DOCSLIB.ORG

Supplementary Information

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supplementary Information ! Time series analysis of two hydrothermal plumes at 9˚50'N East Pacific Rise reveals distinct, heterogeneous bacterial populations Jason B Sylvan1*, Benjamin C Pyenson2, Olivier Rouxel3,4, Christopher R German3 and Katrina J Edwards1 1University of Southern California, Department of Biological Sciences, Marine Environmental Biology Section, 3616 Trousdale Parkway, Los Angeles, CA 90089 2Haverford College, 794 College Avenue, Haverford, PA 19041 3Woods Hole Oceanographic Institution, 266 Woods Hole Rd, Woods Hole, MA 02543 4 Université Européenne de Bretagne, Université de Brest, Institut Universaire Européen de la Mer (IUEM), UMR 6538, Insititut Français de Recherche pour l’Exploitation de la Mer (IFREMER), BP 80 F- 29280 Plouzané, France *email: [email protected] Supplementary Information Sylvan et. al. Supplementary Information "! Table S1- Distribution of OTUs in clone libraries from this study. OTUs with an asterisk (*) next to their name are from the group "other (non-plume)" in Fig. 2. Number of clones from Phylogeny Isolated From OTU Accession Number 1-8 1-13 1-21 2-8 2-13 2-21 Aquificae Desulfurobacterium sp. str. SL19 AY268937 113A07 1 Hydrogenobacter subterraneus str. AB026268 HGP1 28E03 1 Aquifex pyrophilus str. Kol5a M83548 28G03 1 GNO2 Helicobacter anseris str. MIT 04-9362 DQ415545 213F05 1 Firmicutes Spiroplasma culicicola str. AES-1 NR_025701 113F05 1 Umboniibacter marinipuniceus str. KMM 3891 AB467279 113H05 1 4 Streptococcus australis str. ATCC 700641 AY485604 121H11 1 Fusibacter paucivorans str. SEBR oil well NR_024886 4211 213H09* 1 Geobacillus pallidus str. B1 oil resevoir HM030740 213G05* 1 Actinobacteria Rothia mucilaginosa str. J04 tumulus DQ409140 18B07 1 Propionibacterium acnes str. SK137 skin CP001977 121G01 1 Sylvan et. al. Supplementary Information #! Cyanobacteria chloroplast 213E10* 1 Synechococcus 213H01 4 4 9 28H06 1 28F08 2 28F07 1 Synechocystis 213C03* 1 Prochlorococcus 18E05 1 1 28A04 2 213E04* 1 213H02* 1 213A04* 1 Acidobacteria Anaeromyxobacter dehalogenans str. 2CP-1 marine sediment NC_011891 121D12 1 Geobacter sp. str. FRC-32 marine sediment NZ_AASH01000049 113B09 2 Verrucomicrobia Anaeromyxobacter dehalogenans str. 2CP-1 sediment NC_011891 28E02 1 Rubritalea sp. str. MN1-1042 marine sediment AB543685 18E09 2 18A06 1 18A05 1 213D04* 1 Rubromonas marinus str. Pol012 marine sponge DQ302104 18D11 1 18G03 1 unclassified Verrucomicrobia 213E03* 1 Planctomycetes Phycisphaera mikrensis str. NBRC102666 marine alga AB447464 28G11 1 Sylvan et. al. Supplementary Information $! Planctomyces maris str. DSM 8797 marine ABCE01000043 28F10 1 28C09 1 Piruella sp. str. 302 chalk mine X81942 213C10* 1 Piruella marina deep marine X62912 sediments 28C05 1 Piruella sp. str. 139 X81945 28B04 1 28F03 1 Rhodopiruella sp. str. SM49 marine FJ624355 113F02 1 1 18E10 1 4 Deferribacteres Calditerrivibrio nitroreducens str. Yu37-1 hot spring AB364234 18E11 1 Bacteroidetes Owenweeksia hongkongensis str. UST20020801 marine AB125062 18D04 1 113D02 2 28A06 1 Brumimicrobium mesophilum str. YH207 marine sediment DQ660382 113H12 1 Polaribacter dokdonensis str. MED152 marine DQ481463 18E07 1 28E09 1 Flexibacter echinicida str. F11 sea urchin AY006470 18F01 1 213E07 1 1 Algibacter mikhailovii str. LMG 23988 marine AM491809 113G12 1 Sylvan et. al. Supplementary Information %! Winogradskyella sp. str. NF1-23 marine sediment FJ196009 28D10 1 deep-sea sediment clone BD2-17 deep-sea sediment AB015545 28D07 1 28G06 1 Winogradskyella poriferia str. UST030701-295 microbial mat AY848823 28C02 1 28A09 2 18C10 1 Flexibacter tractuosus str. IFO 15981 AB078071 18G08 1 Alvinella pompejana Cytophaga sp. str. Dex80-37 tubes AJ431253 18B01 1 deep-sea sediment clone BD2-2 deep-sea sediment AB015532 113D09 1 Fluviicola taffensis DSM 16823 freshwater CP002542 213B04* 1 Cellulophaga sp. str. MED134 marine AAMZ01000009 18C04 1 Deltaproteobacteria unclassified Deltaproteobacteria 213F03* 1 Desulfatibacillum alkenivorans str. sediment CP001322 AK-01 18D09 1 Geobacter metallireducens str. GS-15 freshwater sediment AAAS03000001 28B07 1 Geobacter bemidjiensis str. Bem freshwater sediment CP001124 113D05 1 Desulfotalea psychrophila str. LSv54 marine sediment NC_006138 18E01 1 113E11 1 Desulfobulbus mediterraneus str. 86FS1 marine sediment AF354663 113B11 1 1 Epsilonproteobacteria Sylvan et. al. Supplementary Information &! Caminibacter mediatlanticus str. TB-2 deep-sea vent NZ_ABCJ01000002 121G08 1 113E08 1 18C07 1 28D01 1 121E07 1 113C03 1 113C10 3 1 Caminibacter profundus str. CR deep-sea vent AJ535664 113E01 1 Caminibacter hydrogeniphilus str. deep-sea vent AJ309655 AM1116 113E07 1 Nautilia profundicola str. AmH deep-sea vent CP001279 113F07 1 Nitratifractor salsuginis str. E9I37-1 deep-sea vent AB175500 28G01 1 1 1 121B08 2 113C07 1 Hydrogenimonas thermophila str. EP1-55-1 deep-sea vent AB105048 28F12 1 Arcobacter sp. str. MA5 abalone AB542077 213D07 1 28H10 1 18F04 1 1 Sulfurimonas autotrophica str. OK10 hydrothermal AB088431 sediments 18G01 3 2 1 1 18C03 1 1 1 28G04 1 18E03 3 1 18C06 1 1 28B05 1 121F08 1 Sulfurimonas denitrificans str. ATCC marine CP000153 33889 113A03 1 18A09 1 2 Sylvan et. al. Supplementary Information '! 213C08 1 18H12 4 2 18F05 1 3 Sulfurimonas autotrophica str. OK5 hydrothermal AB088432 sediments 113B04 1 18B08 2 18D03 3 3 28F05 1 113A02 1 Sulfurovum sp. str. NBC37-1 deep-sea vent AP009179 113A08 3 18B04 1 3 1 18G06 1 1 18A02 2 3 121A12 1 18H07 1 2 113F09 2 113C11 4 1 1 18E08 1 1 113H03 1 113D10 1 18D12 1 28B06 1 28E04 1 113C12 1 28B11 1 18G09 1 7 28F06 1 18D01 1 1 28C04 1 28D12 1 18B11 9 Sulfurovum lithotrophicum str. 42BKT hydrothermal NR_024802 sediments 28D09 1 28C12 1 113G06 2 28C03 1 Sylvan et. al. Supplementary Information !" 221B05 1 18G12 1 18B10 1 1 28B10 1 18G04 1 4 18H01 1 2 1 1 Zetaproteobacteria Mariprofundus ferrooxydans str. PV-1 Loihi Seamount AATS01000005 221C01 1 Alphaproteobacteria Kopriimonas byunsanensis str. KOPRI marine biofilm DQ167245 28B01 1 Erythrobacter longus str. EG6 hypersaline spring AM691106 18D02 1 2 5 1 213A06* 2 213D06* 1 Erythrobacter citreus str. RE25F/1 marine AF118020 221D02* 1 Stella humosa str. DSM 5900 marine NR_025582 213B08* 1 Croceitomaculum antarcticum str. marine EF495229 IMCC3195 113F11 1 Silicibacter sp. str. LS103 marine sponge FJ937914 18C02 2 2 121G02 1 Sulfitobacter dubius str. KMM 3554 sea grass NR_025691 221A01* 22 221F07* 1 221G04* 1 221H02* 1 221A06* 1 221F01* 1 Octadecabacter sp. str. NF3-22 marine FJ196058 213G09* 1 Thalassobius sp. str. ZS6-23 marine FJ196059 18B02 3 3 Sylvan et. al. Supplementary Information !" 18B06 1 Ruegeria atlantica str. SS-05 marine sediments EU624444 28H02 1 28G08 1 28G07 1 1 213B10* 1 213C01* 3 Pseudomonas sp. str. MK12 rhizosphere AY690720 213F02* 2 Maricaulis maris str. ATCC 15269 marine AJ227803 221C05* 1 marine Dinoroseobacter shibae str. DFL 12 dinoflagellates AAVE01000004 213E09* 3 Roseobacter sp. str. P81 marine sediments EU195951 113F03 1 Betaproteobacteria Lautropia sp. str. TeTO human oral cavity FJ823153 121G03 1 Gammaproteobacteria Codakia orbicularis gill symbiont clam symbiont X84979 28F11 1 Calyptogena phaseoliformis symbiont sulfur oxidizing str. KT-2 symbiont AB479082 113G05 1 Legionella pneumophila str. Lens CR628337 113E02 1 121D05 1 Haliea sp. str. SY02 marine sediment GU124598 113D11 1 113B10 1 2 213D03* 1 Vibrio splendidus str. ATCC33789 marine AB038030 213B02* 2 Photobacterium leiognathi str. RM1 squid symbiont AY292947 18A04 1 1 8 213B09* 1 Sylvan et. al. Supplementary Information !"# Pseudoalteromonas sp. str. JL-S1 marine AY745839 18F06 1 113B08 1 2 Colwellia psychrerythraea str. 34H marine CP000083 28C07 1 28C08 1 213C07* 4 213E11* 1 Alcanivorax sp. str. Oha-1 marine AB053130 121E02 4 Marinobacter flavimaris str. SW-145 marine AY517632 121A02 25 15 121B06 10 121E08 2 2 121A01 4 121C06 1 121B03 1 121H05 1 Marinobacter flavimaris str. 2PR54-4 marine EU440995 121H01 1 121B07 1 Marinobacter sp. str. EZ44 Prochlorococcus co- EU591709 culture 121D04 1 1 121D10 2 121B12 2 121H02 1 Marinobacter sp. str. NT N31 marine AB166980 121C12 1 121G09 1 121H07 1 121D01 1 121B05 1 221G02* 1 221G07* 1 221G10* 1 Marinobacter exellens str. KMM 3809 marine sediments AY180101 221E01* 1 Sylvan et. al. Supplementary Information !!" Marinobacter lutaoensis str. T5054 shallow marine vent NR_025116 18D05 2 Halomonas sulfidaeris str. Esulfide1 deep-sea vent AF212204 221A12* 2 Halomonas meridiana str. PR51-13 marine EU441001 221A10* 3 221F06* 1 Umboniibacter marinipuniceus str. KMM 3892 mollusc AB467280 113H01 1 1 Saccharophagus degradans str. 2-40 marine NC_007912 18A03 1 1 113E10 1 213E02* 2 Kangiella koreensis str. DSM 16069 marine tidal flats CP001707 113G04 1 Cellvibrio japonicus str. Ueda107 soil CP000934 113H06 1 Cycloclasticus pugetii str. PS-1 marine sediments NR_025955 113C01 1 Alteromonas genoviensis str. LMG marine biofilm AM887686 24079 221E03* 1 Psychromonas profunda str. 2825 marine sediments AJ416756 213F04* 1 Thioalkalivibrio sp. str. HL-EbGR7 soda lake sediment CP001339 113E12 2 Sylvan et. al. Supplementary Information !"# Table S2 - Diversity indices as calculated by MOTHUR. Ranges given are 95% confidence intervals for each index. # Sample n Chao1 Ace Inverse Simpson 1-8 83 120-446 320-651 31-156 1-13 89 94-249 92-208 60-156 1-21 79 54-207 63-269 5.0-14 2-8 70 144-623 611-1276 38-589 2-13 78 57-145 113-230 22-64 2-21 64 66-440 49-338 4.3-11 Sylvan et. al. Supplementary Information !"# Table S3- Relative hydrothermal component of the particulates collected (calculated as the ratio of Fe to (Fe+Mn+Al)). Samples were not collected from Trap R2 beyond sample R2-11 for Fe/(Fe+Mn+Al). |---------------------------------- Fe/(Fe+Mn+Al) -------------------------------| Trap R1, Trap R1, Trap R2, Trap R2, Sample Bottle Sampling Day >1mm <1mm >1mm <1mm 1 6 0.92 0.93 0.63 0.67 2 12 0.86 0.92 0.56 0.69 3 18 0.85 0.90 0.77 0.71 4 24 0.79 0.91 0.63 0.57 5 30 0.84 0.88 0.71 0.61 6 36 0.90 0.96 0.88 0.68 7 42 0.93 0.97 0.78 0.66 8 48 0.91 0.97 1.02 0.78 9 54 0.94 0.92 0.54 0.62 10 60 0.78 0.90 0.55 0.43 11 66 0.77 0.80 0.54 0.43 12 72 0.93 0.89 13 78 0.96 0.93 14 84 0.91 0.92 15 90 0.92 0.93 16 96 0.95 0.88 17 102 0.83 0.94 18 108 0.90 0.93 19 114 0.95 0.92 20 120 0.97 0.95 21 126 0.88 0.91 mean 0.89 0.92 0.69 0.62 Sylvan et.
Load more

Recommended publications
  • Indagine Sulla Presenza Di Helicobacter Pullorum in Allevamenti Avicoli Italiani
    Alma Mater Studiorum – Università di Bologna DOTTORATO DI RICERCA IN “EPIDEMIOLOGIA E CONTROLLO DELLE ZOONOSI” Ciclo XX Settore scientifico disciplinare di afferenza: VET-05 TITOLO TESI Indagine sulla presenza di Helicobacter pullorum in allevamenti avicoli italiani Presentata da: Dr. Mirko Rossi Coordinatore Dottorato Relatore Prof.Luigi Morganti Prof. Renato Giulio Zanoni Esame finale anno 2008 1 2 Para a Joana Hà-de haver uma cor por descobrir Um juntar de palava escondido Hà-de haver uma chave para abrir A porta deste muro desmedido (Josè Saramago, Hà-de aver…) 3 4 INDICE PARTE GENERALE 7 Capitolo 1 Genere Helicobacter 9 Capitolo 2 Helicobacter pullorum 21 PARTE SPERIMENTALE 31 Presentazione 33 Capitolo 1 Ottimizzazione dei metodi di isolamento di Helicobacter pullorum da matrice policontaminata 35 Capitolo 2 Isolamento di Helicobacter pullorum da contenuto ciecale di broiler, galline ovaiole, tacchini e struzzo, caratterizzazione fenotipica e tipizzazione genotipica degli isolati 55 Capitolo 3 Indagine sulla presenza di Helicobacter pullorum da feci di pazienti umani affetti da patologia gastroenterica 85 Capitolo 4. Antibiotico resistenza in Helicobacter pullorum 93 Conclusioni 119 RINGRAZIAMENTI 123 BIBLIOGRAFIA 125 5 6 PARTE GENERALE 7 8 CAPITOLO 1 Genere Helicobacter 1.1 Tassonomia del genere Helicobacter Il genere Helicobacter è stato originariamente descritto nel 1989 da Goodwin et al . i quali, sulla base di caratteristiche fenotipiche e genotipiche quali la composizione in acidi grassi della membrana cellulare, la sensibilità ad alcuni antibiotici e la sequenza del rRNA, classificarono in questo nuovo genere le specie [Campylobacter pylori ] e [Campylobacter mustelae ], isolate rispettivamente dallo stomaco di uomo (Marshall et al. , 1985) e di furetto (Fox et al ., 1988).
    [Show full text]
  • Biodiversity of Microorganisms Colonizing the Surface of Polystyrene Samples Exposed to Different Aqueous Environments
    sustainability Article Biodiversity of Microorganisms Colonizing the Surface of Polystyrene Samples Exposed to Different Aqueous Environments Tatyana Tourova 1, Diyana Sokolova 1, Tamara Nazina 1,* , Denis Grouzdev 2 , Eugeni Kurshev 3 and Anatoly Laptev 3 1 Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; [email protected] (T.T.); [email protected] (D.S.) 2 Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; [email protected] 3 Federal State Unitary Enterprise “All-Russian Scientific Research Institute of Aviation Materials”, State Research Center of the Russian Federation, 105005 Moscow, Russia; [email protected] (E.K.); [email protected] (A.L.) * Correspondence: [email protected]; Tel.: +7-499-135-03-41 Received: 25 March 2020; Accepted: 29 April 2020; Published: 30 April 2020 Abstract: The contamination of marine and freshwater ecosystems with the items from thermoplastics, including polystyrene (PS), necessitates the search for efficient microbial degraders of these polymers. In the present study, the composition of prokaryotes in biofilms formed on PS samples incubated in seawater and the industrial water of a petrochemical plant were investigated. Using a high-throughput sequencing of the V3–V4 region of the 16S rRNA gene, the predominance of Alphaproteobacteria (Blastomonas), Bacteroidetes (Chryseolinea), and Gammaproteobacteria (Arenimonas and Pseudomonas) in the biofilms on PS samples exposed to industrial water was revealed. Alphaproteobacteria (Erythrobacter) predominated on seawater-incubated PS samples. The local degradation of the PS samples was confirmed by scanning microscopy. The PS-colonizing microbial communities in industrial water differed significantly from the PS communities in seawater.
    [Show full text]
  • Downloaded from the NCBI Genome Portal (Table S1)
    J. Microbiol. Biotechnol. 2021. 31(4): 601–609 https://doi.org/10.4014/jmb.2012.12054 Review Assessment of Erythrobacter Species Diversity through Pan-Genome Analysis with Newly Isolated Erythrobacter sp. 3-20A1M Sang-Hyeok Cho1, Yujin Jeong1, Eunju Lee1, So-Ra Ko3, Chi-Yong Ahn3, Hee-Mock Oh3, Byung-Kwan Cho1,2*, and Suhyung Cho1,2* 1Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea 2KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea 3Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea Erythrobacter species are extensively studied marine bacteria that produce various carotenoids. Due to their photoheterotrophic ability, it has been suggested that they play a crucial role in marine ecosystems. It is essential to identify the genome sequence and the genes of the species to predict their role in the marine ecosystem. In this study, we report the complete genome sequence of the marine bacterium Erythrobacter sp. 3-20A1M. The genome size was 3.1 Mbp and its GC content was 64.8%. In total, 2998 genetic features were annotated, of which 2882 were annotated as functional coding genes. Using the genetic information of Erythrobacter sp. 3-20A1M, we performed pan- genome analysis with other Erythrobacter species. This revealed highly conserved secondary metabolite biosynthesis-related COG functions across Erythrobacter species. Through subsequent secondary metabolite biosynthetic gene cluster prediction and KEGG analysis, the carotenoid biosynthetic pathway was proven conserved in all Erythrobacter species, except for the spheroidene and spirilloxanthin pathways, which are only found in photosynthetic Erythrobacter species.
    [Show full text]
  • Taxon-Specific Aerosolization of Bacteria and Viruses in An
    ARTICLE DOI: 10.1038/s41467-018-04409-z OPEN Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm Jennifer M. Michaud1, Luke R. Thompson 2,3,4, Drishti Kaul5, Josh L. Espinoza5, R. Alexander Richter5, Zhenjiang Zech Xu2, Christopher Lee1, Kevin M. Pham1, Charlotte M. Beall6, Francesca Malfatti6,7, Farooq Azam6, Rob Knight 2,8,9, Michael D. Burkart 1, Christopher L. Dupont5 & Kimberly A. Prather1,6 1234567890():,; Ocean-derived, airborne microbes play important roles in Earth’s climate system and human health, yet little is known about factors controlling their transfer from the ocean to the atmosphere. Here, we study microbiomes of isolated sea spray aerosol (SSA) collected in a unique ocean–atmosphere facility and demonstrate taxon-specific aerosolization of bacteria and viruses. These trends are conserved within taxonomic orders and classes, and temporal variation in aerosolization is similarly shared by related taxa. We observe enhanced transfer into SSA of Actinobacteria, certain Gammaproteobacteria, and lipid-enveloped viruses; conversely, Flavobacteriia, some Alphaproteobacteria, and Caudovirales are generally under- represented in SSA. Viruses do not transfer to SSA as efficiently as bacteria. The enrichment of mycolic acid-coated Corynebacteriales and lipid-enveloped viruses (inferred from genomic comparisons) suggests that hydrophobic properties increase transport to the sea surface and SSA. Our results identify taxa relevant to atmospheric processes and a framework to further elucidate aerosolization mechanisms influencing microbial and viral transport pathways. 1 Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA. 2 Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.
    [Show full text]
  • Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales
    GBE Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales Vandana Viswanathan1,2, Anushree Narjala1, Aravind Ravichandran1, Suvratha Jayaprasad1,and Shivakumara Siddaramappa1,* 1Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru, Karnataka, India 2Manipal University, Manipal, Karnataka, India *Corresponding author: E-mail: [email protected]. Accepted: February 10, 2017 Data deposition: Genome sequences were downloaded from GenBank, and their accession numbers are provided in table 1. Abstract The order Sphingomonadales, containing the families Erythrobacteraceae and Sphingomonadaceae, is a relatively less well-studied phylogenetic branch within the class Alphaproteobacteria. Prophage elements are present in most bacterial genomes and are important determinants of adaptive evolution. An “intact” prophage was predicted within the genome of Sphingomonas hengshuiensis strain WHSC-8 and was designated Prophage IWHSC-8. Loci homologous to the region containing the first 22 open reading frames (ORFs) of Prophage IWHSC-8 were discovered among the genomes of numerous Sphingomonadales.In17genomes, the homologous loci were co-located with an ORF encoding a putative superoxide dismutase. Several other lines of molecular evidence implied that these homologous loci represent an ancient temperate bacteriophage integration, and this horizontal transfer event pre-dated niche-based speciation within the order Sphingomonadales. The “stabilization” of prophages in the genomes of their hosts is an indicator of “fitness” conferred by these elements and natural selection. Among the various ORFs predicted within the conserved prophages, an ORF encoding a putative proline-rich outer membrane protein A was consistently present among the genomes of many Sphingomonadales. Furthermore, the conserved prophages in six Sphingomonas sp. contained an ORF encoding a putative spermidine synthase.
    [Show full text]
  • Helicobacter Pylori: Comparative Genomics and Structure-Function Analysis of the Flagellum Biogenesis Protein HP0958
    UCC Library and UCC researchers have made this item openly available. Please let us know how this has helped you. Thanks! Title Helicobacter pylori: comparative genomics and structure-function analysis of the flagellum biogenesis protein HP0958 Author(s) de Lacy Clancy, Ceara A. Publication date 2014 Original citation de Lacy Clancy, C. A. 2014. Helicobacter pylori: comparative genomics and structure-function analysis of the flagellum biogenesis protein HP0958. PhD Thesis, University College Cork. Type of publication Doctoral thesis Rights © 2014, Ceara A. De Lacy Clancy. http://creativecommons.org/licenses/by-nc-nd/3.0/ Item downloaded http://hdl.handle.net/10468/1684 from Downloaded on 2021-10-10T14:33:51Z Helicobacter pylori: Comparative genomics and structure-function analysis of the flagellum biogenesis protein HP0958 A Thesis Presented in Partial Fulfilment of the Requirements for the Degree of Doctor of Philosophy by Ceara de Lacy Clancy, B.Sc. School of Microbiology National University of Ireland, Cork Supervisor: Prof. Paul W. O’Toole Head of School of Microbiology: Prof. Gerald Fitzgerald February 2014 Table of Contents Table of Contents Abstract ........................................................................................................................ i Chapter 1 Literature Review....................................................................................................... 1 1 Helicobacter pylori .................................................................................................. 2 1.1 Discovery
    [Show full text]
  • A Novel Bacterial Thiosulfate Oxidation Pathway Provides a New Clue About the Formation of Zero-Valent Sulfur in Deep Sea
    The ISME Journal (2020) 14:2261–2274 https://doi.org/10.1038/s41396-020-0684-5 ARTICLE A novel bacterial thiosulfate oxidation pathway provides a new clue about the formation of zero-valent sulfur in deep sea 1,2,3,4 1,2,4 3,4,5 1,2,3,4 4,5 1,2,4 Jing Zhang ● Rui Liu ● Shichuan Xi ● Ruining Cai ● Xin Zhang ● Chaomin Sun Received: 18 December 2019 / Revised: 6 May 2020 / Accepted: 12 May 2020 / Published online: 26 May 2020 © The Author(s) 2020. This article is published with open access Abstract Zero-valent sulfur (ZVS) has been shown to be a major sulfur intermediate in the deep-sea cold seep of the South China Sea based on our previous work, however, the microbial contribution to the formation of ZVS in cold seep has remained unclear. Here, we describe a novel thiosulfate oxidation pathway discovered in the deep-sea cold seep bacterium Erythrobacter flavus 21–3, which provides a new clue about the formation of ZVS. Electronic microscopy, energy-dispersive, and Raman spectra were used to confirm that E. flavus 21–3 effectively converts thiosulfate to ZVS. We next used a combined proteomic and genetic method to identify thiosulfate dehydrogenase (TsdA) and thiosulfohydrolase (SoxB) playing key roles in the conversion of thiosulfate to ZVS. Stoichiometric results of different sulfur intermediates further clarify the function of TsdA − – – – − 1234567890();,: 1234567890();,: in converting thiosulfate to tetrathionate ( O3S S S SO3 ), SoxB in liberating sulfone from tetrathionate to form ZVS and sulfur dioxygenases (SdoA/SdoB) in oxidizing ZVS to sulfite under some conditions.
    [Show full text]
  • Diversity of Mat-Forming Sulfide-Oxidizing Bacteria at Continental Margins
    Diversity of Mat-forming Sulfide-oxidizing Bacteria at Continental Margins Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften - Dr. rer. nat. - dem Fachbereich Biologie/Chemie der Universität Bremen vorgelegt von Stefanie Grünke Bremen, April 2010 Die vorliegende Doktorarbeit wurde in der Zeit von Juni 2006 bis April 2010 am Max- Planck-Institut für Marine Mikrobiologie und am Alfred-Wegener-Institut für Polar- und Meeresforschung angefertigt. 1. Gutachterin: Prof. Dr. Antje Boetius 2. Gutachter: Prof. Dr. Rudolf Amann Tag des Promotionskolloquiums: 4. Juni 2010 Diese Arbeit ist all denjenigen gewidmet, die ihre Segel setzen, um neue Welten gu erkunden. Seien sie sich gewiss, dass auf Sturm immer ruhiges Wasserfolgt. Wertrauen sie auf ihr größtes Gut — ihre Freunde und Familie. Nutgen sie ihre Schwächen, um neue Stärken gu finden. Soll Zuversicht ihr Kompass sein! Summary In the oceans, microbial mats formed by chemosynthetic sulfide-oxidizing bacteria are mostly found in so-called ‘reduced habitats’ that are characterized by chemoclines where energy-rich, reduced substances, like hydrogen sulfide, are transported into oxic or suboxic zones. There, these organisms often thrive in narrow zones or gradients of their electron donor (sulfide) and their electron acceptor (mostly oxygen or nitrate). Through the build up of large biomasses, mat-forming sulfide oxidizers may significantly contribute to primary production in their habitats and dense mats represent efficient benthic filters against the toxic gas hydrogen sulfide. As gradient organisms, these mat-forming sulfide oxidizers seem to be adapted to very defined ecological niches with respect to oxygen (or nitrate) and sulfide gradients. However, many aspects regarding their diversity as well as their geological drivers in marine sulfidic habitats required further investigation.
    [Show full text]
  • Erythrobacter Longus Gen. Nov., Sp. Nov., an Aerobic Bacterium Which Contains Bac Teriochlorophyll A
    INTERNATIONAL JOURNAL OF SYSTEMATICBACTERIOLOGY, Apr. 1982, p. 211-217 Vol. 32, No. 2 0020-771 3/82/020211-07$02.00/0 Erythrobacter longus gen. nov., sp. nov., an Aerobic Bacterium Which Contains Bac teriochlorophyll a TSUNEO SHIBA’ AND US10 SlMIDU’ Otsuchi Murine ReJeurch Center, Ocean Research Institute, University of Tokyo, Akahumu, OtJuchi, hate, 028-11 ,’ and Ocean Research Institute, University of Tokyo, Nukano, Tokyo, 164,’ Japun Four orange-pigmented and seven pink-pigmented strains of bacteria which contained bacteriochlorophyll a were isolated from high-tidal seaweeds, such as Enteromorpha linza (L.) J. Ag. and Porphyra sp. All of the isolates were gram negative. The orange-pigmented bacteria were rods with parallel sides and rounded ends, and the pink-pigmented bacteria were ovoids and short rods. All were motile by means of subpolar flagella. None of the strains produced growth anaerobically in the light. No growth occurred with an atmosphere containing H2 and COz. All of these bacteria grew aerobically and utilized glucose, pyruvate, acetate, butyrate, and glutamate as sole organic carbon sources. The best growth occurred on complex media formulated for heterotrophic marine bacteria. Biotin was required. Oxidase and catalase were present. Small amounts of acid were produced from a wide range of carbohydrates under microaerobic conditions. Gelatin was hydrolyzed. The strains which we investigated fell into the following three clusters: cluster A, all of the orange strains; cluster B, three pink strains; and cluster C, four pink strains. The strains of clusters B and C required thiamine and nicotinic acid and were susceptible to streptomycin. Tween 80 was hydro- lyzed and phosphatase activity was produced by the strains of clusters A and B.
    [Show full text]
  • Utilization of Kelp-Derived Carbon Sources by Kelp Surface-Associated Bacteria
    Vol. 62: 191–199, 2011 AQUATIC MICROBIAL ECOLOGY Published online January 19 doi: 10.3354/ame01477 Aquat Microb Ecol OPENPEN ACCESSCCESS Utilization of kelp-derived carbon sources by kelp surface-associated bacteria Mia M. Bengtsson1, 2,*, Kjersti Sjøtun1, Julia E. Storesund1, Lise Øvreås1, 2 1Department of Biology, and 2Centre for Geobiology, University of Bergen, Box 7803, 5020 Bergen, Norway ABSTRACT: The surfaces of kelp are covered with bacteria that may utilize kelp-produced carbon and thereby contribute significantly to the carbon flux in kelp forest ecosystems. There is scant knowledge about the identity of these bacteria and about which kelp-derived carbon sources they utilize. An enrichment approach, using kelp constituent carbon sources for bacterial cultivation, was used to identify bacterial populations associated with the kelp Laminaria hyperborea that degrade kelp components. In order to assess whether the cultured bacteria are significant under natural con- ditions, partial 16 rRNA gene sequences from the cultured bacteria were compared to sequences obtained from the indigenous bacterial communities inhabiting natural kelp surface biofilms. The results identify different members of the Roseobacter clade of Alphaproteobacteria in addition to members of Gammaproteobacteria that are involved in kelp constituent degradation. These bacteria are observed sporadically on natural kelp surfaces and may represent opportunistic bacteria impor- tant in degradation of dead kelp material. Many of the cultured bacteria appear to be generalists that are able to utilize different kelp carbon sources. This study is the first to link culturable kelp- associated bacteria with their occurrence and possible roles in the natural environment. KEY WORDS: Seaweed · Brown algae · Heterotrophic bacteria · Enrichment cultivation · 16S rRNA · Alginate · Laminaran · Fucoidan Resale or republication not permitted without written consent of the publisher INTRODUCTION kelp material for these consumers (Norderhaug et al.
    [Show full text]
  • Tese Adelina Margarida Parente
    Defences of Helicobacter species against host antimicrobials Adelina Margarida Lima Pereira Rodrigues Parente Dissertation presented to obtain the Ph.D degree in Biochemistry Instituto de Tecnologia Química e Biológica António Xavier | Universidade Nova de Lisboa Oeiras, June, 2016 Defences of Helicobacter species against host antimicrobials Adelina Margarida Lima Pereira Rodrigues Parente Dissertation presented to obtain the Ph.D degree in Biochemistry Instituto de Tecnologia Química e Biológica António Xavier | Universidade Nova de Lisboa Oeiras, June 2016 From left to right: Mónica Oleastro (4th oponente), Gabriel Martins (3 rd opponent), Marta Justino (Co-supervisor) , Miguel Viveiros (2 nd opponent), Adelina Margarida Parente , Lígia Saraiva (supervisor) , Cecília Arraiano (president of the jury), and Maria do Céu Figueiredo (1 st opponent). nd 22 June 2016 Second edition, June 2016 Molecular Mechanisms of Pathogen Resistance Laboratory Instituto de Tecnologia Química e Biológica António Xavier Universidade Nova de Lisboa 2780-157 Portugal ii “Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world” Louis Pasteur iii iv Acknowledgments Firstly, I would like to express my gratitude to the person that allowed me the opportunity to perform a PhD and who also contributed the most for my accomplishment of this thesis by constantly supporting me during these last years. I thus thank my supervisor, Dr. Lígia Saraiva , for her permanent availability whenever I needed guidance, for all the excellent ideas and advices related to my practical work and lastly for all the patience and enthusiasm! I also thank Dr. Lígia for her rigour and enormous help in the writing of this thesis.
    [Show full text]
  • Isolation and Characterization of the First Phage Infecting Ecologically Important Marine Bacteria Erythrobacter Longfei Lu, Lanlan Cai, Nianzhi Jiao and Rui Zhang*
    Lu et al. Virology Journal (2017) 14:104 DOI 10.1186/s12985-017-0773-x RESEARCH Open Access Isolation and characterization of the first phage infecting ecologically important marine bacteria Erythrobacter Longfei Lu, Lanlan Cai, Nianzhi Jiao and Rui Zhang* Abstract Background: Erythrobacter comprises a widespread and ecologically significant genus of marine bacteria. However, no phage infecting Erythrobacter spp. has been reported to date. This study describes the isolation and characterization of phage vB_EliS-R6L from Erythrobacter. Methods: Standard virus enrichment and double-layer agar methods were used to isolate and characterize the phage. Morphology was observed by transmission electron microscopy, and a one-step growth curve assay was performed. The phage genome was sequenced using the Illumina Miseq platform and annotated using standard bioinformatics tools. Phylogenetic analyses were performed based on the deduced amino acid sequences of terminase, endolysin, portal protein, and major capsid protein, and genome recruitment analysis was conducted using Jiulong River Estuary Virome, Pacific Ocean Virome and Global Ocean Survey databases. Results: A novel phage, vB_EliS-R6L, from coastal waters of Xiamen, China, was isolated and found to infect the marine bacterium Erythrobacter litoralis DSM 8509. Morphological observation and genome analysis revealed that phage vB_ EliS-R6L is a siphovirus with a 65.7-kb genome that encodes 108 putative gene products. The phage exhibits growth at a wide range of temperature and pH conditions. Genes encoding five methylase-related proteins were found in the genome, and recognition site predictions suggested its resistance to restriction-modification host systems. Genomic comparisons and phylogenetic analyses indicate that phage vB_EliS-R6L is distinct from other known phages.
    [Show full text]