Lecture 08 (3 2-2021) rares

Kristen DeAngelis
Kristen DeAngelisAssistant Professor at University of Massachusetts Amherst em University of Massachusetts Amherst
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Lecture 08 (3 2-2021) rares
The SARS-CoV-2 genome is highly reduced… and has no 16S ribosomal RNA genes ul Qamar et al., 2020
RARE AND UNCULTURED MICROBES Unit 08, 3.2.2021 Reading for today: Brown Ch. 13 & 14 Reading for next class: Brown Ch. 16, Walter & Ley (moodle) Dr. Kristen DeAngelis Office Hours by appointment deangelis@microbio.umass.edu Poll Q
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. 6
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. 7
Deinococcus/Thermus, Chlamydia & Planctomycetes
Deinococci, Chlamydia & Planctomycetes • There are 13 main phyla, and we are talking about three with few cultured representatives • The Chlamydia & Planctomycetes are closely related • Deinococcus-thermus is one of the more deeply branching phyla.
Phylum Deinococcus-Thermus
Phylum Deinococcus-Thermus • There are two well-known genera in this phylum, Deinococcus and Thermus – These two genera are phenotypically and phylogenetically quite different • Examples – Deinococcus radiodurans – Thermus aquaticus
Deinococcus radiodurans Phylum Deinococcus-Thermus Cell division by septal curtain
Deinococcus radiodurans • 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 – maintains several copies of the each of its two chromosomes, as the mechanism of DNA stress resistance • cells divide by forming a septal curtain – It closes in like the shutter of a camera – There are two perpendicular curtains formedin cell division, producing tetrads
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
Phylum Planctomycetes Fig. 13.12 P. bekefii Fig. 13.13 P. bekefii
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
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
Phylum Chlamydiae
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
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. trachomatis elementary bodies attached to human sperm. From Courtney S. Hossenzadeh in Microbiology Today.
Developmental cycle of Chlamydia
Developmental cycle of Chlamydia • Biphasic life cycle – Elemental bodies are infectious 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
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
Activity for Review of Unit 08.1 Rare phyla Ernst Haeckl’s Tree of Life was wrong because it’s based on morphology. Today, scientists are using Machine Learning to identify microbes by morphology. What are some distinct morphologies, and which organisms are they linked to? 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. 25 Poll Q
Bacterial phyla with few to no cultivated representatives
Bacterial phyla with few to no cultivated representatives • The 13 “main” phyla were described by Carl Woese in his classic 1987 paper • Since then, sequencing revealed 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)
Molecular approaches aka ‘Omics • Amplicon-based sequencing – limited capacity for discovery – Better for phylogenetics because traits can be aligned • Shotgun sequencing – Lots of room for discovery – Half of sequences have no known homology
Assembling whole genomes from metagenomic data using binning • Short sequences are “binned” based on shared characteristics – GC content – taxonomy – Coverage (sequence depth) – K-mer frequency http://dx.doi.org/10.3389/fmicb.2015.01451
Detecting unculturable bacteria • Genomics – sequencing whole genomes, DNA • Transcriptomics – sequencing RNA from genomes • Proteomics – sequencing proteins • Metabolomics – identification of all metabolites, usually by analytical chemistry • Meta- – Add the prefix “meta-” to any of the above, and it refers to sequencing mixed communities instead of single species – For example, Metagenomics – sequencing mixed communities – For example, Metatranscriptomics – sequencing RNA from mixed communities
New Tree of Life
Slides thanks to Jonathan Eisen! @phylogenomics
A “new” tree of life • Shotgun sequencing from a diversity of environments, including filtration to include very small organisms • Based largely on metagenome-assembled genomes (MAGs) • Tree constructed based on aligned and concatenated a set of 16 ribosomal protein sequences from each organism • Two surprising attributes – Topology: Recovery of a two-domain tree of life – Uncultured diversity is the majority (e.g. the CPR)
3 Domain ToLs • Woesian tree (top) – Based on structural RNA sequences • Alternative 3-domain ToL (middle) – Based on protein structures • NOT a ToL (bottom) – No tree places the root in the Eukarya – “Prokaryote” is NOT a monophyletic group – LUCA was not a eukaryote 34 34 Bacteria Archaea Eukaryotes root Bacteria Archaea Eukaryotes root Bacteria Archaea root
Eocyte hypothesis 35
Eocyte hypothesis • some analyses of the protein translation elongation factors, paralogs used to root the 3-domains tree, do not actually recover the 3 domains • These 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.
The two-domain Eocyte ToL vs the three-domain ToL 37 Eukarya Eukarya Bacteria Bacteria Archaea Archaea
• These are competing hypotheses for the origin of the domain 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) most closely related to the eukaryotes. – Paraphyletic = monophyletic except for one group 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. The two-domain Eocyte ToL vs the three-domain ToL
5 Eukaryotic supergroups: • Excavates • Chromalveolates • Plantae • Rhizaria • Unikonts Bacteria Eukaryotes Euryarchaea Crenarchaea
The Eocytes • Domain Eukarya still has 5 supergroups: Excavates, Chromalveolates, Plantae, Rhizaria, & Unikonts – 92 bacterial phyla – we cover 13 in this class ! – 25 Archaeal phyla • Crenarchaeota (aka the Eocytes) • In this tree, Archaea are a polyphyletic group – Euryarchaeota – Other phyla including Thaumarchaeota, Nanoarchaeum, Koryarchaeum 40
Activity for Review of Unit 08.2 Eocyte hypothesis • Based on what you know about how to make a tree, and how to make and root a tree of life, why do you think that there are so many models (trees) of the phylogeny of life? 41
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 Poll Q
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
Hug et al. 2016. Nature Microbiology. New View of the Domain Bacteria • And a new phylum: the Candidate Phyla Radiation – “CPR” – all members have small genomes and most have restricted metabolic capacities. – Most are likely symbionts, with greatly reduced genomes. • A striking feature of this tree is the large number of major lineages without isolated representatives (🔴). – Uncultivated organisms clearly comprise the majority of life’s current diversity • Domain Bacteria includes more major lineages of organisms than the other Domains. – Domain bacteria is the most diverse domain
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 Phyla never grown in the lab Hug et al. 2016. Nature Microbiology.
Why can’t we cultivate these organisms? • Cryptic nutrient requirements • Auxotrophy • Very slow growth rates • Require specific metabolic partners • Require host to assist in reproduction 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 Bacteroids & Spirochetes Hug et al. 2016. Nature Microbiology.
Bacteroidetes and Spirochaetes • Bacteroidetes – Very diverse phylum – 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
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 Green phototrophic bacteria Hug et al. 2016. Nature Microbiology.
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) – Fix C using H2 or sulfur as electron donors for reverse TCA cycle, strict photolithoautotrophs – Energy is generated via cyclic photophosphorylation – Most can fix N • Cyanobacteria – All carry out oxygenic photosynthesis with two photosystems to get energy and reducing power – fix CO2 via the Calvin cycle – Most can fix N
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 Thermophilic bacteria Hug et al. 2016. Nature Microbiology.
Thermophilic bacteria • Aquifex – thermophilic or extremely thermophilic • Thermotoga – thermophilic, anaerobic fermentative organisms
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 Phylum Proteobacteria Hug et al. 2016. Nature Microbiology.
Proteobacteria • Phylum so diverse that they are mostly are discussed by classes – Alphaproteobacteria – Betaproteobacteria – Gammaproteobacteria – Deltaproteobacteria – Epsilonproteobacteria • In the new ToL, the phylum proteobacteria is not monophyletic! – Because of this the classes are identified individually. – For example, the Deltaproteobacteria branch away from the other Proteos.
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 Gram-positive bacteria Hug et al. 2016. Nature Microbiology.
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
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 Deinococci, Chlamydiae & Planctomycetes Hug et al. 2016. Nature Microbiology.
Deinococci, Chlamydiae & Planctomycetes • Deinococcus/Thermus – Deinococcus, extremely DNA-damage stress resistant mesophiles – Thermus, thermophilic oligotrophs • Chlamydiae – Obligate intracellular pathogens or parasites – Reduced genomes • Planctomycetes – Heterotrophic oligotrophs – Compartmentalization via complex inner membranes
Activity for Review of Unit 08.3 Rare bacteria The Candidate Phyla Radiation (CPR) contain the most deeply-rooted organisms in the bacteria. What kind of traits do you predict that they will have? 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) 60
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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. 6

Kristen DeAngelis
Kristen DeAngelisAssistant Professor at University of Massachusetts Amherst em University of Massachusetts Amherst

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Lecture 08 (3 2-2021) rares

  • 1. Be a Microbio Peer Advisor! • Work with a great team. • Practice leadership skills. • Use your unique skills to build community. • Help us all stay connected. • Show your enthusiasm for microbiology. Applications due March 8th! http://bit.ly/micropa_app Or contact Heather Reed at hreed@umass.edu
  • 2. COVID Conversations: A Q&A on the Microbiology of COVID-19 Tuesday, March 16th @ 5 pm Hosted by Dr. Mandy Muller and Dr. Wilmore Webley of the Microbiology Department Register using barcode below or at www.micro.umass.edu !
  • 4. The SARS-CoV-2 genome is highly reduced… and has no 16S ribosomal RNA genes ul Qamar et al., 2020
  • 5. RARE AND UNCULTURED MICROBES Unit 08, 3.2.2021 Reading for today: Brown Ch. 13 & 14 Reading for next class: Brown Ch. 16, Walter & Ley (moodle) Dr. Kristen DeAngelis Office Hours by appointment deangelis@microbio.umass.edu Poll Q
  • 6. 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. 6
  • 7. 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. 7
  • 9. Deinococci, Chlamydia & Planctomycetes • There are 13 main phyla, and we are talking about three with few cultured representatives • The Chlamydia & Planctomycetes are closely related • Deinococcus-thermus is one of the more deeply branching phyla.
  • 11. Phylum Deinococcus-Thermus • There are two well-known genera in this phylum, Deinococcus and Thermus – These two genera are phenotypically and phylogenetically quite different • Examples – Deinococcus radiodurans – Thermus aquaticus
  • 13. Deinococcus radiodurans • 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 – maintains several copies of the each of its two chromosomes, as the mechanism of DNA stress resistance • cells divide by forming a septal curtain – It closes in like the shutter of a camera – There are two perpendicular curtains formedin cell division, producing tetrads
  • 14. 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
  • 15. Phylum Planctomycetes Fig. 13.12 P. bekefii Fig. 13.13 P. bekefii
  • 16. 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
  • 17. 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
  • 19. 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
  • 20. 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. trachomatis elementary bodies attached to human sperm. From Courtney S. Hossenzadeh in Microbiology Today.
  • 22. Developmental cycle of Chlamydia • Biphasic life cycle – Elemental bodies are infectious 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
  • 23. 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
  • 24. Activity for Review of Unit 08.1 Rare phyla Ernst Haeckl’s Tree of Life was wrong because it’s based on morphology. Today, scientists are using Machine Learning to identify microbes by morphology. What are some distinct morphologies, and which organisms are they linked to? 24
  • 25. 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. 25 Poll Q
  • 26. Bacterial phyla with few to no cultivated representatives
  • 27. Bacterial phyla with few to no cultivated representatives • The 13 “main” phyla were described by Carl Woese in his classic 1987 paper • Since then, sequencing revealed 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)
  • 28. Molecular approaches aka ‘Omics • Amplicon-based sequencing – limited capacity for discovery – Better for phylogenetics because traits can be aligned • Shotgun sequencing – Lots of room for discovery – Half of sequences have no known homology
  • 29. Assembling whole genomes from metagenomic data using binning • Short sequences are “binned” based on shared characteristics – GC content – taxonomy – Coverage (sequence depth) – K-mer frequency http://dx.doi.org/10.3389/fmicb.2015.01451
  • 30. Detecting unculturable bacteria • Genomics – sequencing whole genomes, DNA • Transcriptomics – sequencing RNA from genomes • Proteomics – sequencing proteins • Metabolomics – identification of all metabolites, usually by analytical chemistry • Meta- – Add the prefix “meta-” to any of the above, and it refers to sequencing mixed communities instead of single species – For example, Metagenomics – sequencing mixed communities – For example, Metatranscriptomics – sequencing RNA from mixed communities
  • 31. New Tree of Life
  • 32. Slides thanks to Jonathan Eisen! @phylogenomics
  • 33. A “new” tree of life • Shotgun sequencing from a diversity of environments, including filtration to include very small organisms • Based largely on metagenome-assembled genomes (MAGs) • Tree constructed based on aligned and concatenated a set of 16 ribosomal protein sequences from each organism • Two surprising attributes – Topology: Recovery of a two-domain tree of life – Uncultured diversity is the majority (e.g. the CPR)
  • 34. 3 Domain ToLs • Woesian tree (top) – Based on structural RNA sequences • Alternative 3-domain ToL (middle) – Based on protein structures • NOT a ToL (bottom) – No tree places the root in the Eukarya – “Prokaryote” is NOT a monophyletic group – LUCA was not a eukaryote 34 34 Bacteria Archaea Eukaryotes root Bacteria Archaea Eukaryotes root Bacteria Archaea root
  • 36. Eocyte hypothesis • some analyses of the protein translation elongation factors, paralogs used to root the 3-domains tree, do not actually recover the 3 domains • These 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.
  • 37. The two-domain Eocyte ToL vs the three-domain ToL 37 Eukarya Eukarya Bacteria Bacteria Archaea Archaea
  • 38. • These are competing hypotheses for the origin of the domain 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) most closely related to the eukaryotes. – Paraphyletic = monophyletic except for one group 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. The two-domain Eocyte ToL vs the three-domain ToL
  • 39. 5 Eukaryotic supergroups: • Excavates • Chromalveolates • Plantae • Rhizaria • Unikonts Bacteria Eukaryotes Euryarchaea Crenarchaea
  • 40. The Eocytes • Domain Eukarya still has 5 supergroups: Excavates, Chromalveolates, Plantae, Rhizaria, & Unikonts – 92 bacterial phyla – we cover 13 in this class ! – 25 Archaeal phyla • Crenarchaeota (aka the Eocytes) • In this tree, Archaea are a polyphyletic group – Euryarchaeota – Other phyla including Thaumarchaeota, Nanoarchaeum, Koryarchaeum 40
  • 41. Activity for Review of Unit 08.2 Eocyte hypothesis • Based on what you know about how to make a tree, and how to make and root a tree of life, why do you think that there are so many models (trees) of the phylogeny of life? 41
  • 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 Poll Q
  • 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. Hug et al. 2016. Nature Microbiology. New View of the Domain Bacteria • And a new phylum: the Candidate Phyla Radiation – “CPR” – all members have small genomes and most have restricted metabolic capacities. – Most are likely symbionts, with greatly reduced genomes. • A striking feature of this tree is the large number of major lineages without isolated representatives (🔴). – Uncultivated organisms clearly comprise the majority of life’s current diversity • Domain Bacteria includes more major lineages of organisms than the other Domains. – Domain bacteria is the most diverse domain
  • 45. 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 Phyla never grown in the lab Hug et al. 2016. Nature Microbiology.
  • 46. Why can’t we cultivate these organisms? • Cryptic nutrient requirements • Auxotrophy • Very slow growth rates • Require specific metabolic partners • Require host to assist in reproduction 46
  • 47. 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 Bacteroids & Spirochetes Hug et al. 2016. Nature Microbiology.
  • 48. Bacteroidetes and Spirochaetes • Bacteroidetes – Very diverse phylum – 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
  • 49. 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 Green phototrophic bacteria Hug et al. 2016. Nature Microbiology.
  • 50. 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) – Fix C using H2 or sulfur as electron donors for reverse TCA cycle, strict photolithoautotrophs – Energy is generated via cyclic photophosphorylation – Most can fix N • Cyanobacteria – All carry out oxygenic photosynthesis with two photosystems to get energy and reducing power – fix CO2 via the Calvin cycle – Most can fix N
  • 51. 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 Thermophilic bacteria Hug et al. 2016. Nature Microbiology.
  • 52. Thermophilic bacteria • Aquifex – thermophilic or extremely thermophilic • Thermotoga – thermophilic, anaerobic fermentative organisms
  • 53. 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 Phylum Proteobacteria Hug et al. 2016. Nature Microbiology.
  • 54. Proteobacteria • Phylum so diverse that they are mostly are discussed by classes – Alphaproteobacteria – Betaproteobacteria – Gammaproteobacteria – Deltaproteobacteria – Epsilonproteobacteria • In the new ToL, the phylum proteobacteria is not monophyletic! – Because of this the classes are identified individually. – For example, the Deltaproteobacteria branch away from the other Proteos.
  • 55. 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 Gram-positive bacteria Hug et al. 2016. Nature Microbiology.
  • 56. 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
  • 57. 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 Deinococci, Chlamydiae & Planctomycetes Hug et al. 2016. Nature Microbiology.
  • 58. Deinococci, Chlamydiae & Planctomycetes • Deinococcus/Thermus – Deinococcus, extremely DNA-damage stress resistant mesophiles – Thermus, thermophilic oligotrophs • Chlamydiae – Obligate intracellular pathogens or parasites – Reduced genomes • Planctomycetes – Heterotrophic oligotrophs – Compartmentalization via complex inner membranes
  • 59. Activity for Review of Unit 08.3 Rare bacteria The Candidate Phyla Radiation (CPR) contain the most deeply-rooted organisms in the bacteria. What kind of traits do you predict that they will have? 59
  • 60. 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) 60