DOCSLIB.ORG

Supporting Information

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supporting Information Supporting Information Crump et al. 10.1073/pnas.0906149106 Fig. S1. Neighbor joining tree of representative sequences from nine OTUs that appeared in at least five of the six big arctic rivers. The tree was calcu- lated with Jukes-Cantor distances between 16S rRNA gene sequences (Escherichia coli positions 118–796) aligned with the software ARB and sub- jected to a 50% base pair frequency filter in which gaps were treated as valid base pairs when not maximal. Crump et al. www.pnas.org/cgi/content/short/0906149106 1of5 Table S1. Average similarity values (Sorensen’s) between DGGE banding patterns for comparisons within seasons (winter, spring freshet, summer/fall) and between seasons for sampling years 2004 and 2005 Comparison Average n SD SE Within season 2004 0.77 45 0.11 0.02 Within season 2005 0.77 45 0.08 0.01 Within season within year 0.77 90 0.09 0.01 Within season between year 0.72 156 0.09 0.01 Between season 2004 0.50 81 0.13 0.01 Between season 2005 0.53 66 0.11 0.01 Between season within year 0.51 147 0.12 0.01 Between season between years 0.53 184 0.13 0.01 Crump et al. www.pnas.org/cgi/content/short/0906149106 2of5 Table S2. Number of clones from each river library belonging to each OTU grouping as determined with DOTUR at the 97% sequence similarity level No. of Representative rivers All sequence containing clones, for OTU OTU YU KL YE MA LE OB total % Phylum Class Order Family Genus YU201A11 6 10 8 9 4 12 8 51 11.2 Proteobacteria Betaproteobacteria Methylophilales Methylophilaceae Methylophilus MA101D10 6 5 4 5 9 1 7 31 6.8 Bacteroidetes Sphingobacteria Sphingobacteriales Flexibacteraceae Arcicella YE201C08 6 4 1 5 1 5 8 24 5.3 Actinobacteria Actinobacteria Actinomycetales MA101F04 5 2 1 1 10 0 4 18 3.9 Actinobacteria Actinobacteria Actinomycetales YU201B06 5 5 2 2 2 0 4 15 3.3 Actinobacteria Actinobacteria Actinomycetales YU201A10 5 3 0 6 1 1 1 12 2.6 Proteobacteria Betaproteobacteria Burkholderiales Alcaligenaceae MA101A07 5 0 1 2 1 4 2 10 2.2 Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae Rhodoferax MA101E03 5 3 2 2 1 2 0 10 2.2 Actinobacteria Actinobacteria Actinomycetales YU201H04 5 2 1 1 1 1 0 6 1.3 Actinobacteria Actinobacteria Actinomycetales Microbacteriaceae KL201B07 4 0 2 3 2 0 1 8 1.8 Proteobacteria Betaproteobacteria Burkholderiales Burkholderiaceae Polynucleobacter LE201H07 4 1 0 3 3 1 0 8 1.8 Actinobacteria Actinobacteria Actinomycetales YU201D06 4 3 0 1 3 0 1 8 1.8 Proteobacteria Betaproteobacteria Methylophilales Methylophilaceae MA101A06 4 0 1 2 1 0 3 7 1.5 Bacteroidetes Sphingobacteria Sphingobacteriales Flexibacteraceae MA101B02 4 0 1 0 4 1 1 7 1.5 Bacteroidetes Flavobacteria Flavobacteriales Flavobacteriaceae Flavobacterium OB101A12 4 0 1 2 0 1 1 5 1.1 Actinobacteria Actinobacteria Actinomycetales YE201C01 4 0 2 1 0 1 1 5 1.1 Bacteroidetes Flavobacteria Flavobacteriales Flavobacteriaceae Flavobacterium KL201C12 4 0 1 1 0 1 1 4 0.9 Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae Polaromonas KL201C11 3 0 9 1 0 5 0 15 3.3 Bacteroidetes Sphingobacteria Sphingobacteriales Flexibacteraceae Arcicella YE201A01 3 0 6 4 0 2 0 12 2.6 Bacteroidetes Flavobacteria Flavobacteriales Flavobacteriaceae Flavobacterium YU201C09 3 4 0 0 2 2 0 8 1.8 Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae Rhodoferax KL201A10 3 0 1 3 0 0 1 5 1.1 Bacteroidetes KL201F03 3 0 2 1 0 2 0 5 1.1 Proteobacteria Betaproteobacteria Burkholderiales i.s. 5 KL201G07 3 0 3 0 0 1 1 5 1.1 Bacteroidetes Sphingobacteria Sphingobacteriales Flexibacteraceae Spirosoma OB101H10 3 1 1 0 0 0 3 5 1.1 Bacteroidetes Sphingobacteria Sphingobacteriales KL201E07 3 0 1 0 1 2 0 4 0.9 Bacteroidetes Flavobacteria Flavobacteriales Flavobacteriaceae Flavobacterium MA101D05 3 1 0 0 2 0 1 4 0.9 Proteobacteria Betaproteobacteria OB101H05 3 0 1 1 0 0 1 3 0.7 Bacteroidetes YE201C02 3 0 1 1 0 1 0 3 0.7 Proteobacteria Betaproteobacteria Burkholderiales Oxalobacteraceae Herbaspirillum KL201E08 2 0 1 0 2 0 0 3 0.7 Bacteroidetes Sphingobacteria Sphingobacteriales LE201H04 2 1 0 0 0 2 0 3 0.7 Proteobacteria Deltaproteobacteria Bdellovibrionales Bacteriovoracaceae OB101D03 2 0 0 0 0 2 1 3 0.7 Bacteroidetes Flavobacteria Flavobacteriales Flavobacteriaceae Flavobacterium OB101F08 2 1 0 0 0 0 2 3 0.7 Bacteroidetes YU201G06 2 1 0 0 0 0 2 3 0.7 Actinobacteria Actinobacteria Actinomycetales KL201B11 2 0 1 0 0 0 1 2 0.4 Bacteroidetes KL201D09 2 1 1 0 0 0 0 2 0.4 Bacteroidetes KL201E06 2 0 1 0 0 1 0 2 0.4 Bacteroidetes Flavobacteria Flavobacteriales Flavobacteriaceae Flavobacterium KL201G05 2 1 1 0 0 0 0 2 0.4 Proteobacteria Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rhodobacter LE201A12 2 1 0 0 0 1 0 2 0.4 Verrucomicrobia Verrucomicrobiae Verrucomicrobiales Verrucomicrobiaceae Prosthecobacter MA101A01 2 0 0 0 1 1 0 2 0.4 Bacteroidetes Sphingobacteria Sphingobacteriales Flexibacteraceae Leadbetterella YE201H08 2 0 0 1 1 0 0 2 0.4 Bacteroidetes Flavobacteria Flavobacteriales Cryomorphaceae Fluviicola YU201E04 2 1 1 0 0 0 0 2 0.4 Chloroflexi Chloroflexi Chloroflexales YU201F08 2 1 0 0 0 0 1 2 0.4 Proteobacteria Gammaproteobacteria MA101D08 1 0 0 0 5 0 0 5 1.1 Bacteroidetes Sphingobacteria Sphingobacteriales Crenotrichaceae Terrimonas MA101H07 1 0 0 0 5 0 0 5 1.1 Proteobacteria Alphaproteobacteria OB101A05 1 0 0 0 0 0 3 3 0.7 Verrucomicrobia Verrucomicrobiae Verrucomicrobiales Xiphinematobacteriaceae Xiphinematobacteriaceae i.s. KL201F08 1 0 2 0 0 0 0 2 0.4 Bacteroidetes Sphingobacteria Sphingobacteriales Flexibacteraceae Emticicia LE201A03 1 0 0 0 0 2 0 2 0.4 Bacteroidetes Sphingobacteria Sphingobacteriales Flexibacteraceae Spirosoma LE201H05 1 0 0 0 0 2 0 2 0.4 Proteobacteria Betaproteobacteria Burkholderiales OB101A03 1 0 0 0 0 0 2 2 0.4 Bacteroidetes YE201A08 1 0 0 2 0 0 0 2 0.4 Verrucomicrobia Verrucomicrobiae Verrucomicrobiales Verrucomicrobiaceae Verrucomicrobiaceae i.s. YE201B07 1 0 0 2 0 0 0 2 0.4 Bacteroidetes Sphingobacteria Sphingobacteriales Sphingobacteriaceae YE201G11 1 0 0 2 0 0 0 2 0.4 Bacteroidetes YE201H09 1 0 0 2 0 0 0 2 0.4 Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae YU201D10 1 2 0 0 0 0 0 2 0.4 Bacteroidetes KL201A02 1 0 1 0 0 0 0 1 0.2 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Novosphingobium KL201A04 1 0 1 0 0 0 0 1 0.2 OP10 OP10 i.s. KL201A05 1 0 1 0 0 0 0 1 0.2 Bacteroidetes KL201A06 1 0 1 0 0 0 0 1 0.2 Bacteroidetes KL201A07 1 0 1 0 0 0 0 1 0.2 Unknown KL201A12 1 0 1 0 0 0 0 1 0.2 Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae Bdellovibrio Crump et al. www.pnas.org/cgi/content/short/0906149106 3of5 No. of Representative rivers All sequence containing clones, for OTU OTU YU KL YE MA LE OB total % Phylum Class Order Family Genus KL201B03 1 0 1 0 0 0 0 1 0.2 Bacteroidetes Sphingobacteria Sphingobacteriales Flexibacteraceae Dyadobacter KL201C04 1 0 1 0 0 0 0 1 0.2 Proteobacteria Gammaproteobacteria KL201D01 1 0 1 0 0 0 0 1 0.2 Bacteroidetes Sphingobacteria Sphingobacteriales KL201D04 1 0 1 0 0 0 0 1 0.2 Proteobacteria Gammaproteobacteria KL201D10 1 0 1 0 0 0 0 1 0.2 Proteobacteria Deltaproteobacteria Bdellovibrionales Bacteriovoracaceae Bacteriovorax KL201E02 1 0 1 0 0 0 0 1 0.2 Actinobacteria Actinobacteria Actinomycetales KL201E04 1 0 1 0 0 0 0 1 0.2 Proteobacteria Gammaproteobacteria KL201F02 1 0 1 0 0 0 0 1 0.2 Proteobacteria Betaproteobacteria KL201F07 1 0 1 0 0 0 0 1 0.2 Nitrospira Nitrospira Nitrospirales Nitrospiraceae Magnetobacterium KL201F12 1 0 1 0 0 0 0 1 0.2 Proteobacteria Betaproteobacteria KL201G01 1 0 1 0 0 0 0 1 0.2 Bacteroidetes Sphingobacteria Sphingobacteriales Crenotrichaceae KL201G12 1 0 1 0 0 0 0 1 0.2 Unknown KL201H02 1 0 1 0 0 0 0 1 0.2 Verrucomicrobia Verrucomicrobiae Verrucomicrobiales Xiphinematobacteriaceae Xiphinematobacteriaceae i.s. KL201H05 1 0 1 0 0 0 0 1 0.2 Proteobacteria Alphaproteobacteria Rhizobiales KL201H09 1 0 1 0 0 0 0 1 0.2 Bacteroidetes LE201A09 1 0 0 0 0 1 0 1 0.2 Actinobacteria Actinobacteria Actinomycetales LE201B03 1 0 0 0 0 1 0 1 0.2 Bacteroidetes Sphingobacteria Sphingobacteriales Flexibacteraceae LE201B06 1 0 0 0 0 1 0 1 0.2 Firmicutes ‘‘Clostridia’’ Clostridiales i.s. XII Fusibacter LE201B10 1 0 0 0 0 1 0 1 0.2 Unknown LE201C08 1 0 0 0 0 1 0 1 0.2 Proteobacteria Betaproteobacteria LE201D03 1 0 0 0 0 1 0 1 0.2 Actinobacteria Actinobacteria Actinomycetales LE201G11 1 0 0 0 0 1 0 1 0.2 Proteobacteria Betaproteobacteria Methylophilales Methylophilaceae LE201H08 1 0 0 0 0 1 0 1 0.2 Proteobacteria Deltaproteobacteria Bdellovibrionales Bacteriovoracaceae LE201H09 1 0 0 0 0 1 0 1 0.2 Proteobacteria Betaproteobacteria Methylophilales Methylophilaceae Methylophilus LE201H11 1 0 0 0 0 1 0 1 0.2 Proteobacteria Betaproteobacteria MA101A03 1 0 0 0 1 0 0 1 0.2 Unknown MA101A05 1 0 0 0 1 0 0 1 0.2 Bacteroidetes MA101A10 1 0 0 0 1 0 0 1 0.2 Acidobacteria Acidobacteria Acidobacteriales Acidobacteriaceae Gp17 MA101C04 1 0 0 0 1 0 0 1 0.2 Bacteroidetes Sphingobacteria Sphingobacteriales Flexibacteraceae MA101C11 1 0 0 0 1 0 0 1 0.2 Acidobacteria Acidobacteria Acidobacteriales Acidobacteriaceae Gp8 MA101D04 1 0 0 0 1 0 0 1 0.2 Proteobacteria Betaproteobacteria MA101E07 1 0 0 0 1 0 0 1 0.2 Bacteroidetes Sphingobacteria Sphingobacteriales Saprospiraceae MA101E10 1 0 0 0 1 0 0 1 0.2 Actinobacteria Actinobacteria Actinomycetales MA101F07 1 0 0 0 1 0 0 1 0.2 Bacteroidetes Sphingobacteria Sphingobacteriales MA101F12 1 0 0 0 1 0 0 1 0.2 Proteobacteria Alphaproteobacteria MA101G01 1 0 0 0 1 0 0 1 0.2 Bacteroidetes Sphingobacteria Sphingobacteriales Saprospiraceae Haliscomenobacter MA101H02 1 0 0 0 1 0 0 1 0.2 Verrucomicrobia Verrucomicrobiae Verrucomicrobiales Subdivision 3 Subdivision 3 i.s.
Load more

Recommended publications
  • Spatio-Temporal Study of Microbiology in the Stratified Oxic-Hypoxic-Euxinic, Freshwater- To-Hypersaline Ursu Lake
    Spatio-temporal insights into microbiology of the freshwater-to- hypersaline, oxic-hypoxic-euxinic waters of Ursu Lake Baricz, A., Chiriac, C. M., Andrei, A-., Bulzu, P-A., Levei, E. A., Cadar, O., Battes, K. P., Cîmpean, M., enila, M., Cristea, A., Muntean, V., Alexe, M., Coman, C., Szekeres, E. K., Sicora, C. I., Ionescu, A., Blain, D., O’Neill, W. K., Edwards, J., ... Banciu, H. L. (2020). Spatio-temporal insights into microbiology of the freshwater-to- hypersaline, oxic-hypoxic-euxinic waters of Ursu Lake. Environmental Microbiology. https://doi.org/10.1111/1462-2920.14909, https://doi.org/10.1111/1462-2920.14909 Published in: Environmental Microbiology Document Version: Peer reviewed version Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights Copyright 2019 Wiley. This work is made available online in accordance with the publisher’s policies. Please refer to any applicable terms of use of the publisher. General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. If you discover content in the Research Portal that you believe breaches copyright or violates any law, please contact [email protected].
    [Show full text]
  • Community Analysis of Microbial Sharing and Specialization in A
    Downloaded from http://rspb.royalsocietypublishing.org/ on March 15, 2017 Community analysis of microbial sharing rspb.royalsocietypublishing.org and specialization in a Costa Rican ant–plant–hemipteran symbiosis Elizabeth G. Pringle1,2 and Corrie S. Moreau3 Research 1Department of Biology, Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Cite this article: Pringle EG, Moreau CS. 2017 Reno, NV 89557, USA 2Michigan Society of Fellows, University of Michigan, Ann Arbor, MI 48109, USA Community analysis of microbial sharing and 3Department of Science and Education, Field Museum of Natural History, 1400 South Lake Shore Drive, specialization in a Costa Rican ant–plant– Chicago, IL 60605, USA hemipteran symbiosis. Proc. R. Soc. B 284: EGP, 0000-0002-4398-9272 20162770. http://dx.doi.org/10.1098/rspb.2016.2770 Ants have long been renowned for their intimate mutualisms with tropho- bionts and plants and more recently appreciated for their widespread and diverse interactions with microbes. An open question in symbiosis research is the extent to which environmental influence, including the exchange of Received: 14 December 2016 microbes between interacting macroorganisms, affects the composition and Accepted: 17 January 2017 function of symbiotic microbial communities. Here we approached this ques- tion by investigating symbiosis within symbiosis. Ant–plant–hemipteran symbioses are hallmarks of tropical ecosystems that produce persistent close contact among the macroorganism partners, which then have substantial opportunity to exchange symbiotic microbes. We used metabarcoding and Subject Category: quantitative PCR to examine community structure of both bacteria and Ecology fungi in a Neotropical ant–plant–scale-insect symbiosis. Both phloem-feed- ing scale insects and honeydew-feeding ants make use of microbial Subject Areas: symbionts to subsist on phloem-derived diets of suboptimal nutritional qual- ecology, evolution, microbiology ity.
    [Show full text]
  • The Expanded Database of Polysaccharide Utilization Loci Nicolas Terrapon1,2,*, Vincent Lombard1,2, Elodie´ Drula1,2, Pascal Lapebie´ 1,2, Saad Al-Masaudi3, Harry J
    Published online 27 October 2017 Nucleic Acids Research, 2018, Vol. 46, Database issue D677–D683 doi: 10.1093/nar/gkx1022 PULDB: the expanded database of Polysaccharide Utilization Loci Nicolas Terrapon1,2,*, Vincent Lombard1,2, Elodie´ Drula1,2, Pascal Lapebie´ 1,2, Saad Al-Masaudi3, Harry J. Gilbert4 and Bernard Henrissat1,2,3,* 1Architecture et Fonction des Macromolecules´ Biologiques, CNRS, Aix-Marseille Universite,´ F-13288 Marseille, France, 2USC1408 Architecture et Fonction des Macromolecules´ Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France, 3Department of Biological Sciences, King Abdulaziz University, 23218 Jeddah, Saudi Arabia and 4Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK Received September 17, 2017; Revised October 16, 2017; Editorial Decision October 17, 2017; Accepted October 25, 2017 ABSTRACT INTRODUCTION The Polysaccharide Utilization Loci (PUL) database Polysaccharides constitute the main source of carbon for was launched in 2015 to present PUL predictions most organisms on Earth. Because of their enormous struc- in ∼70 Bacteroidetes species isolated from the hu- tural diversity, polysaccharide deconstruction requires the man gastrointestinal tract, as well as PULs derived concerted action of large numbers of specific enzymes. from the experimental data reported in the litera- While most bacteria break down polysaccharides by export- ing their carbohydrate-active enzymes (CAZymes) into the ture. In 2018 PULDB offers access to 820 genomes, extracellular milieu and import the simple sugars produced, sampled from various environments and covering a an inventive solution operates in Gram-negative bacteria of much wider taxonomical range. A Krona dynamic the Bacteroidetes phylum. The genomes of these bacteria chart was set up to facilitate browsing through tax- feature Polysaccharide Utilization Loci, or PULs.
    [Show full text]
  • Table S1. Bacterial Otus from 16S Rrna
    Table S1. Bacterial OTUs from 16S rRNA sequencing analysis including only taxa which were identified to genus level (those OTUs identified as Ambiguous taxa, uncultured bacteria or without genus-level identifications were omitted). OTUs with only a single representative across all samples were also omitted. Taxa are listed from most to least abundant. Pitcher Plant Sample Class Order Family Genus CB1p1 CB1p2 CB1p3 CB1p4 CB5p234 Sp3p2 Sp3p4 Sp3p5 Sp5p23 Sp9p234 sum Gammaproteobacteria Legionellales Coxiellaceae Rickettsiella 1 2 0 1 2 3 60194 497 1038 2 61740 Alphaproteobacteria Rhodospirillales Rhodospirillaceae Azospirillum 686 527 10513 485 11 3 2 7 16494 8201 36929 Sphingobacteriia Sphingobacteriales Sphingobacteriaceae Pedobacter 455 302 873 103 16 19242 279 55 760 1077 23162 Betaproteobacteria Burkholderiales Oxalobacteraceae Duganella 9060 5734 2660 40 1357 280 117 29 129 35 19441 Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas 3336 1991 3475 1309 2819 233 1335 1666 3046 218 19428 Betaproteobacteria Burkholderiales Burkholderiaceae Paraburkholderia 0 1 0 1 16051 98 41 140 23 17 16372 Sphingobacteriia Sphingobacteriales Sphingobacteriaceae Mucilaginibacter 77 39 3123 20 2006 324 982 5764 408 21 12764 Gammaproteobacteria Pseudomonadales Moraxellaceae Alkanindiges 9 10 14 7 9632 6 79 518 1183 65 11523 Betaproteobacteria Neisseriales Neisseriaceae Aquitalea 0 0 0 0 1 1577 5715 1471 2141 177 11082 Flavobacteriia Flavobacteriales Flavobacteriaceae Flavobacterium 324 219 8432 533 24 123 7 15 111 324 10112 Alphaproteobacteria
    [Show full text]
  • A Genomic View of Trophic and Metabolic Diversity in Clade-Specific Lamellodysidea Sponge Microbiomes
    UC San Diego UC San Diego Previously Published Works Title A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes. Permalink https://escholarship.org/uc/item/6z2365ft Journal Microbiome, 8(1) ISSN 2049-2618 Authors Podell, Sheila Blanton, Jessica M Oliver, Aaron et al. Publication Date 2020-06-23 DOI 10.1186/s40168-020-00877-y Peer reviewed eScholarship.org Powered by the California Digital Library University of California Podell et al. Microbiome (2020) 8:97 https://doi.org/10.1186/s40168-020-00877-y RESEARCH Open Access A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes Sheila Podell1 , Jessica M. Blanton1, Aaron Oliver1, Michelle A. Schorn2, Vinayak Agarwal3, Jason S. Biggs4, Bradley S. Moore5,6,7 and Eric E. Allen1,5,7,8* Abstract Background: Marine sponges and their microbiomes contribute significantly to carbon and nutrient cycling in global reefs, processing and remineralizing dissolved and particulate organic matter. Lamellodysidea herbacea sponges obtain additional energy from abundant photosynthetic Hormoscilla cyanobacterial symbionts, which also produce polybrominated diphenyl ethers (PBDEs) chemically similar to anthropogenic pollutants of environmental concern. Potential contributions of non-Hormoscilla bacteria to Lamellodysidea microbiome metabolism and the synthesis and degradation of additional secondary metabolites are currently unknown. Results: This study has determined relative abundance, taxonomic novelty, metabolic
    [Show full text]
  • Leadbetterella Byssophila Type Strain (4M15)
    Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Leadbetterella byssophila type strain (4M15). Permalink https://escholarship.org/uc/item/907989cw Journal Standards in genomic sciences, 4(1) ISSN 1944-3277 Authors Abt, Birte Teshima, Hazuki Lucas, Susan et al. Publication Date 2011-03-04 DOI 10.4056/sigs.1413518 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2011) 4:2-12 DOI:10.4056/sigs.1413518 Complete genome sequence of Leadbetterella byssophila type strain (4M15T) Birte Abt1, Hazuki Teshima2,3, Susan Lucas2, Alla Lapidus2, Tijana Glavina Del Rio2, Matt Nolan2, Hope Tice2, Jan-Fang Cheng2, Sam Pitluck2, Konstantinos Liolios2, Ioanna Pagani2, Natalia Ivanova2, Konstantinos Mavromatis2, Amrita Pati2, Roxane Tapia2,3, Cliff Han2,3, Lynne Goodwin2,3, Amy Chen4, Krishna Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, Manfred Rohde6, Markus Göker1, Brian J. Tindall1, John C. Detter2,3, Tanja Woyke2, James Bristow2, Jonathan A. Eisen2,7, Victor Markowitz4, Philip Hugenholtz2,8, Hans-Peter Klenk1, and Nikos C. Kyrpides2* 1 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Lawrence Livermore National Laboratory, Livermore, California, USA 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA 8 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia *Corresponding author: Nikos C.
    [Show full text]
  • Spatiotemporal Dynamics of Marine Bacterial and Archaeal Communities in Surface Waters Off the Northern Antarctic Peninsula
    Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula Camila N. Signori, Vivian H. Pellizari, Alex Enrich Prast and Stefan M. Sievert The self-archived postprint version of this journal article is available at Linköping University Institutional Repository (DiVA): http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-149885 N.B.: When citing this work, cite the original publication. Signori, C. N., Pellizari, V. H., Enrich Prast, A., Sievert, S. M., (2018), Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula, Deep-sea research. Part II, Topical studies in oceanography, 149, 150-160. https://doi.org/10.1016/j.dsr2.2017.12.017 Original publication available at: https://doi.org/10.1016/j.dsr2.2017.12.017 Copyright: Elsevier http://www.elsevier.com/ Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula Camila N. Signori1*, Vivian H. Pellizari1, Alex Enrich-Prast2,3, Stefan M. Sievert4* 1 Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo (USP). Praça do Oceanográfico, 191. CEP: 05508-900 São Paulo, SP, Brazil. 2 Department of Thematic Studies - Environmental Change, Linköping University. 581 83 Linköping, Sweden 3 Departamento de Botânica, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ). Av. Carlos Chagas Filho, 373. CEP: 21941-902. Rio de Janeiro, Brazil 4 Biology Department, Woods Hole Oceanographic Institution (WHOI). 266 Woods Hole Road, Woods Hole, MA 02543, United States. *Corresponding authors: Camila Negrão Signori Address: Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, São Paulo, Brazil.
    [Show full text]
  • The Prevalence of Foodborne Pathogenic Bacteria on Cutting Boards and Their Ecological Correlation with Background Biota
    AIMS Microbiology, 2(2): 138-151. DOI: 10.3934/microbiol.2016.2.138 Received: 23 April 2016 Accepted: 19 May 2016 Published: 22 May 2016 http://www.aimspress.com/journal/microbiology Research article The prevalence of foodborne pathogenic bacteria on cutting boards and their ecological correlation with background biota Noor-Azira Abdul-Mutalib 1,2,3, Syafinaz Amin Nordin 2, Malina Osman 2, Ahmad Muhaimin Roslan 4, Natsumi Ishida 5, Kenji Sakai 5, Yukihiro Tashiro 5, Kosuke Tashiro 6, Toshinari Maeda 1, and Yoshihito Shirai 1,* 1 Department of Biological Functions and Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0196, Japan 2 Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia 3 Department of Food Service and Management, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia 4 Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia 5 Laboratory of Soil Microbiology, Faculty of Agriculture, Graduate School, Kyushu University, 6- 10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan 6 Laboratory of Molecular Gene Technique, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan * Correspondence: E-mail: [email protected]; Tel.: +6012-9196951; Fax: +603-89471182. Abstract: This study implemented the pyrosequencing technique and real-time quantitative PCR to determine the prevalence of foodborne pathogenic bacteria (FPB) and as well as the ecological correlations of background biota and FPB present on restaurant cutting boards (CBs) collected in Seri Kembangan, Malaysia.
    [Show full text]
  • High Quality Permanent Draft Genome Sequence of Chryseobacterium Bovis DSM 19482T, Isolated from Raw Cow Milk
    Lawrence Berkeley National Laboratory Recent Work Title High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk. Permalink https://escholarship.org/uc/item/4b48v7v8 Journal Standards in genomic sciences, 12(1) ISSN 1944-3277 Authors Laviad-Shitrit, Sivan Göker, Markus Huntemann, Marcel et al. Publication Date 2017 DOI 10.1186/s40793-017-0242-6 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Laviad-Shitrit et al. Standards in Genomic Sciences (2017) 12:31 DOI 10.1186/s40793-017-0242-6 SHORT GENOME REPORT Open Access High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk Sivan Laviad-Shitrit1, Markus Göker2, Marcel Huntemann3, Alicia Clum3, Manoj Pillay3, Krishnaveni Palaniappan3, Neha Varghese3, Natalia Mikhailova3, Dimitrios Stamatis3, T. B. K. Reddy3, Chris Daum3, Nicole Shapiro3, Victor Markowitz3, Natalia Ivanova3, Tanja Woyke3, Hans-Peter Klenk4, Nikos C. Kyrpides3 and Malka Halpern1,5* Abstract Chryseobacterium bovis DSM 19482T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic and lipolytic traits were studied. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA G + C content is 38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105 RNA genes. The C. bovis genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.
    [Show full text]
  • Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz
    Alpine soil bacterial community and environmental filters Bahar Shahnavaz To cite this version: Bahar Shahnavaz. Alpine soil bacterial community and environmental filters. Other [q-bio.OT]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00515414 HAL Id: tel-00515414 https://tel.archives-ouvertes.fr/tel-00515414 Submitted on 6 Sep 2010 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 l’obtention du titre de l'Université Joseph-Fourier - Grenoble 1 École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Par Bahar SHAHNAVAZ Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean MARTIN Examinateur Dr. Yves JOUANNEAU Président du jury Dr. Roberto GEREMIA Directeur de thèse Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) THÈSE Pour l’obtention du titre de Docteur de l’Université de Grenoble École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Bahar SHAHNAVAZ Directeur : Roberto GEREMIA Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr.
    [Show full text]
  • Genomic Homogeneity Between Mycobacterium Avium Subsp. Avium and Mycobacterium Avium Subsp
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln U.S. Department of Agriculture: Agricultural Publications from USDA-ARS / UNL Faculty Research Service, Lincoln, Nebraska 2003 Genomic homogeneity between Mycobacterium avium subsp. avium and Mycobacterium avium subsp. paratuberculosis belies their divergent growth rates John P. Bannantine ARS-USDA, [email protected] Qing Zhang 2University of Minnesota, Minneapolis, [email protected] Ling-Ling Li University of Minnesota, Minneapolis, [email protected] Vivek Kapur University of Minnesota, Minneapolis, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/usdaarsfacpub Bannantine, John P.; Zhang, Qing; Li, Ling-Ling; and Kapur, Vivek, "Genomic homogeneity between Mycobacterium avium subsp. avium and Mycobacterium avium subsp. paratuberculosis belies their divergent growth rates" (2003). Publications from USDA-ARS / UNL Faculty. 2372. https://digitalcommons.unl.edu/usdaarsfacpub/2372 This Article is brought to you for free and open access by the U.S. Department of Agriculture: Agricultural Research Service, Lincoln, Nebraska at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Publications from USDA-ARS / UNL Faculty by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. BMC Microbiology BioMed Central Research article Open Access Genomic homogeneity between Mycobacterium avium subsp. avium and Mycobacterium avium subsp. paratuberculosis belies their
    [Show full text]
  • Nomenclature of Bacteria with Special Reference to the Order Actinomycetales'
    INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY VOL. 21, No. 2 April 1971, pp. 197-206 Printed in U.S.A. Copyright 0 1971 International Association of Microbiological Societies Nomenclature of Bacteria with Special Reference to the Order Actinomycetales' THOMAS G. PRIDHAM Northern Regional Research Laboratory,z Peoria, Illinois 61604 The number of names for streptomycetes that is in the scientific literature now is exceeded only by those for organisms placed in the genus Bacillus Cohn 1872. The genus Streptomyces Waksman and Henrici 1943 may well rank in first place if names in the patent and quasiscientific literature are included. The overwhelming number of names and the lack of a precise definition of a particular species or subspecies, of type or neotype strains, and of certain essential details have brought about problems in assessing the status of many names. The major problems encountered in a 2-year study are discussed, and a simple format is suggested, use of which may help to clarify future nomenclature. Twelve years ago, I presented (29) before ture of Bacteria (20); type strains, where these the First Latin-American Congress for Micro- can be located and obtained, are being as- biology held at Mexico, D.F., some suggestions sembled and recharacterized (35 -38) through on establishing a logical order in streptomycete the International Streptomyces Project, and a classification. minumum set of substrata and tests have been (i) Compilation and evaluation of available recommended for description of A ctino- literature on nomenclature and characterization mycetales in patents (1 1, 12). of streptomycetes. One item upon which insufficient attention (ii) Decision on the proper code of nomen- has been focused is nomenclature.
    [Show full text]