Profiling, Isolation and Characterisation of Beneficial
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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 -
Stress-Tolerance and Taxonomy of Culturable Bacterial Communities Isolated from a Central Mojave Desert Soil Sample
geosciences Article Stress-Tolerance and Taxonomy of Culturable Bacterial Communities Isolated from a Central Mojave Desert Soil Sample Andrey A. Belov 1,*, Vladimir S. Cheptsov 1,2 , Elena A. Vorobyova 1,2, Natalia A. Manucharova 1 and Zakhar S. Ezhelev 1 1 Soil Science Faculty, Lomonosov Moscow State University, Moscow 119991, Russia; [email protected] (V.S.C.); [email protected] (E.A.V.); [email protected] (N.A.M.); [email protected] (Z.S.E.) 2 Space Research Institute, Russian Academy of Sciences, Moscow 119991, Russia * Correspondence: [email protected]; Tel.: +7-917-584-44-07 Received: 28 February 2019; Accepted: 8 April 2019; Published: 10 April 2019 Abstract: The arid Mojave Desert is one of the most significant terrestrial analogue objects for astrobiological research due to its genesis, mineralogy, and climate. However, the knowledge of culturable bacterial communities found in this extreme ecotope’s soil is yet insufficient. Therefore, our research has been aimed to fulfil this lack of knowledge and improve the understanding of functioning of edaphic bacterial communities of the Central Mojave Desert soil. We characterized aerobic heterotrophic soil bacterial communities of the central region of the Mojave Desert. A high total number of prokaryotic cells and a high proportion of culturable forms in the soil studied were observed. Prevalence of Actinobacteria, Proteobacteria, and Firmicutes was discovered. The dominance of pigmented strains in culturable communities and high proportion of thermotolerant and pH-tolerant bacteria were detected. Resistance to a number of salts, including the ones found in Martian regolith, as well as antibiotic resistance, were also estimated. -
Taxonomy and Systematics of Plant Probiotic Bacteria in the Genomic Era
AIMS Microbiology, 3(3): 383-412. DOI: 10.3934/microbiol.2017.3.383 Received: 03 March 2017 Accepted: 22 May 2017 Published: 31 May 2017 http://www.aimspress.com/journal/microbiology Review Taxonomy and systematics of plant probiotic bacteria in the genomic era Lorena Carro * and Imen Nouioui School of Biology, Newcastle University, Newcastle upon Tyne, UK * Correspondence: Email: [email protected]. Abstract: Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics. Keywords: phylogeny; plant; probiotic; PGPR; IAA; ACC; genome; metagenomics Abbreviations: ACC 1-aminocyclopropane-1-carboxylate ANI average nucleotide identity FAO Food and Agriculture Organization DDH DNA-DNA hybridization IAA indol acetic acid JA jasmonic acid OTUs Operational taxonomic units NGS next generation sequencing PGP plant growth promoters WHO World Health Organization PGPR plant growth-promoting rhizobacteria 384 1. -
High-Quality Draft Genome Sequence of Curtobacterium Sp. Strain Ferrero
PROKARYOTES crossm High-Quality Draft Genome Sequence of Curtobacterium sp. Strain Ferrero Ebrahim Osdaghi,a,b Natalia Forero Serna,a* Stephanie Bolot,c,d Marion Fischer-Le Saux,e Marie-Agnès Jacques,e Perrine Portier,e,f Sébastien Carrère,c,d Ralf Koebnika Downloaded from IRD, Cirad, Université de Montpellier, IPME, Montpellier, Francea; Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz, Iranb; INRA, Laboratoire des Interactions Plantes Micro-Organismes (LIPM), UMR 441, Castanet-Tolosan, Francec; CNRS, Laboratoire des Interactions Plantes Micro-Organismes (LIPM), UMR 2594, Castanet-Tolosan, Franced; INRA, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, Francee; CIRM-CFBP, French Collection for Plant-Associated Bacteria, INRA, IRHS, Angers, Francef ABSTRACT Here, we present the high-quality draft genome sequence of Curto- bacterium sp. strain Ferrero, an actinobacterium belonging to a novel species iso- Received 3 November 2017 Accepted 6 http://mra.asm.org/ November 2017 Published 30 November lated as an environmental contaminant in a bacterial cell culture. The assembled 2017 genome of 3,694,888 bp in 49 contigs has a GϩC content of 71.6% and contains Citation Osdaghi E, Forero Serna N, Bolot S, 3,516 predicted genes. Fischer-Le Saux M, Jacques M-A, Portier P, Carrère S, Koebnik R. 2017. High-quality draft genome sequence of Curtobacterium sp. strain Ferrero. Genome Announc 5:e01378-17. he genus Curtobacterium comprises Gram-positive aerobic corynebacteria (family https://doi.org/10.1128/genomeA.01378-17. TMicrobacteriaceae, order Actinomycetales), including at least 11 well-defined species Copyright © 2017 Osdaghi et al. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Adaptive Differentiation and Rapid Evolution of a Soil Bacterium Along a Climate Gradient
Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient Alexander B. Chasea,b,1, Claudia Weihea, and Jennifer B. H. Martinya aDepartment of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697; and bCenter for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, CA 92093 Edited by James M. Tiedje, Michigan State University, East Lansing, MI, and approved March 30, 2021 (received for review January 29, 2021) Microbial community responses to environmental change are largely shifts are due to adaptive differentiation among taxa as a result associated with ecological processes; however, the potential for of past evolutionary divergence. Concurrently, the same selective microbes to rapidly evolve and adapt remains relatively unexplored forces can also shift the abundance of conspecific strains and in natural environments. To assess how ecological and evolutionary alter the allele frequencies of preexisting genetic variation, which processes simultaneously alter the genetic diversity of a microbiome, at this genetic scale is defined as an evolutionary process (14). we conducted two concurrent experiments in the leaf litter layer of Finally, evolution through de novo mutation can provide a new soil over 18 mo across a climate gradient in Southern California. In the source of genetic variation that may allow for further adaptation first experiment, we reciprocally transplanted microbial communities to environmental change. from five sites to test whether ecological shifts in ecotypes of the In this study, we aimed to capture this continuum of ecological abundant bacterium, Curtobacterium, corresponded to past adaptive and evolutionary processes that together produce the response differentiation. -
Diversity and Taxonomic Novelty of Actinobacteria Isolated from The
Diversity and taxonomic novelty of Actinobacteria isolated from the Atacama Desert and their potential to produce antibiotics Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Christian-Albrechts-Universität zu Kiel Vorgelegt von Alvaro S. Villalobos Kiel 2018 Referent: Prof. Dr. Johannes F. Imhoff Korreferent: Prof. Dr. Ute Hentschel Humeida Tag der mündlichen Prüfung: Zum Druck genehmigt: 03.12.2018 gez. Prof. Dr. Frank Kempken, Dekan Table of contents Summary .......................................................................................................................................... 1 Zusammenfassung ............................................................................................................................ 2 Introduction ...................................................................................................................................... 3 Geological and climatic background of Atacama Desert ............................................................. 3 Microbiology of Atacama Desert ................................................................................................. 5 Natural products from Atacama Desert ........................................................................................ 9 References .................................................................................................................................. 12 Aim of the thesis ........................................................................................................................... -
Supplement of Screening of Cloud Microorganisms Isolated at the Puy De Dôme (France) Station for the Production of Biosurfactants
Supplement of Atmos. Chem. Phys., 16, 12347–12358, 2016 http://www.atmos-chem-phys.net/16/12347/2016/ doi:10.5194/acp-16-12347-2016-supplement © Author(s) 2016. CC Attribution 3.0 License. Supplement of Screening of cloud microorganisms isolated at the Puy de Dôme (France) station for the production of biosurfactants Pascal Renard et al. Correspondence to: Anne-Marie Delort ([email protected]) The copyright of individual parts of the supplement might differ from the CC-BY 3.0 licence. Table S1. Strains are isolated during 39 cloud events (from 2004 to 2014) gathered in four categories according to the physicochemical characteristics of the cloud waters (Blue: marine, purple: highly marine, green: continental and black: polluted) as described by Deguillaume et al. (2014). Cloud Nb of Ions (µM) Composition Date pH 2- - - + + 2+ + 2+ Event strains SO 4 NO 3 Cl Acetate Formate Oxalate Succinate Malonate Na NH 4 Mg K Ca 21 Marine 2 2004-01 5.6 NA NA NA NA NA NA NA NA NA NA NA NA NA 23 Polluted 2 2004-02 3.1 NA NA NA NA NA NA NA NA NA NA NA NA NA 29 Marine 1 2004-07 5.5 NA NA NA NA NA NA NA NA NA NA NA NA NA 30 Marine 3 2004-09 7.6 3.8 6.5 12.0 6.0 6.0 0.5 0.1 0.16 19.4 54.9 4.9 4.1 12.0 32 Continental 1 2004-12 5.5 72.1 95.8 31.5 0.0 0.3 0.3 0.1 0.17 74.4 132.4 7.6 9.0 73.7 42 Continental 25 2007-12 4.7 39.7 198.4 20.2 10.2 5.8 2.9 0.6 0.58 19.1 148.2 3.5 11.9 58.0 43 Highly marine 25 2008-01 5.9 9.4 21.4 81.4 11.4 6.7 1.2 0.2 0.28 315.7 35.9 11.8 13.7 26.0 44 Continental 14 2008-02 5.2 24.6 65.9 17.2 26.8 18.0 1.3 0.5 0.39 -
Report on 31 Unrecorded Bacterial Species in Korea That Belong to the Phylum Actinobacteria
Journal of Species Research 5(1):113, 2016 Report on 31 unrecorded bacterial species in Korea that belong to the phylum Actinobacteria JungHye Choi1, JuHee Cha1, JinWoo Bae2, JangCheon Cho3, Jongsik Chun4, WanTaek Im5, Kwang Yeop Jahng6, Che Ok Jeon7, Kiseong Joh8, Seung Bum Kim9, Chi Nam Seong10, JungHoon Yoon11 and ChangJun Cha1,* 1Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Korea 2Department of Biology, Kyung Hee University, Seoul 02447, Korea 3Department of Biological Sciences, Inha University, Incheon 22212, Korea 4School of Biological Sciences, Seoul National University, Seoul 08826, Korea 5Department of Biotechnology, Hankyong National University, Anseong 17579, Korea 6Department of Life Sciences, Chonbuk National University, Jeonju-si 54896, Korea 7Department of Life Science, Chung-Ang University, Seoul 06974, Korea 8Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Korea 9Department of Microbiology, Chungnam National University, Daejeon 34134, Korea 10Department of Biology, Sunchon National University, Suncheon 57922, Korea 11Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon 16419, Korea *Correspondent: [email protected] To discover and characterize indigenous species in Korea, a total of 31 bacterial strains that belong to the phylum Actinobacteria were isolated from various niches in Korea. Each strain showed the high sequence similarity (>99.1%) with the closest bacterial species, forming a robust phylogenetic clade. These strains have not been previously recorded in Korea. According to the recently updated taxonomy of the phylum Actinobacteria based upon 16S rRNA trees, we report 25 genera of 13 families within 5 orders of the class Actinobacteria as actinobacterial species found in Korea. -
Soil Ecotypes Along a Climate Gradient
Emergence of Soil Bacterial Ecotypes Along a Climate Gradient Alexander B. Chase1#, Zulema Gomez-Lunar2, Alberto E. Lopez1, Junhui Li2, Steven D. Allison1,2, Adam C. Martiny1,2, and Jennifer B.H. Martiny1 1Department of Ecology and Evolutionary Biology, University of California, Irvine, California 2Department of Earth System Sciences, University of California, Irvine, California #Address correspondence to: Alexander B. Chase, [email protected] 3300 Biological Sciences III Department of Ecology and Evolutionary Biology University of California Irvine, CA 92697 Running Title: Soil ecotypes along a climate gradient Article Accepted Thi s article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/1462-2920.14405 This article is protected by copyright. All rights reserved. Originality-Significance Statement Microbial community analyses typically rely on delineating operational taxonomic units; however, a great deal of genomic and phenotypic diversity occurs within these taxonomic groupings. Previous work in closely-related marine bacteria demonstrates that fine-scale genetic variation is linked to variation in ecological niches. In this study, we present similar evidence for soil bacteria. We find that an abundant and widespread soil taxon encompasses distinct ecological populations, or ecotypes, as defined by their phenotypic traits. We further validated that differences in these soil ecotypes correspond to variation in their distribution across a regional climate gradient. Thus, there exists genomic and phenotypic diversity within this soil taxon that contributes to niche differentiation. -
Coffee Microbiota and Its Potential Use in Sustainable Crop Management. a Review Duong Benoit, Marraccini Pierre, Jean Luc Maeght, Philippe Vaast, Robin Duponnois
Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review Duong Benoit, Marraccini Pierre, Jean Luc Maeght, Philippe Vaast, Robin Duponnois To cite this version: Duong Benoit, Marraccini Pierre, Jean Luc Maeght, Philippe Vaast, Robin Duponnois. Coffee Mi- crobiota and Its Potential Use in Sustainable Crop Management. A Review. Frontiers in Sustainable Food Systems, Frontiers Media, 2020, 4, 10.3389/fsufs.2020.607935. hal-03045648 HAL Id: hal-03045648 https://hal.inrae.fr/hal-03045648 Submitted on 8 Dec 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. Distributed under a Creative Commons Attribution| 4.0 International License REVIEW published: 03 December 2020 doi: 10.3389/fsufs.2020.607935 Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review Benoit Duong 1,2, Pierre Marraccini 2,3, Jean-Luc Maeght 4,5, Philippe Vaast 6, Michel Lebrun 1,2 and Robin Duponnois 1* 1 LSTM, Univ. Montpellier, IRD, CIRAD, INRAE, SupAgro, Montpellier, France, 2 LMI RICE-2, Univ. Montpellier, IRD, CIRAD, AGI, USTH, Hanoi, Vietnam, 3 IPME, Univ. Montpellier, CIRAD, IRD, Montpellier, France, 4 AMAP, Univ. Montpellier, IRD, CIRAD, INRAE, CNRS, Montpellier, France, 5 Sorbonne Université, UPEC, CNRS, IRD, INRA, Institut d’Écologie et des Sciences de l’Environnement, IESS, Bondy, France, 6 Eco&Sols, Univ. -
Curtobacterium Flaccumfaciens Pv. Flaccumfaciens Not Detected No
European and Mediterranean Plant Protection Organization PM 7/102 (1) Organisation Europe´enne et Me´diterrane´enne pour la Protection des Plantes Diagnostics Diagnostic Curtobacterium flaccumfaciens pv. flaccumfaciens Specific scope Specific approval and amendment This standard describes a diagnostic protocol for Curtobacterium Approved in 2011-09. flaccumfaciens pv. flaccumfaciens.1 of pathogenicity. A flow diagram describing the procedure is Introduction giveninFig.1. Curtobacterium flaccumfaciens pv. flaccumfaciens is the causal agent of the bacterial wilt disease of Phaseolus spp. and is a sys- Identity temic bacterium. The disease was first discovered in the United States (South Dakota) in the 1920s on Phaseolus vulgaris and sub- Name: Curtobacterium flaccumfaciens pv. flaccumfaciens sequently recorded in Australia, Canada, Mexico, South America (Hedges) Collins & Jones. and Tunisia. It has a restricted distributioninRomaniaandRussia. Synonyms:ex-Corynebacterium flaccumfaciens subsp. flaccum- Although it has been recorded in Belgium, Bulgaria, Greece, Hun- faciens (Hedges) Dowson. gary, Poland, Turkey and Ukraine, it has not established and is Taxonomic position: Actinobacteria, Actinomycetales, now considered absent from these countries. It has recently been Microbacteriaceae, Curtobacterium. reported in few fields in South-Eastern Spain (Gonza´lez et al., Notes on taxonomy and nomenclature: In addition to Curto- 2005). Apart from this record, there are few recent records of bacterium flaccumfaciens pv. flaccumfaciens and according to C. flaccumfaciens pv. flaccumfaciens in the EPPO region. the most recent classification (Collins & Jones, 1984; Young No effective chemical methods are known against this disease; et al., 1996, 2004), the species C. flaccumfaciens includes the as C. flaccumfaciens pv. flaccumfaciens is a seed-borne bacte- following pathovars: betae (Cfb), oortii (Cfo), poinsettiae (Cfp) rium, current control methods are based mainly on the use of and ilicis (Cfi).