A Report of 26 Unrecorded Bacterial Species in Korea, Isolated from Urban Streams of the Han River Watershed in 2018
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Corynebacterium Sp.|NML98-0116
1 Limnochorda_pilosa~GCF_001544015.1@NZ_AP014924=Bacteria-Firmicutes-Limnochordia-Limnochordales-Limnochordaceae-Limnochorda-Limnochorda_pilosa 0,9635 Ammonifex_degensii|KC4~GCF_000024605.1@NC_013385=Bacteria-Firmicutes-Clostridia-Thermoanaerobacterales-Thermoanaerobacteraceae-Ammonifex-Ammonifex_degensii 0,985 Symbiobacterium_thermophilum|IAM14863~GCF_000009905.1@NC_006177=Bacteria-Firmicutes-Clostridia-Clostridiales-Symbiobacteriaceae-Symbiobacterium-Symbiobacterium_thermophilum Varibaculum_timonense~GCF_900169515.1@NZ_LT827020=Bacteria-Actinobacteria-Actinobacteria-Actinomycetales-Actinomycetaceae-Varibaculum-Varibaculum_timonense 1 Rubrobacter_aplysinae~GCF_001029505.1@NZ_LEKH01000003=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_aplysinae 0,975 Rubrobacter_xylanophilus|DSM9941~GCF_000014185.1@NC_008148=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_xylanophilus 1 Rubrobacter_radiotolerans~GCF_000661895.1@NZ_CP007514=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_radiotolerans Actinobacteria_bacterium_rbg_16_64_13~GCA_001768675.1@MELN01000053=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_rbg_16_64_13 1 Actinobacteria_bacterium_13_2_20cm_68_14~GCA_001914705.1@MNDB01000040=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_13_2_20cm_68_14 1 0,9803 Thermoleophilum_album~GCF_900108055.1@NZ_FNWJ01000001=Bacteria-Actinobacteria-Thermoleophilia-Thermoleophilales-Thermoleophilaceae-Thermoleophilum-Thermoleophilum_album -
Culturable Bacteria in the Hedera Helix Phylloplane Vincent Stevens1* , Sofie Thijs1 and Jaco Vangronsveld1,2*
Stevens et al. BMC Microbiology (2021) 21:66 https://doi.org/10.1186/s12866-021-02119-z RESEARCH ARTICLE Open Access Diversity and plant growth-promoting potential of (un)culturable bacteria in the Hedera helix phylloplane Vincent Stevens1* , Sofie Thijs1 and Jaco Vangronsveld1,2* Abstract Background: A diverse community of microbes naturally exists on the phylloplane, the surface of leaves. It is one of the most prevalent microbial habitats on earth and bacteria are the most abundant members, living in communities that are highly dynamic. Today, one of the key challenges for microbiologists is to develop strategies to culture the vast diversity of microorganisms that have been detected in metagenomic surveys. Results: We isolated bacteria from the phylloplane of Hedera helix (common ivy), a widespread evergreen, using five growth media: Luria–Bertani (LB), LB01, yeast extract–mannitol (YMA), yeast extract–flour (YFlour), and YEx. We also included a comparison with the uncultured phylloplane, which we showed to be dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Inter-sample (beta) diversity shifted from LB and LB01 containing the highest amount of resources to YEx, YMA, and YFlour which are more selective. All growth media equally favoured Actinobacteria and Gammaproteobacteria, whereas Bacteroidetes could only be found on LB01, YEx, and YMA. LB and LB01 favoured Firmicutes and YFlour was most selective for Betaproteobacteria. At the genus level, LB favoured the growth of Bacillus and Stenotrophomonas, while YFlour was most selective for Burkholderia and Curtobacterium. The in vitro plant growth promotion (PGP) profile of 200 isolates obtained in this study indicates that previously uncultured bacteria from the phylloplane may have potential applications in phytoremediation and other plant-based biotechnologies. -
Isolation, Identification and Investigation of Their Bioactive Potential Inês Filipa Coelho Ribeiro
M DISSERTAÇÃO DE MESTRADO DE DISSERTAÇÃO AMBIENTAIS CONTAMINAÇÃO E TOXICOLOGIA Marine Actinobacteria from the Northern isolation, Coast: Portuguese of their and investigation identification bioactive potential Inês Filipa Coelho Ribeiro 2017 Inês Filipa Coelho Ribeiro. Marine Actinobacteria from the Northern Portuguese Coast: isolation, identification and M.ICBAS 2017 investigation of their bioactive potential Marine Actinobacteria from the Northern Portuguese Coast: isolation, identification and investigation of their bioactive potential Inês Filipa Coelho Ribeiro SEDE ADMINISTRATIVA INSTITUTO DE CIÊNCIAS BIOMÉDICAS ABEL SALAZAR FACULDADE DE CIÊNCIAS INÊS FILIPA COELHO RIBEIRO MARINE ACTINOBACTERIA FROM THE NORTHERN PORTUGUESE COAST: ISOLATION, IDENTIFICATION AND INVESTIGATION OF THEIR BIOACTIVE POTENTIAL Dissertação de Candidatura ao grau de Mestre em Toxicologia e Contaminação Ambientais submetida ao Instituto de Ciências Biomédicas de Abel Salazar da Universidade do Porto. Orientadora – Doutora Maria de Fátima Carvalho Categoria – Investigadora Auxiliar Afiliação – Centro Interdisciplinar de Investigação Marinha e Ambiental da Universidade do Porto Co-orientador – Doutor Filipe Pereira Categoria – Investigador Auxiliar Afiliação – Centro Interdisciplinar de Investigação Marinha e Ambiental da Universidade do Porto ACKNOWLEDGEMENTS First of all, I would like to thank my supervisor, Dr. Fátima Carvalho, who received me and made possible the work done in this thesis. My genuine thanks for all the shared knowledge, for all the trust and dedication and for all you provided me so that my goals were achieved. Thank you for being part of a very important phase for my personal and professional development. I would also like to thank my co-advisor, Dr. Filipe Pereira for his trust, for the support he provided me and for his contribution in the tools of molecular biology that were used in this work. -
Isolation of Rhizobacteria in Southwestern Québec, Canada: An
Isolation of rhizobacteria in Southwestern Québec, Canada: An investigation of their impact on the growth and salinity stress alleviation in Arabidopsis thaliana and crop plants Di Fan Department of Plant Science Faculty of Agricultural and Environmental Sciences Macdonald Campus of McGill University 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Québec H9X 3V9 December 2017 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of DOCTOR OF PHILOSOPHY © Di Fan, Canada, 2017 Table of contents Abstract ................................................................................................. x Résumé ................................................................................................ xiii Acknowledegments ............................................................................. xv Preface ................................................................................................ xviii Contribution of authors ................................................................................ xviii Chapter 1................................................................................................. 1 Introduction ............................................................................................ 1 Chapter 2................................................................................................. 5 Literature Review ................................................................................... 5 2.1 What are root exudates? ......................................................................... -
Characterization of Diverse Mechanisms of Salicin Degradation in Populus Microbiome Isolates
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2019 Characterization of Diverse Mechanisms of Salicin Degradation in Populus Microbiome Isolates Sanjeev Dahal University of Tennessee, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Dahal, Sanjeev, "Characterization of Diverse Mechanisms of Salicin Degradation in Populus Microbiome Isolates. " PhD diss., University of Tennessee, 2019. https://trace.tennessee.edu/utk_graddiss/5720 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Sanjeev Dahal entitled "Characterization of Diverse Mechanisms of Salicin Degradation in Populus Microbiome Isolates." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Life Sciences. Jennifer Morrell-Falvey, Major Professor We have read this dissertation and recommend its acceptance: Dale Pelletier, Sarah Lebeis, Cong Trinh, Daniel Jacobson Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Characterization of Diverse Mechanisms of Salicin Degradation in Populus Microbiome Isolates A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Sanjeev Dahal December 2019 Dedication I would like to dedicate this dissertation, first and foremost to my family. -
Microbial Degradation of Acetaldehyde in Freshwater, Estuarine and Marine Environments
Microbial Degradation of Acetaldehyde in Freshwater, Estuarine and Marine Environments Phillip Robert Kenneth Pichon A thesis submitted for the degree of Doctor of Philosophy in Microbiology School of Life Sciences University of Essex October 2020 This thesis is dedicated to the memory of my mum, Elizabeth “Taylor” Pichon Acknowledgements I would like to begin by thanking my supervisors Professor Terry McGenity, Dr Boyd McKew, Dr Joanna Dixon, and Professor J. Colin Murrell, all of whom have provided invaluable guidance and support throughout this project. Their advice and encouragement have been greatly appreciated during the last four years and I am grateful for all of their contributions to this research. I would also like to thank Dr Michael Steinke for his continued support and insightful discussions during this project. Special thanks also go to Dr Metodi Metodiev and Dr Gergana Metodieva for their help with sample preparation and initial data analysis during the proteomics experiment. I would especially like to thank Farid Benyahia and Tania Cresswell-Maynard for their technical support with a variety of molecular methods, and John Green for his help and expertise in gas chromatography. I would also like to thank all of my friends and colleagues who have worked with me in Labs 5.28 and 5.32 during the last four years. My thanks also to NERC for funding this project and to the EnvEast DTP for providing a range of valuable training opportunities. To my Dad and Roisin, your support and encouragement have helped me through the toughest parts of my project. My love and thanks to you both. -
Revisiting the Taxonomy of the Genus Arcobacter: Getting Order from the Chaos
fmicb-09-02077 September 1, 2018 Time: 10:25 # 1 ORIGINAL RESEARCH published: 04 September 2018 doi: 10.3389/fmicb.2018.02077 Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Chaos Alba Pérez-Cataluña1, Nuria Salas-Massó1, Ana L. Diéguez2, Sabela Balboa2, Alberto Lema2, Jesús L. Romalde2* and Maria J. Figueras1* 1 Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Institut d’Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain, 2 Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain Since the description of the genus Arcobacter in 1991, a total of 27 species have been described, although some species have shown 16S rRNA similarities below 95%, which is the cut-off that usually separates species that belong to different genera. Edited by: The objective of the present study was to reassess the taxonomy of the genus Martha E. Trujillo, Arcobacter using information derived from the core genome (286 genes), a Multilocus Universidad de Salamanca, Spain Sequence Analysis (MLSA) with 13 housekeeping genes, as well as different genomic Reviewed by: John Phillip Bowman, indexes like Average Nucleotide Identity (ANI), in silico DNA–DNA hybridization (isDDH), University of Tasmania, Australia Average Amino-acid Identity (AAI), Percentage of Conserved Proteins (POCPs), and Javier Pascual, Deutsche Sammlung von Relative Synonymous Codon Usage (RSCU). The study included a total of 39 strains Mikroorganismen und Zellkulturen that represent all the 27 species included in the genus Arcobacter together with 13 (DSMZ), Germany strains that are potentially new species, and the analysis of 57 genomes. -
APORTACIONES a LA EPIDEMIOLOGÍA DE Arcobacter Y Helicobacter Spp.: APLICACIÓN DE MÉTODOS MOLECULARES a SU DETECCIÓN E IDENTIFICACIÓN EN ALIMENTOS
Universidad Politécnica de Valencia Departamento de Biotecnología APORTACIONES A LA EPIDEMIOLOGÍA DE Arcobacter Y Helicobacter spp.: APLICACIÓN DE MÉTODOS MOLECULARES A SU DETECCIÓN E IDENTIFICACIÓN EN ALIMENTOS Tesis Doctoral Autor: Isidro Favian Bayas Morejón Directoras: Dra. Ma Antonia Ferrús Pérez Dra. Ana González Pellicer Valencia, Octubre de 2016 DEDICATORIA Este trabajo realizado con mucho esfuerzo lo dedico a mi hijo Anthony Fabián, el cual ha sido la fuerza principal que me impulsó día a día para seguir adelante; a mi amada esposa Rosa Angélica, que de manera incondicional y pese a la distancia me ha apoyado, y me ha dado fuerzas para continuar. A mi querida madre Laura Judith, que sé que desde el cielo me ha estado iluminando en este largo camino. A mí apreciado padre Elías Alberto, a mis queridas hermanas; Rocío, Maritza y Rosario que aunque a la distancia me supieron apoyar. ¡Los quiero mucho! AGRADECIMIENTOS Agradezco a DIOS por brindarme siempre nuevas oportunidades en los caminos de la vida para así aprender día a día lo maravilloso que es vivir. Al finalizar esta tesis es muy satisfactorio expresar mi agradecimiento a mis directoras, Mª Antonia Ferrús y Ana González. Gracias por ofrecerme la oportunidad de trabajar con vosotras, por vuestra dirección, y por supuesto, por haberme guiado con buena voluntad, paciencia, amplio conocimiento y experiencia a lo largo de este trabajo. También quiero agradecer a todos quienes conforman el Departamento de Biotecnología: A Manuel Hernández, Jorge García, Rosa Montes y Ma Ángeles Castillo, gracias por brindarme vuestra confianza y valiosos consejos. A Ana Jiménez y Salut Botella, gracias por haberme permitido compartir con vosotras esa bonita experiencia de impartir y aprender a través de la docencia en prácticas. -
Actinobacterial Diversity in Atacama Desert Habitats As a Road Map to Biodiscovery
Actinobacterial Diversity in Atacama Desert Habitats as a Road Map to Biodiscovery A thesis submitted by Hamidah Idris for the award of Doctor of Philosophy July 2016 School of Biology, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle Upon Tyne, United Kingdom Abstract The Atacama Desert of Northern Chile, the oldest and driest nonpolar desert on the planet, is known to harbour previously undiscovered actinobacterial taxa with the capacity to synthesize novel natural products. In the present study, culture-dependent and culture- independent methods were used to further our understanding of the extent of actinobacterial diversity in Atacama Desert habitats. The culture-dependent studies focused on the selective isolation, screening and dereplication of actinobacteria from high altitude soils from Cerro Chajnantor. Several strains, notably isolates designated H9 and H45, were found to produce new specialized metabolites. Isolate H45 synthesized six novel metabolites, lentzeosides A-F, some of which inhibited HIV-1 integrase activity. Polyphasic taxonomic studies on isolates H45 and H9 showed that they represented new species of the genera Lentzea and Streptomyces, respectively; it is proposed that these strains be designated as Lentzea chajnantorensis sp. nov. and Streptomyces aridus sp. nov.. Additional isolates from sampling sites on Cerro Chajnantor were considered to be nuclei of novel species of Actinomadura, Amycolatopsis, Cryptosporangium and Pseudonocardia. A majority of the isolates produced bioactive compounds that inhibited the growth of one or more strains from a panel of six wild type microorganisms while those screened against Bacillus subtilis reporter strains inhibited sporulation and cell envelope, cell wall, DNA and fatty acid synthesis. -
SAJ NEWS 2601-Rev
SAJ NEWS Vol. 26, No. 1, 2012 Contents Outline of SAJ: Activities and Membership S 2 A message from the chairperson of The Society for Actinomycetes Japan S 3 List of new scientific names and nomenclatural changes in the class Actinobacteria validly published in 2011 S 4 51th Regular Colloquium S 23 The 2012 Annual Meeting of the Society for Actinomycetes Japan S 24 Online access to The Journal of Antibiotics for SAJ members S 25 S1 Outline of SAJ: Activities and Membership The Society for Actinomycetes Japan (SAJ) published in June and December. Actinomycete was established in 1955 and authorized as a scien- researchers in foreign countries are welcome to join tific organization by Science Council of Japan in SAJ. For application of SAJ membership, please 1985. The Society for Applied Genetics of Actino- contact the SAJ secretariat (see below). Annual mycetes, which was established in 1972, merged in membership fees are currently 5,000 yen for active SAJ in 1990. SAJ aims at promoting actinomycete members, 3,000 yen for student members and researches as well as social and scientific exchanges 20,000 yen or more for supporting members (mainly between members domestically and internationally. companies), provided that the fees may be changed The Activities of SAJ have included annual and without advance announcement. regular scientific meetings, workshops and publica- tions of The Journal of Antibiotics (the official The current members (April 2012 - March 2014) journal, joint publication with Japan Antibiotics Re- of the Board of Directors are: Hiroyuki Osada search Association), Actinomycetologica (Newslet- (Chairperson; RIKEN), Masayuki Hayakawa (Vice ter) and laboratory manuals. -
An Inoculum-Dependent Culturing Strategy (IDC) for the Cultivation of Environmental Microbiomes and the Isolation of Novel Endophytic Actinobacteria
The Journal of Antibiotics (2020) 73:66–71 https://doi.org/10.1038/s41429-019-0226-4 BRIEF COMMUNICATION An inoculum-dependent culturing strategy (IDC) for the cultivation of environmental microbiomes and the isolation of novel endophytic Actinobacteria 1,2 1 1 1 Mohamed S. Sarhan ● Elhussein F. Mourad ● Rahma A. Nemr ● Mohamed R. Abdelfadeel ● 3 1 1 1 1 Hassan-Sibroe A. Daanaa ● Hanan H. Youssef ● Hanan A. Goda ● Mervat A. Hamza ● Mohamed Fayez ● 2 4 1 Bettina Eichler-Löbermann ● Silke Ruppel ● Nabil A. Hegazi Received: 5 March 2019 / Revised: 25 July 2019 / Accepted: 4 August 2019 / Published online: 29 August 2019 © The Author(s) 2019. This article is published with open access Abstract The recent introduction of plant-only-based culture media enabled cultivation of not-yet-cultured bacteria that exceed 90% of the plant microbiota communities. Here, we further prove the competence and challenge of such culture media, and further introduce “the inoculum-dependent culturing strategy, IDC”. The strategy depends on direct inoculating plant serial dilutions onto plain water agar plates, allowing bacteria to grow only on the expense of natural nutrients contained in the administered 1234567890();,: 1234567890();,: inoculum. Developed colonies are successively transferred/subcultured onto plant-only-based culture media, which contains natural nutrients very much alike to those found in the prepared plant inocula. Because of its simplicity, the method is recommended as a powerful tool in screening programs that require microbial isolation from a large number of diverse plants. Here, the method comfortably and successfully recovered several isolates of endophytic Actinobacteria represented by the six genera of Curtobacterium spp., Plantibacter spp., Agreia spp., Herbiconiux spp., Rhodococcus spp., and Nocardioides spp. -
Bacterial Communities Within the Microbiome of Three Shark Species in South Florida Waters
Please do not remove this page Bacterial Communities Within the Microbiome of Three Shark Species in South Florida Waters Black, Chelsea Leigh https://scholarship.miami.edu/discovery/delivery/01UOML_INST:ResearchRepository/12356347670002976?l#13356347660002976 Black, C. L. (2020). Bacterial Communities Within the Microbiome of Three Shark Species in South Florida Waters [University of Miami]. https://scholarship.miami.edu/discovery/fulldisplay/alma991031454075202976/01UOML_INST:ResearchR epository Open Downloaded On 2021/09/28 07:30:20 -0400 Please do not remove this page UNIVERSITY OF MIAMI BACTERIAL COMMUNITIES WITHIN THE MICROBIOME OF THREE SHARK SPECIES IN SOUTH FLORIDA WATERS By Chelsea Leigh Black A THESIS Submitted to the Faculty of the University of Miami in partial fulfillment of the requirements for the degree of Master of Science Coral Gables, Florida May 2020 ã2020 Chelsea Leigh Black All Rights Reserved UNIVERSITY OF MIAMI A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science BACTERIAL COMMUNITIES WITHIN THE MICROBIOME OF THREE SHARK SPECIES IN SOUTH FLORIDA WATERS Chelsea Leigh Black Approved: Neil Hammerschlag, Ph.D. Maria Estevanez, M.A, M.B.A. Research Associate Professor Senior Lecturer Marine Ecosystems and Society Marine Ecosystems and Society Liza Merly, Ph.D. Guillermo Prado, Ph.D. Senior Lecturer Dean of the Graduate School Marine Biology and Ecology BLACK, CHELSEA LEIGH (M.S., Marine Ecosystems and Society) (May 2020) Bacterial Communities Within the Microbiome of Three Shark Species in South Florida Waters Abstract of a thesis at the University of Miami. Thesis supervised by Professor Neil Hammerschlag No. of pages in text: (81) Assessing shark health can provide information on species and environmental condition.