DOCSLIB.ORG

Supplementary Figure 1. Chronogram of 308 Archaeal, Bacterial, And

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supplementary Figure 1. Chronogram of 308 Archaeal, Bacterial, And ABCK01000081.1 Lentisphaera araneosa Lentisphaerae−bacterium−GWF2−50−93 CP001998CoraliomargaritaakajimensisDSM45221 CP000975MethylacidiphiluminfernorumV4 Verrucomicrobia−bacterium−GWF2−62−7 Supplementary Figure 1. Chronogram of 308 archaeal, bacterial, and eukaryotic genomes generated using PhyloBayes with a CIR AE001273.1 Chlamydia trachomatis clock model and conservative fossil calibration points. Chronogram was built based on an alignment of concatenated universal, ASLA01000001.1 Omnitrophica bacterium SCGC AAA252−B19 A252B19DRAFT contig 0 0.1 C single-copy genes. Branch lengths indicate time in thousands of years. Error bars represent the 95% confdence intervals for each CP001848.1 Pirellula staleyi DSM 6068 node. TARA−PSW−MAG−00018 AQYQ01000001.1 Hydrogenedentes bacterium Elusimicrobia−bacterium−GWA2−66−18 Elusimicrobia−bacterium−RBG−16−66−12 Elusimicrobia−bacterium−RIFOXYA2−FULL−69−6 Supplementary Figure 1. Chronogram of 308 archaeal, bacterial, and eukaryotic genomes generated using PhyloBayes with a CIR clock model and conservative fossil calibration points. Chronogram was built based on an alignment of concatenated universal, single-copy genes. Branch lengths indicate time in thousands of years. Error bars representElusimicrobia−bacte the 95% confdencerium−GWD2−63−28 intervals for each node. CP001698SpirochaetathermophilaDSM6192 CP001841TreponemaazotonutriciumZAS9 CP001843TreponemaprimitiaZAS2 Treponema−sp−GWA1−62−8 Treponema−sp−RIFOXYC1−FULL−61−9 CP002116SpirochaetasmaragdinaeDSM11293 Spirochaetes−bacterium−GWC2−52−13 Spirochaetes−bacterium−GWB1−36−13 AE006470ChlorobiumtepidumTLS CP001099ChlorobaculumparvumNCIB8327 CP000096ChlorobiumluteolumDSM273 CP000607ChlorobiumphaeovibrioidesDSM265 CP000108ChlorobiumchlorochromatiiCaD3 CP001110PelodictyonphaeoclathratiformeBU1 CP000492ChlorobiumphaeobacteroidesDSM266 CP001097ChlorobiumlimicolaDSM245 CP001108ProsthecochlorisaestuariiDSM271 CP001100ChloroherpetonthalassiumATCC35110 AP006841.1 Bacteroides fragilis AP010656CandidatusAzobacteroidespseudotrichonymphaegenomovarCFP2 CP003418.1 Ignavibacterium album CP003418.1 Ignavibacterium album JCM 16511 ASZK01000001.1 Marinimicrobia bacterium CP018099.1 Caldithrix abyssi LJNC01000001.1 Latescibacteria bacterium candidate−division−Zixibacteria−bacterium−RBG−16−53−22 AQYP01000001.1 Cloacimonetes bacterium JGI 0000039−G13 WWE1 1DRAFT contig 131.132 C CP002158.1 Fibrobacter succinogenes CP007127.1 Gemmatirosa kalamazoonesis strain KBS708 phage−like extrachromosal element AE017180GeobactersulfurreducensPCA CP000698GeobacteruraniireducensRf4 CP001390GeobacterdaltoniiFRC32 CP001124GeobacterbemidjiensisBem CP000482PelobacterpropionicusDSM2379 Geobacteraceae−bacterium−GWC2−48−7 Desulfuromonadales−bacterium−GWD2−54−10 Pelobacteraceae−bacterium−GWB2−53−15 Geobacteraceae−bacterium−GWB2−52−12 Geobacteraceae−bacterium−GWC2−53−11 Geobacteraceae−bacterium−GWC2−55−20 Geobacteraceae−bacterium−GWF2−54−21 CP001089GeobacterlovleyiSZ CP000142PelobactercarbinolicusDSM2380 AP010904DesulfovibriomagneticusRS1 CP001649DesulfovibriosalexigensDSM2638 CP003220DesulfovibriodesulfuricansND132 TARA−PSW−MAG−00013 Desulfovibrionales−bacterium−GWA2−65−9 CP003221DesulfovibrioafricanusstrWalvisBay CP001629DesulfomicrobiumbaculatumDSM4028 CP002683ThermodesulfatatorindicusDSM15286 CP001087DesulfobacteriumautotrophicumHRM2 Desulfobacula−sp−GWF2−41−7 TARA−PSW−MAG−00026 CP001322DesulfatibacillumalkenivoransAK01 CP001940DesulfurivibrioalkaliphilusAHT2 Deltaproteobacteria−bacterium−RIFOXYD12−FULL−53−23 Deltaproteobacteria−bacterium−RIFOXYD12−FULL−55−16 Deltaproteobacteria−bacterium−RIFOXYD12−FULL−56−24 Deltaproteobacteria−bacterium−RIFOXYD12−FULL−50−9 CP002364DesulfobulbuspropionicusDSM2032 CP002085DesulfarculusbaarsiiDSM2075 CP000478SyntrophobacterfumaroxidansMPOB CP002629DesulfobaccaacetoxidansDSM11109 CP000769AnaeromyxobacterspFw1095 HG422173.1 Nitrospina gracilis MGDO01000001.1 Candidatus Tectomicrobia bacterium AM406670AzoarcusspBH72 Rhodocyclales−bacterium−GWA2−65−19 CP000089DechloromonasaromaticaRCB CP001715CandidatusAccumulibacterphosphatiscladeIIAstrUW1 CP003153DechlorosomasuillumPS CP000529PolaromonasnaphthalenivoransCJ2 CP001013LeptothrixcholodniiSP6 CP002039HerbaspirillumseropedicaeSmR1 CP001965SideroxydanslithotrophicusES1 Gallionellales−bacterium−GWA2−59−43 Hydrogenophilales−bacterium−RIFOXYD1−FULL−62−11 BX950851PectobacteriumatrosepticumSCRI1043 CP001654DickeyadadantiiEch703 CP001616TolumonasauensisDSM9187 CP001157AzotobactervinelandiiDJ Pseudomonadales−bacterium−GWC1−66−9 TARA−ION−MAG−00014 TARA−ANW−MAG−00006 TARA−ANW−MAG−00019 CP000544HalorhodospirahalophilaSL1 CP001896AllochromatiumvinosumDSM180 CP002738MethylomonasmethanicaMC09 CP002985AcidithiobacillusferrivoransSS3 AP007255MagnetospirillummagneticumAMB1 CP003046RhodospirillumrubrumF11 AP010946AzospirillumspB510 FQ311868Azospirillumlipoferum4B HE577327AzospirillumbrasilenseSp245 CP000613RhodospirillumcentenumSW CP001189GluconacetobacterdiazotrophicusPA15 AP009384AzorhizobiumcaulinodansORS571 CP000781XanthobacterautotrophicusPy2 CP001016BeijerinckiaindicasubspindicaATCC9039 CP001280MethylocellasilvestrisBL2 CP001349MethylobacteriumnodulansORS2060 AP012206BradyrhizobiumjaponicumUSDA6 CP000494BradyrhizobiumspBTAi1 CU234118BradyrhizobiumspORS278 BA000012MesorhizobiumlotiMAFF303099 CP002279MesorhizobiumopportunistumWSM2075 CP002447MesorhizobiumciceribiovarbiserrulaeWSM1271 CP002292RhodomicrobiumvannieliiATCC17100 CP001312RhodobactercapsulatusSB1003 CP000471MagnetococcusmarinusMC1 DS022297.1 Mariprofundus ferrooxydans AP012048ArcobacterspL CP001999ArcobacternitrofigilisDSM7299 CP002355SulfuricurvumkujienseDSM16994 Sulfuricurvum−sp−GWF2−44−89 Sulfuricurvum−sp−RIFOXYD12−FULL−44−77 Sulfuricurvum−sp−RIFCSPHIGHO2−12−FULL−44−8 Sulfurimonas−sp−GWF2−37−8 Sulfurimonas−sp−RIFOXYD12−FULL−33−39 Candidatus−Lambdaproteobacteria−bacterium−RIFOXYD12−FULL−49−8 Candidatus−Lambdaproteobacteria−bacterium−RIFOXYD2−FULL−50−16 CP001968DenitrovibrioacetiphilusDSM12809 CP002347CalditerrivibrionitroreducensDSM19672 CP002432.1 Desulfurispirillum indicum CP001147ThermodesulfovibrioyellowstoniiDSM11347 LDXN01000001.1 Candidatus Dadabacteria bacterium CP001472.1 Acidobacterium capsulatum LDXP01000001.1 Candidatus Rokubacteria bacterium AE017263.1 Mesoplasma florum L1 complete genome Firmicutes−bacterium−GWE2−51−13 Firmicutes−bacterium−GWF2−51−9 CP003107PaenibacillusterraeHPL003 CP000673ClostridiumkluyveriDSM555 CP001666ClostridiumljungdahliiDSM13528 CP000721ClostridiumbeijerinckiiNCIMB8052 CP002160Clostridiumcellulovorans743B CP002582ClostridiumlentocellumDSM5427 FP929038CoprococcuscatusGD7 CP000724AlkaliphilusmetalliredigensQYMF CP002987AcetobacteriumwoodiiDSM1030 CP000679CaldicellulosiruptorsaccharolyticusDSM8903 CP002219Caldicellulosiruptorhydrothermalis108 CP003001Caldicellulosiruptorlactoaceticus6A CP002171ThermoanaerobacteriumthermosaccharolyticumDSM571 CP000612DesulfotomaculumreducensMI1 CP002780DesulfotomaculumruminisDSM2154 CP002736DesulfotomaculumcarboxydivoransCO1SRB CP002770DesulfotomaculumkuznetsoviiDSM6115 CP000860CandidatusDesulforudisaudaxviatorMP104C CP001720DesulfotomaculumacetoxidansDSM771 CP002028ThermincolapotensJR CP000930HeliobacteriummodesticaldumIce1 CP002547SyntrophobotulusglycolicusDSM8271 CP003108DesulfosporosinusorientisDSM765 CP002048SyntrophothermuslipocalidusDSM12680 Actinobacteria−bacterium−GWC2−53−9 AQYX01000001.1 Atribacteria bacterium Actinobacteria−bacterium−RBG−13−35−12 Candidatus−Margulisbacteria−bacterium−GWD2−39−127 Candidatus−Margulisbacteria−bacterium−GWE2−39−32 BA000019NostocspPCC7120 CP002059Nostocazollae0708 CP001344CyanothecespPCC7425 CP000393TrichodesmiumerythraeumIMS101 CP001291CyanothecespPCC7424 CP002198CyanothecespPCC7822 CP001701CyanothecespPCC8802 CP001842CandidatusAtelocyanobacteriumthalassa TARA−ASW−MAG−00003 CP000239SynechococcusspJA33Ab Candidatus−Melainabacteria−bacterium−GWA2−34−9 CP002801FrankiasymbiontofDatiscaglomerata CP007139.1 Fimbriimonas ginsengisoli CP000804RoseiflexuscastenholziiDSM13941 Chloroflexi−bacterium−RBG−13−52−12 CP011210.1 Microgenomates Beckwithbacteria bacterium GW2011 GWC1 49 16 Candidatus−Gottesmanbacteria−bacterium−RBG−16−52−11 LBRO01000001.1 Candidatus Levybacteria bacterium GW2011 GWB1 36 18 US07 C0001 LBSV01000001.1 Candidatus Roizmanbacteria bacterium GW2011 GWC2 37 13 US40 C0001 LBSJ01000001.1 Candidatus Daviesbacteria bacterium GW2011 GWA1 36 8 US28 C0001 LCAG01000001.1 Candidatus Curtissbacteria bacterium GW2011 GWA1 41 11 UU34 C0001 LBWK01000001.1 Candidate division WS6 bacterium GW2011 GWF2 39 15 UT34 C0001 MEWK01000001.1 Candidate division WWE3 bacterium LBUC01000001.1 Candidatus Falkowbacteria bacterium GW2011 GWF2 38 1205 US73 C0001 LCPI01000001.1 Candidatus Jorgensenbacteria bacterium GW2011 GWA1 48 13 UY26 C0001 LCQM01000001.1 Candidatus Kaiserbacteria bacterium MNZT01000079.1 Candidatus Wirthbacteria bacterium AE000513.1 Deinococcus radiodurans AE009951.2 Fusobacterium nucleatum CP001818.1 Thermanaerovibrio acidaminovorans CP001251.1 Dictyoglomus turgidum MNXV01000056.1 Caldisericum sp. CG2 30 36 11 cg2 3.0 scaffold 1022 c AE000512.1 Thermotoga maritima AP011112HydrogenobacterthermophilusTK6 CP001931ThermocrinisalbusDSM14484 AquifexaeolicusVF5 AQTE01000001.1 Calescamantes bacterium AE000666MethanothermobacterthermautotrophicusstrDeltaH CP001710MethanothermobactermarburgensisstrMarburg CP000742MethanococcusvannieliiSB CP000743MethanococcusaeolicusNankai3 CP002792MethanothermococcusokinawensisIH1 CP002737MethanotorrisigneusKol5 CP001787MethanocaldococcusvulcaniusM7 CP001901MethanocaldococcusspFS40622 L77117MethanocaldococcusjannaschiiDSM2661
Load more

Recommended publications
  • Download This Publication (PDF File)
    PUBLIC LIBRARY of SCIENCE | plosgenetics.org | ISSN 1553-7390 | Volume 2 | Issue 12 | DECEMBER 2006 GENETICS PUBLIC LIBRARY of SCIENCE www.plosgenetics.org Volume 2 | Issue 12 | DECEMBER 2006 Interview Review Knight in Common Armor: 1949 Unraveling the Genetics 1956 An Interview with Sir John Sulston e225 of Human Obesity e188 Jane Gitschier David M. Mutch, Karine Clément Research Articles Natural Variants of AtHKT1 1964 The Complete Genome 2039 Enhance Na+ Accumulation e210 Sequence and Comparative e206 in Two Wild Populations of Genome Analysis of the High Arabidopsis Pathogenicity Yersinia Ana Rus, Ivan Baxter, enterocolitica Strain 8081 Balasubramaniam Muthukumar, Nicholas R. Thomson, Sarah Jeff Gustin, Brett Lahner, Elena Howard, Brendan W. Wren, Yakubova, David E. Salt Matthew T. G. Holden, Lisa Crossman, Gregory L. Challis, About the Cover Drosophila SPF45: A Bifunctional 1974 Carol Churcher, Karen The jigsaw image of representatives Protein with Roles in Both e178 Mungall, Karen Brooks, Tracey of various lines of eukaryote evolution Splicing and DNA Repair Chillingworth, Theresa Feltwell, refl ects the current lack of consensus as Ahmad Sami Chaouki, Helen K. Zahra Abdellah, Heidi Hauser, to how the major branches of eukaryotes Salz Kay Jagels, Mark Maddison, fi t together. The illustrations from upper Sharon Moule, Mandy Sanders, left to bottom right are as follows: a single Mammalian Small Nucleolar 1984 Sally Whitehead, Michael A. scale from the surface of Umbellosphaera; RNAs Are Mobile Genetic e205 Quail, Gordon Dougan, Julian Amoeba, the large amoeboid organism Elements Parkhill, Michael B. Prentice used as an introduction to protists for Michel J. Weber many school children; Euglena, the iconic Low Levels of Genetic 2052 fl agellate that is often used to challenge Soft Sweeps III: The Signature 1998 Divergence across e215 ideas of plants (Euglena has chloroplasts) of Positive Selection from e186 Geographically and and animals (Euglena moves); Stentor, Recurrent Mutation Linguistically Diverse one of the larger ciliates; Cacatua, the Pleuni S.
    [Show full text]
  • Culturing and Targeted Pacbio RS Amplicon Sequencing Reveals a Higher Order Taxonomic Diversity and Global Distribution
    bioRxiv preprint doi: https://doi.org/10.1101/199125; this version posted October 8, 2017. 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. Enigmatic Diphyllatea eukaryotes: Culturing and targeted PacBio RS amplicon sequencing reveals a higher order taxonomic diversity and global distribution Orr Russell J.S.1,2*, Zhao Sen3,4, Klaveness Dag5, Yabuki Akinori6, Ikeda Keiji7, Makoto M. Watanabe7, Shalchian-Tabrizi Kamran1,2* 1 Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway 2 Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway 3 Department of Molecular Oncology, Institute of Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway 4 Medical Faculty, Center for Cancer Biomedicine, University of Oslo University Hospital, Oslo, Norway 5 Section for Aquatic Biology and Toxicology (AQUA), Department of Biosciences, University of Oslo, Oslo, Norway 6 Japan Agency for Marine-Earth Sciences and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan 7 Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan * Corresponding authors: Russell J. S. Orr & Kamran Shalchian-Tabrizi Email: [email protected] Mobile: +4748187013 Email: [email protected] Mobile: +4741045328 Address: Kristine Bonnevies hus, Blindernveien 31, 0371 Oslo, Norway Keywords: Diphyllatea, PacBio, rRNA, phylogeny, diversity, Collodictyon, amplicon, Sulcozoa 1 bioRxiv preprint doi: https://doi.org/10.1101/199125; this version posted October 8, 2017.
    [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]
  • Leishmania\) Martiniquensis N. Sp. \(Kinetoplastida: Trypanosomatidae\
    Parasite 2014, 21, 12 Ó N. Desbois et al., published by EDP Sciences, 2014 DOI: 10.1051/parasite/2014011 urn:lsid:zoobank.org:pub:31F25656-8804-4944-A568-6DB4F52D2217 Available online at: www.parasite-journal.org SHORT NOTE OPEN ACCESS Leishmania (Leishmania) martiniquensis n. sp. (Kinetoplastida: Trypanosomatidae), description of the parasite responsible for cutaneous leishmaniasis in Martinique Island (French West Indies) Nicole Desbois1, Francine Pratlong2, Danie`le Quist3, and Jean-Pierre Dedet2,* 1 CHU de la Martinique, Hoˆpital Pierre-Zobda-Quitman, Poˆle de Biologie de territoire-Pathologie, Unite´de Parasitologie-Mycologie, BP 632, 97261 Fort-de-France Cedex, Martinique, France 2 Universite´Montpellier 1 et CHRU de Montpellier, Centre National de re´fe´rence des leishmanioses, UMR « MIVEGEC » (CNRS 5290, IRD 224, UM1, UM2), De´partement de Parasitologie-Mycologie (Professeur Patrick Bastien), 39 avenue Charles Flahault, 34295 Montpellier Cedex 5, France 3 CHU de la Martinique, Hoˆpital Pierre-Zobda-Quitman, Service de dermatologie, Poˆle de Me´decine-Spe´cialite´s me´dicales, BP 632, 97261 Fort-de-France Cedex, Martinique, France Received 21 November 2013, Accepted 19 February 2014, Published online 14 March 2014 Abstract – The parasite responsible for autochthonous cutaneous leishmaniasis in Martinique island (French West Indies) was first isolated in 1995; its taxonomical position was established only in 2002, but it remained unnamed. In the present paper, the authors name this parasite Leishmania (Leishmania) martiniquensis Desbois, Pratlong & Dedet n. sp. and describe the type strain of this taxon, including its biological characteristics, biochemical and molecular identification, and pathogenicity. This parasite, clearly distinct from all other Euleishmania, and placed at the base of the Leishmania phylogenetic tree, is included in the subgenus Leishmania.
    [Show full text]
  • Sex Is a Ubiquitous, Ancient, and Inherent Attribute of Eukaryotic Life
    PAPER Sex is a ubiquitous, ancient, and inherent attribute of COLLOQUIUM eukaryotic life Dave Speijera,1, Julius Lukešb,c, and Marek Eliášd,1 aDepartment of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands; bInstitute of Parasitology, Biology Centre, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, 370 05 Ceské Budejovice, Czech Republic; cCanadian Institute for Advanced Research, Toronto, ON, Canada M5G 1Z8; and dDepartment of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic Edited by John C. Avise, University of California, Irvine, CA, and approved April 8, 2015 (received for review February 14, 2015) Sexual reproduction and clonality in eukaryotes are mostly Sex in Eukaryotic Microorganisms: More Voyeurs Needed seen as exclusive, the latter being rather exceptional. This view Whereas absence of sex is considered as something scandalous for might be biased by focusing almost exclusively on metazoans. a zoologist, scientists studying protists, which represent the ma- We analyze and discuss reproduction in the context of extant jority of extant eukaryotic diversity (2), are much more ready to eukaryotic diversity, paying special attention to protists. We accept that a particular eukaryotic group has not shown any evi- present results of phylogenetically extended searches for ho- dence of sexual processes. Although sex is very well documented mologs of two proteins functioning in cell and nuclear fusion, in many protist groups, and members of some taxa, such as ciliates respectively (HAP2 and GEX1), providing indirect evidence for (Alveolata), diatoms (Stramenopiles), or green algae (Chlor- these processes in several eukaryotic lineages where sex has oplastida), even serve as models to study various aspects of sex- – not been observed yet.
    [Show full text]
  • University of Oklahoma
    UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By JOSHUA THOMAS COOPER Norman, Oklahoma 2017 MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Boris Wawrik, Chair ______________________________ Dr. J. Phil Gibson ______________________________ Dr. Anne K. Dunn ______________________________ Dr. John Paul Masly ______________________________ Dr. K. David Hambright ii © Copyright by JOSHUA THOMAS COOPER 2017 All Rights Reserved. iii Acknowledgments I would like to thank my two advisors Dr. Boris Wawrik and Dr. J. Phil Gibson for helping me become a better scientist and better educator. I would also like to thank my committee members Dr. Anne K. Dunn, Dr. K. David Hambright, and Dr. J.P. Masly for providing valuable inputs that lead me to carefully consider my research questions. I would also like to thank Dr. J.P. Masly for the opportunity to coauthor a book chapter on the speciation of diatoms. It is still such a privilege that you believed in me and my crazy diatom ideas to form a concise chapter in addition to learn your style of writing has been a benefit to my professional development. I’m also thankful for my first undergraduate research mentor, Dr. Miriam Steinitz-Kannan, now retired from Northern Kentucky University, who was the first to show the amazing wonders of pond scum. Who knew that studying diatoms and algae as an undergraduate would lead me all the way to a Ph.D.
    [Show full text]
  • Phylogenetic Relationships of Rhizoctonia Fungi Within the Cantharellales
    fungal biology 120 (2016) 603e619 journal homepage: www.elsevier.com/locate/funbio Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales Dolores GONZALEZa,*, Marianela RODRIGUEZ-CARRESb, Teun BOEKHOUTc, Joost STALPERSc, Eiko E. KURAMAEd, Andreia K. NAKATANIe, Rytas VILGALYSf, Marc A. CUBETAb aInstituto de Ecologıa, A.C., Red de Biodiversidad y Sistematica, Carretera Antigua a Coatepec No. 351, El Haya, 91070 Xalapa, Veracruz, Mexico bDepartment of Plant Pathology, North Carolina State University, Center for Integrated Fungal Research, Campus Box 7251, Raleigh, NC 27695, USA cCBS Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands dDepartment of Microbial Ecology, Netherlands Institute of Ecology (NIOO/KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands eUNESP, Faculdade de Ci^encias Agronomicas,^ CP 237, 18603-970 Botucatu, SP, Brazil fDepartment of Biology, Duke University, Durham, NC 27708, USA article info abstract Article history: Phylogenetic relationships of Rhizoctonia fungi within the order Cantharellales were studied Received 2 January 2015 using sequence data from portions of the ribosomal DNA cluster regions ITS-LSU, rpb2, tef1, Received in revised form and atp6 for 50 taxa, and public sequence data from the rpb2 locus for 165 taxa. Data sets 1 January 2016 were analysed individually and combined using Maximum Parsimony, Maximum Likeli- Accepted 19 January 2016 hood, and Bayesian Phylogenetic Inference methods. All analyses supported the mono- Available online 29 January 2016 phyly of the family Ceratobasidiaceae, which comprises the genera Ceratobasidium and Corresponding Editor: Thanatephorus. Multi-locus analysis revealed 10 well-supported monophyletic groups that Joseph W. Spatafora were consistent with previous separation into anastomosis groups based on hyphal fusion criteria.
    [Show full text]
  • Multigene Eukaryote Phylogeny Reveals the Likely Protozoan Ancestors of Opis- Thokonts (Animals, Fungi, Choanozoans) and Amoebozoa
    Accepted Manuscript Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opis- thokonts (animals, fungi, choanozoans) and Amoebozoa Thomas Cavalier-Smith, Ema E. Chao, Elizabeth A. Snell, Cédric Berney, Anna Maria Fiore-Donno, Rhodri Lewis PII: S1055-7903(14)00279-6 DOI: http://dx.doi.org/10.1016/j.ympev.2014.08.012 Reference: YMPEV 4996 To appear in: Molecular Phylogenetics and Evolution Received Date: 24 January 2014 Revised Date: 2 August 2014 Accepted Date: 11 August 2014 Please cite this article as: Cavalier-Smith, T., Chao, E.E., Snell, E.A., Berney, C., Fiore-Donno, A.M., Lewis, R., Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa, Molecular Phylogenetics and Evolution (2014), doi: http://dx.doi.org/10.1016/ j.ympev.2014.08.012 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. 1 1 Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts 2 (animals, fungi, choanozoans) and Amoebozoa 3 4 Thomas Cavalier-Smith1, Ema E. Chao1, Elizabeth A. Snell1, Cédric Berney1,2, Anna Maria 5 Fiore-Donno1,3, and Rhodri Lewis1 6 7 1Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
    [Show full text]
  • Metagenomic Characterization of Unicellular Eukaryotes in the Urban Thessaloniki Bay
    Metagenomic characterization of unicellular eukaryotes in the urban Thessaloniki Bay George Tsipas SCHOOL OF ECONOMICS, BUSINESS ADMINISTRATION & LEGAL STUDIES A thesis submitted for the degree of Master of Science (MSc) in Bioeconomy Law, Regulation and Management May, 2019 Thessaloniki – Greece George Tsipas ’’Metagenomic characterization of unicellular eukaryotes in the urban Thessaloniki Bay’’ Student Name: George Tsipas SID: 268186037282 Supervisor: Prof. Dr. Savvas Genitsaris I hereby declare that the work submitted is mine and that where I have made use of another’s work, I have attributed the source(s) according to the Regulations set in the Student’s Handbook. May, 2019 Thessaloniki - Greece Page 2 of 63 George Tsipas ’’Metagenomic characterization of unicellular eukaryotes in the urban Thessaloniki Bay’’ 1. Abstract The present research investigates through metagenomics sequencing the unicellular protistan communities in Thermaikos Gulf. This research analyzes the diversity, composition and abundance in this marine environment. Water samples were collected monthly from April 2017 to February 2018 in the port of Thessaloniki (Harbor site, 40o 37’ 55 N, 22o 56’ 09 E). The extraction of DNA was completed as well as the sequencing was performed, before the downstream read processing and the taxonomic classification that was assigned using PR2 database. A total of 1248 Operational Taxonomic Units (OTUs) were detected but only 700 unicellular eukaryotes were analyzed, excluding unclassified OTUs, Metazoa and Streptophyta. In this research-based study the most abundant and diverse taxonomic groups were Dinoflagellata and Protalveolata. Specifically, the most abundant groups of all samples are Dinoflagellata with 190 OTUs (27.70%), Protalveolata with 139 OTUs (20.26%) Ochrophyta with 73 OTUs (10.64%), Cercozoa with 67 OTUs (9.77%) and Ciliophora with 64 OTUs (9.33%).
    [Show full text]
  • Resource Partitioning Between Phytoplankton and Bacteria in the Coastal Baltic Sea Frontiers in Marine Science, 7: 1-19
    http://www.diva-portal.org This is the published version of a paper published in Frontiers in Marine Science. Citation for the original published paper (version of record): Sörenson, E., Lindehoff, E., Farnelid, H., Legrand, C. (2020) Resource Partitioning Between Phytoplankton and Bacteria in the Coastal Baltic Sea Frontiers in Marine Science, 7: 1-19 https://doi.org/10.3389/fmars.2020.608244 Access to the published version may require subscription. N.B. When citing this work, cite the original published paper. Permanent link to this version: http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-99520 ORIGINAL RESEARCH published: 25 November 2020 doi: 10.3389/fmars.2020.608244 Resource Partitioning Between Phytoplankton and Bacteria in the Coastal Baltic Sea Eva Sörenson, Hanna Farnelid, Elin Lindehoff and Catherine Legrand* Department of Biology and Environmental Science, Linnaeus University Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden Eutrophication coupled to climate change disturbs the balance between competition and coexistence in microbial communities including the partitioning of organic and inorganic nutrients between phytoplankton and bacteria. Competition for inorganic nutrients has been regarded as one of the drivers affecting the productivity of the eutrophied coastal Baltic Sea. Yet, it is unknown at the molecular expression level how resources are competed for, by phytoplankton and bacteria, and what impact this competition has on the community composition. Here we use metatranscriptomics and amplicon sequencing and compare known metabolic pathways of both phytoplankton and bacteria co-occurring during a summer bloom in the archipelago of Åland in the Baltic Sea to examine phytoplankton bacteria resource partitioning.
    [Show full text]
  • Biodiversity of Wood-Decay Fungi in Italy
    AperTO - Archivio Istituzionale Open Access dell'Università di Torino Biodiversity of wood-decay fungi in Italy This is the author's manuscript Original Citation: Availability: This version is available http://hdl.handle.net/2318/88396 since 2016-10-06T16:54:39Z Published version: DOI:10.1080/11263504.2011.633114 Terms of use: Open Access Anyone can freely access the full text of works made available as "Open Access". Works made available under a Creative Commons license can be used according to the terms and conditions of said license. Use of all other works requires consent of the right holder (author or publisher) if not exempted from copyright protection by the applicable law. (Article begins on next page) 28 September 2021 This is the author's final version of the contribution published as: A. Saitta; A. Bernicchia; S.P. Gorjón; E. Altobelli; V.M. Granito; C. Losi; D. Lunghini; O. Maggi; G. Medardi; F. Padovan; L. Pecoraro; A. Vizzini; A.M. Persiani. Biodiversity of wood-decay fungi in Italy. PLANT BIOSYSTEMS. 145(4) pp: 958-968. DOI: 10.1080/11263504.2011.633114 The publisher's version is available at: http://www.tandfonline.com/doi/abs/10.1080/11263504.2011.633114 When citing, please refer to the published version. Link to this full text: http://hdl.handle.net/2318/88396 This full text was downloaded from iris - AperTO: https://iris.unito.it/ iris - AperTO University of Turin’s Institutional Research Information System and Open Access Institutional Repository Biodiversity of wood-decay fungi in Italy A. Saitta , A. Bernicchia , S. P. Gorjón , E.
    [Show full text]
  • Superorganisms of the Protist Kingdom: a New Level of Biological Organization
    Foundations of Science https://doi.org/10.1007/s10699-020-09688-8 Superorganisms of the Protist Kingdom: A New Level of Biological Organization Łukasz Lamża1 © The Author(s) 2020 Abstract The concept of superorganism has a mixed reputation in biology—for some it is a conveni- ent way of discussing supra-organismal levels of organization, and for others, little more than a poetic metaphor. Here, I show that a considerable step forward in the understand- ing of superorganisms results from a thorough review of the supra-organismal levels of organization now known to exist among the “unicellular” protists. Limiting the discussion to protists has enormous advantages: their bodies are very well studied and relatively sim- ple (as compared to humans or termites, two standard examples in most discussions about superorganisms), and they exhibit an enormous diversity of anatomies and lifestyles. This allows for unprecedented resolution in describing forms of supra-organismal organiza- tion. Here, four criteria are used to diferentiate loose, incidental associations of hosts with their microbiota from “actual” superorganisms: (1) obligatory character, (2) specifc spatial localization of microbiota, (3) presence of attachment structures and (4) signs of co-evolu- tion in phylogenetic analyses. Three groups—that have never before been described in the philosophical literature—merit special attention: Symbiontida (also called Postgaardea), Oxymonadida and Parabasalia. Specifcally, it is argued that in certain cases—for Bihos- pites bacati and Calkinsia aureus (symbiontids), Streblomastix strix (an oxymonad), Joe- nia annectens and Mixotricha paradoxa (parabasalids) and Kentrophoros (a ciliate)—it is fully appropriate to describe the whole protist-microbiota assocation as a single organism (“superorganism”) and its elements as “tissues” or, arguably, even “organs”.
    [Show full text]