DOCSLIB.ORG

Archaea;Crenarchaeota;Marine;Other;Other Archaea;Crenarchaeota;Miscellaneous;Other;Other Archaea;Crenarchaeota;Soil;Other;Other

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Archaea;Crenarchaeota;Marine;Other;Other Archaea;Crenarchaeota;Miscellaneous;Other;Other Archaea;Crenarchaeota;Soil;Other;Other Archaea;Crenarchaeota;Marine;Other;Other Archaea;Crenarchaeota;Miscellaneous;Other;Other Archaea;Crenarchaeota;Soil;Other;Other Archaea;Crenarchaeota;South;Other;Other Archaea;Crenarchaeota;terrestrial;Other;Other Archaea;Euryarchaeota;Halobacteria;Halobacteriales;Miscellaneous Archaea;Euryarchaeota;Methanobacteria;Methanobacteriales;Methanobacteriaceae Archaea;Euryarchaeota;Methanomicrobia;Methanocellales;Methanocellaceae Archaea;Euryarchaeota;Methanomicrobia;Methanosarcinales;Methanosarcinaceae Archaea;Euryarchaeota;Thermoplasmata;Thermoplasmatales;Marine Bacteria;Acidobacteria;Acidobacteria;11-24;uncultured Bacteria;Acidobacteria;Acidobacteria;Acidobacteriales;Acidobacteriaceae Bacteria;Acidobacteria;Acidobacteria;BPC102;uncultured Bacteria;Acidobacteria;Acidobacteria;Bryobacter;uncultured Bacteria;Acidobacteria;Acidobacteria;Candidatus;Other Bacteria;Acidobacteria;Acidobacteria;DA023;uncultured Bacteria;Acidobacteria;Acidobacteria;DA023;unidentified Bacteria;Acidobacteria;Acidobacteria;DS-100;uncultured Bacteria;Acidobacteria;Acidobacteria;PAUC26f;uncultured Bacteria;Acidobacteria;Acidobacteria;RB41;uncultured Bacteria;Acidobacteria;Holophagae;32-20;uncultured Bacteria;Acidobacteria;Holophagae;43F-1404R;uncultured Bacteria;Acidobacteria;Holophagae;Holophagales;Holophagaceae Bacteria;Acidobacteria;Holophagae;NS72;uncultured Bacteria;Acidobacteria;Holophagae;SJA-36;uncultured Bacteria;Acidobacteria;Holophagae;Sva0725;uncultured Bacteria;Acidobacteria;Holophagae;iii1-8;uncultured Bacteria;Acidobacteria;RB25;uncultured;Other Bacteria;Actinobacteria;Actinobacteria;Actinobacteridae;Actinomycetales Bacteria;Actinobacteria;Actinobacteria;MB-A2-108;uncultured Bacteria;Actinobacteria;Actinobacteria;Rubrobacteridae;AKIW543 Bacteria;Actinobacteria;Actinobacteria;Rubrobacteridae;Solirubrobacterales Bacteria;Bacteroidetes;Flavobacteria;Flavobacteriales;Cryomorphaceae Bacteria;Bacteroidetes;Flavobacteria;Flavobacteriales;Flavobacteriaceae Bacteria;Bacteroidetes;Sphingobacteria;Sphingobacteriales;AKYH767 Bacteria;Bacteroidetes;Sphingobacteria;Sphingobacteriales;Chitinophagaceae Bacteria;Bacteroidetes;Sphingobacteria;Sphingobacteriales;Cytophagaceae Bacteria;Bacteroidetes;Sphingobacteria;Sphingobacteriales;NS11-12 Bacteria;Bacteroidetes;Sphingobacteria;Sphingobacteriales;PHOS-HE51 Bacteria;Bacteroidetes;Sphingobacteria;Sphingobacteriales;Saprospiraceae Bacteria;Bacteroidetes;Sphingobacteria;Sphingobacteriales;Sphingobacteriaceae Bacteria;Bacteroidetes;Sphingobacteria;Sphingobacteriales;env.OPS Bacteria;Candidate;Other;Other;Other Bacteria;Chlorobi;Chlorobia;Chlorobiales;OPB56 Bacteria;Chlorobi;Chlorobia;Chlorobiales;SJA-28 Bacteria;Chloroflexi;Anaerolineae;Anaerolineales;Anaerolineaceae Bacteria;Chloroflexi;Chloroflexi;Chloroflexales;Chloroflexaceae Bacteria;Chloroflexi;Thermomicrobia;JG30-KF-CM45;uncultured Bacteria;Cyanobacteria;Chloroplast;Auxenochlorella;Other Bacteria;Cyanobacteria;Chloroplast;Vitis;Other Bacteria;Cyanobacteria;Chloroplast;uncultured;Other Bacteria;Cyanobacteria;MLE1-12;uncultured;Other Bacteria;Elusimicrobia;Elusimicrobia;Lineage;Other Bacteria;Firmicutes;Bacilli;Bacillales;Bacillaceae Bacteria;Firmicutes;Bacilli;Bacillales;Paenibacillaceae Bacteria;Firmicutes;Erysipelotrichi;Erysipelotrichales;Erysipelotrichaceae Bacteria;Gemmatimonadetes;Gemmatimonadetes;AT425-EubC11;Other Bacteria;Gemmatimonadetes;Gemmatimonadetes;BD2-11;Other Bacteria;Gemmatimonadetes;Gemmatimonadetes;Gemmatimonadales;Gemmatimonadaceae Bacteria;JL-ETNP-Z39;uncultured;Other;Other Bacteria;Nitrospirae;Nitrospira;Nitrospirales;0319-6A21 Bacteria;Nitrospirae;Nitrospira;Nitrospirales;4-29 Bacteria;Nitrospirae;Nitrospira;Nitrospirales;Nitrospiraceae Bacteria;Planctomycetes;BD7-11;uncultured;Other Bacteria;Planctomycetes;OM190;uncultured;Other Bacteria;Planctomycetes;Phycisphaerae;WD2101;Other Bacteria;Planctomycetes;Planctomycetacia;Planctomycetales;Planctomycetaceae Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Bradyrhizobiaceae Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;DUNssu371 Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Hyphomicrobiaceae Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Methylocystaceae Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Nordella Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Xanthobacteraceae Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Acetobacteraceae Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;DA111 Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;I-10 Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;MND8 Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;MNH4 Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;wr0007 Bacteria;Proteobacteria;Alphaproteobacteria;Sphingomonadales;Sphingomonadaceae Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Burkholderiaceae Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae Bacteria;Proteobacteria;Betaproteobacteria;SC-I-84;uncultured Bacteria;Proteobacteria;Betaproteobacteria;TRA3-20;uncultured Bacteria;Proteobacteria;Deltaproteobacteria;Desulfobacterales;Nitrospinaceae Bacteria;Proteobacteria;Deltaproteobacteria;GR-WP33-30;uncultured Bacteria;Proteobacteria;Deltaproteobacteria;Myxococcales;Nannocystineae Bacteria;Proteobacteria;Gammaproteobacteria;Chromatiales;Chromatiaceae Bacteria;Proteobacteria;Gammaproteobacteria;JTB148;uncultured Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae Bacteria;Proteobacteria;Gammaproteobacteria;Xanthomonadales;Sinobacteraceae Bacteria;Proteobacteria;Gammaproteobacteria;Xanthomonadales;Xanthomonadaceae Eukaryota;;soil;Other;Other Eukaryota;Alveolata;Apicomplexa;Coccidia;Eucoccidiorida Eukaryota;Alveolata;Apicomplexa;Gregarinia;Eugregarinida Eukaryota;Alveolata;Ciliophora;Intramacronucleata;Colpodea Eukaryota;Alveolata;Ciliophora;Intramacronucleata;Spirotrichea Eukaryota;Alveolata;environmental;Other;Other Eukaryota;Amoebozoa;Flabellinea;Flamella; Eukaryota;Amoebozoa;Mycetozoa;Hyperamoeba; Eukaryota;Amoebozoa;Tubulinea;Euamoebida;Echinamoebidae Eukaryota;Amoebozoa;Tubulinea;Euamoebida;Tubulinida Eukaryota;Amoebozoa;Tubulinea;environmental;Other Eukaryota;Dimorpha;;Dimorpha;Other Eukaryota;Fungi;Blastocladiomycota;Blastocladiomycetes;Blastocladiales Eukaryota;Fungi;Chytridiomycota;Chytridiomycetes;Lobulomycetales Eukaryota;Fungi;Chytridiomycota;Chytridiomycetes;Spizellomycetales Eukaryota;Fungi;Chytridiomycota;environmental;Other Eukaryota;Fungi;Dikarya;Ascomycota; Eukaryota;Fungi;Dikarya;Ascomycota;Ascomycota Eukaryota;Fungi;Dikarya;Ascomycota;Saccharomyceta Eukaryota;Fungi;Dikarya;Ascomycota;mitosporic Eukaryota;Fungi;Dikarya;Basidiomycota; Eukaryota;Fungi;Dikarya;Basidiomycota;Agaricomycotina Eukaryota;Fungi;Dikarya;Basidiomycota;Pucciniomycotina Eukaryota;Fungi;Dikarya;Basidiomycota;environmental Eukaryota;Fungi;Fungi;Other;Other Eukaryota;Fungi;Glomeromycota;Glomeromycetes;Glomerales Eukaryota;Fungi;environmental;Other;Other Eukaryota;Heterolobosea;Schizopyrenida;Vahlkampfiidae;Tetramitus Eukaryota;Ichthyosporea;Ichthyophonida;Anurofeca; Eukaryota;Metazoa;Arthropoda;Chelicerata;Arachnida Eukaryota;Metazoa;Arthropoda;Myriapoda;Chilopoda Eukaryota;Metazoa;Nematoda;Chromadorea;Diplogasterida Eukaryota;Metazoa;Nematoda;Chromadorea;Rhabditida Eukaryota;Metazoa;Nematoda;Chromadorea;Tylenchida Eukaryota;Metazoa;Nematoda;Enoplea;Dorylaimida Eukaryota;Metazoa;Nematoda;Enoplea;Enoplida Eukaryota;Metazoa;Nematoda;environmental;Other Eukaryota;Metazoa;environmental;Other;Other Eukaryota;Proleptomonas;;Proleptomonas;Other Eukaryota;Rhizaria;Cercozoa;;Cercozoa Eukaryota;Rhizaria;Cercozoa;;soil Eukaryota;Rhizaria;Cercozoa;Cercomonadida;Cercomonadidae Eukaryota;Rhizaria;Cercozoa;Cercomonadida;Heteromitidae Eukaryota;Rhizaria;Cercozoa;Cercomonadida;environmental Eukaryota;Rhizaria;Cercozoa;Cercomonadida;unclassified Eukaryota;Rhizaria;Cercozoa;Plasmodiophorida;Plasmodiophoridae Eukaryota;Rhizaria;Cercozoa;Plasmodiophorida;environmental Eukaryota;Rhizaria;Cercozoa;Silicofilosea;Euglyphida Eukaryota;Rhizaria;Cercozoa;Silicofilosea;Thaumatomonadida Eukaryota;Rhizaria;Cercozoa;Vampyrellidae;Arachnula Eukaryota;Rhizaria;Cercozoa;environmental;Other Eukaryota;Rhizaria;environmental;Other;Other Eukaryota;Viridiplantae;Chlorophyta;Chlorophyceae; Eukaryota;Viridiplantae;Chlorophyta;Chlorophyceae;Chlamydomonadales Eukaryota;Viridiplantae;Chlorophyta;Chlorophyceae;Chlorococcales Eukaryota;Viridiplantae;Chlorophyta;Chlorophyceae;Chlorosarcinales Eukaryota;Viridiplantae;Chlorophyta;Chlorophyceae;Pseudomuriella Eukaryota;Viridiplantae;Chlorophyta;Chlorophyceae;Pseudotetracystis Eukaryota;Viridiplantae;Chlorophyta;Chlorophyceae;Sphaeropleales Eukaryota;Viridiplantae;Chlorophyta;Trebouxiophyceae;Chlorellales Eukaryota;Viridiplantae;Chlorophyta;Trebouxiophyceae;Interfilum Eukaryota;Viridiplantae;Chlorophyta;Trebouxiophyceae;unclassified Eukaryota;Viridiplantae;Chlorophyta;Ulvophyceae;Acrosiphoniales Eukaryota;Viridiplantae;Chlorophyta;Ulvophyceae;Ulotrichales Eukaryota;Viridiplantae;Chlorophyta;environmental;Other Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Anthocerotophyta Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Bryophyta Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta Eukaryota;Viridiplantae;Streptophyta;Zygnemophyceae;Zygnematales Eukaryota;environmental;Other;Other;Other Eukaryota;stramenopiles;;Leukarachnion;Other Eukaryota;stramenopiles;Bacillariophyta;Bacillariophyceae;Bacillariophycidae Eukaryota;stramenopiles;Hyphochytriomycetes;Hyphochytriaceae;Hyphochytrium Eukaryota;stramenopiles;Oomycetes;Leptomitales;Apodachlya Eukaryota;stramenopiles;Oomycetes;Peronosporales;Phytophthora Eukaryota;stramenopiles;Oomycetes;Pythiales;Pythiaceae Eukaryota;stramenopiles;Oomycetes;Saprolegniales;Saprolegniaceae Unclassified;Coxiella;Other;Other;Other.
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]
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
    [Show full text]
  • Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life
    Smith ScholarWorks Biological Sciences: Faculty Publications Biological Sciences 10-1-2010 Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life Laura Wegener Parfrey University of Massachusetts Amherst Jessica Grant Smith College Yonas I. Tekle Smith College Erica Lasek-Nesselquist Marine Biological Laboratory Hilary G. Morrison Marine Biological Laboratory See next page for additional authors Follow this and additional works at: https://scholarworks.smith.edu/bio_facpubs Part of the Biology Commons Recommended Citation Parfrey, Laura Wegener; Grant, Jessica; Tekle, Yonas I.; Lasek-Nesselquist, Erica; Morrison, Hilary G.; Sogin, Mitchell L.; Patterson, David J.; and Katz, Laura A., "Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life" (2010). Biological Sciences: Faculty Publications, Smith College, Northampton, MA. https://scholarworks.smith.edu/bio_facpubs/126 This Article has been accepted for inclusion in Biological Sciences: Faculty Publications by an authorized administrator of Smith ScholarWorks. For more information, please contact [email protected] Authors Laura Wegener Parfrey, Jessica Grant, Yonas I. Tekle, Erica Lasek-Nesselquist, Hilary G. Morrison, Mitchell L. Sogin, David J. Patterson, and Laura A. Katz This article is available at Smith ScholarWorks: https://scholarworks.smith.edu/bio_facpubs/126 Syst. Biol. 59(5):518–533, 2010 c The Author(s) 2010. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: [email protected] DOI:10.1093/sysbio/syq037 Advance Access publication on July 23, 2010 Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life LAURA WEGENER PARFREY1,JESSICA GRANT2,YONAS I. TEKLE2,6,ERICA LASEK-NESSELQUIST3,4, 3 3 5 1,2, HILARY G.
    [Show full text]
  • Supplementary Information
    doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION METAGENOMIC AND FUNCTIONAL ANALYSIS OF HINDGUT MICROBIOTA OF A WOOD FEEDING HIGHER TERMITE TABLE OF CONTENTS MATERIALS AND METHODS 2 • Glycoside hydrolase catalytic domains and carbohydrate binding modules used in searches that are not represented by Pfam HMMs 5 SUPPLEMENTARY TABLES • Table S1. Non-parametric diversity estimators 8 • Table S2. Estimates of gross community structure based on sequence composition binning, and conserved single copy gene phylogenies 8 • Table S3. Summary of numbers glycosyl hydrolases (GHs) and carbon-binding modules (CBMs) discovered in the P3 luminal microbiota 9 • Table S4. Summary of glycosyl hydrolases, their binning information, and activity screening results 13 • Table S5. Comparison of abundance of glycosyl hydrolases in different single organism genomes and metagenome datasets 17 • Table S6. Comparison of abundance of glycosyl hydrolases in different single organism genomes (continued) 20 • Table S7. Phylogenetic characterization of the termite gut metagenome sequence dataset, based on compositional phylogenetic analysis 23 • Table S8. Counts of genes classified to COGs corresponding to different hydrogenase families 24 • Table S9. Fe-only hydrogenases (COG4624, large subunit, C-terminal domain) identified in the P3 luminal microbiota. 25 • Table S10. Gene clusters overrepresented in termite P3 luminal microbiota versus soil, ocean and human gut metagenome datasets. 29 • Table S11. Operational taxonomic unit (OTU) representatives of 16S rRNA sequences obtained from the P3 luminal fluid of Nasutitermes spp. 30 SUPPLEMENTARY FIGURES • Fig. S1. Phylogenetic identification of termite host species 38 • Fig. S2. Accumulation curves of 16S rRNA genes obtained from the P3 luminal microbiota 39 • Fig. S3. Phylogenetic diversity of P3 luminal microbiota within the phylum Spirocheates 40 • Fig.
    [Show full text]
  • The Vertical Distribution of Sediment Archaeal Community in the (Black Bloom) Disturbing Zhushan Bay of Lake Taihu
    Hindawi Publishing Corporation Archaea Volume 2016, Article ID 8232135, 8 pages http://dx.doi.org/10.1155/2016/8232135 Research Article The Vertical Distribution of Sediment Archaeal Community in the (Black Bloom) Disturbing Zhushan Bay of Lake Taihu Xianfang Fan1,2 and Peng Xing1 1 State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing 210008, China 2State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China Correspondence should be addressed to Peng Xing; [email protected] Received 20 August 2015; Revised 27 November 2015; Accepted 20 December 2015 Academic Editor: William B. Whitman Copyright © 2016 X. Fan and P. Xing. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Using the Illumina sequencing technology, we investigated the vertical distribution of archaeal community in the sediment of Zhushan Bay of Lake Taihu, where the black bloom frequently occurred in summer. Overall, the Miscellaneous Crenarchaeotal Group (MCG), Deep Sea Hydrothermal Vent Group 6 (DHVEG-6), and Methanobacterium dominated the archaeal community. However, we observed significant difference in composition of archaeal community among different depths of the sediment. DHVEG-6 dominated in the surface layer (0–3 cm) sediment. Methanobacterium was the dominating archaeal taxa in the L2 (3– 6 cm) and L3 (6–10) sediment. MCG was most abundant in the L4 (10–15 cm) and L5 (15–20 cm) sediment. Besides, DHVEG-6 was significantly affected by the concentration of total phosphorus ).(TP And loss on ignition (LOI) was an important environmental factor for Methanobacterium.
    [Show full text]
  • THE MASS of L-PYRROLYSINE in METHYLAMINE METHYLTRANSFERASES and the ROLE of ITS IMINE BOND in CATALYSIS DISSERTATION Presented I
    THE MASS OF L-PYRROLYSINE IN METHYLAMINE METHYLTRANSFERASES AND THE ROLE OF ITS IMINE BOND IN CATALYSIS DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in the Graduate School of The Ohio State University by Jitesh Anthony Aloysius Soares, M.S. The Ohio State University 2008 Dissertation Committee: Dr. Joseph A. Krzycki, Advisor Approved by Dr. Charles J. Daniels Dr. Mark Morrison ______________________ Dr. F. Robert Tabita Advisor Graduate Program in Microbiology ABSTRACT Methanosarcina barkeri is an archaeon capable of producing methane from methylamines. Methylamine methyltransferases initiate methanogenesis from methylamines by transferring methyl groups to a cognate corrinoid protein. Each gene encoding a methylamine methyltransferase has been shown to contain a single in-frame amber codon. Further studies have shown that in the monomethylamine methyltransferase, mtmB , the amber codon encodes a novel amino acid, L-pyrrolysine. X-ray crystal structures of MtmB have shown that the structure of this amino acid is a lysine residue with the epsilon-nitrogen in amide linkage to a (4R, 5R)-4-substituted pyrrolyine-5-carboxylate ring. However, these structures did not allow an assignment of the pyrroline ring C4 substituent as a methyl or amine group. In this thesis (Chapter 2) mass spectrometry of chymotryptic digests of methylamine methyltransferases is employed to show that pyrrolysine in present in all three types of methylamine methyltransferase at the position corresponding to the amber codon in their respective genes. The mass of this amber-encoded residue was observed to coincide with the predicted mass of pyrrolysine with a methyl- group at the C4 position.
    [Show full text]
  • Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria)
    bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 2 Genomic analysis of family UBA6911 (Group 18 3 Acidobacteria) expands the metabolic capacities of the 4 phylum and highlights adaptations to terrestrial habitats. 5 6 Archana Yadav1, Jenna C. Borrelli1, Mostafa S. Elshahed1, and Noha H. Youssef1* 7 8 1Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, 9 OK 10 *Correspondence: Noha H. Youssef: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 11 Abstract 12 Approaches for recovering and analyzing genomes belonging to novel, hitherto unexplored 13 bacterial lineages have provided invaluable insights into the metabolic capabilities and 14 ecological roles of yet-uncultured taxa. The phylum Acidobacteria is one of the most prevalent 15 and ecologically successful lineages on earth yet, currently, multiple lineages within this phylum 16 remain unexplored. Here, we utilize genomes recovered from Zodletone spring, an anaerobic 17 sulfide and sulfur-rich spring in southwestern Oklahoma, as well as from multiple disparate soil 18 and non-soil habitats, to examine the metabolic capabilities and ecological role of members of 19 the family UBA6911 (group18) Acidobacteria.
    [Show full text]
  • A Revised Classification of Naked Lobose Amoebae (Amoebozoa
    Protist, Vol. 162, 545–570, October 2011 http://www.elsevier.de/protis Published online date 28 July 2011 PROTIST NEWS A Revised Classification of Naked Lobose Amoebae (Amoebozoa: Lobosa) Introduction together constitute the amoebozoan subphy- lum Lobosa, which never have cilia or flagella, Molecular evidence and an associated reevaluation whereas Variosea (as here revised) together with of morphology have recently considerably revised Mycetozoa and Archamoebea are now grouped our views on relationships among the higher-level as the subphylum Conosa, whose constituent groups of amoebae. First of all, establishing the lineages either have cilia or flagella or have lost phylum Amoebozoa grouped all lobose amoe- them secondarily (Cavalier-Smith 1998, 2009). boid protists, whether naked or testate, aerobic Figure 1 is a schematic tree showing amoebozoan or anaerobic, with the Mycetozoa and Archamoe- relationships deduced from both morphology and bea (Cavalier-Smith 1998), and separated them DNA sequences. from both the heterolobosean amoebae (Page and The first attempt to construct a congruent molec- Blanton 1985), now belonging in the phylum Per- ular and morphological system of Amoebozoa by colozoa - Cavalier-Smith and Nikolaev (2008), and Cavalier-Smith et al. (2004) was limited by the the filose amoebae that belong in other phyla lack of molecular data for many amoeboid taxa, (notably Cercozoa: Bass et al. 2009a; Howe et al. which were therefore classified solely on morpho- 2011). logical evidence. Smirnov et al. (2005) suggested The phylum Amoebozoa consists of naked and another system for naked lobose amoebae only; testate lobose amoebae (e.g. Amoeba, Vannella, this left taxa with no molecular data incertae sedis, Hartmannella, Acanthamoeba, Arcella, Difflugia), which limited its utility.
    [Show full text]
  • Archaeology of Eukaryotic DNA Replication
    Downloaded from http://cshperspectives.cshlp.org/ on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Archaeology of Eukaryotic DNA Replication Kira S. Makarova and Eugene V. Koonin National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 Correspondence: [email protected] Recent advances in the characterization of the archaeal DNA replication system together with comparative genomic analysis have led to the identification of several previously un- characterized archaeal proteins involved in replication and currently reveal a nearly com- plete correspondence between the components of the archaeal and eukaryotic replication machineries. It can be inferred that the archaeal ancestor of eukaryotes and even the last common ancestor of all extant archaea possessed replication machineries that were compa- rable in complexity to the eukaryotic replication system. The eukaryotic replication system encompasses multiple paralogs of ancestral components such that heteromeric complexes in eukaryotes replace archaeal homomeric complexes, apparently along with subfunctionali- zation of the eukaryotic complex subunits. In the archaea, parallel, lineage-specific dupli- cations of many genes encoding replication machinery components are detectable as well; most of these archaeal paralogs remain to be functionally characterized. The archaeal rep- lication system shows remarkable plasticity whereby even some essential components such as DNA polymerase and single-stranded DNA-binding protein are displaced by unrelated proteins with analogous activities in some lineages. ouble-stranded DNA is the molecule that Okazaki fragments (Kornberg and Baker 2005; Dcarries genetic information in all cellular Barry and Bell 2006; Hamdan and Richardson life-forms; thus, replication of this genetic ma- 2009; Hamdan and van Oijen 2010).
    [Show full text]
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
    [Show full text]
  • Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
    Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae
    [Show full text]
  • Multilevel Social Structure and Diet Shape the Gut Microbiota of the Gelada Monkey, the Only Grazing Primate Pål Trosvik 1*, Eric J
    Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate Pål Trosvik 1*, Eric J. de Muinck 1, Eli K. Rueness 1, Peter J. Fashing 2, Evan C. Beierschmitt 3, Kadie R. Callingham 4, Jacob B. Kraus 5, Thomas H. Trew 6, Amera Moges 7, Addisu Mekonnen 1,8 , Vivek V. Venkataraman 9, Nga Nguyen 2 Supplementary information: Supplementary Figures 1-17, Supplementary Tables 1-10. Figure S1. Relative abundances of the eight most prevalent phyla in the gelada samples. Data are shown for all samples combined, as well as split into samples collected during the dry or wet season. The category “Other” includes OTUs that could not be classified to the phylum level with a probability higher than 0.5. Figure S2. Between-sample weighted (a) and unweighted (b) UniFrac distances in gelada samples collected during the dry (n=142) or the wet (n=174) season. Each box represents the interquartile range, with the horizontal lines representing the medians and the whiskers representing 1.5 times the interquartile range. Points outside the whiskers represent outliers. For both comparisons the difference in mean distance was highly significant (t<<0.001 for both comparisons, unpaired t-tests). Figure S3. Non-metric multidimensional scaling of all primate samples based on weighted (a) and unweighted (b) UniFrac distances. The plot shows the two main dimensions of variation, with plotted characters color coded according to sample type. Clustering according to samples type was highly significant, explaining 46.2% and 63.1% of between-sample variation, respectively (p<<0.001 for both tests, PERMANOVA).
    [Show full text]