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! 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.
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  • Erythrobacter Longus Gen. Nov., Sp. Nov., an Aerobic Bacterium Which Contains Bac Teriochlorophyll A

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    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.
  • Utilization of Kelp-Derived Carbon Sources by Kelp Surface-Associated Bacteria

    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.
  • Tese Adelina Margarida Parente

    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.
  • Isolation and Characterization of the First Phage Infecting Ecologically Important Marine Bacteria Erythrobacter Longfei Lu, Lanlan Cai, Nianzhi Jiao and Rui Zhang*

    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.