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Supplementary Table S1. Class comparison of phylum Proteobacteria before and after air surging. The data are prevalence rates (%) in terms of the number of OTUs. Proteobacteria Before After Alphaproteobacteria 5.1 6.2 Betaproteobacteria 38.7 30.3 Deltaproteobacteria 0.4 7.8 Gammaproteobacteria 39.4 1.8 Other Proteobacteria < 0.1 0.5 Total % of Proteobacteria 83.6 46.6 Supplementary Table S2. Comparison of major bacterial communities before and after air surging. The data are prevalence rate (%) in terms of number of OTUs. Air surging OTUs Phylum Class Order Family Genus work (%) number BeforAfte e r Phylum Acidobacter uncultured_Acidobacteria_bact Acidobacteri 11-24 - - 0.0 0.1 ia erium a-OTU01 Phylum Acidobacter Acidobacteri 32-21 uncultured_bacterium - - 0.0 0.2 ia a-OTU03 Phylum Acidobacter Acidobacterial uncultured_bacteri Acidobacteri Acidobacteriaceae uncultured 0.0 0.2 ia es um a-OTU06 Phylum Acidobacter Acidobacteri DA023 uncultured_bacterium - - 0.1 2.0 ia a-OTU13 Phylum Acidobacter Acidobacteri DA052 uncultured_bacterium - - 0.0 0.5 ia a-OTU14 Phylum Acidobacter Acidobacteri Holophagae Holophagales Holophagaceae Geothrix 0.1 0.5 ia a-OTU19 Phylum Acidobacter Acidobacteri Holophagae Holophagales Holophagaceae uncultured 0.2 0.3 ia a-OTU20 Phylum Acidobacter uncultured_bacteriu Acidobacteri Holophagae SJA-36 - 0.0 0.1 ia m a-OTU21 Phylum Acidobacter Acidobacteri SJA-149 - - - 0.0 0.1 ia a-OTU31 Phylum Actinobacte CL500- Actinobacter Acidimicrobiia Acidimicrobiales Acidimicrobiaceae 0.0 1.8 ria 29_marine_group ia-OTU02 1 Phylum Actinobacte Corynebacteria Actinobacter Nocardiaceae Rhodococcus - 0.5 0.1 ria les ia-OTU09 Phylum Actinobacte Candidatus_Plankto Actinobacter Frankiales Sporichthyaceae - 2.4 11.2 ria phila ia-OTU16 Phylum Actinobacte Actinobacter Micrococcales Microbacteriaceae - - 0.0 0.1 ria ia-OTU25 Phylum Actinobacte Actinobacter Micrococcales Micrococcaceae Arthrobacter - 0.1 0.1 ria ia-OTU27 Phylum Actinobacte uncultured_bacteri Actinobacter Micrococcales Micrococcaceae Arthrobacter 0.0 0.2 ria um ia-OTU28 Phylum Actinobacte Actinobacter Micrococcales Micrococcaceae Kocuria - 0.2 0.0 ria ia-OTU29 Phylum Actinobacte Actinobacter OPB41 uncultured_bacterium - - 0.0 0.1 ria ia-OTU31 Phylum Actinobacte Actinobacter PeM15 uncultured_bacterium - - 0.0 0.1 ria ia-OTU32 Phylum Actinobacte Thermoleophil Actinobacter Gaiellales Gaiellaceae Gaiella 0.0 0.1 ria ia ia-OTU42 Phylum Bacteroidete Bacteroidete Cytophagia Cytophagales Cytophagaceae Arcicella 0.6 0.1 s s-OTU04 Phylum Bacteroidete Bacteroidete Cytophagia Cytophagales Cytophagaceae Flexibacter 0.1 0.4 s s-OTU07 Phylum Bacteroidete Bacteroidete Cytophagia Cytophagales Cytophagaceae Hymenobacter 0.3 0.0 s s-OTU08 Phylum Bacteroidete Bacteroidete Flavobacteria Flavobacteriales Flavobacteriaceae Flavobacterium 2.2 0.4 s s-OTU17 Phylum BacteroideteSphingobacteri Bacteroidete Sphingobacteriales Chitinophagaceae - 0.0 1.0 s ia s-OTU18 Phylum BacteroideteSphingobacteri Bacteroidete Sphingobacteriales Chitinophagaceae Hydrotalea 0.4 0.0 s ia s-OTU22 Phylum BacteroideteSphingobacteri Bacteroidete Sphingobacteriales Chitinophagaceae Lacibacter 0.0 0.1 s ia s-OTU23 Phylum BacteroideteSphingobacteri Bacteroidete Sphingobacteriales Chitinophagaceae Sediminibacterium 2.0 1.5 s ia s-OTU24 Phylum BacteroideteSphingobacteri Bacteroidete Sphingobacteriales Chitinophagaceae uncultured 0.0 0.1 s ia s-OTU26 Phylum BacteroideteSphingobacteri uncultured_bacteri Bacteroidete Sphingobacteriales KD3-93 0.0 0.1 s ia um s-OTU29 2 Phylum BacteroideteSphingobacteri NS11- uncultured_bacteri Bacteroidete Sphingobacteriales 0.7 2.4 s ia 12_marine_group um s-OTU31 Phylum BacteroideteSphingobacteri uncultured_bacteri Bacteroidete Sphingobacteriales PHOS-HE51 0.0 0.2 s ia um s-OTU32 Phylum BacteroideteSphingobacteri Bacteroidete Sphingobacteriales Sphingobacteriaceae Mucilaginibacter 0.1 0.0 s ia s-OTU35 Phylum BacteroideteSphingobacteri Bacteroidete Sphingobacteriales Sphingobacteriaceae Sphingobacterium 0.0 0.1 s ia s-OTU39 Phylum BacteroideteSphingobacteri Bacteroidete Sphingobacteriales env.OPS_17 - 0.0 0.1 s ia s-OTU41 Phylum Bacteroidete Bacteroidete WCHB1-32 uncultured_bacterium - - 0.0 5.9 s s-OTU44 Phylum uncultured_bacteri Chlorobi- Chlorobi Chlorobia Chlorobiales OPB56 0.0 0.2 um OTU01 Phylum uncultured_bacteri Chlorobi- Chlorobi Ignavibacteria Ignavibacteriales BSV26 0.0 0.1 um OTU02 Phylum uncultured_bacteri Chlorobi- Chlorobi Ignavibacteria Ignavibacteriales SR-FBR-L83 0.0 0.6 um OTU03 Phylum Chloroflexi- Chloroflexi KD4-96 uncultured_bacterium - - 0.0 2.2 OTU09 Phylum Chloroflexi- Chloroflexi P2-11E uncultured_bacterium - - 0.0 0.2 OTU12 Phylum Chloroflexi- Chloroflexi S085 uncultured_bacterium - - 0.0 0.1 OTU13 Supplementary Table S2. Continued Air surgin g OTUs Phylum Class Order Family Genus work number (%) Bef Af ore ter Phylum SAR202_cla Chloroflexi- Chloroflexi uncultured_bacterium - - 0.0 0.1 de OTU14 Phylum Chloroflexi- Chloroflexi TK10 - - - 0.0 0.2 OTU15 3 Phylum Cyanobacte Cyanobacter MLE1-12 uncultured_bacterium - - 0.8 2.4 ria ia-OTU04 Phylum Cyanobacte Cyanobacter SHA-109 uncultured_bacterium - - 0.0 0.1 ria ia-OTU05 Phylum Elusimicrob uncultured_Termite_gro Elusimicrobi Lineage_IV - - 0.0 0.1 ia up_1_bacterium a-OTU04 Phylum Elusimicrob Elusimicrobi Lineage_IV uncultured_bacterium - - 0.3 1.5 ia a-OTU05 Phylum Firmicutes- Firmicutes Bacilli Bacillales Bacillaceae Anoxybacillus 0.0 0.1 OTU01 Phylum Staphylococcace Firmicutes- Firmicutes Bacilli Bacillales Staphylococcus 0.1 0.0 ae OTU06 Phylum Family_XIII_Inc Firmicutes- Firmicutes Clostridia Clostridiales uncultured 0.0 0.3 ertae_Sedis OTU10 Phylum Gracilibacterace Firmicutes- Firmicutes Clostridia Clostridiales Lutispora 0.0 0.4 ae OTU11 Phylum Gracilibacterace Firmicutes- Firmicutes Clostridia Clostridiales uncultured 0.0 0.1 ae OTU12 Phylum Firmicutes- Firmicutes Clostridia Clostridiales Peptococcaceae Desulfosporosinus 0.0 0.9 OTU14 Phylum Ruminococcace Firmicutes- Firmicutes Clostridia Clostridiales Incertae_Sedis 0.0 0.1 ae OTU15 Phylum Gemmatimo Gemmatim Gemmatimo Gemmatimonadaceae uncultured - 0.0 0.1 nadetes- onadetes nadales OTU03 Phylum Gemmatimo Gemmatim Gemmatimo Gemmatimonadaceae uncultured uncultured_bacterium 0.2 1.5 nadetes- onadetes nadales OTU05 Phylum Nitrospirae- Nitrospirae Nitrospira Nitrospirales - - 0.0 0.6 OTU01 Phylum Nitrospirae- Nitrospirae Nitrospira Nitrospirales 0319-6A21 uncultured_bacterium 0.0 0.4 OTU03 Phylum Nitrospirae- Nitrospirae Nitrospira Nitrospirales Nitrospiraceae Nitrospira 0.2 0.7 OTU06 Phylum Planctomyc Planctomyce OM190 uncultured_bacterium - - 0.0 0.1 etes tes-OTU04 4 Phylum Planctomyc Phycisphaer Phycisphaerace Planctomyce Phycisphaerales SM1A02 0.0 0.2 etes ae ae tes-OTU07 Phylum Planctomyc Planctomyc Planctomycetac Planctomyce Planctomycetales Planctomyces 0.0 0.1 etes etacia eae tes-OTU17 Phylum Planctomyc Planctomyc Planctomycetac Planctomyce Planctomycetales uncultured 0.0 0.1 etes etacia eae tes-OTU20 Phylum Planctomyc Planctomyce vadinHA49 uncultured_bacterium - - 0.0 0.1 etes tes-OTU21 Class Alphaproteo Proteobacte Alphaprote Caulobacteracea Caulobacterales Brevundimonas 0.1 0.1 bacteria- ria obacteria e OTU03 Class Alphaproteo Proteobacte Alphaprote Caulobacteracea Caulobacterales Caulobacter 0.7 0.2 bacteria- ria obacteria e OTU04 Class Alphaproteo Proteobacte Alphaprote Hyphomonadac Caulobacterales Woodsholea 0.0 0.1 bacteria- ria obacteria eae OTU07 Class Alphaproteo Proteobacte Alphaprote DB1-14 - - 0.0 0.4 bacteria- ria obacteria OTU08 Class Alphaproteo Proteobacte Alphaprote Rhizobiales A0839 uncultured_bacterium 0.0 0.1 bacteria- ria obacteria OTU12 Class Alphaproteo Proteobacte Alphaprote Bradyrhizobiace Rhizobiales Bradyrhizobium 0.0 0.1 bacteria- ria obacteria ae OTU14 Class Alphaproteo Proteobacte Alphaprote Methylobacteria Rhizobiales Methylobacterium 0.1 0.1 bacteria- ria obacteria ceae OTU23 Class Alphaproteo Proteobacte Alphaprote Rhodobacterace Rhodobacterales Rhodovulum 1.5 0.2 bacteria- ria obacteria ae OTU33 Class Alphaproteo Proteobacte Alphaprote uncultured_Acetobacter Rhodospirillales KCM-B-60 0.0 0.1 bacteria- ria obacteria aceae_bacterium OTU47 Class Alphaproteo Proteobacte Alphaprote uncultured_Rhodospiril Rhodospirillales KCM-B-60 0.0 0.1 bacteria- ria obacteria lales_bacterium OTU48 5 Class Alphaproteo Proteobacte Alphaprote Rhodospirillace Rhodospirillales Magnetospirillum 0.0 0.2 bacteria- ria obacteria ae OTU51 Class Alphaproteo Proteobacte Alphaprote Rhodospirillace Rhodospirillales uncultured 0.0 0.1 bacteria- ria obacteria ae OTU53 Class Alphaproteo Proteobacte Alphaprote Rhodospirillales wr0007 - 0.1 0.1 bacteria- ria obacteria OTU54 Class Alphaproteo Proteobacte Alphaprote uncultured_alpha_prote Rhodospirillales wr0007 0.0 0.1 bacteria- ria obacteria obacterium OTU55 Class Alphaproteo Proteobacte Alphaprote Rickettsiales Rickettsiaceae uncultured 0.0 0.5 bacteria- ria obacteria OTU67 Class Alphaproteo Proteobacte Alphaprote Sphingomonada Sphingomonadales Novosphingobium 1.7 3.2 bacteria- ria obacteria ceae OTU73 Class Alphaproteo Proteobacte Alphaprote Sphingomonada Sphingomonadales Sphingobium 0.1 0.1 bacteria- ria obacteria ceae OTU74 Class Alphaproteo Proteobacte Alphaprote Sphingomonada Sphingomonadales Sphingomonas 0.3 0.2 bacteria- ria obacteria ceae OTU75 Supplementary Table S2. Continued Air surging OTUs number Phylum Class Order Family Genus work (%) Befo Aft re er Class Proteobact Alphaproteobac Sphingomonada Sphingomonadac Alphaproteobact Sphingopyxis 0.3 0.0 eria teria les eae eria-OTU76 Class Proteobact
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    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.
  • Functional Structure of the Bromeliad Tank Microbiome Is Strongly Shaped by Local Geochemical Conditions

    Functional Structure of the Bromeliad Tank Microbiome Is Strongly Shaped by Local Geochemical Conditions

    Environmental Microbiology (2017) 19(8), 3132–3151 doi:10.1111/1462-2920.13788 Functional structure of the bromeliad tank microbiome is strongly shaped by local geochemical conditions Stilianos Louca,1,2* Saulo M. S. Jacques,3,4 denitrification steps, ammonification, sulfate respira- Aliny P. F. Pires,3 Juliana S. Leal,3,5 tion, methanogenesis, reductive acetogenesis and 6 1,2,7 Angelica L. Gonzalez, Michael Doebeli and anoxygenic phototrophy. Overall, CO2 reducers domi- Vinicius F. Farjalla3 nated in abundance over sulfate reducers, and 1Biodiversity Research Centre, University of British anoxygenic phototrophs largely outnumbered oxy- Columbia, Vancouver, BC, Canada. genic photoautotrophs. Functional community 2Department of Zoology, University of British Columbia, structure correlated strongly with environmental vari- Vancouver, BC, Canada. ables, between and within a single bromeliad species. 3Department of Ecology, Biology Institute, Universidade Methanogens and reductive acetogens correlated Federal do Rio de Janeiro, Rio de Janeiro, Brazil. with detrital volume and canopy coverage, and exhib- 4Programa de Pos-Graduac ¸ao~ em Ecologia e ited higher relative abundances in N. cruenta.A Evoluc¸ao,~ Universidade Estadual do Rio de Janeiro, Rio comparison of bromeliads to freshwater lake sedi- de Janeiro, Brazil. ments and soil from around the world, revealed stark differences in terms of taxonomic as well as func- 5Programa de Pos-Graduac ¸ao~ em Ecologia, tional microbial community structure. Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil. 6Biology Department & Center for Computational & Introduction Integrative Biology, Rutgers University, Camden, NJ, USA. Bromeliads (fam. Bromeliaceae) are plants found through- 7Department of Mathematics, University of British out the neotropics, with many species having rosette-like Columbia, Vancouver, BC, Canada.
  • Full Paper Ilumatobacter Fluminis Gen. Nov., Sp. Nov., a Novel Actinobacterium Isolated from the Sediment of an Estuary

    Full Paper Ilumatobacter Fluminis Gen. Nov., Sp. Nov., a Novel Actinobacterium Isolated from the Sediment of an Estuary

    J. Gen. Appl. Microbiol., 55, 201‒205 (2009) Full Paper Ilumatobacter fl uminis gen. nov., sp. nov., a novel actinobacterium isolated from the sediment of an estuary Atsuko Matsumoto,1 Hiroki Kasai,2 Yoshihide Matsuo,2 Satoshi Ōmura,1 Yoshikazu Shizuri,2 and Yōko Takahashi1,* 1 Kitasato Institute for Life Sciences, Kitasato University, Minato-ku, Tokyo 108‒8641, Japan 2 Marine Biotechnology Institute, Kitasato University, Kamaishi, Iwate 026‒0001, Japan (Received December 1, 2008; Accepted February 2, 2009) Bacterial strain YM22-133T was isolated from the sediment of an estuary and grew in media with an artifi cial seawater base. Strain YM22-133T was Gram-positive, aerobic, non-motile and rod shaped. The cell-wall peptidoglycan contained LL-DAP, glycine, alanine and hydroxyglutamate. The predominant menaquinone was MK-9 (H8), with MK-9 (H0), MK-9 (H2), MK-9 (H4) and MK-9 (H6) present as minor menaquinones. The G+C content of the genomic DNA from the strain was 68 mol%. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain is near- est to Acidimicrobium ferrooxidans DSM 10331T. However, the similarity is relatively low (87.1%) and the physiological characteristics are also different: Acidimicrobium ferrooxidans is thermo- tolerant and acidophilic. Therefore, strain YM22-133T can be classifi ed as a novel genus and species, Ilumatobacter fl uminis gen. nov., sp. nov. (type strain YM22-133T =DSM 18936T=MBIC 08263T). Key Words—Acidimicrobium; Actinobacteria; artifi cial sea water; Ilumatobacter fl uminis gen. nov., sp. nov. Introduction isolated as part of this study. Phylogenetic analysis on the basis of 16S rRNA gene sequence analysis showed Recently, bacteria isolated from marine environ- that the strain is most closely related to the genus Aci- ments have attracted attention due to the recognition dimicrobium (Clark and Norris, 1996).