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Lecture 08 (4 19-2018) rares

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Unit 8: Rare and Uncultured Microbes
LECTURE LEARNING GOALS
1. Describe the phyla containing rare bacteria: Deinococcus/Thermus, Chlamydia & Planctomycetes.
2. Describe the sequencing methods used to understand uncultured microbes. Explain the Eocyte hypothesis and how this model differs from the three domain tree of life.
3. For the cultured microbes, describe major characteristics for the 13 bacterial phyla, and explain why some microbe remain uncultivated.

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Lecture 08 (4 19-2018) rares

  1. 1. RARE AND UNCULTURED MICROBES Unit 08, 4.19.2018 Reading for today: Brown Ch. 13 & 14 Reading for next class: Brown Ch. 16, Walter & Ley (moodle) Dr. Kristen DeAngelis Life Science Labs (LSL) N435 Office Hours Tu & Th 12:30 to 1:30 pm OR by appointment (RSVP appreciated) deangelis@microbio.umass.edu, 413-577-4669 1
  2. 2. Unit 8: Rare and Uncultured Microbes LECTURE LEARNING GOALS 1.  Describe the phyla containing rare bacteria: Deinococcus/Thermus, Chlamydia & Planctomycetes. 2.  Describe the sequencing methods used to understand uncultured microbes. Explain the Eocyte hypothesis and how this model differs from the three domain tree of life. 3.  For the cultured microbes, describe major characteristics for the 13 bacterial phyla, and explain why some microbe remain uncultivated. 2
  3. 3. Unit 8: Rare and Uncultured Microbes LECTURE LEARNING GOALS 1.  Describe the phyla containing rare bacteria: Deinococcus/Thermus, Chlamydia & Planctomycetes. 2.  Describe the sequencing methods used to understand uncultured microbes. Explain the Eocyte hypothesis and how this model differs from the three domain tree of life. 3.  For the cultured microbes, describe major characteristics for the 13 bacterial phyla, and explain why some microbe remain uncultivated. 3
  4. 4. Deinococcus/Thermus, Chlamydia & Planctomycetes
  5. 5. Deinococci, Chlamydia & Planctomycetes •  There are 13 main phyla, and we are talking about three with few cultured representatives •  The Chlamydia & Planctomycetes are very closely related •  Deinococcus-thermus is one of the more deeply branching phyla.
  6. 6. Phylum Deinococcus-Thermus
  7. 7. Phylum Deinococcus-Thermus •  There are two well-known genera in this phylum, Deinococcus and Thermus •  These organisms are phenotypically and phylogenetically quite different •  The members of the two main orders of this phylum are each very closely related •  Examples –  Deinococcus radiodurans –  Thermus aquaticus
  8. 8. Deinococcus and relatives •  Diversity of the order Deinococcus is low, with a small collection (~18) very closely related species •  Metabolism –  Aerobic heterotrophs –  Mostly mesophiles –  Extreme resistance to DNA-damaging stress: UV radiation, desiccation, oxidizing agents, and mutagens •  Habitat –  Found in soil, sediment, rainwater, sewage, dust –  Rare members of these communities –  Most isolates from irradiated samples (food, clean rooms, and nuclear reactor cooling pools)
  9. 9. Deinococcus radiodurans Phylum Deinococcus-Thermus !"##$%&'&(&)*$+,$!"#$%&'-./01&*$$
  10. 10. Deinococcus radiodurans •  Just like the time and temperature of autoclaving is determined by the need to kill endospores, so the dose of gamma-irradiation for food is based on the need to kill D. rad –  isolated from cans of spoiled meat that had been irradiated –  maintains several copies of the each of its two chromosomes, as the mechanism of DNA stress resistance •  D. radiodurans survives high exposure to gamma- irradiation –  E. coli can withstand up to 500 Gy (Grays, Joules per kilogram) –  For comparison 10 Gy is lethal to humans •  cells divide by forming a septal curtain –  It closes in like the shutter of a camera –  There are two curtains formed producing tetrads
  11. 11. Thermus and relatives •  More diversity than in the order Deinococcus with four genera and many isolates •  Metabolism –  Thermophilic heterotrophs –  Oligotrophs, prefer low nutrient concentrations –  Obligate aerobes or facultative anaerobes •  Habitat –  Neutral to slightly alkaline hot springs –  55oC – 80oC –  Some halophiles, some deep sea hydrothermal vents
  12. 12. Thermus aquaticus Phylum Deinococcus-Thermus •  Isolated from many alkaline hot springs in Yellowstone NP •  Pink colonies, especially when grown in light due to pigments •  Its DNA polymerase is highly heat resistant and error-correcting –  Taq polymerase is commonly used in PCR
  13. 13. Phylum Planctomycetes Fig.  13.12  P.  bekefii   Fig.  13.13  P.  bekefii  
  14. 14. Phylum Planctomycetes •  Diversity is unclear, because they are so few cultivated •  Metabolism of almost all are aerobic, heterotrophic, mesophilic oligotrophs •  Habitats are mostly aquatic and especially eutrophic environments, though sequences are detected in a wide range of environments including wastewater and soils •  Example: Blastopirellula marina
  15. 15. Blastopirellula marina Phylum Planctomycetes •  Common freshwater species •  Reproduce by budding •  Internal membrane-defined compartmentalization –  Central pirellulosome contains the riboplasm and nucleoid (genome) –  Riboplasm contains ribosomes and DNA –  Paryphoplasm contains RNA but not ribosomes
  16. 16. Phylum Chlamydiae
  17. 17. Phylum Chlamydiae •  Low phylogenetic and phenotypic diversity –  Few cultured representatives –  Uncultured diversity seems to be much greater •  Metabolism –  Greatly reduced genomes –  Remain capable of •  information processing (transcription, translation, replication) •  cell envelope •  central metabolism •  Habitat: Obligate intracellular parasites transmitted via small, metabolically inert particles
  18. 18. Chlamydia trachomatis Phylum Chlamydiae •  Human pathogen that causes the most common sexually transmitted disease (STD) in the U.S. •  Most infections are asymptomatic, but untreated infections can cause sterility •  Repeated ocular infection in children can cause blindness C.  trachoma1s  elementary  bodies  a3ached  to  human  sperm.   From  Courtney  S.  Hossenzadeh  in  Microbiology  Today.  
  19. 19. Developmental cycle of Chlamydia
  20. 20. Developmental cycle of Chlamydia •  Biphasic life cycle –  Elemental bodies are infectious, small and metabolically inert –  Replication bodies are much larger, noninfectious and osmotically fragile •  RBs live inside the cell, metabolize, grow and and divide within the endocytic vessicles •  When resources in the cell become limited, most RBs differentiate into EBs and are released from the cell •  Not all infectious cycles end in host cell lysis; some species are released by exocytosis
  21. 21. Reductive evolution •  Over evolutionary time, parasites rely more on the host for the things it needs and may simplify its genome •  This reduction allows the organism to devote more resources to reproduction
  22. 22. Reductive evolution •  Over evolutionary time, parasites rely more on the host for the things it needs and may simplify its genome •  This reduction allows the organism to devote more resources to reproduction •  Examples of reductive evolution in bacteria include –  Chlamydia: phylum of intracellular parasites –  Rikettsias: genus of class Alphaproteobacteria, include mitochondria –  Mycoplasmas: genus of phylum Firmicutes capable of gliding motility
  23. 23. Activity for Review of ! Unit 08.1 Rare phyla Match the rare phylum-bacteria with its relatively unique morphology. Taxa may be used more than once. " " 1.! Elemental bodies" 2.! Extreme tolerance to UV irradiation" 3.! Pirrelulosomes" 4.! Riboplasm" 5.! Taq polymerase " 6.! Division by septal curtain" a)! Blastopirellula marina" b)! Chlamydia" c)! Thermus aquaticus! d)! Deinoccus radiodurans! 23
  24. 24. Unit 8: Rare and Uncultured Microbes LECTURE LEARNING GOALS 1.  Describe the phyla containing rare bacteria: Deinococcus/Thermus, Chlamydia & Planctomycetes. 2.  Describe the sequencing methods used to understand uncultured microbes. Explain the Eocyte hypothesis and how this model differs from the three domain tree of life. 3.  For the cultured microbes, describe major characteristics for the 13 bacterial phyla, and explain why some microbe remain uncultivated. 24
  25. 25. Bacterial phyla with few to no cultivated representatives
  26. 26. Bacterial phyla with few to no cultivated representatives •  The 13 “main” phyla were described by Carl Woese in his classic 1987 paper –  The addition of Aquifex is a more recent addition •  Improvements in sequencing reveal that microbial diversity is much greater than this! •  Most cultivated, characterized bacteria fall into one of five phyla –  Proteoabcteria, Firmicutes, Actinobacteria, Bacteroidetes and Cyanobacteria –  Animal diversity is similar: most animal species belong to a few animal phyla e.g. nematodes (round worms) and arthropods (insects)
  27. 27. Molecular  approaches  aka  ‘Omics   Random  primers  “shotgun”  amplify  all  sequences  
  28. 28. Detecting unculturable bacteria •  Amplicon-based sequencing –  limited capacity for discovery •  Shotgun sequencing is performed with no primers or with random hexamers –  Lots of room for discovery –  Half of sequences have no known homology •  Genomics – sequencing whole genomes •  Metagenomics – sequencing mixed communities •  Transcriptomics – sequencing RNA from genomes •  Metatranscriptomics – sequencing RNA from mixed communities
  29. 29. Assembling whole genomes from metagenomic data using binning •  Puts shotgun sequences into “bins” based on shared characteristics –  GC content –  Coverage –  K-mer frequency –  taxonomy h3p://dx.doi.org/10.3389/fmicb.2015.01451  
  30. 30. New Tree of Life
  31. 31. Slides  thanks  to  Jonathan  Eisen!  @phylogenomics  
  32. 32. A new tree of life •  A striking feature of this tree is the large number of major lineages without isolated representatives (red dots). •  Candidate Phyla Radiation (CPR) –  Based on hundreds of genomes from genome- resolved metagenomics and single-cell genomics methods to date –  all members have relatively small genomes and most have somewhat (if not highly) restricted metabolic capacities. –  Most are likely symbionts, so they have greatly reduced genomes.
  33. 33. 0.4 Candidate Phyla Radiation Microgenomates Parcubacteria Bacteria RBX1 WOR1 Cyanobacteria Melainabacteria PVC superphylum Major lineage lacking isolated representative: Major lineages with isolated representative: italics Dojkabacteria WS6 Peregrinibacteria Gracilibacteria BD1-5, GN02 Absconditabacteria SR1 Katanobacteria WWE3 Berkelbacteria SM2F11 CPR1 CPR3 Nomurabacteria Kaiserbacteria Adlerbacteria Campbellbacteria Wirthbacteria Chloroflexi Armatimonadetes Giovannonibacteria Wolfebacteria Jorgensenbacteria Azambacteria Yanofskybacteria Moranbacteria Magasanikbacteria Uhrbacteria Falkowbacteria Saccharibacteria Woesebacteria Amesbacteria Shapirobacteria Collierbacteria Pacebacteria Beckwithbacteria Roizmanbacteria Gottesmanbacteria Levybacteria Daviesbacteria Curtissbacteria Spirochaetes Firmicutes (Tenericutes) Bacteroidetes Chlorobi Gammaproteobacteria Alphaproteobacteria Betaproteobacteria Actinobacteria Planctomycetes Chlamydiae, Lentisphaerae, Verrucomicrobia Omnitrophica Aminicentantes Rokubacteria NC10 Elusimicrobia Poribacteria Ignavibacteria Dadabacteria TM6 Atribacteria Gemmatimonadetes Cloacimonetes Fibrobacteres Nitrospirae Latescibacteria TA06 Caldithrix Marinimicrobia WOR-3 Zixibacteria Synergistetes Fusobacteria Aquificae Calescamantes Deinococcus-Therm. Caldiserica Dictyoglomi Deltaprotebacteria (Thermodesulfobacteria) Epsilonproteobacteria Deferribacteres Chrysiogenetes Tectomicrobia, Modulibacteria Nitrospinae Acidobacteria Zetaproteo. Thermotogae Acidithiobacillia Hydrogenedentes NKB19 BRC1 New  View  of  the  Domain  Bacteria     •  The  phyla  we  study  make  up  a  small   porRon  of  the  total  esRmated   phylogeneRc  diversity   •  The  total  funcRonal  diversity  is  sRll   unknown.   Hug  et  al.  2016.  Nature  Microbiology.    
  34. 34. Hug  et  al.  2016.  Nature  Microbiology.     New View of the Domain Bacteria •  the CPR, in combination with other lineages that lack isolated representatives (red dots in Fig. 2), clearly comprises the majority of life’s current diversity •  Domain Bacteria includes more major lineages of organisms than the other Domains. •  We do not attribute the smaller scope of the Archaea relative to Bacteria to sampling bias because metagenomics and single-cell genomics methods detect members of both domains equally well.
  35. 35. Eocyte hypothesis 35 Eukarya   Eukarya   Bacteria   Bacteria   Archaea   Archaea  
  36. 36. Eocyte hypothesis •  The two-domain Eocyte tree and the three-domain tree are competing hypotheses for the origin of Eukarya. •  (A) The rooted 3-domains tree posits that the Archaea, consisting of 2 kingdoms Euryarchaeota and Crenarchaeota (eocytes), are monophyletic and more closely related to the eukaryotes than to Bacteria. •  (B) An alternative hypothesis, the eocyte tree, posits that the Archaea are paraphyletic, with the eocytes (Crenarchaeota) alone most closely related to the eukaryotes. •  In both hypotheses the root was placed in the Bacteria in accord with the results of published reciprocal rooting studies using ancient paralogous proteins. •  Cox, C. J., Foster, P. G., Hirt, R. P., Harris, S. R., Embley, T. M. (2008). "The archaebacterial origin of eukaryotes". Proc Natl Acad Sci U S A 105 (51): 20356-61.
  37. 37. Eocyte hypothesis 37
  38. 38. Eocyte hypothesis •  some analyses of the paralogous protein translation elongation factors, used to root the 3-domains tree, do not actually recover the 3 domains •  Instead, they show a tree where the eukaryotic proteins branch as phylum of Archaea called the Crenarchaeota (aka the eocytes) •  shapes of ribosomes in the Crenarchaeota and eukaryotes are more similar to each other than to either bacteria or the second major kingdom of archaea, the Euryarchaeota.
  39. 39. ;'<=>%:?2@9' !=#":*:2=#!A' •! UH-1'10"($ •! !4/)21#'")#10"($ •! X#1*01"$ •! A4&:1/&1$ •! Y*&>)*0($$
  40. 40. The eocytes •  This two-domain Eocyte tree and the three- domain tree are competing hypotheses for the origin of Eukarya. •  Still has 5 eukaryotic supergroups: Excavates, Chromalveolates, Plantae, Rhizaria, & Unikonts –  92 bacterial phyla – we cover 13 in this class –  25 Archaeal phyla •  Crenarchaeota (aka the eocytes) •  Archaea are a paraphyletic group –  Euryarchaeota –  Other phyla including Thaumarchaeota, Nanoarchaeum, Koryarchaeum 40
  41. 41. Activity for Review of ! Unit 08.2 Eocyte hypothesis Which are true of the eocyte hypothesis?" a.! It presents a competing view of the origin of the domain Eukarya." b.! It presents a competing view of the structure of the domain Eukarya." c.! It suggests that the closest relatives to the Eukarya are the eocytes." d.! It is a different understanding of the root of the tree of life and thus LUCA." 41
  42. 42. Unit 8: Rare and Uncultured Microbes LECTURE LEARNING GOALS 1.  Describe the phyla containing rare bacteria: Deinococcus/Thermus, Chlamydia & Planctomycetes. 2.  Describe the sequencing methods used to understand uncultured microbes. Explain the Eocyte hypothesis and how this model differs from the three domain tree of life. 3.  For the cultured microbes, describe major characteristics for the 13 bacterial phyla, and explain why some microbe remain uncultivated. 42
  43. 43. 0.4 Candidate Phyla Radiation Microgenomates Parcubacteria Bacteria RBX1 WOR1 Cyanobacteria Melainabacteria PVC superphylum Major lineage lacking isolated representative: Major lineages with isolated representative: italics Dojkabacteria WS6 Peregrinibacteria Gracilibacteria BD1-5, GN02 Absconditabacteria SR1 Katanobacteria WWE3 Berkelbacteria SM2F11 CPR1 CPR3 Nomurabacteria Kaiserbacteria Adlerbacteria Campbellbacteria Wirthbacteria Chloroflexi Armatimonadetes Giovannonibacteria Wolfebacteria Jorgensenbacteria Azambacteria Yanofskybacteria Moranbacteria Magasanikbacteria Uhrbacteria Falkowbacteria Saccharibacteria Woesebacteria Amesbacteria Shapirobacteria Collierbacteria Pacebacteria Beckwithbacteria Roizmanbacteria Gottesmanbacteria Levybacteria Daviesbacteria Curtissbacteria Spirochaetes Firmicutes (Tenericutes) Bacteroidetes Chlorobi Gammaproteobacteria Alphaproteobacteria Betaproteobacteria Actinobacteria Planctomycetes Chlamydiae, Lentisphaerae, Verrucomicrobia Omnitrophica Aminicentantes Rokubacteria NC10 Elusimicrobia Poribacteria Ignavibacteria Dadabacteria TM6 Atribacteria Gemmatimonadetes Cloacimonetes Fibrobacteres Nitrospirae Latescibacteria TA06 Caldithrix Marinimicrobia WOR-3 Zixibacteria Synergistetes Fusobacteria Aquificae Calescamantes Deinococcus-Therm. Caldiserica Dictyoglomi Deltaprotebacteria (Thermodesulfobacteria) Epsilonproteobacteria Deferribacteres Chrysiogenetes Tectomicrobia, Modulibacteria Nitrospinae Acidobacteria Zetaproteo. Thermotogae Acidithiobacillia Hydrogenedentes NKB19 BRC1 Hug  et  al.  2016.  Nature  Microbiology.     New  View  of   the  Domain  Bacteria  
  44. 44. 0.4 Candidate Phyla Radiation Microgenomates Parcubacteria Bacteria RBX1 WOR1 Cyanobacteria Melainabacteria PVC superphylum Major lineage lacking isolated representative: Major lineages with isolated representative: italics Dojkabacteria WS6 Peregrinibacteria Gracilibacteria BD1-5, GN02 Absconditabacteria SR1 Katanobacteria WWE3 Berkelbacteria SM2F11 CPR1 CPR3 Nomurabacteria Kaiserbacteria Adlerbacteria Campbellbacteria Wirthbacteria Chloroflexi Armatimonadetes Giovannonibacteria Wolfebacteria Jorgensenbacteria Azambacteria Yanofskybacteria Moranbacteria Magasanikbacteria Uhrbacteria Falkowbacteria Saccharibacteria Woesebacteria Amesbacteria Shapirobacteria Collierbacteria Pacebacteria Beckwithbacteria Roizmanbacteria Gottesmanbacteria Levybacteria Daviesbacteria Curtissbacteria Spirochaetes Firmicutes (Tenericutes) Bacteroidetes Chlorobi Gammaproteobacteria Alphaproteobacteria Betaproteobacteria Actinobacteria Planctomycetes Chlamydiae, Lentisphaerae, Verrucomicrobia Omnitrophica Aminicentantes Rokubacteria NC10 Elusimicrobia Poribacteria Ignavibacteria Dadabacteria TM6 Atribacteria Gemmatimonadetes Cloacimonetes Fibrobacteres Nitrospirae Latescibacteria TA06 Caldithrix Marinimicrobia WOR-3 Zixibacteria Synergistetes Fusobacteria Aquificae Calescamantes Deinococcus-Therm. Caldiserica Dictyoglomi Deltaprotebacteria (Thermodesulfobacteria) Epsilonproteobacteria Deferribacteres Chrysiogenetes Tectomicrobia, Modulibacteria Nitrospinae Acidobacteria Zetaproteo. Thermotogae Acidithiobacillia Hydrogenedentes NKB19 BRC1 0.4 Candidate Phyla Radiation Microgenomates cubacteria Bacteria PVC superphylum Major lineage lacking isolated representative: Major lineages with isolated representative: italics egrinibacteria acilibacteria BD1-5, GN02 onditabacteria SR1 Katanobacteria WWE3 CPR3 Nomurabacteria Kaiserbacteria CampbellbacteriaChloroflexi Armatimonadetes ebacteria ensenbacteria asanikbacteria charibacteria WoesebacteriaWoesebacteriaW Amesbacteria obacteria ollierbacteria ebacteria withbacteria oizmanbacteria vybacteria Daviesbacteria vybacteria viesbacteria vybacteria Curtissbacteria Spi Firmicutes (TenericutesTenericutesT )enericutes)enericutes Bacteroidetes Chlorobi Gammaproteobacteria Alphaproteobacteria Betaproteobacteria Actinobacteria Planctomycetes Chlamydiae, Lentisphaerae, VerruVerruV comicrobia Omnitrophica Aminicentantes Rokubacteria Elusimic Poribacteria Ignavibacteria TM6 Atribacteria Gemmatimonadetes Cloacimonetes Fibrobacteres Latescibacteria TA06TA06T Caldithrix Marinimicrobia WOR-3 Zixibacteria Synergistetes Fusobacteria Aquificae Calescamantes Deinococcus-T-T- herm. Caldiserica Dictyoglomi Deltaprotebacteria ( Deltap ( Deltap T Deltap T Deltap hermodesul Deltap hermodesul Deltap fobacteria)fobacteria)f Epsilonproteobacteria Deferribacteferribactef TectomicTectomicT robia, Modulibacteria Nit obia, Modulibacteria Nit obia, Modulibacteria rospinae obia, Modulibacteria ospinae obia, Modulibacteria Acidobacteria Zetaproteo. Thermotogae Acidithiobacillia Hydrogenedentes NKB19 BRC1 ochaetesochaetesochaetes !"#$%&'()(*&+*,-'&.'&/"(&$%0& Candidate P Parcubacteria RBX1 WOR1 Cyanobacteria Melainabacteria Peregrinibacteria Gracilibacteria BD1-5, GN Absconditabacteria SR1 Berkelbacteria SM2F11 Kaiserbacteria Adlerbacteria Campbellbacteria Giovannonibacteria WolWolW febacteriafebacteriaf Jorgensenbacteria Azambacteria YanofsYanofsY kybacteriakybacteriak Moranbacteria Magasanikbacteria Uhrbacteria Falkowbacteria Saccharibacteria Shapirobacteriaobacteria irmicutes Dojkabacteria WS6 CPR1 Wirthbacteria Amesbacteria Shapirobacteria Collierbacteria Pacebacteria Beckwithbacteriakwithbacteriak Roizmanbacteria Gottesmanbacteria Levybacteria Shapir Elusimicrobia vibacteria aldithrix ubacteria NC10NC10ubacteria obia, Modulibacteria ospinae obia, Modulibacteria ospinae obia, Modulibacteria ubacteria NC10NC10 obia, Modulibacteria ospinae obia, Modulibacteria ospinae obia, Modulibacteria Spirochaetes Dadabacteria Nitrospi adabacteria ospi adabacteria rae otebacteria obacteria)obacteria) oteobacteria erribacteres Chrysiogenetes Nitrospinae enedentes NKB19 adabacteria ae ospinae adabacteria siogenetessiogenetessiogenetessiogenetes adabacteria ae ospinae 9.<$"0$1#6$NJIS6$T10./"$;&-/)+&)#)<,6$$
  45. 45. Why can’t we cultivate these organisms? •  Cryptic micronutrient requirements •  Auxotrophy •  Very slow growth rates •  Require specific metabolic partners •  Require host to assist in reproduction •  the CPR, in combination with other lineages that lack isolated representatives (red dots in Fig. 2), clearly comprises the majority of life’s current diversity –  Domain Bacteria includes more major lineages of organisms than the other Domains. –  We do not attribute the smaller scope of the Archaea relative to Bacteria to sampling bias because metagenomics and single-cell genomics methods detect members of both domains equally well. 45
  46. 46. 0.4 Candidate Phyla Radiation Microgenomates Parcubacteria Bacteria RBX1 WOR1 Cyanobacteria Melainabacteria PVC superphylum Major lineage lacking isolated representative: Major lineages with isolated representative: italics Dojkabacteria WS6 Peregrinibacteria Gracilibacteria BD1-5, GN02 Absconditabacteria SR1 Katanobacteria WWE3 Berkelbacteria SM2F11 CPR1 CPR3 Nomurabacteria Kaiserbacteria Adlerbacteria Campbellbacteria Wirthbacteria Chloroflexi Armatimonadetes Giovannonibacteria Wolfebacteria Jorgensenbacteria Azambacteria Yanofskybacteria Moranbacteria Magasanikbacteria Uhrbacteria Falkowbacteria Saccharibacteria Woesebacteria Amesbacteria Shapirobacteria Collierbacteria Pacebacteria Beckwithbacteria Roizmanbacteria Gottesmanbacteria Levybacteria Daviesbacteria Curtissbacteria Spirochaetes Firmicutes (Tenericutes) Bacteroidetes Chlorobi Gammaproteobacteria Alphaproteobacteria Betaproteobacteria Actinobacteria Planctomycetes Chlamydiae, Lentisphaerae, Verrucomicrobia Omnitrophica Aminicentantes Rokubacteria NC10 Elusimicrobia Poribacteria Ignavibacteria Dadabacteria TM6 Atribacteria Gemmatimonadetes Cloacimonetes Fibrobacteres Nitrospirae Latescibacteria TA06 Caldithrix Marinimicrobia WOR-3 Zixibacteria Synergistetes Fusobacteria Aquificae Calescamantes Deinococcus-Therm. Caldiserica Dictyoglomi Deltaprotebacteria (Thermodesulfobacteria) Epsilonproteobacteria Deferribacteres Chrysiogenetes Tectomicrobia, Modulibacteria Nitrospinae Acidobacteria Zetaproteo. Thermotogae Acidithiobacillia Hydrogenedentes NKB19 BRC1 siogenetes 0.4 Candidate Phyla Radiation Microgenomates Parcubacteria Bacteria RBX1 WOR1 Cyanobacteria Melainabacteria PVC superphylum Major lineage lacking isolated representative: Major lineages with isolated representative: italics Dojkabacteria WS6 Peregrinibacteria Gracilibacteria BD1-5, GN02 Absconditabacteria SR1 Katanobacteria WWE3 Berkelbacteria SM2F11 CPR1 CPR3 Nomurabacteria Kaiserbacteria Adlerbacteria Campbellbacteria Wirthbacteria Chloroflexi Armatimonadetes Giovannonibacteria WolWolW febacteriafebacteriaf Jorgensenbacteria Azambacteria YanofsYanofsY kybacteriakybacteriak Moranbacteria Magasanikbacteria Uhrbacteria Falkowbacteria Saccharibacteria WoesebacteriaWoesebacteriaW Amesbacteria Shapirobacteriaobacteria Collierbacteria Pacebacteria Beckwithbacteriakwithbacteriak Roizmanbacteria Gottesmanbacteria Levybacteria Daviesbacteria vybacteria viesbacteria vybacteria Curtissbacteria Spirochaetesochaetesochaetes Firmicutes (TenericutesTenericutesT )enericutes)enericutes Bacteroidetes Chlorobi Gammaproteobacteria Alphaproteobacteria Betaproteobacteria Actinobacteria Planctomycetes Chlamydiae, Lentisphaerae, VerruVerruV comicrobia Omnitrophica Aminicentantes Rokubacteria NC10 Poribacteria Ignavibacteria Dadabacteria TM6 Atribacteria Gemmatimonadetes Cloacimonetes Fibrobacteres Nitrospi adabacteria ospi adabacteria r Latescibacteria TA06TA06T Marinimicrobia WOR-3 Zixibacteria Synergistetes Fusobacteria Aquificae Calescamantes Deinococcus-T-T- herm. Caldiserica Dictyoglomi Deltaprotebacteria ( Deltap ( Deltap T Deltap T Deltap hermodesul Deltap hermodesul Deltap fobacteria)obacteria)fobacteria)f Epsilonproteobacteria Deferribacteferribactef res Chrysiogenetes TectomicTectomicT robia, Modulibacteria Nit obia, Modulibacteria Nit obia, Modulibacteria rospinae obia, Modulibacteria ospinae obia, Modulibacteria Acidobacteria Zetaproteo. Thermotogae Acidithiobacillia Hydrogenedentes NKB19 BRC1 C 8%9$":2)B!'C'D#):294"$"!' ylum oidetes etes ae, obia Elusimicrobia Ignavibacteria Caldithrixaldithrix adabacteria rae es siogenetessiogenetessiogenetessiogenetes ospinae 9.<$"0$1#6$NJIS6$T10./"$;&-/)+&)#)<,6$$
  47. 47. Bacteroidetes and Spirochaetes •  Bacteroidetes –  Very diverse phylum of mostly anaerobic fermenters –  Common in guts of animals •  Spirochaetes –  Found in sediments and some are pathogens –  Mostly heterotrophs with internal polar flagella –  May be progenitors for eukaryotic flagella
  48. 48. 0.4 Candidate Phyla Radiation Microgenomates Parcubacteria Bacteria RBX1 WOR1 Cyanobacteria Melainabacteria PVC superphylum Major lineage lacking isolated representative: Major lineages with isolated representative: italics Dojkabacteria WS6 Peregrinibacteria Gracilibacteria BD1-5, GN02 Absconditabacteria SR1 Katanobacteria WWE3 Berkelbacteria SM2F11 CPR1 CPR3 Nomurabacteria Kaiserbacteria Adlerbacteria Campbellbacteria Wirthbacteria Chloroflexi Armatimonadetes Giovannonibacteria Wolfebacteria Jorgensenbacteria Azambacteria Yanofskybacteria Moranbacteria Magasanikbacteria Uhrbacteria Falkowbacteria Saccharibacteria Woesebacteria Amesbacteria Shapirobacteria Collierbacteria Pacebacteria Beckwithbacteria Roizmanbacteria Gottesmanbacteria Levybacteria Daviesbacteria Curtissbacteria Spirochaetes Firmicutes (Tenericutes) Bacteroidetes Chlorobi Gammaproteobacteria Alphaproteobacteria Betaproteobacteria Actinobacteria Planctomycetes Chlamydiae, Lentisphaerae, Verrucomicrobia Omnitrophica Aminicentantes Rokubacteria NC10 Elusimicrobia Poribacteria Ignavibacteria Dadabacteria TM6 Atribacteria Gemmatimonadetes Cloacimonetes Fibrobacteres Nitrospirae Latescibacteria TA06 Caldithrix Marinimicrobia WOR-3 Zixibacteria Synergistetes Fusobacteria Aquificae Calescamantes Deinococcus-Therm. Caldiserica Dictyoglomi Deltaprotebacteria (Thermodesulfobacteria) Epsilonproteobacteria Deferribacteres Chrysiogenetes Tectomicrobia, Modulibacteria Nitrospinae Acidobacteria Zetaproteo. Thermotogae Acidithiobacillia Hydrogenedentes NKB19 BRC1 0.4 Candidate Phyla Radiation Microgenomates Parcubacteria Bacteria RBX1 OR1 Cyanobacteria Melainabacteria PVC superphylum Major lineage lacking isolated representative: Major lineages with isolated representative: italics Dojkabacteria WS6 Peregrinibacteria Gracilibacteria BD1-5, GN02 Absconditabacteria SR1 Katanobacteria WWE3 Berkelbacteria SM2F11 CPR1 CPR3 Nomurabacteria Kaiserbacteria Adlerbacteria Campbellbacteria Wirthbacteria Chloroflexi Armatimonadetes Giovannonibacteria WolWolW febacteriafebacteriaf Jorgensenbacteria Azambacteria YanofsYanofsY kybacteriakybacteriak Moranbacteria Magasanikbacteria Uhrbacteria Falkowbacteria Saccharibacteria WoesebacteriaWoesebacteriaW Amesbacteria Shapirobacteriaobacteria Collierbacteria Pacebacteria Beckwithbacteriakwithbacteriak Roizmanbacteria Gottesmanbacteria Levybacteria Daviesbacteria vybacteria viesbacteria vybacteria Curtissbacteria Spirochaetesochaetesochaetes Firmicutes (TenericutesTenericutesT )enericutes)enericutes Bacteroidetes Chlorobi Gammaproteobacteria Alphaproteobacteria Betaproteobacteria Actinobacteria Planctomycetes Chlamydiae, Lentisphaerae, VerruVerruV comicrobia Omnitrophica Aminicentantes Rokubacteria NC10 Poribacteria Ignavibacteria Dadabacteria TM6 Atribacteria Gemmatimonadetes Cloacimonetes Fibrobacteres Nitrospi adabacteria ospi adabacteria rae Latescibacteria TA06TA06T Marinimicrobia WOR-3 Zixibacteria Synergistetes Fusobacteria Aquificae Calescamantes Deinococcus-T-T- herm. Caldiserica Dictyoglomi Deltaprotebacteria ( Deltap ( Deltap T Deltap T Deltap hermodesul Deltap hermodesul Deltap fobacteria)obacteria)fobacteria)f Epsilonproteobacteria Deferribacteferribactef res Chrysiogenetessiogenetessiogenetessiogenetes TectomicTectomicT robia, Modulibacteria Nit obia, Modulibacteria Nit obia, Modulibacteria rospinae obia, Modulibacteria ospinae obia, Modulibacteria Acidobacteria Zetaproteo. Thermotogae Acidithiobacillia Hydrogenedentes NKB19 BRC1 y C E:""7'#42$2$:2#4)9'F%9$":)%' R WOR1 Cyanobacteria Melainabacteria ylum oidetes etes ae, obia Elusimicrobia Ignavibacteria Caldithrixaldithrix 9.<$"0$1#6$NJIS6$T10./"$;&-/)+&)#)<,6$$
  49. 49. Green phototrophic bacteria •  Chloroflexi (green non-sulfurs) –  thermophilic phototrophs and heterotrophs –  Single type of photosystem, Cyclic photophosphorylation to get energy (ATP) from light, Most fix C via the hydroxypropionate pathway •  Chlorobi (green sulfurs) –  Small number of closely related species –  Strict photolithoautotrophs, H2 or sulfur are electron donors for reverse TCA cycle to fix C –  Energy is generated via cyclic photophosphorylation –  Most can fix N •  Cyanobacteria –  functionally diverse but phylogenetically closely related –  All carry out oxygenic photosynthesis with two photosystems to get energy and reducing power for fixing CO2 via the Calvin cycle –  Most can fix N
  50. 50. 0.4 Candidate Phyla Radiation Microgenomates Parcubacteria Bacteria RBX1 WOR1 Cyanobacteria Melainabacteria PVC superphylum Major lineage lacking isolated representative: Major lineages with isolated representative: italics Dojkabacteria WS6 Peregrinibacteria Gracilibacteria BD1-5, GN02 Absconditabacteria SR1 Katanobacteria WWE3 Berkelbacteria SM2F11 CPR1 CPR3 Nomurabacteria Kaiserbacteria Adlerbacteria Campbellbacteria Wirthbacteria Chloroflexi Armatimonadetes Giovannonibacteria Wolfebacteria Jorgensenbacteria Azambacteria Yanofskybacteria Moranbacteria Magasanikbacteria Uhrbacteria Falkowbacteria Saccharibacteria Woesebacteria Amesbacteria Shapirobacteria Collierbacteria Pacebacteria Beckwithbacteria Roizmanbacteria Gottesmanbacteria Levybacteria Daviesbacteria Curtissbacteria Spirochaetes Firmicutes (Tenericutes) Bacteroidetes Chlorobi Gammaproteobacteria Alphaproteobacteria Betaproteobacteria Actinobacteria Planctomycetes Chlamydiae, Lentisphaerae, Verrucomicrobia Omnitrophica Aminicentantes Rokubacteria NC10 Elusimicrobia Poribacteria Ignavibacteria Dadabacteria TM6 Atribacteria Gemmatimonadetes Cloacimonetes Fibrobacteres Nitrospirae Latescibacteria TA06 Caldithrix Marinimicrobia WOR-3 Zixibacteria Synergistetes Fusobacteria Aquificae Calescamantes Deinococcus-Therm. Caldiserica Dictyoglomi Deltaprotebacteria (Thermodesulfobacteria) Epsilonproteobacteria Deferribacteres Chrysiogenetes Tectomicrobia, Modulibacteria Nitrospinae Acidobacteria Zetaproteo. Thermotogae Acidithiobacillia Hydrogenedentes NKB19 BRC1 0.4 Candidate Phyla Radiation Microgenomates Parcubacteria Bacteria RBX1 WOR1 Cyanobacteria Melainabacteria PVC superphylum Major lineage lacking isolated representative: Major lineages with isolated representative: italics Dojkabacteria WS6 Peregrinibacteria Gracilibacteria BD1-5, GN02 Absconditabacteria SR1 Katanobacteria WWE3 Berkelbacteria SM2F11 CPR1 CPR3 Nomurabacteria Kaiserbacteria Adlerbacteria Campbellbacteria Wirthbacteria Chloroflexi Armatimonadetes Giovannonibacteria WolWolW febacteriafebacteriaf Jorgensenbacteria Azambacteria YanofsYanofsY kybacteriakybacteriak Moranbacteria Magasanikbacteria Uhrbacteria Falkowbacteria Saccharibacteria WoesebacteriaWoesebacteriaW Amesbacteria Shapirobacteriaobacteria Collierbacteria Pacebacteria Beckwithbacteriakwithbacteriak Roizmanbacteria Gottesmanbacteria Levybacteria Daviesbacteria vybacteria viesbacteria vybacteria Curtissbacteria Spirochaetesochaetesochaetes Firmicutes (TenericutesTenericutesT )enericutes)enericutes Bacteroidetes Chlorobi Gammaproteobacteria Alphaproteobacteria Betaproteobacteria Actinobacteria Planctomycetes Chlamydiae, Lentisphaerae, VerruVerruV comicrobia Omnitrophica Aminicentantes Rokubacteria NC10 Elusimicrobia Poribacteria Ignavibacteria Dadabacteria TM6 Atribacteria Gemmatimonadetes Cloacimonetes Fibrobacteres Nitrospi adabacteria ospi adabacteria rae Latescibacteria TA06TA06T Caldithrixaldithrix Marinimicrobia WOR-3 Zixibacteria Synergistetes Fusobacteria Aquificae Calescamantes Deinococcus-T-T- herm. Caldiserica Dictyoglomi Deltaprotebacteria ( Deltap ( Deltap T Deltap T Deltap hermodesul Deltap hermodesul Deltap fobacteria)obacteria)fobacteria)f Epsilonproteobacteria Deferribacteferribactef res Chrysiogenetessiogenetessiogenetessiogenetes TectomicTectomicT robia, Modulibacteria Nit obia, Modulibacteria Nit obia, Modulibacteria rospinae obia, Modulibacteria ospinae obia, Modulibacteria Acidobacteria Zetaproteo. Thermotogae Acidithiobacillia Hydrogenedentes NKB19 BRC1 G4":62#4)&)9'F%9$":)%' 9.<$"0$1#6$NJIS6$T10./"$;&-/)+&)#)<,6$$
  51. 51. Thermophilic bacteria •  Aquifex – thermophilic or extremely thermophilic •  Thermotoga – thermophilic, anaerobic fermentative organisms
  52. 52. 0.4 Candidate Phyla Radiation Microgenomates Parcubacteria Bacteria RBX1 WOR1 Cyanobacteria Melainabacteria PVC superphylum Major lineage lacking isolated representative: Major lineages with isolated representative: italics Dojkabacteria WS6 Peregrinibacteria Gracilibacteria BD1-5, GN02 Absconditabacteria SR1 Katanobacteria WWE3 Berkelbacteria SM2F11 CPR1 CPR3 Nomurabacteria Kaiserbacteria Adlerbacteria Campbellbacteria Wirthbacteria Chloroflexi Armatimonadetes Giovannonibacteria Wolfebacteria Jorgensenbacteria Azambacteria Yanofskybacteria Moranbacteria Magasanikbacteria Uhrbacteria Falkowbacteria Saccharibacteria Woesebacteria Amesbacteria Shapirobacteria Collierbacteria Pacebacteria Beckwithbacteria Roizmanbacteria Gottesmanbacteria Levybacteria Daviesbacteria Curtissbacteria Spirochaetes Firmicutes (Tenericutes) Bacteroidetes Chlorobi Gammaproteobacteria Alphaproteobacteria Betaproteobacteria Actinobacteria Planctomycetes Chlamydiae, Lentisphaerae, Verrucomicrobia Omnitrophica Aminicentantes Rokubacteria NC10 Elusimicrobia Poribacteria Ignavibacteria Dadabacteria TM6 Atribacteria Gemmatimonadetes Cloacimonetes Fibrobacteres Nitrospirae Latescibacteria TA06 Caldithrix Marinimicrobia WOR-3 Zixibacteria Synergistetes Fusobacteria Aquificae Calescamantes Deinococcus-Therm. Caldiserica Dictyoglomi Deltaprotebacteria (Thermodesulfobacteria) Epsilonproteobacteria Deferribacteres Chrysiogenetes Tectomicrobia, Modulibacteria Nitrospinae Acidobacteria Zetaproteo. Thermotogae Acidithiobacillia Hydrogenedentes NKB19 BRC1 0.4 Candidate Phyla Radiation Parcubacteria Bacteria RBX1 WOR1 Cyanobacteria Melainabacteria PVC superphylum Peregrinibacteria Gracilibacteria BD1-5, GN02 Absconditabacteria SR1 Berkelbacteria SM2F11 Nomurabacteria Kaiserbacteria Adlerbacteria CampbellbacteriaChloroflexi Armatimonadetes Giovannonibacteria WolWolW febacteriafebacteriaf Jorgensenbacteria Azambacteria YanofsYanofsY kybacteriakybacteriak Moranbacteria Magasanikbacteria Uhrbacteria Falkowbacteria Saccharibacteria WoesebacteriaWoesebacteriaW Firmicutes (TenericutesTenericutesT )enericutes)enericutes Bacteroidetes Chlorobi Gammaproteobacteria Alphap Betaproteobacteria Actinobacteria Planctomycetes Chlamydiae, Lentisphaerae, VerruVerruV comicrobia Omnitrophica Aminicentantes Rokubacteria NC10 Elusimicrobia Poribacteria Ignavibacteria Atribacteria Gemmatimonadetes Cloacimonetes Fibrobacteres Nitrospi Latescibacteria TA06TA06T Caldithrixaldithrix Marinimicrobia WOR-3 Zixibacteria Synergistetes Fusobacteria Aquificae Calescamantes Deinococcus-T-T- herm. Caldiserica Dictyoglomi Deltap ( Deltap ( Deltap T Deltap T Deltap Epsilonp TectomicTectomicT robia, Modulibacteria Nit obia, Modulibacteria Nit obia, Modulibacteria Acidobacteria Thermotogae H BRC1 H4?&=6'!*,/(,0%1/(*.%& Spirochaetes Alphaproteobacteria Dadabacteria TM6 ospi adabacteria ospi adabacteria Deltaprotebacteria T Deltap T Deltap hermodesul Deltap hermodesul Deltap fobacteria)fobacteria)f Epsilonproteobacteria Deferribacteferribactef Chr Zetaproteo. Acidithiobacillia ydrogenedentes NKB19 Z A oteobacteria oteobacteria ochaetesochaetesochaetes erribacteres hrysiogenetessiogenetessiogenetessiogenetes enedentes NKB19 adabacteria ospirae obia, Modulibacteria Nit obia, Modulibacteria Nit obia, Modulibacteria rospinae obia, Modulibacteria ospinae obia, Modulibacteria cidobacteria adabacteria ospi adabacteria ospi adabacteria obacteria) hr adabacteria obacteria)obacteria) hrysiogenetes 9.<$"0$1#6$NJIS6$T10./"$;&-/)+&)#)<,6$$
  53. 53. Proteobacteria •  Phylum so diverse that mostly are discussed by classes –  Alphaproteobacteria –  Betaproteobacteria –  Gammaproteobacteria –  Deltaproteobacteria –  Epsilonproteobacteria •  In this new view, the phylum proteobacteria is no longer monophyletic! Because of this the classes are identified individually. For example, the Deltaproteobacteria branch away from the other Proteos.
  54. 54. 0.4 Candidate Phyla Radiation Microgenomates Parcubacteria Bacteria RBX1 WOR1 Cyanobacteria Melainabacteria PVC superphylum Major lineage lacking isolated representative: Major lineages with isolated representative: italics Dojkabacteria WS6 Peregrinibacteria Gracilibacteria BD1-5, GN02 Absconditabacteria SR1 Katanobacteria WWE3 Berkelbacteria SM2F11 CPR1 CPR3 Nomurabacteria Kaiserbacteria Adlerbacteria Campbellbacteria Wirthbacteria Chloroflexi Armatimonadetes Giovannonibacteria Wolfebacteria Jorgensenbacteria Azambacteria Yanofskybacteria Moranbacteria Magasanikbacteria Uhrbacteria Falkowbacteria Saccharibacteria Woesebacteria Amesbacteria Shapirobacteria Collierbacteria Pacebacteria Beckwithbacteria Roizmanbacteria Gottesmanbacteria Levybacteria Daviesbacteria Curtissbacteria Spirochaetes Firmicutes (Tenericutes) Bacteroidetes Chlorobi Gammaproteobacteria Alphaproteobacteria Betaproteobacteria Actinobacteria Planctomycetes Chlamydiae, Lentisphaerae, Verrucomicrobia Omnitrophica Aminicentantes Rokubacteria NC10 Elusimicrobia Poribacteria Ignavibacteria Dadabacteria TM6 Atribacteria Gemmatimonadetes Cloacimonetes Fibrobacteres Nitrospirae Latescibacteria TA06 Caldithrix Marinimicrobia WOR-3 Zixibacteria Synergistetes Fusobacteria Aquificae Calescamantes Deinococcus-Therm. Caldiserica Dictyoglomi Deltaprotebacteria (Thermodesulfobacteria) Epsilonproteobacteria Deferribacteres Chrysiogenetes Tectomicrobia, Modulibacteria Nitrospinae Acidobacteria Zetaproteo. Thermotogae Acidithiobacillia Hydrogenedentes NKB19 BRC1 0.4 Candidate Phyla Radiation Microgenomates Parcubacteria Bacteria RBX1 WOR1 Cyanobacteria Melainabacteria PVC superphylum Major lineage lacking isolated representative: Major lineages with isolated representative: italics Dojkabacteria WS6 Peregrinibacteria Gracilibacteria BD1-5, GN02 Absconditabacteria SR1 Katanobacteria WWE3 Berkelbacteria SM2F11 CPR1 CPR3 Nomurabacteria Kaiserbacteria Adlerbacteria Campbellbacteria Wirthbacteria Armatimonadetes Giovannonibacteria WolWolW febacteriafebacteriaf Jorgensenbacteria Azambacteria YanofsYanofsY kybacteriakybacteriak Moranbacteria Magasanikbacteria Uhrbacteria Falkowbacteria Saccharibacteria WoesebacteriaWoesebacteriaW Amesbacteria Shapirobacteriaobacteria Collierbacteria Pacebacteria Beckwithbacteriakwithbacteriak Roizmanbacteria Gottesmanbacteria Levybacteria Daviesbacteria vybacteria viesbacteria vybacteria Curtissbacteria Spirochaetesochaetesochaetes (TenericutesTenericutesT )enericutes)enericutes Bacteroidetes Chlorobi Gammaproteobacteria Alphaproteobacteria Betaproteobacteria Actinobacteria Planctomycetes Chlamydiae, Lentisphaerae, VerruVerruV comicrobia Omnitrophica Aminicentantes Rokubacteria NC10 Elusimicrobia Poribacteria Ignavibacteria Dadabacteria TM6 Atribacteria Gemmatimonadetes Cloacimonetes Fibrobacteres Nitrospi adabacteria ospi adabacteria rae Latescibacteria TA06TA06T Caldithrixaldithrix Marinimicrobia WOR-3 Zixibacteria Synergistetes Fusobacteria Aquificae Calescamantes Deinococcus-T-T- herm. Caldiserica Dictyoglomi Deltaprotebacteria ( Deltap ( Deltap T Deltap T Deltap hermodesul Deltap hermodesul Deltap fobacteria)obacteria)fobacteria)f Epsilonproteobacteria Deferribacteferribactef res Chrysiogenetessiogenetessiogenetessiogenetes TectomicTectomicT robia, Modulibacteria Nit obia, Modulibacteria Nit obia, Modulibacteria rospinae obia, Modulibacteria ospinae obia, Modulibacteria Acidobacteria Zetaproteo. Thermotogae Acidithiobacillia Hydrogenedentes NKB19 BRC1 E:%6I#2!)@J"'F%9$":)%' Armatimonadetes Firmicutes Chloroflexi herm. 9.<$"0$1#6$NJIS6$T10./"$;&-/)+&)#)<,6$$
  55. 55. Gram-positive bacteria •  Firmicutes – aka low G+C Gram positive bacteria – Almost all Heterotrophs, Anaerobes use substrate-level phosphorylation rather than anaerobic respiration •  Actinobacteria – Aka high G+C Gram positive bacteria – Filamentous, aerobic respirers – Known antibiotic producers
  56. 56. 0.4 Candidate Phyla Radiation Microgenomates Parcubacteria Bacteria RBX1 WOR1 Cyanobacteria Melainabacteria PVC superphylum Major lineage lacking isolated representative: Major lineages with isolated representative: italics Dojkabacteria WS6 Peregrinibacteria Gracilibacteria BD1-5, GN02 Absconditabacteria SR1 Katanobacteria WWE3 Berkelbacteria SM2F11 CPR1 CPR3 Nomurabacteria Kaiserbacteria Adlerbacteria Campbellbacteria Wirthbacteria Chloroflexi Armatimonadetes Giovannonibacteria Wolfebacteria Jorgensenbacteria Azambacteria Yanofskybacteria Moranbacteria Magasanikbacteria Uhrbacteria Falkowbacteria Saccharibacteria Woesebacteria Amesbacteria Shapirobacteria Collierbacteria Pacebacteria Beckwithbacteria Roizmanbacteria Gottesmanbacteria Levybacteria Daviesbacteria Curtissbacteria Spirochaetes Firmicutes (Tenericutes) Bacteroidetes Chlorobi Gammaproteobacteria Alphaproteobacteria Betaproteobacteria Actinobacteria Planctomycetes Chlamydiae, Lentisphaerae, Verrucomicrobia Omnitrophica Aminicentantes Rokubacteria NC10 Elusimicrobia Poribacteria Ignavibacteria Dadabacteria TM6 Atribacteria Gemmatimonadetes Cloacimonetes Fibrobacteres Nitrospirae Latescibacteria TA06 Caldithrix Marinimicrobia WOR-3 Zixibacteria Synergistetes Fusobacteria Aquificae Calescamantes Deinococcus-Therm. Caldiserica Dictyoglomi Deltaprotebacteria (Thermodesulfobacteria) Epsilonproteobacteria Deferribacteres Chrysiogenetes Tectomicrobia, Modulibacteria Nitrospinae Acidobacteria Zetaproteo. Thermotogae Acidithiobacillia Hydrogenedentes NKB19 BRC1 0.4 Candidate Phyla Radiation Microgenomates Parcubacteria Bacteria RBX1 WOR1 Cyanobacteria Melainabacteria PVC superphylum Major lineage lacking isolated representative: Major lineages with isolated representative: italics Dojkabacteria WS6 Peregrinibacteria Gracilibacteria BD1-5, GN02 Absconditabacteria SR1 Katanobacteria WWE3 Berkelbacteria SM2F11 CPR1 CPR3 Nomurabacteria Kaiserbacteria Adlerbacteria Campbellbacteria Wirthbacteria Chloroflexi Armatimonadetes Giovannonibacteria WolWolW febacteriafebacteriaf Jorgensenbacteria Azambacteria YanofsYanofsY kybacteriakybacteriak Moranbacteria Magasanikbacteria Uhrbacteria Falkowbacteria Saccharibacteria WoesebacteriaWoesebacteriaW Amesbacteria Shapirobacteriaobacteria Collierbacteria Pacebacteria Beckwithbacteriakwithbacteriak Roizmanbacteria Gottesmanbacteria Levybacteria Daviesbacteria vybacteria viesbacteria vybacteria Curtissbacteria Spirochaetesochaetesochaetes Firmicutes (TenericutesTenericutesT )enericutes)enericutes Bacteroidetes Chlorobi Gammaproteobacteria Alphaproteobacteria Betaproteobacteria Actinobacteria Planctomycetes Chlamydiae, Lentisphaerae, VerruVerruV comicrobia Omnit Aminicentantes Rokubacteria NC10 Elusimicrobia Poribacteria Ignavibacteria Dadabacteria TM6 Atribacteria Gemmatimonadetes Cloacimonetes Fibrobacteres Nitrospi adabacteria ospi adabacteria rae Latescibacteria TA06TA06T Caldithrixaldithrix Marinimicrobia WOR-3 Zixibacteria Synergistetes Fusobacteria Aquificae Calescamantes Deinococcus-T-T- herm. Caldiserica Dictyoglomi Deltaprotebacteria ( Deltap ( Deltap T Deltap T Deltap hermodesul Deltap hermodesul Deltap fobacteria)obacteria)fobacteria)f Epsilonproteobacteria Deferribacteferribactef res Chrysiogenetessiogenetessiogenetessiogenetes TectomicTectomicT robia, Modulibacteria Nit obia, Modulibacteria Nit obia, Modulibacteria rospinae obia, Modulibacteria ospinae obia, Modulibacteria Acidobacteria Zetaproteo. Thermotogae Acidithiobacillia Hydrogenedentes NKB19 BRC1 >%(6/-/--(Z$).4,0<5(,%$[$!4,6-*/0<-%*%2& mnit entantes Rokubacteria NC10 mnitrophica R kubacteria NC10 9.<$"0$1#6$NJIS6$T10./"$;&-/)+&)#)<,6$$
  57. 57. Deinococci, Chlamydiae & Planctomycetes •  Deinococci –  Includes Deinococcus, extremely DNA- damage stress resistant mesophiles, and Thermus, thermophilic oligotrophs •  Chlamydiae –  Obligate intracellular pathogens or parasites –  Reduced genomes •  Planctomycetes –  Heterotrophic oligotrophs –  Compartmentalization via complex inner membranes
  58. 58. Activity for Review of ! Unit 08.3 Rare bacteria 1.! What are some reasons why bacteria from the rare phyla remain uncultivated?" 2.! For each pair of phyla below, circle the phylum that is the most phylogenetically diverse." •! Proteobacteria or Chlorflexi" •! Deinococcus or Firmicutes" •! Chlorobi or Bacteroidetes" •! Candidate Phylum Radiation or Chlamydia" 58
  59. 59. Unit 8: Rare and Uncultured Microbes LECTURE LEARNING GOALS 1.  Describe the phyla containing rare bacteria: Deinococcus/Thermus, Chlamydia & Planctomycetes. 2.  Describe the sequencing methods used to understand uncultured microbes. Explain the Eocyte hypothesis and how this model differs from the three domain tree of life. 3.  For the cultured microbes, describe major characteristics for the 13 bacterial phyla, and explain why some microbe remain uncultivated. Next class is Unit 9: Diversity of the Human Microbiome Reading for next class: Brown Ch. 16, Walter & Ley (moodle) 59
  60. 60. Molecular approaches aka ‘Omics •  Genomics – sequencing whole genomes •  Metagenomics – sequencing mixed communities •  Transcriptomics – sequencing RNA from genomes •  Metatranscriptomics – sequencing RNA from mixed communities
  61. 61. 16S ribosomal RNA primers Kuczynski  et  al  2012,  Nature  Reviews  Gene1cs  13,  47-­‐58    
  62. 62. Kuczynski  et  al  2012,  Nature  Reviews  Gene1cs  13,  47-­‐58     Molecular  approaches  aka  ‘Omics   Random  primers  “shotgun”  amplify  all  sequences  

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