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Metaproteogenomic Insights Beyond Bacterial Response to Naphthalene
ORIGINAL ARTICLE ISME Journal – Original article Metaproteogenomic insights beyond bacterial response to 5 naphthalene exposure and bio-stimulation María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V. del Pozo, José María Vieites, Martin von Bergen, José Luis R. Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H. Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert and Manuel Ferrer 10 Supporting Online Material includes Text (Supporting Materials and Methods) Tables S1 to S9 Figures S1 to S7 1 SUPPORTING TEXT Supporting Materials and Methods Soil characterisation Soil pH was measured in a suspension of soil and water (1:2.5) with a glass electrode, and 5 electrical conductivity was measured in the same extract (diluted 1:5). Primary soil characteristics were determined using standard techniques, such as dichromate oxidation (organic matter content), the Kjeldahl method (nitrogen content), the Olsen method (phosphorus content) and a Bernard calcimeter (carbonate content). The Bouyoucos Densimetry method was used to establish textural data. Exchangeable cations (Ca, Mg, K and 10 Na) extracted with 1 M NH 4Cl and exchangeable aluminium extracted with 1 M KCl were determined using atomic absorption/emission spectrophotometry with an AA200 PerkinElmer analyser. The effective cation exchange capacity (ECEC) was calculated as the sum of the values of the last two measurements (sum of the exchangeable cations and the exchangeable Al). Analyses were performed immediately after sampling. 15 Hydrocarbon analysis Extraction (5 g of sample N and Nbs) was performed with dichloromethane:acetone (1:1) using a Soxtherm extraction apparatus (Gerhardt GmbH & Co. -
Taxonomy of the Azotobacteraceae Determined by Using Immunoelectrophoresis Y
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Apr. 1983, p. 147-156 Vol. 33, No. 2 0020-7713/83/020147-10$02. WO Copyright 0 1983, International Union of Microbiological Societies a Taxonomy of the Azotobacteraceae Determined by Using Immunoelectrophoresis Y. T. TCHAN,'* Z. WYSZOMIRSKA-DREHER,' P. B. NEW,' AND J.-C. ZHOU' Department of Microbiology, University of Sydney, New South Wales, 2006, Australia, and Hua-ckung Agricultural College, Wuhan, People's Republic of China' The similarities of various strains of Azotobacter spp. and Azomonas spp. to reference strains of Azotobacter paspali, Azotobacter vinelandii, Azotobacter chroococcum, Azomonas agilis, Azomonas insignis, and Azomonas macrocyto- genes were determined by rocket line immunoelectrophoresis. The strains of Azotobacter paspali and Azotobacter vinelandii used were immunologically more homogeneous than the strains of Azotobacter chroococcum studied, possibly due to the more diverse geographical origins of the Azotobacter chroococcum strains. Low values were obtained for the mean immunological distances (1 - proportion of immunoprecipitation bands shared between strains) between Azotobacter paspali and Azotobacter vinelandii strains, suggesting that these two species are immunologically closely related. Immunological distances from the Azotobacter chroococcum reference strain were similar for Azotobacter paspali and for other undisputed members of the genus Azotobacter, which makes it reasonable to retain Azotobacter paspali in this genus. When the three Azotobacter antisera were used, all Azotobacter species had mean immunological distances of less than 0.5, whereas the Azomonas species were immunologically more distant , showing that the six species of Azotobacter form an immunologically related group which is distinct from the Azomonas species. Our results with the three Azomonas antisera show that each species of Azoinonas is immunologically distant from the other species, as well as from the Azotobacter species. -
Bourbon Gumbo” 10/13/2016
“Bourbon Gumbo” 10/13/2016 Microbial Analysis Report Table of Contents Executive Summary ----------------------------------------------------------------------------------------------------------------2 Background ---------------------------------------------------------------------------------------------------------------------2 Results ---------------------------------------------------------------------------------------------------------------------------2 Coliforms ------------------------------------------------------------------------------------------------------------------------4 Non-Coliforms that can trigger Coliform test ----------------------------------------------------------------------------4 Fecal Indicator Bacteria -------------------------------------------------------------------------------------------------------4 Potential Pathogens ------------------------------------------------------------------------------------------------------------4 Freshwater or Marine Bacteria (potential sign of surface water intrusion) -------------------------------------------4 Nitrogen Fixing Bacteria ------------------------------------------------------------------------------------------------------5 Carbon Fixing Bacteria --------------------------------------------------------------------------------------------------------5 Ammonia Oxidizing Bacteria ------------------------------------------------------------------------------------------------5 Nitrite Oxidizing Bacteria ----------------------------------------------------------------------------------------------------5 -
Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Lincoln University Research Archive G C A T T A C G G C A T genes Review Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae Tomasz St˛epkowski 1,*, Joanna Banasiewicz 1, Camille E. Granada 2, Mitchell Andrews 3 and Luciane M. P. Passaglia 4 1 Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland; [email protected] 2 Universidade do Vale do Taquari—UNIVATES, Rua Avelino Tallini, 171, 95900-000 Lajeado, RS, Brazil; [email protected] 3 Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand; [email protected] 4 Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul. Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970 Porto Alegre, RS, Brazil; [email protected] * Correspondence: [email protected]; Tel.: +48-509-453-708 Received: 31 January 2018; Accepted: 5 March 2018; Published: 14 March 2018 Abstract: The legume tribe Genisteae comprises 618, predominantly temperate species, showing an amphi-Atlantic distribution that was caused by several long-distance dispersal events. Seven out of the 16 authenticated rhizobial genera can nodulate particular Genisteae species. Bradyrhizobium predominates among rhizobia nodulating Genisteae legumes. Bradyrhizobium strains that infect Genisteae species belong to both the Bradyrhizobium japonicum and Bradyrhizobium elkanii superclades. In symbiotic gene phylogenies, Genisteae bradyrhizobia are scattered among several distinct clades, comprising strains that originate from phylogenetically distant legumes. -
Revised Taxonomy of the Family Rhizobiaceae, and Phylogeny of Mesorhizobia Nodulating Glycyrrhiza Spp
Division of Microbiology and Biotechnology Department of Food and Environmental Sciences University of Helsinki Finland Revised taxonomy of the family Rhizobiaceae, and phylogeny of mesorhizobia nodulating Glycyrrhiza spp. Seyed Abdollah Mousavi Academic Dissertation To be presented, with the permission of the Faculty of Agriculture and Forestry of the University of Helsinki, for public examination in lecture hall 3, Viikki building B, Latokartanonkaari 7, on the 20th of May 2016, at 12 o’clock noon. Helsinki 2016 Supervisor: Professor Kristina Lindström Department of Environmental Sciences University of Helsinki, Finland Pre-examiners: Professor Jaakko Hyvönen Department of Biosciences University of Helsinki, Finland Associate Professor Chang Fu Tian State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University, China Opponent: Professor J. Peter W. Young Department of Biology University of York, England Cover photo by Kristina Lindström Dissertationes Schola Doctoralis Scientiae Circumiectalis, Alimentariae, Biologicae ISSN 2342-5423 (print) ISSN 2342-5431 (online) ISBN 978-951-51-2111-0 (paperback) ISBN 978-951-51-2112-7 (PDF) Electronic version available at http://ethesis.helsinki.fi/ Unigrafia Helsinki 2016 2 ABSTRACT Studies of the taxonomy of bacteria were initiated in the last quarter of the 19th century when bacteria were classified in six genera placed in four tribes based on their morphological appearance. Since then the taxonomy of bacteria has been revolutionized several times. At present, 30 phyla belong to the domain “Bacteria”, which includes over 9600 species. Unlike many eukaryotes, bacteria lack complex morphological characters and practically phylogenetically informative fossils. It is partly due to these reasons that bacterial taxonomy is complicated. -
Genome of Rhizobium Leucaenae Strains CFN 299T and CPAO 29.8
Ormeño-Orrillo et al. BMC Genomics (2016) 17:534 DOI 10.1186/s12864-016-2859-z RESEARCHARTICLE Open Access Genome of Rhizobium leucaenae strains CFN 299T and CPAO 29.8: searching for genes related to a successful symbiotic performance under stressful conditions Ernesto Ormeño-Orrillo1†, Douglas Fabiano Gomes2,3†, Pablo del Cerro4, Ana Tereza Ribeiro Vasconcelos5, Carlos Canchaya6, Luiz Gonzaga Paula Almeida5, Fabio Martins Mercante7, Francisco Javier Ollero4, Manuel Megías4 and Mariangela Hungria2* Abstract Background: Common bean (Phaseolus vulgaris L.) is the most important legume cropped worldwide for food production and its agronomic performance can be greatly improved if the benefits from symbiotic nitrogen fixation are maximized. The legume is known for its high promiscuity in nodulating with several Rhizobium species, but those belonging to the Rhizobium tropici “group” are the most successful and efficient in fixing nitrogen in tropical acid soils. Rhizobium leucaenae belongs to this group, which is abundant in the Brazilian “Cerrados” soils and frequently submitted to several environmental stresses. Here we present the first high-quality genome drafts of R. leucaenae, including the type strain CFN 299T and the very efficient strain CPAO 29.8. Our main objective was to identify features that explain the successful capacity of R. leucaenae in nodulating common bean under stressful environmental conditions. Results: The genomes of R. leucaenae strains CFN 299T and CPAO 29.8 were estimated at 6.7–6.8 Mbp; 7015 and 6899 coding sequences (CDS) were predicted, respectively, 6264 of which are common to both strains. The genomes of both strains present a large number of CDS that may confer tolerance of high temperatures, acid soils, salinity and water deficiency. -
Enhanced Productivity of Serine Alkaline Protease by Bacillus Sp
Malaysian Journal of Microbiology, Vol 6(2) 2010, pp. 133-139 http://dx.doi.org/10.21161/mjm.20109 Studies on nodulation, biochemical analysis and protein profiles of Rhizobium isolated from Indigofera species Kumari B. S., Ram M. R.* and Mallaiah K. V. Department of Microbiology, Acharya Nagarjuna University Nagarjuna Nagar-522 510, Guntur Dist, Andhra Pradesh, India. E-mail: [email protected] Received 3 July 2009; received in revised form 6 November 2009; accepted 20 November 2009 _______________________________________________________________________________________________ ABSTRACT Nodulation characteristics in five species of Indigofera viz., I .trita, I. linnaei, I. astragalina, I. parviflora and I. viscosa was studied at regular intervals on the plants raised in garden soil. Among the species studied, highest average number of nodules per plant of 23 with maximum sized nodules of 8.0 mm diameter was observed in I. astragalina. Biochemical analysis of root nodules of I. astragalina revealed that the leghaemoglobin content of nodules and nitrogen content of root, shoot, leaves and nodules were gradually increased up to 60 DAS, and then decreased with increase in age. Rhizobium isolates of five species of Indigofera were isolated and screened for enzymatic activities and total cellular protein profiles. All the five isolates showed nitrate reductase, citrase, tryptophanase and catalase activity while much variation was observed for enzymes like gelatinase, urease, caseinase, lipase, amylase, lysine decarboxylase and protease activities. Among the isolates studied, only the isolate from I. viscosa has the ability to solubilize the insoluble tricalcium phosphate. All the Rhizobium isolates exhibit similarity in protein content, except the isolate from I. viscosa which showed one additional protein band. -
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. -
Specificity in Legume-Rhizobia Symbioses
International Journal of Molecular Sciences Review Specificity in Legume-Rhizobia Symbioses Mitchell Andrews * and Morag E. Andrews Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand; [email protected] * Correspondence: [email protected]; Tel.: +64-3-423-0692 Academic Editors: Peter M. Gresshoff and Brett Ferguson Received: 12 February 2017; Accepted: 21 March 2017; Published: 26 March 2017 Abstract: Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N2) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. Bradyrhizobium spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but Mimosa spp. show specificity towards Burkholderia in central and southern Brazil, Rhizobium/Ensifer in central Mexico and Cupriavidus in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae (Rhizobium), the genus level for Cytisus (Bradyrhizobium), Lupinus (Bradyrhizobium) and the New Zealand native Sophora spp. (Mesorhizobium) and species level for Cicer arietinum (Mesorhizobium), Listia bainesii (Methylobacterium) and Listia angolensis (Microvirga). -
Ep 2434019 A1
(19) & (11) EP 2 434 019 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 28.03.2012 Bulletin 2012/13 C12N 15/82 (2006.01) C07K 14/395 (2006.01) C12N 5/10 (2006.01) G01N 33/50 (2006.01) (2006.01) (2006.01) (21) Application number: 11160902.0 C07K 16/14 A01H 5/00 C07K 14/39 (2006.01) (22) Date of filing: 21.07.2004 (84) Designated Contracting States: • Kamlage, Beate AT BE BG CH CY CZ DE DK EE ES FI FR GB GR 12161, Berlin (DE) HU IE IT LI LU MC NL PL PT RO SE SI SK TR • Taman-Chardonnens, Agnes A. 1611, DS Bovenkarspel (NL) (30) Priority: 01.08.2003 EP 03016672 • Shirley, Amber 15.04.2004 PCT/US2004/011887 Durham, NC 27703 (US) • Wang, Xi-Qing (62) Document number(s) of the earlier application(s) in Chapel Hill, NC 27516 (US) accordance with Art. 76 EPC: • Sarria-Millan, Rodrigo 04741185.5 / 1 654 368 West Lafayette, IN 47906 (US) • McKersie, Bryan D (27) Previously filed application: Cary, NC 27519 (US) 21.07.2004 PCT/EP2004/008136 • Chen, Ruoying Duluth, GA 30096 (US) (71) Applicant: BASF Plant Science GmbH 67056 Ludwigshafen (DE) (74) Representative: Heistracher, Elisabeth BASF SE (72) Inventors: Global Intellectual Property • Plesch, Gunnar GVX - C 6 14482, Potsdam (DE) Carl-Bosch-Strasse 38 • Puzio, Piotr 67056 Ludwigshafen (DE) 9030, Mariakerke (Gent) (BE) • Blau, Astrid Remarks: 14532, Stahnsdorf (DE) This application was filed on 01-04-2011 as a • Looser, Ralf divisional application to the application mentioned 13158, Berlin (DE) under INID code 62. -
The Ever-Expanding Pseudomonas Genus: Description of 43
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 14 July 2021 doi:10.20944/preprints202107.0335.v1 Article The Ever-Expanding Pseudomonas Genus: Description of 43 New Species and Partition of the Pseudomonas Putida Group Léa Girard1+, Cédric Lood1,2+, Monica Höfte3, Peter Vandamme4, Hassan Rokni-Zadeh5, Vera van Noort1,6, Rob Lavigne2*, René De Mot1,* 1 Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Aren- berg 20, 3001 Leuven, Belgium; [email protected] (L.G.), [email protected] (C.L.), [email protected] (V.v.N.) 2 Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium; [email protected] 3 Department of Plants and Crops, Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium 4 Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; [email protected] 5 Zanjan Pharmaceutical Biotechnology Research Center, Zanjan University of Medical Sciences, 45139-56184 Zanjan, Iran; [email protected] 6 Institute of Biology, Leiden University, Sylviusweg 72, 2333 Leiden, The Netherlands + The authors contributed equally to this work. * Correspondence: [email protected], +3216379524; [email protected] ; Tel.: +3216329681 Abstract: The genus Pseudomonas hosts an extensive genetic diversity and is one of the largest genera among Gram-negative bacteria. Type strains of Pseudomonas are well-known to represent only a small fraction of this diversity and the number of available Pseudomonas genome sequences is increasing rapidly. Consequently, new Pseudomonas species are regularly reported and the number of species within the genus is in constant evolution. -
Amanda Azarias Guimarães
AMANDA AZARIAS GUIMARÃES GENOTYPIC, PHENOTYPIC AND SYMBIOTIC CHARACTERIZATION OF BRADYRHIZOBIUM STRAINS ISOLATED FROM AMAZONIA AND MINAS GERAIS SOILS LAVRAS – MG 2013 AMANDA AZARIAS GUIMARÃES GENOTYPIC, PHENOTYPIC AND SYMBIOTIC CHARACTERIZATION OF BRADYRHIZOBIUM STRAINS ISOLATED FROM AMAZONIA AND MINAS GERAIS SOILS Tese apresentada à Universidade Federal de Lavras, como parte das exigências do Programa de Pós- Graduação em Ciência do Solo, área de concentração em Biologia, Microbiologia e Processos Biológicos do Solo, para a obtenção do título de Doutor. Orientadora PhD. Fatima Maria de Souza Moreira LAVRAS - MG 2013 Ficha Catalográfica Elaborada pela Divisão de Processos Técnicos da Biblioteca da UFLA Guimarães, Amanda Azarias. Genotypic, phenotypic and symbiotic characterization of Bradyrhizobium strains isolated from Amazonia and Minas Gerais soils / Amanda Azarias Guimarães. – Lavras : UFLA, 2013. 88 p. : il. Tese (doutorado) – Universidade Federal de Lavras, 2013. Orientador: Fatima Maria de Souza Moreira. Bibliografia. 1. Bactérias fixadoras de nitrogênio. 2. Taxonomia. 3. Genes housekeeping. 4. Hibridização DNA:DNA. 5. Biologia do solo. I. Universidade Federal de Lavras. II. Título. CDD – 631.46 AMANDA AZARIAS GUIMARÃES GENOTYPIC, PHENOTYPIC AND SYMBIOTIC CHARACTERIZATION OF BRADYRHIZOBIUM STRAINS ISOLATED FROM AMAZONIA AND MINAS GERAIS SOILS (CARACTERIZAÇÃO GENÉTICA, FENOTÍPICA E SIMBIÓTICA DE ESTIRPES DE Bradyrhizobium ISOLADAS DE SOLOS DA AMAZÔNIA E MINAS GERAIS) Tese apresentada à Universidade Federal de Lavras, como parte das exigências do Programa de Pós- Graduação em Ciência do Solo, área de concentração em Biologia, Microbiologia e Processos Biológicos do Solo, para a obtenção do título de Doutor. APROVADA em 18 de fevereiro de 2013. PhD. Anne Willems UGent PhD. Patrícia Gomes Cardoso UFLA PhD. Lucy Seldin UFRJ PhD .