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BiS2C: Lecture 9: Microbial Diversity

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Slides for BIS2C at UC Davis Spring 2016.
Lecture by Jonathan Eisen.
Topic: Microbial Diversity.

Published in: Science
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BiS2C: Lecture 9: Microbial Diversity

  1. 1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Lecture 9: Microbial Diversity BIS 002C Biodiversity & the Tree of Life Spring 2016 Prof. Jonathan Eisen 1
  2. 2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Where we are going and where we have been • Previous Lecture: !8: The Tree of Life II • Current Lecture: !9: Microbial Diversity • Next Lecture: !10: The Not Quite a Tree Tree of Life 2
  3. 3. Lectures 9-13 Microbial Diversity • The Tree of Life is mostly microbial • Diverse methods are available for studying microbial diversity • Most of the diversity of microbial life is poorly characterized • The Tree of Life is not actually a tree • The biological diversity (form, function, etc) seen in microbes is immense • Microbes run (kind of) the planet • Microbial interactions (with each other and non- microbes) also help run the planet 3
  4. 4. Lectures 9 • The Tree of Life is mostly microbial • Diverse methods are available for studying microbial diversity • Most of the diversity of microbial life is poorly characterized • The Tree of Life is not actually a tree • The biological diversity (form, function, etc) seen in microbes is immense • Microbes run (kind of) the planet • Microbial interactions (with each other and non- microbes) also help run the planet 4
  5. 5. Lectures 10 • The Tree of Life is mostly microbial • Diverse methods are available for studying microbial diversity • Most of the diversity of microbial life is poorly characterized • The Tree of Life is not actually a tree • The biological diversity (form, function, etc) seen in microbes is immense • Microbes run (kind of) the planet • Microbial interactions (with each other and non- microbes) also help run the planet 5
  6. 6. Lecture 11 • The Tree of Life is mostly microbial • Diverse methods are available for studying microbial diversity • Most of the diversity of microbial life is poorly characterized • The Tree of Life is not actually a tree • The biological diversity (form, function, etc) seen in microbes is immense • Microbes run (kind of) the planet • Microbial interactions (with each other and non- microbes) also help run the planet 6
  7. 7. Lectures 12-13 • The Tree of Life is mostly microbial • Diverse methods are available for studying microbial diversity • Most of the diversity of microbial life is poorly characterized • The Tree of Life is not actually a tree • The biological diversity (form, function, etc) seen in microbes is immense • Microbes run (kind of) the planet • Microbial interactions (with each other and non- microbes) also help run the planet 7
  8. 8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Lecture 9: Microbial Diversity • The Tree of Life is mostly microbial • Diverse methods are available for studying microbial diversity • Most of the diversity of microbial life is poorly characterized 8
  9. 9. Unrooted Tree of Life (from ~ 2004) 9 adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
  10. 10. 10adapted from Baldauf, et al., in Assembling the Tree of Life, 2004 P Plants
 Two Weeks Unrooted Tree of Life (from ~ 2004)
  11. 11. 11adapted from Baldauf, et al., in Assembling the Tree of Life, 2004 F Fungi One Week P Unrooted Tree of Life (from ~ 2004)
  12. 12. 12adapted from Baldauf, et al., in Assembling the Tree of Life, 2004 A Animals Two Weeks P Unrooted Tree of Life (from ~ 2004)
  13. 13. 13adapted from Baldauf, et al., in Assembling the Tree of Life, 2004 1.5 Weeks Unrooted Tree of Life (from ~ 2004)
  14. 14. Unrooted Tree of Life 14adapted from Baldauf, et al., in Assembling the Tree of Life, 2004 1.5 Weeks Mostly Microbes
  15. 15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 The Bacteria and Archaea via Textbook v.10 15
  16. 16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Eukaryotic Groups via Textbook v.10 16
  17. 17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Eukaryote Groups - More Detail 1717
  18. 18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Microbial Diversity • The Tree of Life is mostly microbial • Diverse methods are available for studying microbial diversity • Most of the diversity of microbial life is poorly characterized 18
  19. 19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 20 Field Observations Are Important Tools
  20. 20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 • Field studies of multicellular organisms are of course common • Show binoculars, butterfly nets, etc • Field studies of microbes are also possible but a bit more challenging 21 Field Observations Important in Microbial Studies
  21. 21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 • More detail on some of these in Labs 2 and 3 22
  22. 22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 !23 Culturing Microbes
  23. 23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Culturing • More On This in Lectures 11-12 • Some in Labs 2-3 24
  24. 24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 DNA Sequencing • All cellular organisms have genomes made up of DNA • All cellular organisms transcribe DNA into RNA and then translate RNA into protein • Sequencing involves reading the string of letters in DNA, RNA or protein • Sequencing is usually done on DNA • Sequencing gets cheaper and faster VERY fast • Sequencing is very useful is studying microbial diversity 25
  25. 25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 26 Sequencing Has Gone Crazy
  26. 26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 rRNA Sequencing for Phylogenetic Analysis 27 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG EukaryotesBacteria ?????Archaea
  27. 27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Clicker 28
  28. 28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Which of the following is NOT a reason that analysis of rRNA is useful for inferring a Tree of Life A: rRNAs are universal homologies B: rRNAs can be sequenced C: rRNAs are transcribed from DNA D: rRNAs have functional roles in ribosomes E: rRNAs don't vary between species 29
  29. 29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Which of the following is NOT a reason that analysis of rRNA is useful for inferring a Tree of Life A: rRNAs are universal homologies B: rRNAs can be sequenced C: rRNAs are transcribed from DNA D: rRNAs have functional roles in ribosomes E: rRNAs don't vary between species 30
  30. 30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Genome Sequencing Improves Phylogenetic Analysis 31 ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG EukaryotesBacteria ?????Archaea DNA DNADNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG
  31. 31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Genome Sequencing Has Many Other Uses 32 ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG DNA DNADNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG
  32. 32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Genome Sequencing Has Many Other Uses 33 ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG DNA DNADNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Some Discussion of this in Lecture 10
  33. 33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 2002 Most Genomes from a Few Groups 34 Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  34. 34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 2002-2007: TIGR Tree of Life Project 35 Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Naomi Ward Karen Nelson
  35. 35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 2007-2014: Genomic Encyclopedia 36 Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  36. 36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 2007-2014: Genomic Encyclopedia 37 Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree BUT …
  37. 37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Microbial Diversity • The Tree of Life is mostly microbial • Diverse methods are available for studying microbial diversity • Most of the diversity of microbial life is poorly characterized 38
  38. 38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Great Plate Count Anomaly 39 <<<< Culturing Observation CountCount
  39. 39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Great Plate Count Anomaly 39 <<<< Culturing Observation CountCount http://www.google.com/url? sa=i&rct=j&q=&esrc=s&source=images&c d=&docid=rLu5sL207WlE1M&tbnid=CRLQ YP7d9d_TcM:&ved=0CAUQjRw&url=http %3A%2F%2Fwww.biol.unt.edu %2F~jajohnson %2FDNA_sequencing_process&ei=hFu7U_ TyCtOqsQSu9YGwBg&psig=AFQjCNG-8EB dEljE7- yHFG2KPuBZt8kIPw&ust=14048739512114 24 DNA
  40. 40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 rRNA Sequencing from Environmental Samples 40 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG EukaryotesBacteria ?????Archaea
  41. 41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Metagenomics Improves Phylogenetic Resolution 41 metagenomics ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG EukaryotesBacteria Archaea Jo Handelsman
  42. 42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Metagenomics Has Many Other Purposes 42 metagenomics ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG inputs of fixed carbon or nitrogen from external sources. As with Leptospirillum group I, both Leptospirillum group II and III have the genes needed to fix carbon by means of the Calvin–Benson– Bassham cycle (using type II ribulose 1,5-bisphosphate carboxy- lase–oxygenase). All genomes recovered from the AMD system contain formate hydrogenlyase complexes. These, in combination with carbon monoxide dehydrogenase, may be used for carbon fixation via the reductive acetyl coenzyme A (acetyl-CoA) pathway by some, or all, organisms. Given the large number of ABC-type sugar and amino acid transporters encoded in the Ferroplasma type Figure 4 Cell metabolic cartoons constructed from the annotation of 2,180 ORFs identified in the Leptospirillum group II genome (63% with putative assigned function) and 1,931 ORFs in the Ferroplasma type II genome (58% with assigned function). The cell cartoons are shown within a biofilm that is attached to the surface of an acid mine drainage stream (viewed in cross-section). Tight coupling between ferrous iron oxidation, pyrite dissolution and acid generation is indicated. Rubisco, ribulose 1,5-bisphosphate carboxylase–oxygenase. THF, tetrahydrofolate. articles NATURE | doi:10.1038/nature02340 | www.nature.com/nature 5©2004 NaturePublishing Group Some Discussion of this in Lecture 13
  43. 43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 43 Sequencing Has Gone Crazy
  44. 44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Hug et al. 2016 • Dowloaded 10,000+ genomes from various databases (including many I generated) • 1000+ new genomes • Searched these genomes for a set universal homologous genes (ribosomal proteins) (based on AMPHORA) • Aligned the sequences of these genes between species • Maximum likelihood tree 44 Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48 Laura Hug U. Waterloo Jill Banfield UC Berkeley
  45. 45. Hug et al 2016 !45 Hug et al. 2016 Tree of Life 92 Bacterial Phyla 25 Archaeal Phyla 5 Eukaryotic Supergroups Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48 Laura Hug U. Waterloo Jill Banfield UC Berkeley
  46. 46. !46 Hug et al 2016Hug et al. 2016 Bacteria Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48
  47. 47. Taxa Covered in Textbook !47 Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48
  48. 48. !48 Hug et al 2016Phyla Never Grown in the Lab Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48
  49. 49. Hug et al 2016 !49 Hug et al. 2016 Archaea and Eukaryotes Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48
  50. 50. Hug et al 2016 !50 Hug et al. 2016 Archaea Phyla Never Grown in the Lab Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48
  51. 51. Major Groups by Evolutionary Distance !51
  52. 52. The Dark Matter of Biology !52 0.2 Korarchaeota Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci Archaeoglobi, Methanomicrobia, Halobacteria Aciduliprofundum, Thermoplasmata Uncultured Thermoplasmata Thermoplasmata Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota Cyanobacteria, Melainabacteria Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria Microgenomates Daviesbacteria Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Microgenomates Shapirobacteria Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Microgenomates Gottesmanbacteria KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi Thermotogae Omnitrophica Omnitrophica Spirochaetes Spirochaetes Hydrogenedentes NKB19 Deltaproteobacteria Epsilonproteobacteria TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria Planctomycetes Chlamydiae Lentisphaerae Verrucomicrobia Verrucomicrobia RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) Aigarchaeota, Cand. Caldiarchaeum subterraneum Unclassified archaea Parcubacteria Candidate Phyla Radiation Cyanobacteria, Melainabacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi q ,q , Thermotogae A ifi C Omnitrophica Omnitrophica pp Spirochaetes Spirochaetes S i h t Hydrogenedentes NKB19 Deltaproteobacteria H d d t N Epsilonproteobacteria b TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria D f bD f b , , p ,, , p , Planctomycetes pp Chlamydiae y Lentisphaerae C a ydCh Verrucomicrobia Verrucomicrobia pp RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) , y g, y g Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria ( ) Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 b M Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) O h Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria gg Microgenomates Daviesbacteria gg Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Mi t L b t i Microgenomates Shapirobacteria Mi t W bMi t Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Mi Sh i b i Microgenomates Gottesmanbacteria t R i b t i g yg y KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria te a Parcubacteria Parcubacteria Parcubacteria Parcubacteria AbscAbs Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria gg Parcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria P b i Candidate Phyla Radiation Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci E43 Archaeoglobi, Methanomicrobia, Halobacteria , , ,, , , Aciduliprofundum, Thermoplasmata gg Uncultured Thermoplasmata p ,p , Thermoplasmata p Unclassified archaea Korarchaeota , Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota b l b Aigarchaeota, FFA Cand. Caldiarchaeum subterraneum C b t i M l i b t i Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Th h , Th h t Eukaryotes Bacteria Archaea Katanobacteria WWE3 Bootstrap ≥ 85% 85% > Bootstrap ≥ 50% Woesearchaeota, Nanoarchaeota gure 2 | A reformatted view of the tree in Fig. 1 in which each major lineage represents the same amount of evolutionary distance. The threshold for oups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups and hers are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resulting oups to have special taxonomic status. The massive scale of diversity in the CPR and the large fraction of major lineages that lack isolated representatives ed dots) are apparent from this analysis. Bootstrap support values are indicated by circles on nodes—black for support of 85% and above, grey for support om 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newick rmat in Supplementary Dataset 2. NATURE MICROBIOLOGY DOI: 10.1038/NMICROBIOL.2016.48 LETTERS ATURE MICROBIOLOGY | www.nature.com/naturemicrobiology 3 © 2016 Macmillan Publishers Limited. All rights reserved 2 Korarchaeota Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci Archaeoglobi, Methanomicrobia, Halobacteria Aciduliprofundum, Thermoplasmata Uncultured Thermoplasmata Thermoplasmata Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota Cyanobacteria, Melainabacteria Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria Microgenomates Daviesbacteria Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Microgenomates Shapirobacteria Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Microgenomates Gottesmanbacteria KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi Thermotogae Omnitrophica Omnitrophica Spirochaetes Spirochaetes Hydrogenedentes NKB19 Deltaproteobacteria Epsilonproteobacteria TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria Planctomycetes Chlamydiae Lentisphaerae Verrucomicrobia Verrucomicrobia RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) Aigarchaeota, Cand. Caldiarchaeum subterraneum Unclassified archaea Parcubacteria Candidate Phyla Radiation Cyanobacteria, Melainabacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi q ,q , Thermotogae A ifi C Omnitrophica Omnitrophica pp Spirochaetes Spirochaetes S i h t Hydrogenedentes NKB19 Deltaproteobacteria H d d t N Epsilonproteobacteria b TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria D f bD f b , , p ,, , p , Planctomycetes pp Chlamydiae y Lentisphaerae C a ydCh Verrucomicrobia Verrucomicrobia pp RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) , y g, y g Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria ( ) Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 b M Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) O h Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria gg Microgenomates Daviesbacteria gg Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Mi t L b t i Microgenomates Shapirobacteria Mi t W bMi t Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Mi Sh i b i Microgenomates Gottesmanbacteria t R i b t i g yg y KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria te a Parcubacteria Parcubacteria Parcubacteria Parcubacteria AbscAbs Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria gg Parcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria P b i Candidate Phyla Radiation Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci E43 Archaeoglobi, Methanomicrobia, Halobacteria , , ,, , , Aciduliprofundum, Thermoplasmata gg Uncultured Thermoplasmata p ,p , Thermoplasmata p Unclassified archaea Korarchaeota , Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota b l b Aigarchaeota, FFA Cand. Caldiarchaeum subterraneum C b t i M l i b t i Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Th h , Th h t Eukaryotes Bacteria Archaea Katanobacteria WWE3 Bootstrap ≥ 85% 85% > Bootstrap ≥ 50% Woesearchaeota, Nanoarchaeota reformatted view of the tree in Fig. 1 in which each major lineage represents the same amount of evolutionary distance. The threshold for ured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups and plit into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resulting ve special taxonomic status. The massive scale of diversity in the CPR and the large fraction of major lineages that lack isolated representatives re apparent from this analysis. Bootstrap support values are indicated by circles on nodes—black for support of 85% and above, grey for support 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newick pplementary Dataset 2. E MICROBIOLOGY DOI: 10.1038/NMICROBIOL.2016.48 LETTERS ROBIOLOGY | www.nature.com/naturemicrobiology 3 © 2016 Macmillan Publishers Limited. All rights reserved 0.2 Korarchaeota Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci Archaeoglobi, Methanomicrobia, Halobacteria Aciduliprofundum, Thermoplasmata Uncultured Thermoplasmata Thermoplasmata Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota Cyanobacteria, Melainabacteria Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria Microgenomates Daviesbacteria Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Microgenomates Shapirobacteria Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Microgenomates Gottesmanbacteria KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi Thermotogae Omnitrophica Omnitrophica Spirochaetes Spirochaetes Hydrogenedentes NKB19 Deltaproteobacteria Epsilonproteobacteria TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria Planctomycetes Chlamydiae Lentisphaerae Verrucomicrobia Verrucomicrobia RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) Aigarchaeota, Cand. Caldiarchaeum subterraneum Unclassified archaea Parcubacteria Candidate Phyla Radiation Cyanobacteria, Melainabacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi q ,q , Thermotogae A ifi C Omnitrophica Omnitrophica pp Spirochaetes Spirochaetes S i h t Hydrogenedentes NKB19 Deltaproteobacteria H d d t N Epsilonproteobacteria b TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria D f bD f b , , p ,, , p , Planctomycetes pp Chlamydiae y Lentisphaerae C a ydCh Verrucomicrobia Verrucomicrobia pp RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) , y g, y g Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria ( ) Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 b M Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) O h Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria gg Microgenomates Daviesbacteria gg Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Mi t L b t i Microgenomates Shapirobacteria Mi t W bMi t Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Mi Sh i b i Microgenomates Gottesmanbacteria t R i b t i g yg y KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria te a Parcubacteria Parcubacteria Parcubacteria Parcubacteria AbscAbs Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria gg Parcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria P b i Candidate Phyla Radiation Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci E43 Archaeoglobi, Methanomicrobia, Halobacteria , , ,, , , Aciduliprofundum, Thermoplasmata gg Uncultured Thermoplasmata p ,p , Thermoplasmata p Unclassified archaea Korarchaeota , Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota b l b Aigarchaeota, FFA Cand. Caldiarchaeum subterraneum C b t i M l i b t i Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Th h , Th h t Eukaryotes Bacteria Archaea Katanobacteria WWE3 Bootstrap ≥ 85% 85% > Bootstrap ≥ 50% Woesearchaeota, Nanoarchaeota Figure 2 | A reformatted view of the tree in Fig. 1 in which each major lineage represents the same amount of evolutionary distance. The threshold for groups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups and others are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resulting groups to have special taxonomic status. The massive scale of diversity in the CPR and the large fraction of major lineages that lack isolated representatives (red dots) are apparent from this analysis. Bootstrap support values are indicated by circles on nodes—black for support of 85% and above, grey for support from 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newick format in Supplementary Dataset 2. NATURE MICROBIOLOGY DOI: 10.1038/NMICROBIOL.2016.48 LETTERS NATURE MICROBIOLOGY | www.nature.com/naturemicrobiology 3 © 2016 Macmillan Publishers Limited. All rights reserved 0.2 Korarchaeota Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci Archaeoglobi, Methanomicrobia, Halobacteria Aciduliprofundum, Thermoplasmata Uncultured Thermoplasmata Thermoplasmata Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota Cyanobacteria, Melainabacteria Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria Microgenomates Daviesbacteria Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Microgenomates Shapirobacteria Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Microgenomates Gottesmanbacteria KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi Thermotogae Omnitrophica Omnitrophica Spirochaetes Spirochaetes Hydrogenedentes NKB19 Deltaproteobacteria Epsilonproteobacteria TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria Planctomycetes Chlamydiae Lentisphaerae Verrucomicrobia Verrucomicrobia RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) Aigarchaeota, Cand. Caldiarchaeum subterraneum Unclassified archaea Parcubacteria Candidate Phyla Radiation Cyanobacteria, Melainabacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi q ,q , Thermotogae A ifi C Omnitrophica Omnitrophica pp Spirochaetes Spirochaetes S i h t Hydrogenedentes NKB19 Deltaproteobacteria H d d t N Epsilonproteobacteria b TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria D f bD f b , , p ,, , p , Planctomycetes pp Chlamydiae y Lentisphaerae C a ydCh Verrucomicrobia Verrucomicrobia pp RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) , y g, y g Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria ( ) Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 b M Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) O h Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria gg Microgenomates Daviesbacteria gg Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Mi t L b t i Microgenomates Shapirobacteria Mi t W bMi t Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Mi Sh i b i Microgenomates Gottesmanbacteria t R i b t i g yg y KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria te a Parcubacteria Parcubacteria Parcubacteria Parcubacteria AbscAbs Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria gg Parcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria P b i Candidate Phyla Radiation Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci E43 Archaeoglobi, Methanomicrobia, Halobacteria , , ,, , , Aciduliprofundum, Thermoplasmata gg Uncultured Thermoplasmata p ,p , Thermoplasmata p Unclassified archaea Korarchaeota , Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota b l b Aigarchaeota, FFA Cand. Caldiarchaeum subterraneum C b t i M l i b t i Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Th h , Th h t Eukaryotes Bacteria Archaea Katanobacteria WWE3 Bootstrap ≥ 85% 85% > Bootstrap ≥ 50% Woesearchaeota, Nanoarchaeota Figure 2 | A reformatted view of the tree in Fig. 1 in which each major lineage represents the same amount of evolutionary distance. The threshold for groups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups and others are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resulting groups to have special taxonomic status. The massive scale of diversity in the CPR and the large fraction of major lineages that lack isolated representatives (red dots) are apparent from this analysis. Bootstrap support values are indicated by circles on nodes—black for support of 85% and above, grey for support from 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newick format in Supplementary Dataset 2. NATURE MICROBIOLOGY DOI: 10.1038/NMICROBIOL.2016.48 LETTERS NATURE MICROBIOLOGY | www.nature.com/naturemicrobiology 3 © 2016 Macmillan Publishers Limited. All rights reserved Korarchaeota Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci Archaeoglobi, Methanomicrobia, Halobacteria Aciduliprofundum, Thermoplasmata Uncultured Thermoplasmata Thermoplasmata Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota Cyanobacteria, Melainabacteria Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria Microgenomates Daviesbacteria Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Microgenomates Shapirobacteria Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Microgenomates Gottesmanbacteria KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi Thermotogae Omnitrophica Omnitrophica Spirochaetes Spirochaetes Hydrogenedentes NKB19 Deltaproteobacteria Epsilonproteobacteria TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria Planctomycetes Chlamydiae Lentisphaerae Verrucomicrobia Verrucomicrobia RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) Aigarchaeota, Cand. Caldiarchaeum subterraneum Unclassified archaea Parcubacteria Candidate Phyla Radiation Cyanobacteria, Melainabacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi q ,q , Thermotogae A ifi C Omnitrophica Omnitrophica pp Spirochaetes Spirochaetes S i h t Hydrogenedentes NKB19 Deltaproteobacteria H d d t N Epsilonproteobacteria b TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria D f bD f b , , p ,, , p , Planctomycetes pp Chlamydiae y Lentisphaerae C a ydCh Verrucomicrobia Verrucomicrobia pp RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) , y g, y g Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria ( ) Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 b M Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) O h Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria gg Microgenomates Daviesbacteria gg Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Mi t L b t i Microgenomates Shapirobacteria Mi t W bMi t Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Mi Sh i b i Microgenomates Gottesmanbacteria t R i b t i g yg y KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria te a Parcubacteria Parcubacteria Parcubacteria Parcubacteria AbscAbs Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria gg Parcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria P b i Candidate Phyla Radiation Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci E43 Archaeoglobi, Methanomicrobia, Halobacteria , , ,, , , Aciduliprofundum, Thermoplasmata gg Uncultured Thermoplasmata p ,p , Thermoplasmata p Unclassified archaea Korarchaeota , Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota b l b Aigarchaeota, FFA Cand. Caldiarchaeum subterraneum C b t i M l i b t i Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Th h , Th h t Eukaryotes Bacteria Archaea Katanobacteria WWE3 Bootstrap ≥ 85% 85% > Bootstrap ≥ 50% Woesearchaeota, Nanoarchaeota matted view of the tree in Fig. 1 in which each major lineage represents the same amount of evolutionary distance. The threshold for edges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups and multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resulting cial taxonomic status. The massive scale of diversity in the CPR and the large fraction of major lineages that lack isolated representatives rent from this analysis. Bootstrap support values are indicated by circles on nodes—black for support of 85% and above, grey for support he complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newick ntary Dataset 2. CROBIOLOGY DOI: 10.1038/NMICROBIOL.2016.48 LETTERS 0.2 Korarchaeota Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci Archaeoglobi, Methanomicrobia, Halobacteria Aciduliprofundum, Thermoplasmata Uncultured Thermoplasmata Thermoplasmata Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota Cyanobacteria, Melainabacteria Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria Microgenomates Daviesbacteria Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Microgenomates Shapirobacteria Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Microgenomates Gottesmanbacteria KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi Thermotogae Omnitrophica Omnitrophica Spirochaetes Spirochaetes Hydrogenedentes NKB19 Deltaproteobacteria Epsilonproteobacteria TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria Planctomycetes Chlamydiae Lentisphaerae Verrucomicrobia Verrucomicrobia RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) Aigarchaeota, Cand. Caldiarchaeum subterraneum Unclassified archaea Parcubacteria Candidate Phyla Radiation Cyanobacteria, Melainabacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi q ,q , Thermotogae A ifi C Omnitrophica Omnitrophica pp Spirochaetes Spirochaetes S i h t Hydrogenedentes NKB19 Deltaproteobacteria H d d t N Epsilonproteobacteria b TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria D f bD f b , , p ,, , p , Planctomycetes pp Chlamydiae y Lentisphaerae C a ydCh Verrucomicrobia Verrucomicrobia pp RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) , y g, y g Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria ( ) Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 b M Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) O h Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria gg Microgenomates Daviesbacteria gg Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Mi t L b t i Microgenomates Shapirobacteria Mi t W bMi t Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Mi Sh i b i Microgenomates Gottesmanbacteria t R i b t i g yg y KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria te a Parcubacteria Parcubacteria Parcubacteria Parcubacteria AbscAbs Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria gg Parcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria P b i Candidate Phyla Radiation Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci E43 Archaeoglobi, Methanomicrobia, Halobacteria , , ,, , , Aciduliprofundum, Thermoplasmata gg Uncultured Thermoplasmata p ,p , Thermoplasmata p Unclassified archaea Korarchaeota , Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota b l b Aigarchaeota, FFA Cand. Caldiarchaeum subterraneum C b t i M l i b t i Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Th h , Th h t Eukaryotes Bacteria Archaea Katanobacteria WWE3 Bootstrap ≥ 85% 85% > Bootstrap ≥ 50% Woesearchaeota, Nanoarchaeota Figure 2 | A reformatted view of the tree in Fig. 1 in which each major lineage represents the same amount of evolutionary distance. The threshold for groups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups and others are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resulting groups to have special taxonomic status. The massive scale of diversity in the CPR and the large fraction of major lineages that lack isolated representatives (red dots) are apparent from this analysis. Bootstrap support values are indicated by circles on nodes—black for support of 85% and above, grey for support from 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newick format in Supplementary Dataset 2. NATURE MICROBIOLOGY DOI: 10.1038/NMICROBIOL.2016.48 LETTERS NATURE MICROBIOLOGY | www.nature.com/naturemicrobiology 3 © 2016 Macmillan Publishers Limited. All rights reserved 0.2 Korarchaeota Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci Archaeoglobi, Methanomicrobia, Halobacteria Aciduliprofundum, Thermoplasmata Uncultured Thermoplasmata Thermoplasmata Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota Cyanobacteria, Melainabacteria Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria Microgenomates Daviesbacteria Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Microgenomates Shapirobacteria Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Microgenomates Gottesmanbacteria KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi Thermotogae Omnitrophica Omnitrophica Spirochaetes Spirochaetes Hydrogenedentes NKB19 Deltaproteobacteria Epsilonproteobacteria TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria Planctomycetes Chlamydiae Lentisphaerae Verrucomicrobia Verrucomicrobia RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) Aigarchaeota, Cand. Caldiarchaeum subterraneum Unclassified archaea Parcubacteria Candidate Phyla Radiation Cyanobacteria, Melainabacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi q ,q , Thermotogae A ifi C Omnitrophica Omnitrophica pp Spirochaetes Spirochaetes S i h t Hydrogenedentes NKB19 Deltaproteobacteria H d d t N Epsilonproteobacteria b TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria D f bD f b , , p ,, , p , Planctomycetes pp Chlamydiae y Lentisphaerae C a ydCh Verrucomicrobia Verrucomicrobia pp RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) , y g, y g Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria ( ) Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 b M Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) O h Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria gg Microgenomates Daviesbacteria gg Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Mi t L b t i Microgenomates Shapirobacteria Mi t W bMi t Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Mi Sh i b i Microgenomates Gottesmanbacteria t R i b t i g yg y KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria te a Parcubacteria Parcubacteria Parcubacteria Parcubacteria AbscAbs Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria gg Parcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria P b i Candidate Phyla Radiation Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci E43 Archaeoglobi, Methanomicrobia, Halobacteria , , ,, , , Aciduliprofundum, Thermoplasmata gg Uncultured Thermoplasmata p ,p , Thermoplasmata p Unclassified archaea Korarchaeota , Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota b l b Aigarchaeota, FFA Cand. Caldiarchaeum subterraneum C b t i M l i b t i Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Th h , Th h t Eukaryotes Bacteria Archaea Katanobacteria WWE3 Bootstrap ≥ 85% 85% > Bootstrap ≥ 50% Woesearchaeota, Nanoarchaeota Figure 2 | A reformatted view of the tree in Fig. 1 in which each major lineage represents the same amount of evolutionary distance. The threshold for groups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups and others are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resulting groups to have special taxonomic status. The massive scale of diversity in the CPR and the large fraction of major lineages that lack isolated representatives (red dots) are apparent from this analysis. Bootstrap support values are indicated by circles on nodes—black for support of 85% and above, grey for support from 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newick format in Supplementary Dataset 2. NATURE MICROBIOLOGY DOI: 10.1038/NMICROBIOL.2016.48 LETTERS NATURE MICROBIOLOGY | www.nature.com/naturemicrobiology 3 © 2016 Macmillan Publishers Limited. All rights reserved cteria esebacteria cteria bacteria,Pacebacteria,Collierbacteria eria CandidatePhylaRadiation cteria esebacteria cteria b bacteria,Pacebacteria,Collierbacteria i eria CandidatePhylaRadiation cteria esebacteria cteria bacteria,Pacebacteria,Collierbacteria eria CandidatePhylaRadiation cteria esebacteria cteria b bacteria,Pacebacteria,Collierbacteria i eria CandidatePhylaRadiation Korarchaeota Woesearchaeota,Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri,Methanococci,Methanobacteria,Hadesarchaea,Thermococci Archaeoglobi,Methanomicrobia,Halobacteria Aciduliprofundum,Thermoplasmata UnculturedThermoplasmata Thermoplasmata Opisthokonta,Excavata,Archaeplastida Chromalveolata,Amoebozoa Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota Cyanobacteria,Melainabacteria Deinococcus-Thermus Aquificae,CalescamantesEM19 Caldiserica,Dictyoglomi Thermotogae RBX-1 WOR-1 Firmicutes,Tenericutes,Armatimonadetes,Chloroflexi,Actinobacteria Fusobacteria,Synergistetes Unculturedbacteria(CPRIF32) bacteria(OP9) BRC1,Poribacteria Aigarchaeota,Cand.Caldiarchaeumsubterraneum Cyanobacteria,Melainabacteria Deinococcus-Thermus Aquificae,CalescamantesEM19 Caldiserica,Dictyoglomi q ,q , Thermotogae A ifi C RBX-1 WOR-1 Firmicutes,Tenericutes,Armatimonadetes,Chloroflexi,Actinobacteria Fusobacteria,Synergistetes Unculturedbacteria(CPRIF32) , y g, y g bacteria(OP9) BRC1,Poribacteria ( ) Woesearchaeota,Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri,Methanococci,Methanobacteria,Hadesarchaea,Thermococci E43 Archaeoglobi,Methanomicrobia,Halobacteria , , ,, , , Aciduliprofundum,Thermoplasmata gg UnculturedThermoplasmata p ,p , Thermoplasmata p Korarchaeota , Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota b l b Aigarchaeota, FFA Cand.Caldiarchaeumsubterraneum C b t i M l i b t i Opisthokonta,Excavata,Archaeplastida Chromalveolata,Amoebozoa Th h , Th h t Eukaryotes Bacteria ArchaeaWoesearchaeota,Nanoarchaeota Korarchaeota Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci Archaeoglobi, Methanomicrobia, Halobacteria Aciduliprofundum, Thermoplasmata Uncultured Thermoplasmata Thermoplasmata Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota Cyanobacteria, Melainabacteria Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria Microgenomates Daviesbacteria Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Microgenomates Shapirobacteria Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Microgenomates Gottesmanbacteria KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi Thermotogae Omnitrophica Omnitrophica Spirochaetes Spirochaetes Hydrogenedentes NKB19 Deltaproteobacteria Epsilonproteobacteria TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria Planctomycetes Chlamydiae Lentisphaerae Verrucomicrobia Verrucomicrobia RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) Aigarchaeota, Cand. Caldiarchaeum subterraneum Unclassified archaea Parcubacteria Candidate Phyla Radiation Cyanobacteria, Melainabacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi q ,q , Thermotogae A ifi C Omnitrophica Omnitrophica pp Spirochaetes Spirochaetes S i h t Hydrogenedentes NKB19 Deltaproteobacteria H d d t N Epsilonproteobacteria b TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria D f bD f b , , p ,, , p , Planctomycetes pp Chlamydiae y Lentisphaerae C a ydCh Verrucomicrobia Verrucomicrobia pp RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) , y g, y g Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria ( ) Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 b M Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) O h Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria gg Microgenomates Daviesbacteria gg Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Mi t L b t i Microgenomates Shapirobacteria Mi t W bMi t Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Mi Sh i b i Microgenomates Gottesmanbacteria t R i b t i g yg y KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria te a Parcubacteria Parcubacteria Parcubacteria Parcubacteria AbscAbs Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria gg Parcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria P b i Candidate Phyla Radiation Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci E43 Archaeoglobi, Methanomicrobia, Halobacteria , , ,, , , Aciduliprofundum, Thermoplasmata gg Uncultured Thermoplasmata p ,p , Thermoplasmata p Unclassified archaea Korarchaeota , Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota b l b Aigarchaeota, FFA Cand. Caldiarchaeum subterraneum C b t i M l i b t i Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Th h , Th h t Eukaryotes Bacteria Archaea Katanobacteria WWE3 Bootstrap ≥ 85% 85% > Bootstrap ≥ 50% Woesearchaeota, Nanoarchaeota of the tree in Fig. 1 in which each major lineage represents the same amount of evolutionary distance. The threshold for an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups and tinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resulting ic status. The massive scale of diversity in the CPR and the large fraction of major lineages that lack isolated representatives s analysis. Bootstrap support values are indicated by circles on nodes—black for support of 85% and above, grey for support ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newick et 2. OLOGY DOI: 10.1038/NMICROBIOL.2016.48 LETTERS ature.com/naturemicrobiology 3 © 2016 Macmillan Publishers Limited. All rights reserved Korarchaeota Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci Archaeoglobi, Methanomicrobia, Halobacteria Aciduliprofundum, Thermoplasmata Uncultured Thermoplasmata Thermoplasmata Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota Cyanobacteria, Melainabacteria Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria Microgenomates Daviesbacteria Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Microgenomates Shapirobacteria Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Microgenomates Gottesmanbacteria KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi Thermotogae Omnitrophica Omnitrophica Spirochaetes Spirochaetes Hydrogenedentes NKB19 Deltaproteobacteria Epsilonproteobacteria TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria Planctomycetes Chlamydiae Lentisphaerae Verrucomicrobia Verrucomicrobia RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) Aigarchaeota, Cand. Caldiarchaeum subterraneum Unclassified archaea Parcubacteria Candidate Phyla Radiation Cyanobacteria, Melainabacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi q ,q , Thermotogae A ifi C Omnitrophica Omnitrophica pp Spirochaetes Spirochaetes S i h t Hydrogenedentes NKB19 Deltaproteobacteria H d d t N Epsilonproteobacteria b TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria D f bD f b , , p ,, , p , Planctomycetes pp Chlamydiae y Lentisphaerae C a ydCh Verrucomicrobia Verrucomicrobia pp RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) , y g, y g Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria ( ) Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 b M Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) O h Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria gg Microgenomates Daviesbacteria gg Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Mi t L b t i Microgenomates Shapirobacteria Mi t W bMi t Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Mi Sh i b i Microgenomates Gottesmanbacteria t R i b t i g yg y KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria te a Parcubacteria Parcubacteria Parcubacteria Parcubacteria AbscAbs Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria gg Parcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria P b i Candidate Phyla Radiation Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci E43 Archaeoglobi, Methanomicrobia, Halobacteria , , ,, , , Aciduliprofundum, Thermoplasmata gg Uncultured Thermoplasmata p ,p , Thermoplasmata p Unclassified archaea Korarchaeota , Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota b l b Aigarchaeota, FFA Cand. Caldiarchaeum subterraneum C b t i M l i b t i Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Th h , Th h t Eukaryotes Bacteria Archaea Katanobacteria WWE3 Bootstrap ≥ 85% 85% > Bootstrap ≥ 50% Woesearchaeota, Nanoarchaeota view of the tree in Fig. 1 in which each major lineage represents the same amount of evolutionary distance. The threshold for ) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups and ple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resulting xonomic status. The massive scale of diversity in the CPR and the large fraction of major lineages that lack isolated representatives om this analysis. Bootstrap support values are indicated by circles on nodes—black for support of 85% and above, grey for support mplete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newick Dataset 2. OBIOLOGY DOI: 10.1038/NMICROBIOL.2016.48 LETTERS www.nature.com/naturemicrobiology 3 © 2016 Macmillan Publishers Limited. All rights reserved Korarchaeota Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci Archaeoglobi, Methanomicrobia, Halobacteria Aciduliprofundum, Thermoplasmata Uncultured Thermoplasmata Thermoplasmata Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota Cyanobacteria, Melainabacteria Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria Microgenomates Daviesbacteria Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Microgenomates Shapirobacteria Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Microgenomates Gottesmanbacteria KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi Thermotogae Omnitrophica Omnitrophica Spirochaetes Spirochaetes Hydrogenedentes NKB19 Deltaproteobacteria Epsilonproteobacteria TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria Planctomycetes Chlamydiae Lentisphaerae Verrucomicrobia Verrucomicrobia RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) Aigarchaeota, Cand. Caldiarchaeum subterraneum Unclassified archaea Parcubacteria Candidate Phyla Radiation Cyanobacteria, Melainabacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi q ,q , Thermotogae A ifi C Omnitrophica Omnitrophica pp Spirochaetes Spirochaetes S i h t Hydrogenedentes NKB19 Deltaproteobacteria H d d t N Epsilonproteobacteria b TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria D f bD f b , , p ,, , p , Planctomycetes pp Chlamydiae y Lentisphaerae C a ydCh Verrucomicrobia Verrucomicrobia pp RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) , y g, y g Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria ( ) Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 b M Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) O h Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria gg Microgenomates Daviesbacteria gg Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Mi t L b t i Microgenomates Shapirobacteria Mi t W bMi t Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Mi Sh i b i Microgenomates Gottesmanbacteria t R i b t i g yg y KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria te a Parcubacteria Parcubacteria Parcubacteria Parcubacteria AbscAbs Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria gg Parcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria P b i Candidate Phyla Radiation Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci E43 Archaeoglobi, Methanomicrobia, Halobacteria , , ,, , , Aciduliprofundum, Thermoplasmata gg Uncultured Thermoplasmata p ,p , Thermoplasmata p Unclassified archaea Korarchaeota , Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota b l b Aigarchaeota, FFA Cand. Caldiarchaeum subterraneum C b t i M l i b t i Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Th h , Th h t Eukaryotes Bacteria Archaea Katanobacteria WWE3 Bootstrap ≥ 85% 85% > Bootstrap ≥ 50% Woesearchaeota, Nanoarchaeota e tree in Fig. 1 in which each major lineage represents the same amount of evolutionary distance. The threshold for erage branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups and groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resulting tus. The massive scale of diversity in the CPR and the large fraction of major lineages that lack isolated representatives alysis. Bootstrap support values are indicated by circles on nodes—black for support of 85% and above, grey for support omal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newick OGY DOI: 10.1038/NMICROBIOL.2016.48 LETTERS om/naturemicrobiology 3 © 2016 Macmillan Publishers Limited. All rights reserved Korarchaeota Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci Archaeoglobi, Methanomicrobia, Halobacteria Aciduliprofundum, Thermoplasmata Uncultured Thermoplasmata Thermoplasmata Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota Cyanobacteria, Melainabacteria Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria Microgenomates Daviesbacteria Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Microgenomates Shapirobacteria Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Microgenomates Gottesmanbacteria KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi Thermotogae Omnitrophica Omnitrophica Spirochaetes Spirochaetes Hydrogenedentes NKB19 Deltaproteobacteria Epsilonproteobacteria TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria Planctomycetes Chlamydiae Lentisphaerae Verrucomicrobia Verrucomicrobia RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) Aigarchaeota, Cand. Caldiarchaeum subterraneum Unclassified archaea Parcubacteria Candidate Phyla Radiation Cyanobacteria, Melainabacteria Deinococcus-Thermus Aquificae, Calescamantes EM19 Caldiserica, Dictyoglomi q ,q , Thermotogae A ifi C Omnitrophica Omnitrophica pp Spirochaetes Spirochaetes S i h t Hydrogenedentes NKB19 Deltaproteobacteria H d d t N Epsilonproteobacteria b TM6 Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, GammaproteobacteriaChrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria D f bD f b , , p ,, , p , Planctomycetes pp Chlamydiae y Lentisphaerae C a ydCh Verrucomicrobia Verrucomicrobia pp RBX-1 WOR-1 Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes Uncultured bacteria (CP RIF32) , y g, y g Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres Cloacamonetes Atribacteria (OP9) BRC1, Poribacteria ( ) Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06 b M Elusimicrobia Uncultured bacteria Uncultured bacteria (CP RIF1) O h Dojkabacteria WS6 CPR3 Katanobacteria WWE3 Katanobacteria WWE3 Microgenomates Roizmanbacteria Microgenomates Roizmanbacteria Microgenomates Microgenomates Curtissbacteria gg Microgenomates Daviesbacteria gg Microgenomates Levybacteria Microgenomates Woesebacteria Microgenomates Amesbacteria Mi t L b t i Microgenomates Shapirobacteria Mi t W bMi t Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria Mi Sh i b i Microgenomates Gottesmanbacteria t R i b t i g yg y KAZAN CPR2, Saccharibacteria TM7 Berkelbacteria Berkelbacteria Berkelbacteria Berkelbacteria CPR Uncultured unclassified bacteria Peregrinibacteria Peregrinibacteria Absconditabacteria SR1 Gracilibacteria BD1-5 / GNO2 SM2F11 Parcubacteria Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteria te a Parcubacteria Parcubacteria Parcubacteria Parcubacteria AbscAbs Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria gg Parcubacteria Parcubacteria Moranbacteria Parcubacteria Parcubacteria Yanofskybacteria P b i Candidate Phyla Radiation Diapherotrites Nanohaloarchaeota Unclassified archaea Pacearchaeota Woesearchaeota, Nanoarchaeota Woesearchaeota Altiarchaeales Z7ME43 Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, Thermococci E43 Archaeoglobi, Methanomicrobia, Halobacteria , , ,, , , Aciduliprofundum, Thermoplasmata gg Uncultured Thermoplasmata p ,p , Thermoplasmata p Unclassified archaea Korarchaeota , Crenarchaeota Crenarchaeota Thorarchaeota Lokiarchaeota YNPFFA Thaumarchaeota Thaumarchaeota b l b Aigarchaeota, FFA Cand. Caldiarchaeum subterraneum C b t i M l i b t i Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa Th h , Th h t Eukaryotes Bacteria Archaea Katanobacteria WWE3 Bootstrap ≥ 85% 85% > Bootstrap ≥ 50% Woesearchaeota, Nanoarchaeota view of the tree in Fig. 1 in which each major lineage represents the same amount of evolutionary distance. The threshold for ) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups and ple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resulting xonomic status. The massive scale of diversity in the CPR and the large fraction of major lineages that lack isolated representatives om this analysis. Bootstrap support values are indicated by circles on nodes—black for support of 85% and above, grey for support mplete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newick Dataset 2. OBIOLOGY DOI: 10.1038/NMICROBIOL.2016.48 LETTERS www.nature.com/naturemicrobiology 3 © 2016 Macmillan Publishers Limited. All rights reserved
  53. 53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Also many uncultured eukaryotic groups 5353
  54. 54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Details • Dowloaded 10,000+ genomes from various databases (including many I generated) • 1000+ new genomes • Searched these genomes for a set universal homologous genes (ribosomal proteins) (based on AMPHORA) • Aligned the sequences of these genes between species • Maximum likelihood tree 54
  55. 55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Details • If you want to do things like this • Learn biology but also • Bioinformatics • Programming • Data science • Quantitative biology • Statistics 55
  56. 56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Reminder These trees are based on analysis of ribosomal proteins. They represent only a small subset of all the genes in a genome. 56
  57. 57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Microbial Diversity • We do not have time to cover all of these groups of microbes in lecture • These groups barely scratch the surface of the true diversity • Examples of Biological Diversity of Microbes • Focus on the Big Picture Patterns of This Diversity 57
  58. 58. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Clicker 58
  59. 59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Clicker Which of the following is an example of universal homology A: Ether-linked lipids B: Peptidoglycan C: Ester-linked lipids D: Transcription of DNA into RNA E: Translation of RNA in the nucleus 59
  60. 60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Clicker Which of the following is an example of universal homology A: Ether-linked lipids B: Peptidoglycan C: Ester-linked lipids D: Transcription of DNA into RNA E: Translation of RNA in the nucleus 60
  61. 61. Bacterial Diversity: Gram Positive vs. Negative 61 Outside of cell Outside of cell Inside of cell Inside of cell Cell envelope Cell wall (peptidoglycan) Plasma membrane Outer membrane of cell envelope Periplasmic space Peptidoglycan layer Periplasmic space Plasma membrane 5 µm 5 µm Gram Positive Gram Negative
  62. 62. Bacterial and Archaeal Shapes Archaea cell membranes have lipids with fatty acids linked to glycerol by ether linkages (a synapomorphy of archaea): 62
  63. 63. Ester Linkages Bacterial and eukaryotic cell membranes have lipids with fatty acids connected to glycerol by ester linkages: 63
  64. 64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Diversity of Form • Bacteria and archaea way more diverse in morphology (e.g., size, shape) than many appreciate • Morphological diversity in NPAF eukaryotes also immense (NPAF = non plant, animal, or fungal) • Diversity of movement connected to diversity of form • Many examples of convergent evolution in morphology, related features 64
  65. 65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Bacteria: Major Cell Forms • Among the Bacteria and Archaea, three shapes are common: ! Sphere or coccus (plural cocci), occur singly or in plates, blocks, or clusters. ! Rod—bacillus (plural bacilli) ! Helical • Rods and helical shapes may form chains or clusters. 65
  66. 66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Bacteria: Other Forms 66
  67. 67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Archaea: Examples of Forms 67
  68. 68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Motility of Vibrio (a member of the Proteobacteria phylum) 68
  69. 69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Corkscrew Movement of Spiraling (A Cyanobacterium) 69
  70. 70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 •Most are marine and are important photoautotrophic primary producers •Mixture of pigments give them a golden brown color. •Have two flagella, one in an equatorial groove, the other in a longitudinal groove. Alveolates: Dinoflagellates 70 Certium tenue Coral symbiont
  71. 71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Chromalveolates: Haptophytes • Haptophytes 71 Coccolithophores (haptophytes) can also form immense blooms in the ocean. Blooms can reduce the amount of sunlight that penetrates deeper waters. Emiliania huxleyi—one of smallest unicellular eukaryotes. May contribute to global warming through its metabolism.
  72. 72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Alveolates: Ciliates 72 Movement in a ciliate from the gut of a termite • All have numerous cilia, • Most are heterotrophic; very diverse group. • Have complex body forms and two types of nuclei.
  73. 73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Stramenopiles: Diatoms •Unicellular, but many associate in filaments. •Have carotenoids and appear yellow or brown. •Excellent fossil record •Most are photoautotrophic •Responsible for 20% of all carbon fixation. •Oil, gas source 73 A colony of the diatom, Bacillaria paradoxa
  74. 74. Rhizaria: Foraminiferans Sand beaches in the tropics • Secrete shells of calcium carbonate. • Discarded shells make up limestone. • Create some beach sands • Used to date & characterize sedimentary rocks. • Some live as plankton, others at sea bottom. • Thread-like, branched pseudopods extend through pores in the shell and form a sticky net that captures smaller plankton. 74
  75. 75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Rhizaria: Radiolarians • Have thin, stiff pseudopods reinforced by microtubules. • The pseudopods increase surface area for exchange of materials; and help the cell float. • Exclusively marine, most secrete glassy endoskeletons, many with elaborate designs. 75
  76. 76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Unikonts: Opisthokonts: Choanoflagellates •Choanoflagellates are sister to the animals. •Some are colonial and resemble a type of cell found in sponges. 76 The choanoflagellate Salpingoeca sp. feeding
  77. 77. Convergent Evolution • Look Like Fungi 77
  78. 78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Figure 30.14 Sexual Life Cycles of Chytrids and Zygospore Fungi (Part 1) 78
  79. 79. Stramenopiles: Oomcyetes Phytophthora Potato Late Blight • Non-photosynthetic. • Are absorptive heterotrophs • Once were classed as fungi, but are unrelated. 79 Sudden Oak Death
  80. 80. Amoebozoans: Plasmodial Slime Molds • Individual motile cells can form single, multinucleate cell (plasmodium) • Ingest food by endocytosis • Form spores on stalks called fruiting bodies. • Found in cool, moist habitats 80
  81. 81. Amoebozoans: Cellular Slime Molds • Life cycle consists of individual motile cells that ingest food by endocytosis • This is followed by the formation of single, multicellular fruiting structure • Each cell retains its own plasma membrane and individuality 81 Karyo
  82. 82. Multicellularity • Many lineages, not just PAF (plants, animals and fungi) include multicellular representatives • Mechanisms responsible for multicellularity different in different groups (why might that be)? 82
  83. 83. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Many Fungi Multicellular 83
  84. 84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Animals 84
  85. 85. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Plants 8
  86. 86. Amoebozoans: Cellular Slime Molds • Life cycle consists of individual motile cells that ingest food by endocytosis • This is followed by the formation of single, multicellular fruiting structure • Each cell retains its own plasma membrane and individuality 86 Karyo
  87. 87. •All are multicellular; some get very large (e.g., giant kelp). •The carotenoid fucoxanthin imparts the brown color. •Almost exclusively marine. Stramenopiles: Brown Algae 87 A community of brown algae: The marine kelp forest
  88. 88. Amoebozoans: Plasmodial Slime Molds • Individual motile cells can form single, multinucleate cell (plasmodium) • Ingest food by endocytosis • Form spores on stalks called fruiting bodies. • Found in cool, moist habitats 88
  89. 89. Plantae: Red Algae 89 • Most red algae are marine and multicellular. • Red pigment is phycoerythrin. •Many reproduce with spores Motile spores from Purpureofilum Audouinella pacifica Spyridia
  90. 90. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 The chlorophytes are the sister group to charophytes and land plants. Synapomorphies include chlorophyll a and b, and starch as a storage product. More than 17,000 species; marine, freshwater, and terrestrial. Unicellular to large 90 Plantae: Chlorophytes Movement in the green alga Volvox Micrasterias
  91. 91. Multicellular Bacteria (Stigmatella, a Proteobacterium) Photo 26.24 Fruiting body of gliding bacterium Stigmatella aurantiaca. SEM. 91
  92. 92. Biofilms are common in bacteria 92
  93. 93. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Photo 26.4 Filaments of photoautotrophic cyanobacteria, 93
  94. 94. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 More on Multicellularity Later in BIS2C 94
  95. 95. Diversity of Processes • Microbes are able to make use of or alter just about any chemical bond found on Earth • This allows a wide range of niches, and a wide diversity of roles in ecosystems • Also diverse mechanisms for surviving and thriving in “harsh” conditions • Humans and other organisms have taken advantage of this diversity in many ways 95
  96. 96. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 The Unusual 105°C CH3 CO, 80°CH2S, pH 0, 95°C High salt CO2 4°Clow pH 96
  97. 97. The Influential Carbon cycle Nitrogen cycle 97
  98. 98. The Consumable • = 98 Feed microbes a little carbon and they can make some nice things
  99. 99. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Functional Diversity Covered in Labs 2 and 3 and Lecture 11-13 99
  100. 100. Interactions • Microbes have diverse interactions with other organisms (both microbes and macrobes) • Symbiosis is an intimate association between at least two different organisms in which at least one of them benefits 100
  101. 101. The Bad 101
  102. 102. Alveolates: Apicomplexans • All parasitic • Have a mass of organelles at one tip —the apical complex that help the parasite enter the host’s cells. 102 Apical complex • Plasmodium falciparum- Malaria kills 700,000-2,000,000 people per year—75% of them are African children
  103. 103. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Red tide caused by dinoflagellates (Gonyaulax sp.). 103
  104. 104. Excavates: Diplomonads and Parabisalids • Unicellular • Lack mitochondria and most are anaerobic. This is a derived condition • Giardia lamblia - a diplomonad - is a human parasite • Trichomonas vaginalis - parabasalid - STD 104
  105. 105. Excavates: Heteroloboseans • Amoeboid body form. • Naegleria can enter humans and cause a fatal nervous system disease - “brain eating” • Some can transform between amoeboid and flagellated stages. 105

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