolated from a Sewage Sludge Compost–Soil Microcosm
International Journal of Systematic and Evolutionary Microbiology (2014), 64, 131–137 DOI 10.1099/ijs.0.049874-0 Massilia umbonata sp. nov., able to accumulate poly-b-hydroxybutyrate, isolated from a sewage sludge compost–soil microcosm Marina Rodrı´guez-Dı´az,1,23 Federico Cerrone,33 Mar Sa´nchez-Peinado,3 Lucı´a SantaCruz-Calvo,3 Clementina Pozo1,3 and Jesu´s Gonza´lez Lo´pez1,3 Correspondence 1Department of Microbiology, University of Granada, Granada, Spain Clementina Pozo 2Max-Planck-Institut fu¨r Marine Mikrobiologie, Celsiusstrasse 1, 28359 Bremen, Germany [email protected] 3Water Research Institute, University of Granada, Granada, Spain A bacterial strain, designated strain LP01T, was isolated from a laboratory-scale microcosm packed with a mixture of soil and sewage sludge compost designed to study the evolution of microbial biodiversity over time. The bacterial strain was selected for its potential ability to store polyhydroxyalkanoates (PHAs) as intracellular granules. The cells were aerobic, Gram-stain- negative, non-endospore-forming motile rods. Phylogenetically, the strain was classified within the genus Massilia, as its 16S rRNA gene sequence had similarity of 99.2 % with respect to those of Massilia albidiflava DSM 17472T and M. lutea DSM 17473T. DNA–DNA hybridization showed low relatedness of strain LP01T to the type strains of other, phylogenetically related species of the genus Massilia. It contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1v7c and/or iso-C15 : 0 2-OH) as the major fatty acid(s). It was found to contain small amounts of the fatty acids C18 : 0 and C14 : 0 2-OH, a feature that served to distinguish it from its closest phylogenetic relatives within the genus Massilia. -
An Insight Into Beneficial Pseudomonas Bacteria
Chapter 5 An Insight Into Beneficial Pseudomonas bacteria Galina Novik, Victoria Savich and Elena Kiseleva Additional information is available at the end of the chapter http://dx.doi.org/10.5772/60502 Abstract Pseudomonas is a widespread bacterial genus embracing a vast number of species. Various genosystematic methods are used to identify Pseudomonas and differentiate these bacteria from species of the same genus and species of other genera. Ability to degrade and produce a whole spectrum of compounds makes these species perspec‐ tive in industrial applications. It also makes possible to use various media, including wastes, for cultivation of Pseudomonas. Pseudomonads may be applied in bioreme‐ diation, production of polymers and low-molecular-weight compounds, biocontrol. Recent studies open up new frontiers for further use of Pseudomonas in various areas. Keywords: Pseudomonas bacteria, physiology, taxonomy, application 1. Introduction Pseudomonas is one of the most studied species of bacteria. They were first identified at the end of 19th century by Migula as Gram-negative, rod-shaped and polar-flagellated bacteria. Since that time description of genus Pseudomonas has widened; development of new methods allowed to study in detail the morphology and physiology of these bacteria. However, the morphological characteristics of Pseudomonas are common to many bacterial genera and so are of little value in the positive identification of members of the genus. Advanced nucleic acid- based methods allow to differentiate it from other similar genera and reveal taxonomic relationships among various bacterial species including Pseudomonas. Genus Pseudomonas is represented by species that occupy a wide range of niches owing to metabolic and physiological diversity.