DOCSLIB.ORG

Transfer of Pseudomonas Aminovorans (Den Dooren De Jong 1926) to Aminobacter Gen

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Transfer of Pseudomonas Aminovorans (Den Dooren De Jong 1926) to Aminobacter Gen INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1992, p. 84-92 Vol. 42, No. 1 0020-771319210 10084-09$02.00/0 Copyright 0 1992, International Union of Microbiological Societies Transfer of Pseudomonas aminovorans (den Dooren de Jong 1926) to Aminobacter gen. nov. as Arninobacter aminovorans comb. nov. and Description of Aminobacter aganoensis sp. nov. and Aminobactev niigataensis sp. nov. TEIZI URAKAMI,l* HISAYA ARAKI,2 HIROMI OYANAGI,* KEN-ICHIRO SUZUKI,3 AND KAZUO KOMAGATA4 Biochemicals Division, Mitsubishi Gas Chemical Co., Seavans-N Building, 1-2-1, Shibaura, Minato-ku, Tokyo 105,' Niigata Research Laboratory, Mitsubishi Gas Chemical Co., Niigata 950-31 ,2 Japan Collection of Microorganisms, The Institute of Physical and Chemical Research, Wacho-shi, Saitama 351-01,3 and Institute of Applied Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo I 13,4Japan We compared non-methane-, non-methanol-, and methylamine-utilizing bacteria, including Pseudomonas aminovorans, a tetramethylammonium-utilizing bacterium, and an N,N-dimethylformamide-utilizingbacte- rium. These bacteria are gram-negative, nonsporeforming, subpolarly flagellated, rod-shaped organisms. Reproduction occurs by budding. The DNA base compositions are 62 to 64 mol% guanine plus cytosine. The cellular fatty acids contain a large amount of acid. The major hydroxy acid is 3-OH C1z:oacid. The major ubiquinone is ubiquinone Q-lo. These bacteria are clearly separated from authentic Pseudomonas species (Pseudornonas Jiuorescens rRNA group) on the basis of utilization of methylamine, morphological and chemotaxonomic characteristics, DNA-DNA homology, and rRNA-DNA homology. They were divided into three subgroups on the basis of their physiological characteristics and DNA-DNA homology data. A new genus, Aminobacter, and three new species, Aminobacter aminovorans comb. nov., Aminobacter aganoensis sp. nov., and Aminobacter niigataensis sp. nov., are proposed. The type species of Aminobacter gen. nov. is A. aminovorans, with type strain JCM 7852. The type strain of A. aganoensis is strain TH-3 (= JCM 7854), and the type strain of A. niigataensis is strain DM-81 (= JCM 7853). Although a large number of methane- and methylamine- philus (41, 42), and Paracoccus aminovorans (41, 42) were utilizing bacteria (and a large number of methanol- and described. Strains TH-3T and DM-81T were non-methane-, methylamine-utilizing bacteria have been described (23, 29, non-methanol-, monomethylamine-, dimethylamine-, and 43-54), only a few non-methane-, non-methanol-, and meth- trimethylamine-utilizing, nonsporeforming, gram-negative, ylamine-utilizing have been found to date (4, 10, 13, 22, 29, subpolar1y flagellated, rod-shaped organisms with a ubiqui- 32, 4042). Pseudomonas aminovorans (4), Pseudomonas none Q-10 system, a cellular fatty acid composition which sp. strain MA (32), and Pseudomonas sp. strain MS (22) included a large amount of C18:' acid, a hydroxy fatty acid have been reported to be gram-negative methylamine-utiliz- composition which included a large amount of 3-hydroxy ing bacteria. These three bacteria were distinguished from C12:* acid, and a DNA base composition ranging from 62 to methane- and met hanol-utilizing bacteria on the basis of 64 mol% guanine plus cytosine (G+C) (40, 42). These their failure to utilize methanol and methane. De Ley et al. characteristics were identical for Pseudomonas amino- (5) studied the rRNA cistron similarities of Pseudomonas vorans JCM 7852T, Pseudomonas sp. strain MA, and Pseu- and Pseudomonas-like strains and reported that the type domonas sp. strain MS, as reported previously (47, 48). strain of P. aminovorans was actually a member of the In this study, we characterized five methylamine-utilizing Rhizobium loti rRNA branch and not a member of the genus bacteria, including strains TH-3T and DM-81T, and clarified Pseudomonas. Furthermore, Green and Gillis (12) observed the differentiation of these organisms from authentic Pseu- the budding multiplication of P. aminovorans strains and domonas species; in this paper we propose the transfer of discussed the relationship of these organisms to R. loti and Pseudomonas aminovorans to a new genus, Aminobacter, Blastobacter species. However, these authors did not make as Aminobacter aminovorans and the establishment of two formal taxonomic proposals concerning Pseudomonas ami- new species, Aminobacter aganoensis and Aminobacter novorans. Recently, Tsuji et al. (39) described the results niigataensis. of a 16s rRNA sequence analysis performed to determine the phylogenetic relationships among methylotrophs; in this analysis they included methanol- and methylamine-utilizing MATERIALS AND METHODS Methylophilus, Methylobacterium, and Hyphomicrobium strains, but non-methane-, non-methanol-, and methyl- Bacterial strains. The strains which we studied are listed in amine-utilizing bacteria were not studied. Table 1. Strain TH-3T was isolated as a TMAH-utilizing Previously, we described the biodegradation of tetrameth- bacterium, and strain DM-81T was isolated as a DMF- ylammonium hydroxide (TMAH) and N,N-dimethylforma- utilizing bacterium (40, 42). Pseudomonas aminovorans mide (DMF) by bacteria (40, 42); in this work strains TH-3T JCM 7852T (= NCIB 9039T = NCTC 10684T = ATCC 23314T) (4), Pseudomonas sp. strain ATCC 23819 (= strain (T = type strain), DM-81T, and TH-15, Paracoccus amino- MA = NCIB 11590) (32), and Pseudomonas sp. strain ATCC 25262 (= strain MS = NCIB 11591) (22) are non-methane-, non-methanol-, and methylamine-utilizing bacteria (47, 48). * Corresponding author. Pseudomonas diminuta JCM 2788T (= ATCC 11568T = 84 VOL.42, 1992 AMINOBACTER GEN. NOV. 85 TABLE 1. Differentiating physiological characteristics of methylamine-utilizing bacteria Utilization of: Production Nitrate Growth in of acid from Strain reduction Dimethylamine Formamide ~~~~~.$DMF TMAH ~~~~~s,” Pseudomonas - + - aminovorans JCM 78XT Pseudomonas sp. strain - + - ATCC 23819 Pseudomonas sp. strain - + - ATCC 25262 TH-3T Wa w or - + DM-81T W w or - + + + - a w, weak. IAM 1513T), Pseudomonas vesicularis IF0 12165T (= acid composition and hydroxy fatty acid composition were ATCC 11426T = IAM 12105T), Sphingomonas paucimobilis determined as described previously (49). (Pseudomonas paucimobilis [17, 591) IF0 13935T (= ATCC Quinone and quinone homologs. Cells of reference strains 29837T = NCTC 11030T), Sphingomonas paucimobilis (Fla- that were cultivated aerobically for 2 days were used for the vobacterium devorans [17, 591) NCIB 8195 (= ATCC 10829 quinone analysis. Quinone systems were determined as = DSM 30198 = CCM 72), Sphingomonas capsulata (Fla- described previously (47). In the abbreviations used for vobacterium capsulatum [17, 591) NCIB 9890T (= ATCC ubiquinones, Q indicates ubiquinone, and the number indi- 14666T = IF0 12533T), Pseudomonas aeruginosa JCM cates the number of isoprenoid units in the side chain (e.g., 5962T (= ATCC 10145T = NCIB 8295T = NCTC 10332T = Q-9, Q-lo, etc.). NRRL B-771T), and Pseudomonas jluorescens NCIB 9046T DNA base composition. Cells that were cultivated aerobi- (= ATCC 13525T = CCM 21FiT = DSM 50090T = JCM cally for 2 days were used for the DNA analysis. DNA was 5963T) were used as reference strains. Strains TH-3T and extracted by using the method of Saito and Miura (31), and DM-81T and the three methylamine-utilizing bacteria resem- the G+C content was determined by reversed-phase high- bled Pseudomonas diminuta , Pseudomonas vesicularis , S. performance liquid chromatography as described by paucimobilis, and S. capsulata on the basis of their cellular Tamaoka and Komagata (36). fatty acid compositions and quinone systems (16, 25, 26, 58, DNA-DNA hybridization. DNA-DNA hybridization was 59). Pseudomonas aeruginosa and Pseudomonas Jzuo- carried out at 68°C by using the method of Kaneko et al. (21). rescens are typical species of the genus Pseudomonas. The The DNAs of strains TH-3T and DM-81T, Pseudomonas bacterial strains were maintained on PYG agar (pH 7.0) (41). aminovorans JCM 7852T, Pseudomonas diminuta JCM Identification methods. PYG agar was used for precultur- 27MT, and S. paucimobilis IF0 13935T were labeled with ing and as the basal medium for strains TH-3T and DM-81T, [1‘,2’, 5-3H]dCTP by the nick translation method, using a Pseudomonas aminovorans, Pseudomonas sp. strain ATCC type TRK 7000 kit (Amersham International plc, Amersham, 23819, and Pseudomonas sp. strain ATCC 25262. Unless United Kingdom). otherwise stated, the strains were cultivated aerobically in PYG broth at 30°C. Cell form, Gram reaction, motility, and RESULTS multiplication were determined by using cells grown on PYG agar. Motility was observed by using the hanging drop Phenotypic characteristics of methylamine-utilizing bacte- method. Flagellar morphology and multiplication were de- ria. The methylamine-utilizing bacteria (strains TH-3T and termined by the staining method of Toda (37), using a light DM-81T, Pseudomonas aminovorans JCM 7852T, Pseudo- microscope, and by using an electron microscope when the monas sp. strain ATCC 23819, and Pseudomonas sp. strain organisms were negatively stained with 2% phosphotungstic ATCC 25262) were gram-negative, nonsporeforming, rod- acid (pH 7.0). Granules of poly-P-hydroxybutyrate in cells shaped, methylamine-utilizing organisms that were 0.5 to 0.9 cultivated in medium containing 0.5% (wt/vol) DL-P-hy- by 1.0 to 3.0 pm and had rounded ends. Nonmucoid colonies droxy-n-butyric acid (sodium salt) were stained by using the were formed on PYG, nutrient, or methylamine-containing
Load more

Recommended publications
  • Use of Endophytic and Rhizosphere Bacteria to Improve
    Use of Endophytic and Rhizosphere Bacteria To Improve Phytoremediation of Arsenic-Contaminated Industrial Soils by Autochthonous Betula celtiberica Victoria Mesa, Alejandro Navazas, Ricardo González, Aida González, Nele Weyens, Béatrice Lauga, Jose Luis R. Gallego, Jesús Sánchez, Ana Isabel Peláez To cite this version: Victoria Mesa, Alejandro Navazas, Ricardo González, Aida González, Nele Weyens, et al.. Use of Endophytic and Rhizosphere Bacteria To Improve Phytoremediation of Arsenic-Contaminated Indus- trial Soils by Autochthonous Betula celtiberica. Applied and Environmental Microbiology, American Society for Microbiology, 2017, 83 (8), 10.1128/AEM.03411-16. hal-01644095 HAL Id: hal-01644095 https://hal.archives-ouvertes.fr/hal-01644095 Submitted on 11 Jan 2018 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. ENVIRONMENTAL MICROBIOLOGY crossm Use of Endophytic and Rhizosphere Bacteria To Improve Phytoremediation of Arsenic-Contaminated Industrial Soils Downloaded from by Autochthonous Betula celtiberica Victoria Mesa,a Alejandro Navazas,b,c Ricardo González-Gil,b Aida González,b Nele Weyens,c Béatrice Lauga,d Jose Luis R. Gallego,e Jesús Sánchez,a Ana Isabel Peláeza a Departamento de Biología Funcional–IUBA, Universidad de Oviedo, Oviedo, Spain ; Departamento de Biología http://aem.asm.org/ de Organismos y Sistemas–IUBA, Universidad de Oviedo, Oviedo, Spainb; Centre for Environmental Sciences (CMK), Hasselt University, Hasselt, Belgiumc; Equipe Environnement et Microbiologie (EEM), CNRS/Univ.
    [Show full text]
  • (2016) Nitrogen-Fixing Bacterial Communities in Invasive Legume Nodules and Associated Soils Are Similar Across Introduced and Native Range Populations in Australia
    MURDOCH RESEARCH REPOSITORY This is the author’s final version of the work, as accepted for publication following peer review but without the publisher’s layout or pagination. The definitive version is available at http://dx.doi.org/10.1111/jbi.12752 Birnbaum, C., Bissett, A., Thrall, P.H. and Leishman, M.R. (2016) Nitrogen-fixing bacterial communities in invasive legume nodules and associated soils are similar across introduced and native range populations in Australia. Journal of Biogeography, 43 (8). pp. 1631-1644. http://researchrepository.murdoch.edu.au/32675/ Copyright: © 2016 John Wiley & Sons Ltd. It is posted here for your personal use. No further distribution is permitted. 1 1 Original Article 2 Nitrogen fixing bacterial communities in invasive legume nodules and associated 3 soils are similar across introduced and native range populations in Australia 4 Running head: Bacterial communities of legumes in Australia 5 6 KEYWORDS: Acacia; Australia; free-living nitrogen fixers; invasion; legumes; 7 mutualism; rhizobia 8 9 Christina Birnbaum1,3 *, Andrew Bissett2, Peter H. Thrall2, Michelle R. 10 Leishman1 11 12 1Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, 13 Australia 14 15 2 CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia 16 17 3Present address: School of Veterinary and Life Sciences, 90 South Street, Murdoch 18 University, Perth, Western Australia 6150, Australia 19 20 *Christina Birnbaum 21 22 Corresponding author’s e-mail address: [email protected], 23 [email protected] 24 2 25 26 Word count=7459 27 28 ABSTRACT 29 Aim 30 Understanding interactions between invasive legumes and soil biota in both native and 31 introduced ranges could assist in managing biological invasions.
    [Show full text]
  • Specialized Metabolites from Methylotrophic Proteobacteria Aaron W
    Specialized Metabolites from Methylotrophic Proteobacteria Aaron W. Puri* Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT, USA. *Correspondence: [email protected] htps://doi.org/10.21775/cimb.033.211 Abstract these compounds and strategies for determining Biosynthesized small molecules known as special- their biological functions. ized metabolites ofen have valuable applications Te explosion in bacterial genome sequences in felds such as medicine and agriculture. Con- available in public databases as well as the availabil- sequently, there is always a demand for novel ity of bioinformatics tools for analysing them has specialized metabolites and an understanding of revealed that many bacterial species are potentially their bioactivity. Methylotrophs are an underex- untapped sources for new molecules (Cimerman- plored metabolic group of bacteria that have several cic et al., 2014). Tis includes organisms beyond growth features that make them enticing in terms those traditionally relied upon for natural product of specialized metabolite discovery, characteriza- discovery, and recent studies have shown that tion, and production from cheap feedstocks such examining the biosynthetic potential of new spe- as methanol and methane gas. Tis chapter will cies indeed reveals new classes of compounds examine the predicted biosynthetic potential of (Pidot et al., 2014; Pye et al., 2017). Tis strategy these organisms and review some of the specialized is complementary to synthetic biology approaches metabolites they produce that have been character- focused on activating BGCs that are not normally ized so far. expressed under laboratory conditions in strains traditionally used for natural product discovery, such as Streptomyces (Rutledge and Challis, 2015).
    [Show full text]
  • International Committee on Systematics Of
    ICSP - MINUTES de Lajudie and Martinez-Romero, Int J Syst Evol Microbiol 2017;67:516– 520 DOI 10.1099/ijsem.0.001597 International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Agrobacterium and Rhizobium Minutes of the meeting, 7 September 2014, Tenerife, Spain Philippe de Lajudie1,* and Esperanza Martinez-Romero2 MINUTE 1. CALL TO ORDER (Chinese Agricultural University, Beijing, China) was later elected (online, November 2015) as a member of the subcom- The closed meeting was called by the Chairperson, E. Marti- mittee. It was agreed to invite representative scientist(s) from nez-Romero, at 14:00 on 7 September 2014 during the 11th Africa who have published validated novel rhizobial/agrobac- European Nitrogen Fixation Conference in Costa Adeje, Ten- terial species descriptions to become members of the subcom- erife, Spain. mittee. Several tentative names came up. MINUTE 2. RECORD OF ATTENDANCE MINUTE 6. THE HOME PAGE The members present were J. P. W. Young, E. Martinez- The website of the subcommittee can be accessed at http:// Romero, P. Vinuesa, B. Eardly and P. de Lajudie. K. Lind- edzna.ccg.unam.mx/rhizobialtaxonomy. It would be very ström was represented by S. A. Mousavi. All subcommittee useful to list genome sequenced type strains on the website. members had the opportunity to participate in the online discussions. K. Lindström, secretary of the subcommittee since 1996, resigned from this responsibility, but expressed MINUTE 7. GUIDELINES FOR THE her willingness to continue to act as an active subcommittee DESCRIPTION OF NEW TAXA member. P. Vinuesa agreed to act as a temporary secretary Some years ago, E.
    [Show full text]
  • Pseudomonas Gessardii Sp. Nov. and Pseudornonas Migulae Sp. Nov., Two New Species Isolated from Natural Mineral Waters
    International Journal of Systematic Bacteriology (1 999), 49, 1 559-1 572 Printed in Great Britain Pseudomonas gessardii sp. nov. and Pseudornonas migulae sp. nov., two new species isolated from natural mineral waters Sophie Verhille,l Nader Batda,' Fouad Dabboussi,' Monzer Hamze,* Daniel Izard' and Henri Leclerc' Author for correspondence: Henri Leclerc. Tel: + 33 3 20 52 94 28. Fax: + 33 3 20 52 93 61. e-mail : leclerc(@univ-lille2.fr Service de Bact6riologie- Twenty-f ive non-identif ied fluorescent Pseudomonas strains isolated from Hygihne, Facult6 de natural mineral waters were previously clustered into three phenotypic Medecine Henri Warembourg (p81e subclusters, Xlllb, XVa and XVc. These strains were characterized genotypically recherche), 1 place de in the present study. DNA-DNA hybridization results and DNA base Verdun, 59045 Lille Cedex, composition analysis revealed that these strains were members of two new France species, for which the names Pseudomonas gessardii sp. nov. (type strain CIP * Facult6 de Sant6 Publique, 1054693 and Pseudomonas migulae sp. nov. (type strain CIP 1054703 are U n iversite Liba na ise, Tripoli, Lebanon and CNRS proposed. P. gessardii included 13 strains from phenotypic subclusters XVa and Liban, Beirut, Lebanon XVc. P. migulae included 10 strains from phenotypic subcluster Xlllb. The levels of DNA-DNA relatedness ranged from 71 to 100% for P. gessardii and from 74 to 100% for P. migulae. The G+C content of the DNA of each type strain was 58 mol%. DNA similarity levels, measured with 67 reference strains of Pseudomonas species, were below 55%, with ATm values of 13 "C or more.
    [Show full text]
  • C, Compound-Utilizing Bacteria, the So-Called Methylotrophs Or Methano
    J. Gen. Appl. Microbiol., 42, 431-437 (1996) Short Communication POLYAMINE I)ISTRIBUTION PATTERNS IN C, COMPOUND-UTILIZING EUBACTERIA AND ACIDOPHILIC EUBACTERIA KOEI HAMANA* AND NORIAKI KISHIMOTO' College of Medical Care and Technology, Gunma University, Maebashi 371, Japan ' Mimasaka Women's Junior College, Tsuyama 708, Japan (Received January 30, 1996; Accepted September 5, 1996) C, compound-utilizing bacteria, the so-called methylotrophs or methano- trophs, are a diverse group of Gram-negative proteobacteria which obligately or facultatively oxidize methane, methanol and methylamine as sole sources of carbon and energy. The class Proteobacteria is phylogenetically comprised of alpha, beta, gamma, delta and epsilon subclasses; furthermore, each subclass is divided into several clusters corresponding to orders or families (19). Methylobacterium, Methylosinus, and Methylocystis belong to the alpha-2 subclass (12, 21). Methylo- bacillus, Methylophilus, and Methylovorus are located in the beta subclass (12). Methylococcus, Methylobacter, Methylomicrobium, and Methylomonas are the mem- bers of the family Methylococcaceae of the gamma subclass (1,12). The phylo- genetic position of Methylophaga within the Proteobacteria, however, is still not clear. A methanol oxidizer, Ancylobacter aquaticus was confirmed as belonging to the alpha subclass (22). Non-methane-, non-methanol-, and methylamine-utilizing proteobacteria; a genus, Aminobacter, and three species, A. aminovorans, A. agano- ensis, and A. niigataensis, probably belong to the alpha subclass (20). A study of a non-methane-, methanol-, and methylamine-utilizing, budding proteobacterium, Hyphomicrobium, belonging to the alpha subclass, was published recently (23). New members of acidophilic chemo-organotrophic proteobacteria belonging to the genus Acidiphilium (14,16,25) and the genus Acidocella transferred from * Address reprint requests to: Dr .
    [Show full text]
  • International Committee on Systematics of Prokaryotes Subcommittee for the Taxonomy of Rhizobium and Agrobacterium Minutes of the Meeting, Budapest, 25 August 2016
    This is a repository copy of International Committee on Systematics of Prokaryotes Subcommittee for the Taxonomy of Rhizobium and Agrobacterium Minutes of the meeting, Budapest, 25 August 2016. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/131619/ Version: Accepted Version Article: de Lajudie, Philippe M and Young, J Peter W orcid.org/0000-0001-5259-4830 (2017) International Committee on Systematics of Prokaryotes Subcommittee for the Taxonomy of Rhizobium and Agrobacterium Minutes of the meeting, Budapest, 25 August 2016. International Journal of Systematic and Evolutionary Microbiology. pp. 2485-2494. ISSN 1466-5034 https://doi.org/10.1099/ijsem.0.002144 Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ International Committee on Systematics of Prokaryotes Subcommittee for the Taxonomy of Rhizobium-Agrobacterium Minutes of the meeting, Budapest, August 25th, 2016 Philippe de Lajudie, Secretary. J. Peter W. Young, Chairperson. Minute 1. Call to order.
    [Show full text]
  • Bacterial Clade with the Ribosomal RNA Operon on a Small Plasmid Rather Than the Chromosome
    Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome Mizue Anda1,2, Yoshiyuki Ohtsubo1, Takashi Okubo, Masayuki Sugawara, Yuji Nagata, Masataka Tsuda, Kiwamu Minamisawa3, and Hisayuki Mitsui3 Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan Edited by E. Peter Greenberg, University of Washington, Seattle, WA, and approved October 15, 2015 (received for review July 21, 2015) rRNA is essential for life because of its functional importance in protein (5.2 Mb in total) contains nine circular replicons: the main synthesis. The rRNA (rrn) operon encoding 16S, 23S, and 5S rRNAs is chromosome (3.7 Mb) and eight other replicons (designated locatedonthe“main” chromosome in all bacteria documented to date pAU20a to pAU20g and pAU20rrn)(Table1andFig. S1). The and is frequently used as a marker of chromosomes. Here, our genome five smallest replicons, pAU20d to pAU20g and pAU20rrn, analysis of a plant-associated alphaproteobacterium, Aureimonas sp. could be distinguished from the chromosome by their lower G+C rrn AU20, indicates that this strain has its sole operon on a small contents, suggesting that they had distinct evolutionary origins. The (9.4 kb), high-copy-number replicon. We designated this unusual repli- genome contained a single rrn operon, 55 tRNA genes, and 4,785 rrn rrn concarryingthe operon on the background of an -lacking chro- protein-coding genes (Table 1). Surprisingly, the rrn operon, which mosome (RLC) as the rrn-plasmid. Four of 12 strains close to AU20 also consisted of genes for 16S rRNA, tRNAIle,tRNAAla, 23S rRNA, had this RLC/rrn-plasmid organization.
    [Show full text]
  • Transfer of Pseudomonas Aminovorans (Den Dooren De Jong 1926) to Aminobacter Gen
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1992, p. 84-92 Vol. 42, No. 1 0020-771319210 10084-09$02.00/0 Copyright 0 1992, International Union of Microbiological Societies Transfer of Pseudomonas aminovorans (den Dooren de Jong 1926) to Aminobacter gen. nov. as Arninobacter aminovorans comb. nov. and Description of Aminobacter aganoensis sp. nov. and Aminobactev niigataensis sp. nov. TEIZI URAKAMI,l* HISAYA ARAKI,2 HIROMI OYANAGI,* KEN-ICHIRO SUZUKI,3 AND KAZUO KOMAGATA4 Biochemicals Division, Mitsubishi Gas Chemical Co., Seavans-N Building, 1-2-1, Shibaura, Minato-ku, Tokyo 105,' Niigata Research Laboratory, Mitsubishi Gas Chemical Co., Niigata 950-31 ,2 Japan Collection of Microorganisms, The Institute of Physical and Chemical Research, Wacho-shi, Saitama 351-01,3 and Institute of Applied Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo I 13,4Japan We compared non-methane-, non-methanol-, and methylamine-utilizing bacteria, including Pseudomonas aminovorans, a tetramethylammonium-utilizing bacterium, and an N,N-dimethylformamide-utilizingbacte- rium. These bacteria are gram-negative, nonsporeforming, subpolarly flagellated, rod-shaped organisms. Reproduction occurs by budding. The DNA base compositions are 62 to 64 mol% guanine plus cytosine. The cellular fatty acids contain a large amount of acid. The major hydroxy acid is 3-OH C1z:oacid. The major ubiquinone is ubiquinone Q-lo. These bacteria are clearly separated from authentic Pseudomonas species (Pseudornonas Jiuorescens rRNA group) on the basis of utilization of methylamine, morphological and chemotaxonomic characteristics, DNA-DNA homology, and rRNA-DNA homology. They were divided into three subgroups on the basis of their physiological characteristics and DNA-DNA homology data. A new genus, Aminobacter, and three new species, Aminobacter aminovorans comb.
    [Show full text]
  • Of Mammals and Bacteria in a Rainforest: Temporal Dynamics of Soil Bacteria in Response to Simulated N Pulse from Mammalian Urine
    Received: 25 January 2017 | Accepted: 19 September 2017 DOI: 10.1111/1365-2435.12998 RESEARCH ARTICLE Of mammals and bacteria in a rainforest: Temporal dynamics of soil bacteria in response to simulated N pulse from mammalian urine Erika Buscardo1,2,3 | József Geml4,5 | Steven K. Schmidt6 | Artur L. C. Silva7 | Rommel T. J. Ramos7 | Silvanira M. R. Barbosa7 | Soraya S. Andrade7 | Ricardo Dalla Costa8 | Anete P. Souza2 | Helena Freitas1 | Hillândia B. Cunha3 | Laszlo Nagy2,3 1Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal; 2Department of Plant Biology, University of Campinas, Campinas, Brazil; 3Large-scale Biosphere-Atmosphere Programme, National Amazonian Research Institute (INPA), Manaus, Brazil; 4Biodiversity Dynamics Research Group, Naturalis Biodiversity Center, Leiden, The Netherlands; 5Faculty of Sciences, Leiden University, Leiden, The Netherlands; 6Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA; 7Department of Genetics, Federal University of Pará, Belém, Brazil and 8Thermo Fisher Scientific, São Paulo, Brazil Correspondence Erika Buscardo Abstract Email: [email protected] 1. Pulse-type perturbation through excreta by animals creates a mosaic of short-term Funding information high nutrient-load patches in the soil. How this affects microbial community com- Conselho Nacional de Desenvolvimento position and how long these impacts last are important for microbial community Científico e Tecnológico, Grant/Award Number: CNPq No. 480568/2011; Fundação dynamics and nutrient cycling. para a Ciência e a Tecnologia, Grant/Award 2. Our study focused on the short-term responses to N by bacterial communities and Number: SFRH/BPD/77795/2011 ‘functional groups’ associated with the N cycle in a lowland evergreen tropical rain- Handling Editor: Rachel Gallery forest.
    [Show full text]
  • Identification of Dimethylamine Monooxygenase in Marine Bacteria Reveals a Metabolic Bottleneck in the Methylated Amine Degradation Pathway
    OPEN The ISME Journal (2017) 11, 1592–1601 www.nature.com/ismej ORIGINAL ARTICLE Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the methylated amine degradation pathway Ian Lidbury1, Michaela A Mausz1, David J Scanlan and Yin Chen School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, UK Methylated amines (MAs) are ubiquitous in the marine environment and their subsequent flux into the atmosphere can result in the formation of aerosols and ultimately cloud condensation nuclei. Therefore, these compounds have a potentially important role in climate regulation. Using Ruegeria pomeroyi as a model, we identified the genes encoding dimethylamine (DMA) monooxygenase (dmmABC) and demonstrate that this enzyme degrades DMA to monomethylamine (MMA). Although only dmmABC are required for enzyme activity in recombinant Escherichia coli, we found that an additional gene, dmmD, was required for the growth of R. pomeroyi on MAs. The dmmDABC genes are absent from the genomes of multiple marine bacteria, including all representatives of the cosmopolitan SAR11 clade. Consequently, the abundance of dmmDABC in marine metagenomes was substantially lower than the genes required for other metabolic steps of the MA degradation pathway. Thus, there is a genetic and potential metabolic bottleneck in the marine MA degradation pathway. Our data provide an explanation for the observation that DMA-derived secondary organic aerosols (SOAs) are among the most abundant SOAs detected in fine marine particles over the North and Tropical Atlantic Ocean. The ISME Journal (2017) 11, 1592–1601; doi:10.1038/ismej.2017.31; published online 17 March 2017 Introduction (Ge et al., 2011).
    [Show full text]
  • Structuring Factors of Microbial Communities in the Atmospheric Boundary Layer Romie Tignat-Perrier
    Structuring factors of microbial communities in the atmospheric boundary layer Romie Tignat-Perrier To cite this version: Romie Tignat-Perrier. Structuring factors of microbial communities in the atmospheric boundary layer. Ocean, Atmosphere. Université Grenoble Alpes, 2019. English. NNT : 2019GREAU034. tel-02496882 HAL Id: tel-02496882 https://tel.archives-ouvertes.fr/tel-02496882 Submitted on 3 Mar 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. THÈSE Pour obtenir le grade de DOCTEUR DE LA COMMUNAUTE UNIVERSITE GRENOBLE ALPES Spécialité : Sciences de la Terre et Univers, Environnement Arrêté ministériel : 25 mai 2016 Présentée par Romie TIGNAT-PERRIER Thèse dirigée par Aurélien DOMMERGUE, Maître de Conférences, Institut des Géosciences de l’Environnement, Université Grenoble Alpes, et Catherine LAROSE, Chargée de Recherche, Laboratoire Ampère de l’Ecole Centrale de Lyon Thèse préparée au sein de l’Institut des Géosciences de l’Environnement à Grenoble dans l'École Doctorale Terre Univers Environnement Facteurs de structuration des communautés microbiennes de la couche limite atmosphérique Thèse soutenue publiquement le 22 novembre 2019, devant le jury composé de : Dr. Viviane DESPRES HDR, Max Planck Institute for Chemistry Biochemistry Department – Mainz (Allemagne), Rapportrice Dr.
    [Show full text]