BiS2C: Lecture 9: Microbial Diversity
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Transcript of BiS2C: Lecture 9: Microbial Diversity
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
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
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
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
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
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
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
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
Unrooted Tree of Life (from ~ 2004)
9adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
10adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
P PlantsTwo Weeks
Unrooted Tree of Life (from ~ 2004)
11adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
FFungi
One Week
P
Unrooted Tree of Life (from ~ 2004)
12adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
AAnimals
Two Weeks
P
Unrooted Tree of Life (from ~ 2004)
13adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
1.5 Weeks
Unrooted Tree of Life (from ~ 2004)
Unrooted Tree of Life
14adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
1.5 Weeks Mostly Microbes
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
The Bacteria and Archaea via Textbook v.10
15
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 20
Field Observations Are Important Tools
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
• More detail on some of these in Labs 2 and 3
22
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
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 diversity25
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
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
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
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
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
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
2002 Most Genomes from a Few Groups
34Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
2002-2007: TIGR Tree of Life Project
35Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
Naomi Ward
KarenNelson
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
2007-2014: Genomic Encyclopedia
36Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
2007-2014: Genomic Encyclopedia
37Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
BUT …
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Great Plate Count Anomaly
39
<<<<
Culturing Observation
CountCount
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&cd=&docid=rLu5sL207WlE1M&tbnid=CRLQYP7d9d_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
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
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
JoHandelsman
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 withLeptospirillum group I, both Leptospirillum group II and III have thegenes 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 combinationwith carbon monoxide dehydrogenase, may be used for carbonfixation via the reductive acetyl coenzyme A (acetyl-CoA) pathwayby some, or all, organisms. Given the large number of ABC-typesugar 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 Nature Publishing Group
Some Discussion of this in Lecture 13
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 tree44
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
Hug et al 2016
!45
Hug et al. 2016 Tree of Life
92 Bacterial Phyla25 Archaeal Phyla5 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
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
Taxa Covered in Textbook
!47Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48
!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
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
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
The Dark Matter of Biology
!52
0.2
Korarchaeota
DiapherotritesNanohaloarchaeota
Unclassified archaea Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciArchaeoglobi, Methanomicrobia, Halobacteria
Aciduliprofundum, ThermoplasmataUncultured Thermoplasmata
ThermoplasmataOpisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa
CrenarchaeotaCrenarchaeota
Thorarchaeota Lokiarchaeota
YNPFFA
Thaumarchaeota Thaumarchaeota
Cyanobacteria, Melainabacteria
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates 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 SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, MagasanikbacteriaParcubacteriaParcubacteria
Parcubacteria
ParcubacteriaParcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria
Parcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomi Thermotogae
Omnitrophica Omnitrophica
Spirochaetes Spirochaetes
Hydrogenedentes NKB19 Deltaproteobacteria
Epsilonproteobacteria TM6
Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, 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
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)
Aigarchaeota, Cand. Caldiarchaeum subterraneum
Unclassified archaea
Parcubacteria
Candidate Phyla Radiation
Cyanobacteria, Melainabacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomiq ,q ,
ThermotogaeA ifi C
Omnitrophica Omnitrophica
pp
Spirochaetes SpirochaetesS i h t
Hydrogenedentes NKB19 Deltaproteobacteria
H d d t N
Epsilonproteobacteriab
TM6Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres
Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria
D f bD f b, , p ,, , p ,
Planctomycetespp
Chlamydiaey
LentisphaeraeC a yd Ch
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, TA06b M
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)O h
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates Roizmanbacteria
MicrogenomatesMicrogenomates Curtissbacteria
ggMicrogenomates Daviesbacteria
gg
Microgenomates Levybacteria
Microgenomates Woesebacteria Microgenomates AmesbacteriaMi t L b t i
Microgenomates ShapirobacteriaMi t W bMi t
Microgenomates Beckwithbacteria, Pacebacteria, CollierbacteriaMi Sh i b i
Microgenomates Gottesmanbacteriat R i b t i
g yg y
KAZAN CPR2, Saccharibacteria TM7
Berkelbacteria
Berkelbacteria
Berkelbacteria Berkelbacteria
CPR Uncultured unclassified bacteria Peregrinibacteria
Peregrinibacteria
Absconditabacteria SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteriate a
ParcubacteriaParcubacteria
Parcubacteria
Parcubacteria AbscAbs
Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria
ggParcubacteriaParcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
P b i
Candidate Phyla Radiation
DiapherotritesNanohaloarchaeota
Unclassified archaea
Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciE43
Archaeoglobi, Methanomicrobia, Halobacteria, , ,, , ,
Aciduliprofundum, Thermoplasmatagg
Uncultured Thermoplasmatap ,p ,
Thermoplasmatap
Unclassified archaea
Korarchaeota
,
CrenarchaeotaCrenarchaeota
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 tEukaryotes
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 forgroups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups andothers are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resultinggroups 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 supportfrom 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newickformat 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
DiapherotritesNanohaloarchaeota
Unclassified archaea Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciArchaeoglobi, Methanomicrobia, Halobacteria
Aciduliprofundum, ThermoplasmataUncultured Thermoplasmata
ThermoplasmataOpisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa
CrenarchaeotaCrenarchaeota
Thorarchaeota Lokiarchaeota
YNPFFA
Thaumarchaeota Thaumarchaeota
Cyanobacteria, Melainabacteria
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates 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 SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, MagasanikbacteriaParcubacteriaParcubacteria
Parcubacteria
ParcubacteriaParcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria
Parcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomi Thermotogae
Omnitrophica Omnitrophica
Spirochaetes Spirochaetes
Hydrogenedentes NKB19 Deltaproteobacteria
Epsilonproteobacteria TM6
Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, 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
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)
Aigarchaeota, Cand. Caldiarchaeum subterraneum
Unclassified archaea
Parcubacteria
Candidate Phyla Radiation
Cyanobacteria, Melainabacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomiq ,q ,
ThermotogaeA ifi C
Omnitrophica Omnitrophica
pp
Spirochaetes SpirochaetesS i h t
Hydrogenedentes NKB19 Deltaproteobacteria
H d d t N
Epsilonproteobacteriab
TM6Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres
Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria
D f bD f b, , p ,, , p ,
Planctomycetespp
Chlamydiaey
LentisphaeraeC a yd Ch
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, TA06b M
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)O h
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates Roizmanbacteria
MicrogenomatesMicrogenomates Curtissbacteria
ggMicrogenomates Daviesbacteria
gg
Microgenomates Levybacteria
Microgenomates Woesebacteria Microgenomates AmesbacteriaMi t L b t i
Microgenomates ShapirobacteriaMi t W bMi t
Microgenomates Beckwithbacteria, Pacebacteria, CollierbacteriaMi Sh i b i
Microgenomates Gottesmanbacteriat R i b t i
g yg y
KAZAN CPR2, Saccharibacteria TM7
Berkelbacteria
Berkelbacteria
Berkelbacteria Berkelbacteria
CPR Uncultured unclassified bacteria Peregrinibacteria
Peregrinibacteria
Absconditabacteria SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteriate a
ParcubacteriaParcubacteria
Parcubacteria
Parcubacteria AbscAbs
Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria
ggParcubacteriaParcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
P b i
Candidate Phyla Radiation
DiapherotritesNanohaloarchaeota
Unclassified archaea
Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciE43
Archaeoglobi, Methanomicrobia, Halobacteria, , ,, , ,
Aciduliprofundum, Thermoplasmatagg
Uncultured Thermoplasmatap ,p ,
Thermoplasmatap
Unclassified archaea
Korarchaeota
,
CrenarchaeotaCrenarchaeota
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 tEukaryotes
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 forgroups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups andothers are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resultinggroups 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 supportfrom 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newickformat 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
DiapherotritesNanohaloarchaeota
Unclassified archaea Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciArchaeoglobi, Methanomicrobia, Halobacteria
Aciduliprofundum, ThermoplasmataUncultured Thermoplasmata
ThermoplasmataOpisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa
CrenarchaeotaCrenarchaeota
Thorarchaeota Lokiarchaeota
YNPFFA
Thaumarchaeota Thaumarchaeota
Cyanobacteria, Melainabacteria
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates 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 SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, MagasanikbacteriaParcubacteriaParcubacteria
Parcubacteria
ParcubacteriaParcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria
Parcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomi Thermotogae
Omnitrophica Omnitrophica
Spirochaetes Spirochaetes
Hydrogenedentes NKB19 Deltaproteobacteria
Epsilonproteobacteria TM6
Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, 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
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)
Aigarchaeota, Cand. Caldiarchaeum subterraneum
Unclassified archaea
Parcubacteria
Candidate Phyla Radiation
Cyanobacteria, Melainabacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomiq ,q ,
ThermotogaeA ifi C
Omnitrophica Omnitrophica
pp
Spirochaetes SpirochaetesS i h t
Hydrogenedentes NKB19 Deltaproteobacteria
H d d t N
Epsilonproteobacteriab
TM6Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres
Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria
D f bD f b, , p ,, , p ,
Planctomycetespp
Chlamydiaey
LentisphaeraeC a yd Ch
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, TA06b M
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)O h
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates Roizmanbacteria
MicrogenomatesMicrogenomates Curtissbacteria
ggMicrogenomates Daviesbacteria
gg
Microgenomates Levybacteria
Microgenomates Woesebacteria Microgenomates AmesbacteriaMi t L b t i
Microgenomates ShapirobacteriaMi t W bMi t
Microgenomates Beckwithbacteria, Pacebacteria, CollierbacteriaMi Sh i b i
Microgenomates Gottesmanbacteriat R i b t i
g yg y
KAZAN CPR2, Saccharibacteria TM7
Berkelbacteria
Berkelbacteria
Berkelbacteria Berkelbacteria
CPR Uncultured unclassified bacteria Peregrinibacteria
Peregrinibacteria
Absconditabacteria SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteriate a
ParcubacteriaParcubacteria
Parcubacteria
Parcubacteria AbscAbs
Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria
ggParcubacteriaParcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
P b i
Candidate Phyla Radiation
DiapherotritesNanohaloarchaeota
Unclassified archaea
Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciE43
Archaeoglobi, Methanomicrobia, Halobacteria, , ,, , ,
Aciduliprofundum, Thermoplasmatagg
Uncultured Thermoplasmatap ,p ,
Thermoplasmatap
Unclassified archaea
Korarchaeota
,
CrenarchaeotaCrenarchaeota
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 tEukaryotes
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 forgroups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups andothers are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resultinggroups 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 supportfrom 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newickformat 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
DiapherotritesNanohaloarchaeota
Unclassified archaea Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciArchaeoglobi, Methanomicrobia, Halobacteria
Aciduliprofundum, ThermoplasmataUncultured Thermoplasmata
ThermoplasmataOpisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa
CrenarchaeotaCrenarchaeota
Thorarchaeota Lokiarchaeota
YNPFFA
Thaumarchaeota Thaumarchaeota
Cyanobacteria, Melainabacteria
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates 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 SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, MagasanikbacteriaParcubacteriaParcubacteria
Parcubacteria
ParcubacteriaParcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria
Parcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomi Thermotogae
Omnitrophica Omnitrophica
Spirochaetes Spirochaetes
Hydrogenedentes NKB19 Deltaproteobacteria
Epsilonproteobacteria TM6
Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, 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
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)
Aigarchaeota, Cand. Caldiarchaeum subterraneum
Unclassified archaea
Parcubacteria
Candidate Phyla Radiation
Cyanobacteria, Melainabacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomiq ,q ,
ThermotogaeA ifi C
Omnitrophica Omnitrophica
pp
Spirochaetes SpirochaetesS i h t
Hydrogenedentes NKB19 Deltaproteobacteria
H d d t N
Epsilonproteobacteriab
TM6Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres
Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria
D f bD f b, , p ,, , p ,
Planctomycetespp
Chlamydiaey
LentisphaeraeC a yd Ch
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, TA06b M
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)O h
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates Roizmanbacteria
MicrogenomatesMicrogenomates Curtissbacteria
ggMicrogenomates Daviesbacteria
gg
Microgenomates Levybacteria
Microgenomates Woesebacteria Microgenomates AmesbacteriaMi t L b t i
Microgenomates ShapirobacteriaMi t W bMi t
Microgenomates Beckwithbacteria, Pacebacteria, CollierbacteriaMi Sh i b i
Microgenomates Gottesmanbacteriat R i b t i
g yg y
KAZAN CPR2, Saccharibacteria TM7
Berkelbacteria
Berkelbacteria
Berkelbacteria Berkelbacteria
CPR Uncultured unclassified bacteria Peregrinibacteria
Peregrinibacteria
Absconditabacteria SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteriate a
ParcubacteriaParcubacteria
Parcubacteria
Parcubacteria AbscAbs
Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria
ggParcubacteriaParcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
P b i
Candidate Phyla Radiation
DiapherotritesNanohaloarchaeota
Unclassified archaea
Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciE43
Archaeoglobi, Methanomicrobia, Halobacteria, , ,, , ,
Aciduliprofundum, Thermoplasmatagg
Uncultured Thermoplasmatap ,p ,
Thermoplasmatap
Unclassified archaea
Korarchaeota
,
CrenarchaeotaCrenarchaeota
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 tEukaryotes
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 forgroups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups andothers are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resultinggroups 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 supportfrom 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newickformat 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
DiapherotritesNanohaloarchaeota
Unclassified archaea Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciArchaeoglobi, Methanomicrobia, Halobacteria
Aciduliprofundum, ThermoplasmataUncultured Thermoplasmata
ThermoplasmataOpisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa
CrenarchaeotaCrenarchaeota
Thorarchaeota Lokiarchaeota
YNPFFA
Thaumarchaeota Thaumarchaeota
Cyanobacteria, Melainabacteria
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates 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 SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, MagasanikbacteriaParcubacteriaParcubacteria
Parcubacteria
ParcubacteriaParcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria
Parcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomi Thermotogae
Omnitrophica Omnitrophica
Spirochaetes Spirochaetes
Hydrogenedentes NKB19 Deltaproteobacteria
Epsilonproteobacteria TM6
Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, 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
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)
Aigarchaeota, Cand. Caldiarchaeum subterraneum
Unclassified archaea
Parcubacteria
Candidate Phyla Radiation
Cyanobacteria, Melainabacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomiq ,q ,
ThermotogaeA ifi C
Omnitrophica Omnitrophica
pp
Spirochaetes SpirochaetesS i h t
Hydrogenedentes NKB19 Deltaproteobacteria
H d d t N
Epsilonproteobacteriab
TM6Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres
Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria
D f bD f b, , p ,, , p ,
Planctomycetespp
Chlamydiaey
LentisphaeraeC a yd Ch
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, TA06b M
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)O h
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates Roizmanbacteria
MicrogenomatesMicrogenomates Curtissbacteria
ggMicrogenomates Daviesbacteria
gg
Microgenomates Levybacteria
Microgenomates Woesebacteria Microgenomates AmesbacteriaMi t L b t i
Microgenomates ShapirobacteriaMi t W bMi t
Microgenomates Beckwithbacteria, Pacebacteria, CollierbacteriaMi Sh i b i
Microgenomates Gottesmanbacteriat R i b t i
g yg y
KAZAN CPR2, Saccharibacteria TM7
Berkelbacteria
Berkelbacteria
Berkelbacteria Berkelbacteria
CPR Uncultured unclassified bacteria Peregrinibacteria
Peregrinibacteria
Absconditabacteria SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteriate a
ParcubacteriaParcubacteria
Parcubacteria
Parcubacteria AbscAbs
Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria
ggParcubacteriaParcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
P b i
Candidate Phyla Radiation
DiapherotritesNanohaloarchaeota
Unclassified archaea
Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciE43
Archaeoglobi, Methanomicrobia, Halobacteria, , ,, , ,
Aciduliprofundum, Thermoplasmatagg
Uncultured Thermoplasmatap ,p ,
Thermoplasmatap
Unclassified archaea
Korarchaeota
,
CrenarchaeotaCrenarchaeota
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 tEukaryotes
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 forgroups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups andothers are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resultinggroups 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 supportfrom 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newickformat 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
DiapherotritesNanohaloarchaeota
Unclassified archaea Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciArchaeoglobi, Methanomicrobia, Halobacteria
Aciduliprofundum, ThermoplasmataUncultured Thermoplasmata
ThermoplasmataOpisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa
CrenarchaeotaCrenarchaeota
Thorarchaeota Lokiarchaeota
YNPFFA
Thaumarchaeota Thaumarchaeota
Cyanobacteria, Melainabacteria
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates 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 SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, MagasanikbacteriaParcubacteriaParcubacteria
Parcubacteria
ParcubacteriaParcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria
Parcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomi Thermotogae
Omnitrophica Omnitrophica
Spirochaetes Spirochaetes
Hydrogenedentes NKB19 Deltaproteobacteria
Epsilonproteobacteria TM6
Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, 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
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)
Aigarchaeota, Cand. Caldiarchaeum subterraneum
Unclassified archaea
Parcubacteria
Candidate Phyla Radiation
Cyanobacteria, Melainabacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomiq ,q ,
ThermotogaeA ifi C
Omnitrophica Omnitrophica
pp
Spirochaetes SpirochaetesS i h t
Hydrogenedentes NKB19 Deltaproteobacteria
H d d t N
Epsilonproteobacteriab
TM6Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres
Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria
D f bD f b, , p ,, , p ,
Planctomycetespp
Chlamydiaey
LentisphaeraeC a yd Ch
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, TA06b M
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)O h
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates Roizmanbacteria
MicrogenomatesMicrogenomates Curtissbacteria
ggMicrogenomates Daviesbacteria
gg
Microgenomates Levybacteria
Microgenomates Woesebacteria Microgenomates AmesbacteriaMi t L b t i
Microgenomates ShapirobacteriaMi t W bMi t
Microgenomates Beckwithbacteria, Pacebacteria, CollierbacteriaMi Sh i b i
Microgenomates Gottesmanbacteriat R i b t i
g yg y
KAZAN CPR2, Saccharibacteria TM7
Berkelbacteria
Berkelbacteria
Berkelbacteria Berkelbacteria
CPR Uncultured unclassified bacteria Peregrinibacteria
Peregrinibacteria
Absconditabacteria SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteriate a
ParcubacteriaParcubacteria
Parcubacteria
Parcubacteria AbscAbs
Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria
ggParcubacteriaParcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
P b i
Candidate Phyla Radiation
DiapherotritesNanohaloarchaeota
Unclassified archaea
Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciE43
Archaeoglobi, Methanomicrobia, Halobacteria, , ,, , ,
Aciduliprofundum, Thermoplasmatagg
Uncultured Thermoplasmatap ,p ,
Thermoplasmatap
Unclassified archaea
Korarchaeota
,
CrenarchaeotaCrenarchaeota
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 tEukaryotes
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 forgroups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups andothers are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resultinggroups 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 supportfrom 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newickformat 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
DiapherotritesNanohaloarchaeota
Unclassified archaea Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciArchaeoglobi, Methanomicrobia, Halobacteria
Aciduliprofundum, ThermoplasmataUncultured Thermoplasmata
ThermoplasmataOpisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa
CrenarchaeotaCrenarchaeota
Thorarchaeota Lokiarchaeota
YNPFFA
Thaumarchaeota Thaumarchaeota
Cyanobacteria, Melainabacteria
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates 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 SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, MagasanikbacteriaParcubacteriaParcubacteria
Parcubacteria
ParcubacteriaParcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria
Parcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomi Thermotogae
Omnitrophica Omnitrophica
Spirochaetes Spirochaetes
Hydrogenedentes NKB19 Deltaproteobacteria
Epsilonproteobacteria TM6
Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, 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
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)
Aigarchaeota, Cand. Caldiarchaeum subterraneum
Unclassified archaea
Parcubacteria
Candidate Phyla Radiation
Cyanobacteria, Melainabacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomiq ,q ,
ThermotogaeA ifi C
Omnitrophica Omnitrophica
pp
Spirochaetes SpirochaetesS i h t
Hydrogenedentes NKB19 Deltaproteobacteria
H d d t N
Epsilonproteobacteriab
TM6Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres
Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria
D f bD f b, , p ,, , p ,
Planctomycetespp
Chlamydiaey
LentisphaeraeC a yd Ch
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, TA06b M
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)O h
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates Roizmanbacteria
MicrogenomatesMicrogenomates Curtissbacteria
ggMicrogenomates Daviesbacteria
gg
Microgenomates Levybacteria
Microgenomates Woesebacteria Microgenomates AmesbacteriaMi t L b t i
Microgenomates ShapirobacteriaMi t W bMi t
Microgenomates Beckwithbacteria, Pacebacteria, CollierbacteriaMi Sh i b i
Microgenomates Gottesmanbacteriat R i b t i
g yg y
KAZAN CPR2, Saccharibacteria TM7
Berkelbacteria
Berkelbacteria
Berkelbacteria Berkelbacteria
CPR Uncultured unclassified bacteria Peregrinibacteria
Peregrinibacteria
Absconditabacteria SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteriate a
ParcubacteriaParcubacteria
Parcubacteria
Parcubacteria AbscAbs
Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria
ggParcubacteriaParcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
P b i
Candidate Phyla Radiation
DiapherotritesNanohaloarchaeota
Unclassified archaea
Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciE43
Archaeoglobi, Methanomicrobia, Halobacteria, , ,, , ,
Aciduliprofundum, Thermoplasmatagg
Uncultured Thermoplasmatap ,p ,
Thermoplasmatap
Unclassified archaea
Korarchaeota
,
CrenarchaeotaCrenarchaeota
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 tEukaryotes
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 forgroups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups andothers are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resultinggroups 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 supportfrom 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newickformat 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
DiapherotritesNanohaloarchaeota
Unclassified archaea Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciArchaeoglobi, Methanomicrobia, Halobacteria
Aciduliprofundum, ThermoplasmataUncultured Thermoplasmata
ThermoplasmataOpisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa
CrenarchaeotaCrenarchaeota
Thorarchaeota Lokiarchaeota
YNPFFA
Thaumarchaeota Thaumarchaeota
Cyanobacteria, Melainabacteria
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates 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 SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, MagasanikbacteriaParcubacteriaParcubacteria
Parcubacteria
ParcubacteriaParcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria
Parcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomi Thermotogae
Omnitrophica Omnitrophica
Spirochaetes Spirochaetes
Hydrogenedentes NKB19 Deltaproteobacteria
Epsilonproteobacteria TM6
Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, 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
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)
Aigarchaeota, Cand. Caldiarchaeum subterraneum
Unclassified archaea
Parcubacteria
Candidate Phyla Radiation
Cyanobacteria, Melainabacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomiq ,q ,
ThermotogaeA ifi C
Omnitrophica Omnitrophica
pp
Spirochaetes SpirochaetesS i h t
Hydrogenedentes NKB19 Deltaproteobacteria
H d d t N
Epsilonproteobacteriab
TM6Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres
Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria
D f bD f b, , p ,, , p ,
Planctomycetespp
Chlamydiaey
LentisphaeraeC a yd Ch
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, TA06b M
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)O h
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates Roizmanbacteria
MicrogenomatesMicrogenomates Curtissbacteria
ggMicrogenomates Daviesbacteria
gg
Microgenomates Levybacteria
Microgenomates Woesebacteria Microgenomates AmesbacteriaMi t L b t i
Microgenomates ShapirobacteriaMi t W bMi t
Microgenomates Beckwithbacteria, Pacebacteria, CollierbacteriaMi Sh i b i
Microgenomates Gottesmanbacteriat R i b t i
g yg y
KAZAN CPR2, Saccharibacteria TM7
Berkelbacteria
Berkelbacteria
Berkelbacteria Berkelbacteria
CPR Uncultured unclassified bacteria Peregrinibacteria
Peregrinibacteria
Absconditabacteria SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteriate a
ParcubacteriaParcubacteria
Parcubacteria
Parcubacteria AbscAbs
Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria
ggParcubacteriaParcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
P b i
Candidate Phyla Radiation
DiapherotritesNanohaloarchaeota
Unclassified archaea
Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciE43
Archaeoglobi, Methanomicrobia, Halobacteria, , ,, , ,
Aciduliprofundum, Thermoplasmatagg
Uncultured Thermoplasmatap ,p ,
Thermoplasmatap
Unclassified archaea
Korarchaeota
,
CrenarchaeotaCrenarchaeota
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 tEukaryotes
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 forgroups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups andothers are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resultinggroups 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 supportfrom 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newickformat 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
DiapherotritesNanohaloarchaeota
Unclassified archaea Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciArchaeoglobi, Methanomicrobia, Halobacteria
Aciduliprofundum, ThermoplasmataUncultured Thermoplasmata
ThermoplasmataOpisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa
CrenarchaeotaCrenarchaeota
Thorarchaeota Lokiarchaeota
YNPFFA
Thaumarchaeota Thaumarchaeota
Cyanobacteria, Melainabacteria
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates 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 SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, MagasanikbacteriaParcubacteriaParcubacteria
Parcubacteria
ParcubacteriaParcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria
Parcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomi Thermotogae
Omnitrophica Omnitrophica
Spirochaetes Spirochaetes
Hydrogenedentes NKB19 Deltaproteobacteria
Epsilonproteobacteria TM6
Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, 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
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)
Aigarchaeota, Cand. Caldiarchaeum subterraneum
Unclassified archaea
Parcubacteria
Candidate Phyla Radiation
Cyanobacteria, Melainabacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomiq ,q ,
ThermotogaeA ifi C
Omnitrophica Omnitrophica
pp
Spirochaetes SpirochaetesS i h t
Hydrogenedentes NKB19 Deltaproteobacteria
H d d t N
Epsilonproteobacteriab
TM6Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres
Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria
D f bD f b, , p ,, , p ,
Planctomycetespp
Chlamydiaey
LentisphaeraeC a yd Ch
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, TA06b M
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)O h
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates Roizmanbacteria
MicrogenomatesMicrogenomates Curtissbacteria
ggMicrogenomates Daviesbacteria
gg
Microgenomates Levybacteria
Microgenomates Woesebacteria Microgenomates AmesbacteriaMi t L b t i
Microgenomates ShapirobacteriaMi t W bMi t
Microgenomates Beckwithbacteria, Pacebacteria, CollierbacteriaMi Sh i b i
Microgenomates Gottesmanbacteriat R i b t i
g yg y
KAZAN CPR2, Saccharibacteria TM7
Berkelbacteria
Berkelbacteria
Berkelbacteria Berkelbacteria
CPR Uncultured unclassified bacteria Peregrinibacteria
Peregrinibacteria
Absconditabacteria SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteriate a
ParcubacteriaParcubacteria
Parcubacteria
Parcubacteria AbscAbs
Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria
ggParcubacteriaParcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
P b i
Candidate Phyla Radiation
DiapherotritesNanohaloarchaeota
Unclassified archaea
Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciE43
Archaeoglobi, Methanomicrobia, Halobacteria, , ,, , ,
Aciduliprofundum, Thermoplasmatagg
Uncultured Thermoplasmatap ,p ,
Thermoplasmatap
Unclassified archaea
Korarchaeota
,
CrenarchaeotaCrenarchaeota
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 tEukaryotes
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 forgroups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups andothers are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resultinggroups 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 supportfrom 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newickformat 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
DiapherotritesNanohaloarchaeota
Unclassified archaea Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciArchaeoglobi, Methanomicrobia, Halobacteria
Aciduliprofundum, ThermoplasmataUncultured Thermoplasmata
ThermoplasmataOpisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa
CrenarchaeotaCrenarchaeota
Thorarchaeota Lokiarchaeota
YNPFFA
Thaumarchaeota Thaumarchaeota
Cyanobacteria, Melainabacteria
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates 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 SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, MagasanikbacteriaParcubacteriaParcubacteria
Parcubacteria
ParcubacteriaParcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria
Parcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomi Thermotogae
Omnitrophica Omnitrophica
Spirochaetes Spirochaetes
Hydrogenedentes NKB19 Deltaproteobacteria
Epsilonproteobacteria TM6
Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, 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
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)
Aigarchaeota, Cand. Caldiarchaeum subterraneum
Unclassified archaea
Parcubacteria
Candidate Phyla Radiation
Cyanobacteria, Melainabacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomiq ,q ,
ThermotogaeA ifi C
Omnitrophica Omnitrophica
pp
Spirochaetes SpirochaetesS i h t
Hydrogenedentes NKB19 Deltaproteobacteria
H d d t N
Epsilonproteobacteriab
TM6Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres
Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria
D f bD f b, , p ,, , p ,
Planctomycetespp
Chlamydiaey
LentisphaeraeC a yd Ch
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, TA06b M
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)O h
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates Roizmanbacteria
MicrogenomatesMicrogenomates Curtissbacteria
ggMicrogenomates Daviesbacteria
gg
Microgenomates Levybacteria
Microgenomates Woesebacteria Microgenomates AmesbacteriaMi t L b t i
Microgenomates ShapirobacteriaMi t W bMi t
Microgenomates Beckwithbacteria, Pacebacteria, CollierbacteriaMi Sh i b i
Microgenomates Gottesmanbacteriat R i b t i
g yg y
KAZAN CPR2, Saccharibacteria TM7
Berkelbacteria
Berkelbacteria
Berkelbacteria Berkelbacteria
CPR Uncultured unclassified bacteria Peregrinibacteria
Peregrinibacteria
Absconditabacteria SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteriate a
ParcubacteriaParcubacteria
Parcubacteria
Parcubacteria AbscAbs
Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria
ggParcubacteriaParcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
P b i
Candidate Phyla Radiation
DiapherotritesNanohaloarchaeota
Unclassified archaea
Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciE43
Archaeoglobi, Methanomicrobia, Halobacteria, , ,, , ,
Aciduliprofundum, Thermoplasmatagg
Uncultured Thermoplasmatap ,p ,
Thermoplasmatap
Unclassified archaea
Korarchaeota
,
CrenarchaeotaCrenarchaeota
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 tEukaryotes
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 forgroups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups andothers are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resultinggroups 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 supportfrom 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newickformat 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
DiapherotritesNanohaloarchaeota
Unclassified archaea Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciArchaeoglobi, Methanomicrobia, Halobacteria
Aciduliprofundum, ThermoplasmataUncultured Thermoplasmata
ThermoplasmataOpisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa
CrenarchaeotaCrenarchaeota
Thorarchaeota Lokiarchaeota
YNPFFA
Thaumarchaeota Thaumarchaeota
Cyanobacteria, Melainabacteria
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates 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 SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, MagasanikbacteriaParcubacteriaParcubacteria
Parcubacteria
ParcubacteriaParcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria
Parcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomi Thermotogae
Omnitrophica Omnitrophica
Spirochaetes Spirochaetes
Hydrogenedentes NKB19 Deltaproteobacteria
Epsilonproteobacteria TM6
Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, 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
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)
Aigarchaeota, Cand. Caldiarchaeum subterraneum
Unclassified archaea
Parcubacteria
Candidate Phyla Radiation
Cyanobacteria, Melainabacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomiq ,q ,
ThermotogaeA ifi C
Omnitrophica Omnitrophica
pp
Spirochaetes SpirochaetesS i h t
Hydrogenedentes NKB19 Deltaproteobacteria
H d d t N
Epsilonproteobacteriab
TM6Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres
Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria
D f bD f b, , p ,, , p ,
Planctomycetespp
Chlamydiaey
LentisphaeraeC a yd Ch
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, TA06b M
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)O h
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates Roizmanbacteria
MicrogenomatesMicrogenomates Curtissbacteria
ggMicrogenomates Daviesbacteria
gg
Microgenomates Levybacteria
Microgenomates Woesebacteria Microgenomates AmesbacteriaMi t L b t i
Microgenomates ShapirobacteriaMi t W bMi t
Microgenomates Beckwithbacteria, Pacebacteria, CollierbacteriaMi Sh i b i
Microgenomates Gottesmanbacteriat R i b t i
g yg y
KAZAN CPR2, Saccharibacteria TM7
Berkelbacteria
Berkelbacteria
Berkelbacteria Berkelbacteria
CPR Uncultured unclassified bacteria Peregrinibacteria
Peregrinibacteria
Absconditabacteria SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteriate a
ParcubacteriaParcubacteria
Parcubacteria
Parcubacteria AbscAbs
Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria
ggParcubacteriaParcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
P b i
Candidate Phyla Radiation
DiapherotritesNanohaloarchaeota
Unclassified archaea
Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciE43
Archaeoglobi, Methanomicrobia, Halobacteria, , ,, , ,
Aciduliprofundum, Thermoplasmatagg
Uncultured Thermoplasmatap ,p ,
Thermoplasmatap
Unclassified archaea
Korarchaeota
,
CrenarchaeotaCrenarchaeota
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 tEukaryotes
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 forgroups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups andothers are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resultinggroups 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 supportfrom 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newickformat 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
DiapherotritesNanohaloarchaeota
Unclassified archaea Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciArchaeoglobi, Methanomicrobia, Halobacteria
Aciduliprofundum, ThermoplasmataUncultured Thermoplasmata
ThermoplasmataOpisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa
CrenarchaeotaCrenarchaeota
Thorarchaeota Lokiarchaeota
YNPFFA
Thaumarchaeota Thaumarchaeota
Cyanobacteria, Melainabacteria
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates 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 SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, MagasanikbacteriaParcubacteriaParcubacteria
Parcubacteria
ParcubacteriaParcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria
Parcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomi Thermotogae
Omnitrophica Omnitrophica
Spirochaetes Spirochaetes
Hydrogenedentes NKB19 Deltaproteobacteria
Epsilonproteobacteria TM6
Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, 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
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)
Aigarchaeota, Cand. Caldiarchaeum subterraneum
Unclassified archaea
Parcubacteria
Candidate Phyla Radiation
Cyanobacteria, Melainabacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomiq ,q ,
ThermotogaeA ifi C
Omnitrophica Omnitrophica
pp
Spirochaetes SpirochaetesS i h t
Hydrogenedentes NKB19 Deltaproteobacteria
H d d t N
Epsilonproteobacteriab
TM6Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres
Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria
D f bD f b, , p ,, , p ,
Planctomycetespp
Chlamydiaey
LentisphaeraeC a yd Ch
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, TA06b M
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)O h
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates Roizmanbacteria
MicrogenomatesMicrogenomates Curtissbacteria
ggMicrogenomates Daviesbacteria
gg
Microgenomates Levybacteria
Microgenomates Woesebacteria Microgenomates AmesbacteriaMi t L b t i
Microgenomates ShapirobacteriaMi t W bMi t
Microgenomates Beckwithbacteria, Pacebacteria, CollierbacteriaMi Sh i b i
Microgenomates Gottesmanbacteriat R i b t i
g yg y
KAZAN CPR2, Saccharibacteria TM7
Berkelbacteria
Berkelbacteria
Berkelbacteria Berkelbacteria
CPR Uncultured unclassified bacteria Peregrinibacteria
Peregrinibacteria
Absconditabacteria SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteriate a
ParcubacteriaParcubacteria
Parcubacteria
Parcubacteria AbscAbs
Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria
ggParcubacteriaParcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
P b i
Candidate Phyla Radiation
DiapherotritesNanohaloarchaeota
Unclassified archaea
Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciE43
Archaeoglobi, Methanomicrobia, Halobacteria, , ,, , ,
Aciduliprofundum, Thermoplasmatagg
Uncultured Thermoplasmatap ,p ,
Thermoplasmatap
Unclassified archaea
Korarchaeota
,
CrenarchaeotaCrenarchaeota
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 tEukaryotes
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 forgroups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups andothers are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resultinggroups 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 supportfrom 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newickformat 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
DiapherotritesNanohaloarchaeota
Unclassified archaea Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciArchaeoglobi, Methanomicrobia, Halobacteria
Aciduliprofundum, ThermoplasmataUncultured Thermoplasmata
ThermoplasmataOpisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa
CrenarchaeotaCrenarchaeota
Thorarchaeota Lokiarchaeota
YNPFFA
Thaumarchaeota Thaumarchaeota
Cyanobacteria, Melainabacteria
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates 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 SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, MagasanikbacteriaParcubacteriaParcubacteria
Parcubacteria
ParcubacteriaParcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria
Parcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomi Thermotogae
Omnitrophica Omnitrophica
Spirochaetes Spirochaetes
Hydrogenedentes NKB19 Deltaproteobacteria
Epsilonproteobacteria TM6
Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, 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
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)
Aigarchaeota, Cand. Caldiarchaeum subterraneum
Unclassified archaea
Parcubacteria
Candidate Phyla Radiation
Cyanobacteria, Melainabacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomiq ,q ,
ThermotogaeA ifi C
Omnitrophica Omnitrophica
pp
Spirochaetes SpirochaetesS i h t
Hydrogenedentes NKB19 Deltaproteobacteria
H d d t N
Epsilonproteobacteriab
TM6Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres
Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria
D f bD f b, , p ,, , p ,
Planctomycetespp
Chlamydiaey
LentisphaeraeC a yd Ch
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, TA06b M
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)O h
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates Roizmanbacteria
MicrogenomatesMicrogenomates Curtissbacteria
ggMicrogenomates Daviesbacteria
gg
Microgenomates Levybacteria
Microgenomates Woesebacteria Microgenomates AmesbacteriaMi t L b t i
Microgenomates ShapirobacteriaMi t W bMi t
Microgenomates Beckwithbacteria, Pacebacteria, CollierbacteriaMi Sh i b i
Microgenomates Gottesmanbacteriat R i b t i
g yg y
KAZAN CPR2, Saccharibacteria TM7
Berkelbacteria
Berkelbacteria
Berkelbacteria Berkelbacteria
CPR Uncultured unclassified bacteria Peregrinibacteria
Peregrinibacteria
Absconditabacteria SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteriate a
ParcubacteriaParcubacteria
Parcubacteria
Parcubacteria AbscAbs
Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria
ggParcubacteriaParcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
P b i
Candidate Phyla Radiation
DiapherotritesNanohaloarchaeota
Unclassified archaea
Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciE43
Archaeoglobi, Methanomicrobia, Halobacteria, , ,, , ,
Aciduliprofundum, Thermoplasmatagg
Uncultured Thermoplasmatap ,p ,
Thermoplasmatap
Unclassified archaea
Korarchaeota
,
CrenarchaeotaCrenarchaeota
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 tEukaryotes
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 forgroups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups andothers are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resultinggroups 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 supportfrom 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newickformat 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
DiapherotritesNanohaloarchaeota
Unclassified archaea Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciArchaeoglobi, Methanomicrobia, Halobacteria
Aciduliprofundum, ThermoplasmataUncultured Thermoplasmata
ThermoplasmataOpisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa
CrenarchaeotaCrenarchaeota
Thorarchaeota Lokiarchaeota
YNPFFA
Thaumarchaeota Thaumarchaeota
Cyanobacteria, Melainabacteria
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates 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 SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, MagasanikbacteriaParcubacteriaParcubacteria
Parcubacteria
ParcubacteriaParcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria
Parcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomi Thermotogae
Omnitrophica Omnitrophica
Spirochaetes Spirochaetes
Hydrogenedentes NKB19 Deltaproteobacteria
Epsilonproteobacteria TM6
Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, 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
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)
Aigarchaeota, Cand. Caldiarchaeum subterraneum
Unclassified archaea
Parcubacteria
Candidate Phyla Radiation
Cyanobacteria, Melainabacteria
Deinococcus-Thermus Aquificae, Calescamantes EM19
Caldiserica, Dictyoglomiq ,q ,
ThermotogaeA ifi C
Omnitrophica Omnitrophica
pp
Spirochaetes SpirochaetesS i h t
Hydrogenedentes NKB19 Deltaproteobacteria
H d d t N
Epsilonproteobacteriab
TM6Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres
Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria
D f bD f b, , p ,, , p ,
Planctomycetespp
Chlamydiaey
LentisphaeraeC a yd Ch
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, TA06b M
ElusimicrobiaUncultured bacteria
Uncultured bacteria (CP RIF1)O h
Dojkabacteria WS6 CPR3
Katanobacteria WWE3 Katanobacteria WWE3
Microgenomates RoizmanbacteriaMicrogenomates Roizmanbacteria
MicrogenomatesMicrogenomates Curtissbacteria
ggMicrogenomates Daviesbacteria
gg
Microgenomates Levybacteria
Microgenomates Woesebacteria Microgenomates AmesbacteriaMi t L b t i
Microgenomates ShapirobacteriaMi t W bMi t
Microgenomates Beckwithbacteria, Pacebacteria, CollierbacteriaMi Sh i b i
Microgenomates Gottesmanbacteriat R i b t i
g yg y
KAZAN CPR2, Saccharibacteria TM7
Berkelbacteria
Berkelbacteria
Berkelbacteria Berkelbacteria
CPR Uncultured unclassified bacteria Peregrinibacteria
Peregrinibacteria
Absconditabacteria SR1Gracilibacteria BD1-5 / GNO2
SM2F11Parcubacteria
Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteriate a
ParcubacteriaParcubacteria
Parcubacteria
Parcubacteria AbscAbs
Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria
ggParcubacteriaParcubacteria Moranbacteria
ParcubacteriaParcubacteria Yanofskybacteria
P b i
Candidate Phyla Radiation
DiapherotritesNanohaloarchaeota
Unclassified archaea
Pacearchaeota
Woesearchaeota, Nanoarchaeota
Woesearchaeota
AltiarchaealesZ7ME43
Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciE43
Archaeoglobi, Methanomicrobia, Halobacteria, , ,, , ,
Aciduliprofundum, Thermoplasmatagg
Uncultured Thermoplasmatap ,p ,
Thermoplasmatap
Unclassified archaea
Korarchaeota
,
CrenarchaeotaCrenarchaeota
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 tEukaryotes
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 forgroups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups andothers are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resultinggroups 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 supportfrom 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newickformat 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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Also many uncultured eukaryotic groups
5353
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
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
• Statistics55
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
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
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
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
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
Bacterial and Archaeal Shapes
Archaea cell membranes have lipids with fatty acids linked to glycerol by ether linkages (a synapomorphy of archaea):
62
Ester Linkages
Bacterial and eukaryotic cell membranes have lipids with fatty acids connected to glycerol by ester linkages:
63
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
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Motility of Vibrio (a member of the Proteobacteria phylum)
68
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Corkscrew Movement of Spiraling (A Cyanobacterium)
69
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
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.
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.
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
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
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
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
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
Stramenopiles: Oomcyetes
Phytophthora
Potato Late Blight
• Non-photosynthetic. • Are absorptive heterotrophs • Once were classed as fungi, but
are unrelated.
79Sudden Oak Death
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
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
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
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
•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
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
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
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
Chlamydomonas
90
Plantae: Chlorophytes
Movement in the green alga Volvox
Micrasterias
Multicellular Bacteria (Stigmatella, a Proteobacterium)
Photo 26.24 Fruiting body of gliding bacterium Stigmatella aurantiaca. SEM.91
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Photo 26.4 Filaments of photoautotrophic cyanobacteria,
93
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
More on Multicellularity Later in BIS2C
94
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
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Functional Diversity Covered in
Labs 2 and 3 and Lecture 11-13
99
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
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Red tide caused by dinoflagellates (Gonyaulax sp.).
103
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
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
Excavates: Kinetoplastids
• Unicellular parasites with two flagella and a single mitochondrion.
• Mitochondrion contains a kinetoplast - structure with multiple, circular DNA molecules
• Includes trypanosomes and agents of chagas, sleeping sickness, Leishmaniasis
Trypanosoma sp.mixed with blood cells
106
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Interactions Covered in
Lecture 12-13 and Labs 3 and 3
109
Organelle Diversity
• A key feature of eukaryotes is the possession of diverse organelles
• Two key ones we will focus on are mitochondria and chloroplasts
• Pay particular attention to where (what organisms) they are found or not found in eukaryotes
110
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
112
Excavates: Euglenids
• Have flagella. • Some are
photosynthetic, some always heterotrophic, and some can switch.
113
Movement in the euglenoid Eutreptia
•All are multicellular; some get very large (e.g., giant kelp). •The carotenoid fucoxanthin imparts the brown color. •Almost exclusively marine.
Stramenopiles: Brown Algae
114
A community of brown algae: The marine kelp forest
•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
115
Certium tenue
Coral symbiont
Stramenopiles: Diatoms
116
A colony of the diatom, Bacillaria paradoxa
•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
Rhizaria: Cercozoans
Some cercozoans are aquatic, others live in soil.
They have diverse forms and habitats.
One group has chloroplasts derived from a green alga by secondary endosymbiosis.
Euglyphid
117
Chlorarachnion reptans
Plantae: Red Algae
118
• Most red algae are marine and multicellular. • Red pigment is phycoerythrin. •Many reproduce with spores
Motile spores from Purpureofilum
Audouinella pacifica
Spyridia
Plantae: Chlorophytes• Sister group to charophytes and land plants.
• Synapomorphies include chlorophyll a and b, and starch as a storage product.
• >17,000 species; marine, freshwater, and terrestrial. Unicellular to large multicellular forms.
Chlamydomonas
119
Movement in the green alga Volvox
Micrasterias
Plantae: Glaucophytes
• Unicellular, freshwater organisms
• The chloroplast retains a bit of peptidoglycan between the inner and outer membrane.
120