DOCSLIB.ORG

Tree Scale: 1

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Tree scale: 1 bchZ ADVR d Bacteria d ADVR bchZ bchZ ADVR d Bacteria d ADVR bchZ bchZ LWQS d Bacteria d LWQS bchZ bchZ LWQS d Bacteria d LWQS bchZ bchZ LJCR d Bacteria Bacteria d NQWI bchZ bchZ NQWI d Bacteria d NQWI bchZ bchZ DCSM d Bacteria d DCSM bchZ bchZ DCSM d Bacteria d DCSM bchZ p Chloroflexota c Chlo c Chloroflexota p bchZ AZXV d Bacteria Bacteria d AZXV bchZ p Chloroflexota c Chlo c Chloroflexota p bchZ JPIM d Bacteria p Bacteria d JPIM bchZ bchZ AZXV d Bacteria Bacteria d AZXV bchZ bchZ DBCF d Bacteria bchZ DBCF d Bacteria Chlo c Chloroflexota p p Chloroflexota c Chlo c Chloroflexota p 1.0 bchZ MPJE d BacteriabchZ LVWG d Bacteria 0.9 bchZ LVWG d Bacteria bchZ LUZT d Bacteria p Chloroflexota c Chlor Chlo c Chloroflexota p bchZ AASE d Bacteria Chlo c Chloroflexota p bchZ LUZT d Bacteria p Chloroflexota c Chlo c Chloroflexota p bchZ MPJE d Bacteria Chlo c Chloroflexota p p Chloroflexota c Chlor c Chloroflexota p roflexia o Chloroflexale o roflexia roflexia o Chloroflexale o roflexia Chloroflexota c Chloro c Chloroflexota 1.0 Chlor c Chloroflexota p bchZ LMBR d Bacteria roflexia o Chloroflexale o roflexia p Chloroflexota c Chlo Chloroflexale o roflexia bchZ LMBR d Bacteria p Chloroflexota c Chlo bchZ LMXM d Bacteria p Bacteroidota c Chloro p Bacteroidota c Chlor 1.0 p Bacteroidota c Chlor p Bacteroidota c Chloro p Bacteroidota c Chloro p Bacteroidota c Chloro oflexia o Chloroflexales Chloroflexale o roflexia p Bacteroidota c Chloro Chloroflexale o roflexia roflexia o Chloroflexale o roflexia p Bacteroidota c Chlor Chloroflexale o roflexia oflexia o Chloroflexales o oflexia s f Chloroflexaceae g O g Chloroflexaceae f s oflexia o Chloroflexales o oflexia flexia o Chloroflexales Chloroflexales o flexia bchZ JPGV d Bacteriap Bacteroidota c Chlor O g Chloroflexaceae f s p Acidobacteriota c Bla s f Chloroflexaceae g C g Chloroflexaceae f s s f Chloroflexaceae g C g Chloroflexaceae f s roflexia o Chloroflexale roflexia o Chloroflexale bia o Chlorobialesobia f Ch o Chlorobiales f C obia o Chlorobiales f C bia o Chlorobiales f Ch bia o Chlorobiales f Ch bia o Chlorobiales f Ch bchZ LNAA d Bacteria C g Chloroflexaceae f s f Roseiflexaceae g Ko obia o Chlorobiales f C bia o Chlorobiales f Ch C g Chloroflexaceae f s stocatellia o Chloracido dastool Co OHK bchZ p Bacteroidota c Chloro U g Chloroflexaceae f s bchZ Chloranaerofilum bchZ obia o Chlorobiales f C U g Chloroflexaceae f s bchZ OHK Co dastool Ch g Chloroflexaceae f f Chloroflexaceae g Ch g Chloroflexaceae f f Chloroflexaceae g Ch g Chloroflexaceae f scillochloris s Oscilloch s scillochloris scillochloris s Oscilloch s scillochloris hloroflexus s Chloroflex s hloroflexus hloroflexus s Chloroflex s hloroflexus bchZ Chloroploca asiat Chloroploca bchZ s f Roseiflexaceae g U s f Roseiflexaceae g U dastool Co OHK bchZ bchZ OHK Co maxb.04 Co OHK bchZ lorobiaceae g Chlorobihlorobiaceae g Chlorob casten roseiflexus bchZ hlorobiaceae g Chlorob bchZ OHK Co maxb.09 bchZ Chlorobaculum p aggr chloroflexus bchZ bchZ OHK Co dastool p Acidobacteriota c Bla lorobiaceae g Chlorobi lorobiaceae g Chlorobi bchZ RSAS01 1/2-492 RSAS01 bchZ hlorobiaceae g Chlorob lorobiaceae g Chloroba 1/2 64 metab Nak bchZ bacteriales f Chloracido bchZ TC 152 1/1-483 bchZ OHK C C 18 1/1- bia o Chlorobialeshlorobiaceae f Ch g Chlorob lorobiaceae g Chloroba uleothrix s Kouleothrix bchZ TC 71 1/1-474 1/2-485 s hloroploca bchZ OHK Co maxb.00 1/2-490 s hloroploca bchZ QWQY01 1/2-486 1/2-492 RYFF01 bchZ metabat 40 1/2-492 40 metabat bchZ Nak concoct 8 1/2 bchZ Chlorothrix 1/1-48 Chlorothrix bchZ corporosum 1/2-482 corporosum bchZ Roseiflexus sp 1/ BA1466 s 1/1-480 s BA1466 loroflexus s 1/2-481 s loroflexus metabat 10 1/1-470 1/2-484 s loroflexus BA1466 s 1/1-477 s BA1466 1/2-4 265 maxb J bchZ loroflexus s 1/2-480 s loroflexus bchZ RYFE01 1/2-491 RYFE01 bchZ bchZ RYFD01 1/2-489 RYFD01 bchZ loris trichoides 1/2-487 trichoides loris loris trichoides 1/2-489 trichoides loris us islandicus 1/2-484 islandicus us bchZ TC 22 1/1-473 1/2-480 islandicus us bchZ PDNY02 1/1-455 bchZ Roseilinea gracile 1/2-488 B79 ica concoct 110 1/2-482 110 concoct bchZ DOMF01 1/1-451 BA965 s 1/2-489 BA965 s 1/2-488 bchZ J150 1/2-480 J150 bchZ um s Chlorobium ferroo bchZ PNIR01 1/2-481 stocatellia o Chloracido bchZ Pelodictyon phae ium s Chlorobium luteo bchZ JP3 C 13 1/1-475 bchZ Anaerolinea YNP bchZ RFGY01 1/1-475 bchZ Chlorobium ferrooium s Chlorobium luteo 1/2-493 3 holzii 1/2-483 holzii bchZ PDNX01 1/1-446 1/2-481 egans um s Chlorobium ferroo bchZ SDGU01arvulum 1/1-448 1/1-448 bchZ J metab 75 1/1-4 um s Chlorobium ferroo 4 1/1-475 bacteriaceae g Chlorac metabat 77 1/2-480 ium s Chlorobium limic bchZ PDNZ01 1/1-448 bchZ RXYK01 1/1-448 Bacteri d NWMW bchZ loroherpetonaceae g G bchZbchZ DPAN01 RXYJ01 1/1-448 1/1-450 ium s Chlorobium limic culum s 1/1-450 bchZ JP3 7 1/1-471 -484 culum s 1/1-445 476 bchZ bog 1492 GCA 00 aurantiaca 1/2-457 bchZ AUBA d Bacteria Bacteria d AUBA bchZ 4 1/2-476 82 bchZ SJPA01 1/1-447 2-481 -479 1 bacteriales f Chloracido Bacteria d JONN bchZ oclathratiforme 1/1-447 1/1-481 xidans 1/1-452 Bacteria d LSHQ bchZ lum 1/1-446 idobacterium s Chlorac xidans 1/1-452 lum 1/1-450 p Bacteria d AHIR bchZ 1/1-477 bchZ PHFL01 1/1-450 xidansxidans 1/1-450 1/1-450 ola A 1/1-450 71 BChlB s 1/1-450 bchZ HeliobacteriumbchZ m Chloracidobacter ola A 1/1-447 Al c Proteobacteria p a 3136655.1 20110800 S Bacteria d AHHA bchZ bchZ WPS2 33 1/1-465 Bacteria d LMKT bchZ bchZ WPS2 29 1/1-474 bchZ WPS2 33 1/1-452 Alph c Proteobacteria p bacteriaceae g Chlorac bchZ WPS2 29 1/1-460 Alp c Proteobacteria p bchZ NCSQ d Bacteria d NCSQ bchZ bchZ PLFC01 1/1-470 Bacteria d LLZQ bchZ idobacterium thermoph p Proteobacteria c Alp c Proteobacteria p bchZ PLBH01 1/1-457 Bacteria d PIUM bchZ bchZ NYUA d Bacteria d NYUA bchZ bchZ SLXT01 1/1-471 Alpha c Proteobacteria odesticaldum 1/1-458ium thermophilum 1/2-4 Bacteria d NCEB bchZ 3S 1/1-469 Bacteria d ATVO bchZ phaproteobacteria o Sp o phaproteobacteria p Proteobacteria c Alph c Proteobacteria p bchZ JNIX d Bacteria p Bacteria d JNIX bchZ idobacterium s 1/2-485 Alph c Proteobacteria p aproteobacteria o Sphi o aproteobacteria ilum A 1/2-485 Sph o haproteobacteria p Proteobacteria c Alp c Proteobacteria p p Proteobacteria c Alph c Proteobacteria p p Proteobacteria c Alph c Proteobacteria p haproteobacteria o Sph o haproteobacteria 80 Alp c Proteobacteria p proteobacteria o Sphin o proteobacteria p Proteobacteria c Alp c Proteobacteria p p Proteobacteria c Alph c Proteobacteria p bchZ NKJA d Bacteria Bacteria d NKJA bchZ hingomonadales f Sphi f hingomonadales aproteobacteria o Sphi o aproteobacteria Proteobacteria c Alpha c Proteobacteria bchZ JPOM d Bacteria d JPOM bchZ bchZ NOXT d Bacteria d NOXT bchZ aproteobacteria o Sphi o aproteobacteria bchZ LSHM d Bacteria d LSHM bchZ ngomonadales f Sphing f ngomonadales bchZ ANFY d Bacteria Bacteria d ANFY bchZ bchZ LJHP d Bacteria p Bacteria d LJHP bchZ haproteobacteria o Cau o haproteobacteria ingomonadales f Sphin f ingomonadales aproteobacteria o Sphi o aproteobacteria aproteobacteria o Rhod o aproteobacteria bchZ LXQI d Bacteria p Bacteria d LXQI bchZ haproteobacteria o Sph o haproteobacteria ingomonadales f Sphin f ingomonadales haproteobacteria o Cau o haproteobacteria 1.0 bchZ LSHH d Bacteria Bacteria d LSHH bchZ gomonadales f Sphingo f gomonadales aproteobacteria o Sphi o aproteobacteria 1.0 p Proteobacteria c Alph c Proteobacteria p 0.8 1.0 0.9 proteobacteria o Caulo o proteobacteria p Proteobacteria c Alp c Proteobacteria p p Proteobacteria c Alp c Proteobacteria p ngomonadales f Sphing f ngomonadales ngomonadaceae g Sph g ngomonadaceae p Proteobacteria c Alp c Proteobacteria p 0.8 1.0 0.8 ngomonadales f Sphing f ngomonadales bchZ JROG d Bacteria d JROG bchZ 1.0 1.0 0.9 1/1-475 0.9 p Proteobacteria c Alph c Proteobacteria p 1.0 Proteobacteria c Alpha c Proteobacteria omonadaceae g Novos g omonadaceae bchZ MIAJ d Bacteria p Bacteria d MIAJ bchZ 1/1-454 gomonadaceae g Sphi g gomonadaceae lobacterales f Hyphomo f lobacterales 1/1-454 0.4 p Bacteria d MIAJ bchZ Proteobacteria c Alpha c Proteobacteria p Proteobacteria c Alph c Proteobacteria p ospirillales f Magnetosp f ospirillales 1.0 ngomonadales f Sphing f ngomonadales delafieldii 1/1-467 1/1-440 1.0 0.7 0.9 ingomonadales f Sphin f ingomonadales lobacterales f Caulobac f lobacterales 0.8 0.4 Sphing f ngomonadales -448 1.0 gomonadaceae g Sphi g gomonadaceae monadaceae g Sphing g monadaceae monas A jaspsi 1/1-475 0.8 0.7 -448 1.0 1.0 ter B marinus 1/1-475 aproteobacteria o Caul o aproteobacteria 0.8 Sph o haproteobacteria 0.9 1.0 bacterales f Caulobacte f bacterales haproteobacteria o Sph o haproteobacteria p Proteobacteria c Alp c Proteobacteria p hingobium capsulatum 0.9 0.4 Cau o haproteobacteria 0.9 omonadaceae g Sphin g omonadaceae gobium subterraneum 0.5 1.0 Sphingom s ingomonas 1.0 Sphin g omonadaceae proteobacteria o Sphin o proteobacteria aproteobacteria o Sphi o aproteobacteria 0.9 Alpha c Proteobacteria ingobium subterraneum 0.6 1.0 Novosph s phingobium 1.0 Alpha c Proteobacteria 0.8 1.0 Sphingo s A ngomonas gobium fuchskuhlense 1.0 Aquidulcib g nadaceae aproteobacteria o Sphi o aproteobacteria omonas s Blastomonas 1.0 um bathyomarinum 1/1 1.0 Sphin o proteobacteria irillaceae g Telmatospir g irillaceae um bathyomarinum 1/1 1.0 omonadaceae g Novos g omonadaceae teraceae g Brevundimo g teraceae ngomonas A s Sphingo 1.0 Sanda g omonadaceae 1.0 1.0 Sphi g gomonadaceae obacter B s Erythrobac r D litoralis 1/1-475 1.0 0.9 Sphingom s ngomonas omonas s Sphingomon s omonas sphingobium s Novosp 1.0 1.0 1.0
Recommended publications
  • A Study on the Phototrophic Microbial Mat Communities of Sulphur Mountain Thermal Springs and Their Association with the Endangered, Endemic Snail Physella Johnsoni

    A Study on the Phototrophic Microbial Mat Communities of Sulphur Mountain Thermal Springs and Their Association with the Endangered, Endemic Snail Physella Johnsoni

    A Study on the Phototrophic Microbial Mat Communities of Sulphur Mountain Thermal Springs and their Association with the Endangered, Endemic Snail Physella johnsoni By Michael Bilyj A thesis submitted to the Faculty of Graduate Studies in partial fulfillment of the requirements for the degree of Master of Science Department of Microbiology Faculty of Science University of Manitoba Winnipeg, Manitoba October 2011 © Copyright 2011, Michael A. Bilyj 1 Abstract The seasonal population fluctuation of anoxygenic phototrophs and the diversity of cyanobacteria at the Sulphur Mountain thermal springs of Banff, Canada were investigated and compared to the drastic population changes of the endangered snail Physella johnsoni. A new species and two strains of Rhodomicrobium were taxonomically characterized in addition to new species of Rhodobacter and Erythromicrobium. Major mat-forming organisms included Thiothrix-like species, oxygenic phototrophs of genera Spirulina, Oscillatoria, and Phormidium and purple nonsulfur bacteria Rhodobacter, Rhodopseudomonas and Rhodomicrobium. Aerobic anoxygenic phototrophs comprised upwards of 9.6 x 104 CFU/cm2 of mat or 18.9% of total aerobic heterotrophic bacterial isolates at certain sites, while maximal purple nonsulfur and purple sulfur bacteria were quantified at 3.2 x 105 and 2.0 x 106 CFU/cm2 of mat, respectively. Photosynthetic activity measurements revealed incredibly productive carbon fixation rates averaging 40.5 mg C/cm2/24 h. A temporal mismatch was observed for mat area and prokaryote-based organics to P. johnsoni population flux in a ―tracking inertia‖ manner. 2 Acknowledgements It is difficult to express sufficient gratitude to my supervisor Dr. Vladimir Yurkov for his unfaltering patience, generosity and motivation throughout this entire degree.
  • Multilayered Horizontal Operon Transfers from Bacteria Reconstruct a Thiamine Salvage Pathway in Yeasts

    Multilayered Horizontal Operon Transfers from Bacteria Reconstruct a Thiamine Salvage Pathway in Yeasts

    Multilayered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts Carla Gonçalvesa and Paula Gonçalvesa,1 aApplied Molecular Biosciences Unit-UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal Edited by Edward F. DeLong, University of Hawaii at Manoa, Honolulu, HI, and approved September 22, 2019 (received for review June 14, 2019) Horizontal acquisition of bacterial genes is presently recognized as nisms presumed to have facilitated a transition from bacterial an important contribution to the adaptation and evolution of operon transcription to eukaryotic-style gene expression were eukaryotic genomes. However, the mechanisms underlying ex- proposed, such as gene fusion giving rise to multifunctional pro- pression and consequent selection and fixation of the prokaryotic teins (6, 23, 24), increase in intergenic distances between genes to genes in the new eukaryotic setting are largely unknown. Here we generate room for eukaryotic promoters, and independent tran- show that genes composing the pathway for the synthesis of the scription producing mRNAs with poly(A) tails have been dem- essential vitamin B1 (thiamine) were lost in an ancestor of a yeast onstrated (22). In the best documented study, which concerns a lineage, the Wickerhamiella/Starmerella (W/S) clade, known to bacterial siderophore biosynthesis operon acquired by yeasts be- harbor an unusually large number of genes of alien origin. The longing to the Wickerhamiella/Starmerella (W/S) clade, the bacte- thiamine pathway was subsequently reassembled, at least twice, rial genes acquired as an operon were shown to be functional (22). by multiple HGT events from different bacterial donors involving Thiamine, commonly known as vitamin B1, is essential for all both single genes and entire operons.
  • Anaerobic Digestion of the Microalga Spirulina at Extreme Alkaline Conditions: Biogas Production, Metagenome, and Metatranscriptome

    Anaerobic Digestion of the Microalga Spirulina at Extreme Alkaline Conditions: Biogas Production, Metagenome, and Metatranscriptome

    ORIGINAL RESEARCH published: 22 June 2015 doi: 10.3389/fmicb.2015.00597 Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome Vímac Nolla-Ardèvol 1*, Marc Strous 1, 2, 3 and Halina E. Tegetmeyer 1, 3, 4 1 Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld, Bielefeld, Germany, 2 Department of Geoscience, University of Calgary, Calgary, AB, Canada, 3 Microbial Fitness Group, Max Planck Institute for Marine Microbiology, Bremen, Germany, 4 HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany A haloalkaline anaerobic microbial community obtained from soda lake sediments was Edited by: Mark Alexander Lever, used to inoculate anaerobic reactors for the production of methane rich biogas. The ETH Zürich, Switzerland microalga Spirulina was successfully digested by the haloalkaline microbial consortium + Reviewed by: at alkaline conditions (pH 10, 2.0 M Na ). Continuous biogas production was observed Aharon Oren, and the obtained biogas was rich in methane, up to 96%. Alkaline medium acted The Hebrew University of Jerusalem, Israel as a CO2 scrubber which resulted in low amounts of CO2 and no traces of H2S Ronald Oremland, in the produced biogas. A hydraulic retention time (HRT) of 15 days and 0.25 g United States Geological Survey, USA Spirulina L−1 day−1 organic loading rate (OLR) were identified as the optimal operational *Correspondence: Vímac Nolla-Ardèvol, parameters. Metagenomic and metatranscriptomic analysis showed that the hydrolysis Institute for Genome Research and of the supplied substrate was mainly carried out by Bacteroidetes of the “ML635J-40 Systems Biology, Center for aquatic group” while the hydrogenotrophic pathway was the main producer of methane Biotechnology, University of Bielefeld, Office G2-152, Universitätstraße 27, in a methanogenic community dominated by Methanocalculus.
  • Roseisalinus Antarcticus Gen. Nov., Sp. Nov., a Novel Aerobic Bacteriochlorophyll A-Producing A-Proteobacterium Isolated from Hypersaline Ekho Lake, Antarctica

    Roseisalinus Antarcticus Gen. Nov., Sp. Nov., a Novel Aerobic Bacteriochlorophyll A-Producing A-Proteobacterium Isolated from Hypersaline Ekho Lake, Antarctica

    International Journal of Systematic and Evolutionary Microbiology (2005), 55, 41–47 DOI 10.1099/ijs.0.63230-0 Roseisalinus antarcticus gen. nov., sp. nov., a novel aerobic bacteriochlorophyll a-producing a-proteobacterium isolated from hypersaline Ekho Lake, Antarctica Matthias Labrenz,13 Paul A. Lawson,2 Brian J. Tindall,3 Matthew D. Collins2 and Peter Hirsch1 Correspondence 1Institut fu¨r Allgemeine Mikrobiologie, Christian-Albrechts-Universita¨t, Kiel, Germany Matthias Labrenz 2School of Food Biosciences, University of Reading, PO Box 226, Reading RG6 6AP, UK matthias.labrenz@ 3DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder io-warnemuende.de Weg 1b, D-38124 Braunschweig, Germany A Gram-negative, aerobic to microaerophilic rod was isolated from 10 m depths of the hypersaline, heliothermal and meromictic Ekho Lake (East Antarctica). The strain was oxidase- and catalase-positive, metabolized a variety of carboxylic acids and sugars and produced lipase. Cells had an absolute requirement for artificial sea water, which could not be replaced by NaCl. A large in vivo absorption band at 870 nm indicated production of bacteriochlorophyll a. The predominant fatty acids of this organism were 16 : 0 and 18 : 1v7c, with 3-OH 10 : 0, 16 : 1v7c and 18 : 0 in lower amounts. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine. Ubiquinone 10 was produced. The DNA G+C content was 67 mol%. 16S rRNA gene sequence comparisons indicated that the isolate represents a member of the Roseobacter clade within the a-Proteobacteria. The organism showed no particular relationship to any members of this clade but clustered on the periphery of the genera Jannaschia, Octadecabacter and ‘Marinosulfonomonas’ and the species Ruegeria gelatinovorans.
  • Article-Associated Bac- Teria and Colony Isolation in Soft Agar Medium for Bacteria Unable to Grow at the Air-Water Interface

    Article-Associated Bac- Teria and Colony Isolation in Soft Agar Medium for Bacteria Unable to Grow at the Air-Water Interface

    Biogeosciences, 8, 1955–1970, 2011 www.biogeosciences.net/8/1955/2011/ Biogeosciences doi:10.5194/bg-8-1955-2011 © Author(s) 2011. CC Attribution 3.0 License. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea C. Jeanthon1,2, D. Boeuf1,2, O. Dahan1,2, F. Le Gall1,2, L. Garczarek1,2, E. M. Bendif1,2, and A.-C. Lehours3 1Observatoire Oceanologique´ de Roscoff, UMR7144, INSU-CNRS – Groupe Plancton Oceanique,´ 29680 Roscoff, France 2UPMC Univ Paris 06, UMR7144, Adaptation et Diversite´ en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France 3CNRS, UMR6023, Microorganismes: Genome´ et Environnement, Universite´ Blaise Pascal, 63177 Aubiere` Cedex, France Received: 21 April 2011 – Published in Biogeosciences Discuss.: 5 May 2011 Revised: 7 July 2011 – Accepted: 8 July 2011 – Published: 20 July 2011 Abstract. Aerobic anoxygenic phototrophic (AAP) bac- detected in the eastern basin, reflecting the highest diver- teria play significant roles in the bacterioplankton produc- sity of pufM transcripts observed in this ultra-oligotrophic tivity and biogeochemical cycles of the surface ocean. In region. To our knowledge, this is the first study to document this study, we applied both cultivation and mRNA-based extensively the diversity of AAP isolates and to unveil the ac- molecular methods to explore the diversity of AAP bacte- tive AAP community in an oligotrophic marine environment. ria along an oligotrophic gradient in the Mediterranean Sea By pointing out the discrepancies between culture-based and in early summer 2008. Colony-forming units obtained on molecular methods, this study highlights the existing gaps in three different agar media were screened for the production the understanding of the AAP bacteria ecology, especially in of bacteriochlorophyll-a (BChl-a), the light-harvesting pig- the Mediterranean Sea and likely globally.
  • Polyamine Profiles of Some Members of the Alpha Subclass of the Class Proteobacteria: Polyamine Analysis of Twenty Recently Described Genera

    Polyamine Profiles of Some Members of the Alpha Subclass of the Class Proteobacteria: Polyamine Analysis of Twenty Recently Described Genera

    Microbiol. Cult. Coll. June 2003. p. 13 ─ 21 Vol. 19, No. 1 Polyamine Profiles of Some Members of the Alpha Subclass of the Class Proteobacteria: Polyamine Analysis of Twenty Recently Described Genera Koei Hamana1）＊，Azusa Sakamoto1），Satomi Tachiyanagi1）， Eri Terauchi1）and Mariko Takeuchi2） 1）Department of Laboratory Sciences, School of Health Sciences, Faculty of Medicine, Gunma University, 39 ─ 15 Showa-machi 3 ─ chome, Maebashi, Gunma 371 ─ 8514, Japan 2）Institute for Fermentation, Osaka, 17 ─ 85, Juso-honmachi 2 ─ chome, Yodogawa-ku, Osaka, 532 ─ 8686, Japan Cellular polyamines of 41 newly validated or reclassified alpha proteobacteria belonging to 20 genera were analyzed by HPLC. Acetic acid bacteria belonging to the new genus Asaia and the genera Gluconobacter, Gluconacetobacter, Acetobacter and Acidomonas of the alpha ─ 1 sub- group ubiquitously contained spermidine as the major polyamine. Aerobic bacteriochlorophyll a ─ containing Acidisphaera, Craurococcus and Paracraurococcus（alpha ─ 1）and Roseibium （alpha-2）contained spermidine and lacked homospermidine. New Rhizobium species, including some species transferred from the genera Agrobacterium and Allorhizobium, and new Sinorhizobium and Mesorhizobium species of the alpha ─ 2 subgroup contained homospermidine as a major polyamine. Homospermidine was the major polyamine in the genera Oligotropha, Carbophilus, Zavarzinia, Blastobacter, Starkeya and Rhodoblastus of the alpha ─ 2 subgroup. Rhodobaca bogoriensis of the alpha ─ 3 subgroup contained spermidine. Within the alpha ─ 4 sub- group, the genus Sphingomonas has been divided into four clusters, and species of the emended Sphingomonas（cluster I）contained homospermidine whereas those of the three newly described genera Sphingobium, Novosphingobium and Sphingopyxis（corresponding to clusters II, III and IV of the former Sphingomonas）ubiquitously contained spermidine.
  • APP201895 APP201895__Appli

    APP201895 APP201895__Appli

    APPLICATION FORM DETERMINATION Determine if an organism is a new organism under the Hazardous Substances and New Organisms Act 1996 Send by post to: Environmental Protection Authority, Private Bag 63002, Wellington 6140 OR email to: [email protected] Application number APP201895 Applicant Neil Pritchard Key contact NPN Ltd www.epa.govt.nz 2 Application to determine if an organism is a new organism Important This application form is used to determine if an organism is a new organism. If you need help to complete this form, please look at our website (www.epa.govt.nz) or email us at [email protected]. This application form will be made publicly available so any confidential information must be collated in a separate labelled appendix. The fee for this application can be found on our website at www.epa.govt.nz. This form was approved on 1 May 2012. May 2012 EPA0159 3 Application to determine if an organism is a new organism 1. Information about the new organism What is the name of the new organism? Briefly describe the biology of the organism. Is it a genetically modified organism? Pseudomonas monteilii Kingdom: Bacteria Phylum: Proteobacteria Class: Gamma Proteobacteria Order: Pseudomonadales Family: Pseudomonadaceae Genus: Pseudomonas Species: Pseudomonas monteilii Elomari et al., 1997 Binomial name: Pseudomonas monteilii Elomari et al., 1997. Pseudomonas monteilii is a Gram-negative, rod- shaped, motile bacterium isolated from human bronchial aspirate (Elomari et al 1997). They are incapable of liquefing gelatin. They grow at 10°C but not at 41°C, produce fluorescent pigments, catalase, and cytochrome oxidase, and possesse the arginine dihydrolase system.
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater

    Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater

    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
  • Roseibacterium Beibuensis Sp. Nov., a Novel Member of Roseobacter Clade Isolated from Beibu Gulf in the South China Sea

    Roseibacterium Beibuensis Sp. Nov., a Novel Member of Roseobacter Clade Isolated from Beibu Gulf in the South China Sea

    Curr Microbiol (2012) 65:568–574 DOI 10.1007/s00284-012-0192-6 Roseibacterium beibuensis sp. nov., a Novel Member of Roseobacter Clade Isolated from Beibu Gulf in the South China Sea Yujiao Mao • Jingjing Wei • Qiang Zheng • Na Xiao • Qipei Li • Yingnan Fu • Yanan Wang • Nianzhi Jiao Received: 6 April 2012 / Accepted: 25 June 2012 / Published online: 31 July 2012 Ó Springer Science+Business Media, LLC 2012 Abstract A novel aerobic, bacteriochlorophyll-contain- similarity), followed by Dinoroseobacter shibae DFL 12T ing bacteria strain JLT1202rT was isolated from Beibu Gulf (95.4 % similarity). The phylogenetic distance of pufM genes in the South China Sea. Cells were gram-negative, non- between strain JLT1202rT and R. elongatum OCh 323T was motile, and short-ovoid to rod-shaped with two narrower 9.4 %, suggesting that strain JLT1202rT was distinct from the poles. Strain JLT1202rT formed circular, opaque, wine-red only strain of the genus Roseibacterium. Based on the vari- colonies, and grew optimally at 3–4 % NaCl, pH 7.5–8.0 abilities of phylogenetic and phenotypic characteristics, strain and 28–30 °C. The strain was catalase, oxidase, ONPG, JLT1202rT stands for a novel species of the genus Roseibac- gelatin, and Voges–Proskauer test positive. In vivo terium and the name R. beibuensis sp. nov. is proposed with absorption spectrum of bacteriochlorophyll a presented two JLT1202rT as the type strain (=JCM 18015T = CGMCC peaks at 800 and 877 nm. The predominant cellular fatty 1.10994T). acid was C18:1 x7c and significant amounts of C16:0,C18:0, C10:0 3-OH, C16:0 2-OH, and 11-methyl C18:1 x7c were present.
  • Which Organisms Are Used for Anti-Biofouling Studies

    Which Organisms Are Used for Anti-Biofouling Studies

    Table S1. Semi-systematic review raw data answering: Which organisms are used for anti-biofouling studies? Antifoulant Method Organism(s) Model Bacteria Type of Biofilm Source (Y if mentioned) Detection Method composite membranes E. coli ATCC25922 Y LIVE/DEAD baclight [1] stain S. aureus ATCC255923 composite membranes E. coli ATCC25922 Y colony counting [2] S. aureus RSKK 1009 graphene oxide Saccharomycetes colony counting [3] methyl p-hydroxybenzoate L. monocytogenes [4] potassium sorbate P. putida Y. enterocolitica A. hydrophila composite membranes E. coli Y FESEM [5] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) K. pneumonia ATCC13883 P. aeruginosa BAA-1744 composite membranes E. coli Y SEM [6] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) graphene oxide E. coli ATCC25922 Y colony counting [7] S. aureus ATCC9144 P. aeruginosa ATCCPAO1 composite membranes E. coli Y measuring flux [8] (unspecified/unique sample type) graphene oxide E. coli Y colony counting [9] (unspecified/unique SEM sample type) LIVE/DEAD baclight S. aureus stain (unspecified/unique sample type) modified membrane P. aeruginosa P60 Y DAPI [10] Bacillus sp. G-84 LIVE/DEAD baclight stain bacteriophages E. coli (K12) Y measuring flux [11] ATCC11303-B4 quorum quenching P. aeruginosa KCTC LIVE/DEAD baclight [12] 2513 stain modified membrane E. coli colony counting [13] (unspecified/unique colony counting sample type) measuring flux S. aureus (unspecified/unique sample type) modified membrane E. coli BW26437 Y measuring flux [14] graphene oxide Klebsiella colony counting [15] (unspecified/unique sample type) P. aeruginosa (unspecified/unique sample type) graphene oxide P. aeruginosa measuring flux [16] (unspecified/unique sample type) composite membranes E.
  • Diversity of Cultivated and Metabolically Active Aerobic Anoxygenic Phototrophic Bacteria Along an Oligotrophic Gradientthe in Mediterranean Sea C

    Diversity of Cultivated and Metabolically Active Aerobic Anoxygenic Phototrophic Bacteria Along an Oligotrophic Gradientthe in Mediterranean Sea C

    Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Biogeosciences Discuss., 8, 4421–4457, 2011 Biogeosciences www.biogeosciences-discuss.net/8/4421/2011/ Discussions doi:10.5194/bgd-8-4421-2011 © Author(s) 2011. CC Attribution 3.0 License. This discussion paper is/has been under review for the journal Biogeosciences (BG). Please refer to the corresponding final paper in BG if available. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea C. Jeanthon1,2, D. Boeuf1,2, O. Dahan1,2, F. Le Gall1,2, L. Garczarek1,2, E. M. Bendif1,2, and A.-C. Lehours3 1INSU-CNRS, UMR 7144, Observatoire Oceanologique´ de Roscoff, Groupe Plancton Oceanique,´ 29680 Roscoff, France 2UPMC Univ Paris 06, UMR 7144, Adaptation et Diversite´ en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France 3CNRS, UMR 6023, Microorganismes: Genome´ et Environnement, Universite´ Blaise Pascal, 63177 Aubiere` Cedex, France Received: 21 April 2011 – Accepted: 29 April 2011 – Published: 5 May 2011 Correspondence to: C. Jeanthon (jeanthon@sb-roscoff.fr) Published by Copernicus Publications on behalf of the European Geosciences Union. 4421 Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Abstract Aerobic anoxygenic phototrophic (AAP) bacteria play significant roles in the bacterio- plankton productivity and biogeochemical cycles of the surface ocean. In this study, we applied both cultivation and mRNA-based molecular methods to explore the diversity of 5 AAP bacteria along an oligotrophic gradient in the Mediterranean Sea in early summer 2008. Colony-forming units obtained on three different agar media were screened for the production of bacteriochlorophyll-a (BChl-a), the light-harvesting pigment of AAP bacteria.
  • Characterization of Bacterial Communities Associated

    Characterization of Bacterial Communities Associated

    www.nature.com/scientificreports OPEN Characterization of bacterial communities associated with blood‑fed and starved tropical bed bugs, Cimex hemipterus (F.) (Hemiptera): a high throughput metabarcoding analysis Li Lim & Abdul Hafz Ab Majid* With the development of new metagenomic techniques, the microbial community structure of common bed bugs, Cimex lectularius, is well‑studied, while information regarding the constituents of the bacterial communities associated with tropical bed bugs, Cimex hemipterus, is lacking. In this study, the bacteria communities in the blood‑fed and starved tropical bed bugs were analysed and characterized by amplifying the v3‑v4 hypervariable region of the 16S rRNA gene region, followed by MiSeq Illumina sequencing. Across all samples, Proteobacteria made up more than 99% of the microbial community. An alpha‑proteobacterium Wolbachia and gamma‑proteobacterium, including Dickeya chrysanthemi and Pseudomonas, were the dominant OTUs at the genus level. Although the dominant OTUs of bacterial communities of blood‑fed and starved bed bugs were the same, bacterial genera present in lower numbers were varied. The bacteria load in starved bed bugs was also higher than blood‑fed bed bugs. Cimex hemipterus Fabricus (Hemiptera), also known as tropical bed bugs, is an obligate blood-feeding insect throughout their entire developmental cycle, has made a recent resurgence probably due to increased worldwide travel, climate change, and resistance to insecticides1–3. Distribution of tropical bed bugs is inclined to tropical regions, and infestation usually occurs in human dwellings such as dormitories and hotels 1,2. Bed bugs are a nuisance pest to humans as people that are bitten by this insect may experience allergic reactions, iron defciency, and secondary bacterial infection from bite sores4,5.