bis2c: lecture 9: microbial diversity

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016

Lecture 9: Microbial Diversity

BIS 002C Biodiversity & the Tree of Life

Spring 2016

Prof. Jonathan Eisen

1


Where we are going and where we have been

• Previous Lecture: !8: The Tree of Life II

• Current Lecture: !9: Microbial Diversity

• Next Lecture: !10: The Not Quite a Tree Tree of Life

2

Lectures 9-13 Microbial Diversity

• The Tree of Life is mostly microbial

• Diverse methods are available for studying microbial diversity

• Most of the diversity of microbial life is poorly characterized

• The Tree of Life is not actually a tree

• The biological diversity (form, function, etc) seen in microbes is immense

• Microbes run (kind of) the planet

• Microbial interactions (with each other and non-microbes) also help run the planet

3

Lectures 9








4

Lectures 10








5

Lecture 11








6

Lectures 12-13








7


Lecture 9: Microbial Diversity




8

Unrooted Tree of Life (from ~ 2004)

9adapted from Baldauf, et al., in Assembling the Tree of Life, 2004


P PlantsTwo Weeks



FFungi

One Week

P



AAnimals

Two Weeks

P



1.5 Weeks


Unrooted Tree of Life


1.5 Weeks Mostly Microbes


The Bacteria and Archaea via Textbook v.10

15


Eukaryotic Groups via Textbook v.10

16


Eukaryote Groups - More Detail

1717


Microbial Diversity




18

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 20

Field Observations Are Important Tools


• Field studies of multicellular organisms are of course common

• Show binoculars, butterfly nets, etc

• Field studies of microbes are also possible but a bit more challenging

21

Field Observations Important in Microbial Studies


• More detail on some of these in Labs 2 and 3

22

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 !23

Culturing Microbes


Culturing

• More On This in Lectures 11-12

• Some in Labs 2-3

24


DNA Sequencing

• All cellular organisms have genomes made up of DNA

• All cellular organisms transcribe DNA into RNA and then translate RNA into protein

• Sequencing involves reading the string of letters in DNA, RNA or protein

• Sequencing is usually done on DNA • Sequencing gets cheaper and faster VERY

fast • Sequencing is very useful is studying

microbial diversity25


Sequencing Has Gone Crazy


rRNA Sequencing for Phylogenetic Analysis

27

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG

Taxa Characters S ACUGCACCUAUCGUUCG

E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG

EukaryotesBacteria ?????Archaea


Clicker

28


Which of the following is NOT a reason that analysis of rRNA is useful for inferring a Tree of Life

A: rRNAs are universal homologies B: rRNAs can be sequenced C: rRNAs are transcribed from DNA D: rRNAs have functional roles in ribosomes E: rRNAs don't vary between species

29


Which of the following is NOT a reason that analysis of rRNA is useful for inferring a Tree of Life

A: rRNAs are universal homologies B: rRNAs can be sequenced C: rRNAs are transcribed from DNA D: rRNAs have functional roles in ribosomes E: rRNAs don't vary between species

30


Genome Sequencing Improves Phylogenetic Analysis

31

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG


DNA DNADNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG


Genome Sequencing Has Many Other Uses

32

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

DNA DNADNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG


Genome Sequencing Has Many Other Uses

33

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

DNA DNADNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG

Some Discussion of this in Lecture 10


2002 Most Genomes from a Few Groups

34Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree


2002-2007: TIGR Tree of Life Project


Naomi Ward

KarenNelson


2007-2014: Genomic Encyclopedia



2007-2014: Genomic Encyclopedia


BUT …


Microbial Diversity




38


Great Plate Count Anomaly

39

<<<<

Culturing Observation

CountCount


Great Plate Count Anomaly

39

<<<<

Culturing Observation

CountCount

http://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&docid=rLu5sL207WlE1M&tbnid=CRLQYP7d9d_TcM:&ved=0CAUQjRw&url=http

%3A%2F%2Fwww.biol.unt.edu%2F~jajohnson

%2FDNA_sequencing_process&ei=hFu7U_TyCtOqsQSu9YGwBg&psig=AFQjCNG-8EB

dEljE7-yHFG2KPuBZt8kIPw&ust=14048739512114

24

DNA


rRNA Sequencing from Environmental Samples

40

rRNA rRNArRNA

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG


Taxa Characters S ACUGCACCUAUCGUUCG

E ACUCCAGCUAUCGAUCG

C ACCCCAGCUCUCGCUCG



Metagenomics Improves Phylogenetic Resolution

41

metagenomics

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG


EukaryotesBacteria Archaea

JoHandelsman


Metagenomics Has Many Other Purposes

42

metagenomics

ACUGC ACCUAU CGUUCG

ACUCC AGCUAU CGAUCG

ACCCC AGCUCU CGCUCG


inputs of fixed carbon or nitrogen from external sources. As withLeptospirillum group I, both Leptospirillum group II and III have thegenes needed to fix carbon by means of the Calvin–Benson–Bassham cycle (using type II ribulose 1,5-bisphosphate carboxy-lase–oxygenase). All genomes recovered from the AMD system

contain formate hydrogenlyase complexes. These, in combinationwith carbon monoxide dehydrogenase, may be used for carbonfixation via the reductive acetyl coenzyme A (acetyl-CoA) pathwayby some, or all, organisms. Given the large number of ABC-typesugar and amino acid transporters encoded in the Ferroplasma type

Figure 4 Cell metabolic cartoons constructed from the annotation of 2,180 ORFs

identified in the Leptospirillum group II genome (63% with putative assigned function) and

1,931 ORFs in the Ferroplasma type II genome (58% with assigned function). The cell

cartoons are shown within a biofilm that is attached to the surface of an acid mine

drainage stream (viewed in cross-section). Tight coupling between ferrous iron oxidation,

pyrite dissolution and acid generation is indicated. Rubisco, ribulose 1,5-bisphosphate

carboxylase–oxygenase. THF, tetrahydrofolate.

articles

NATURE | doi:10.1038/nature02340 | www.nature.com/nature 5© 2004 Nature Publishing Group

Some Discussion of this in Lecture 13


Sequencing Has Gone Crazy


Hug et al. 2016

• Dowloaded 10,000+ genomes from various databases (including many I generated)

• 1000+ new genomes

• Searched these genomes for a set universal homologous genes (ribosomal proteins) (based on AMPHORA)

• Aligned the sequences of these genes between species

• Maximum likelihood tree44

Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48

Laura Hug U. Waterloo

Jill Banfield UC Berkeley

http://dx.doi.org/10.1038/nmicrobiol.2016.48

Hug et al 2016

!45

Hug et al. 2016 Tree of Life

92 Bacterial Phyla25 Archaeal Phyla5 Eukaryotic Supergroups


Laura Hug U. Waterloo

Jill Banfield UC Berkeley


!46

Hug et al 2016Hug et al. 2016 Bacteria



Taxa Covered in Textbook

!47Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48


!48

Hug et al 2016Phyla Never Grown in the Lab



Hug et al 2016

!49

Hug et al. 2016 Archaea and Eukaryotes



Hug et al 2016

!50

Hug et al. 2016 Archaea Phyla Never Grown in the Lab



Major Groups by Evolutionary Distance

!51

The Dark Matter of Biology

!52

0.2

Korarchaeota

DiapherotritesNanohaloarchaeota

Unclassified archaea Pacearchaeota

Woesearchaeota, Nanoarchaeota

Woesearchaeota

AltiarchaealesZ7ME43

Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciArchaeoglobi, Methanomicrobia, Halobacteria

Aciduliprofundum, ThermoplasmataUncultured Thermoplasmata

ThermoplasmataOpisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa

CrenarchaeotaCrenarchaeota

Thorarchaeota Lokiarchaeota

YNPFFA

Thaumarchaeota Thaumarchaeota

Cyanobacteria, Melainabacteria

Dojkabacteria WS6 CPR3

Katanobacteria WWE3 Katanobacteria WWE3

Microgenomates RoizmanbacteriaMicrogenomates Roizmanbacteria

Microgenomates Microgenomates Curtissbacteria Microgenomates Daviesbacteria

Microgenomates Levybacteria

Microgenomates Woesebacteria Microgenomates Amesbacteria

Microgenomates Shapirobacteria Microgenomates Beckwithbacteria, Pacebacteria, Collierbacteria

Microgenomates Gottesmanbacteria

KAZAN CPR2, Saccharibacteria TM7

Berkelbacteria

Berkelbacteria

Berkelbacteria Berkelbacteria

CPR Uncultured unclassified bacteria Peregrinibacteria

Peregrinibacteria

Absconditabacteria SR1Gracilibacteria BD1-5 / GNO2

SM2F11Parcubacteria

Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, MagasanikbacteriaParcubacteriaParcubacteria

Parcubacteria

ParcubacteriaParcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, KaiserbacteriaParcubacteria

Parcubacteria Moranbacteria

ParcubacteriaParcubacteria Yanofskybacteria

Deinococcus-Thermus Aquificae, Calescamantes EM19

Caldiserica, Dictyoglomi Thermotogae

Omnitrophica Omnitrophica

Spirochaetes Spirochaetes

Hydrogenedentes NKB19 Deltaproteobacteria

Epsilonproteobacteria TM6

Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot.

NC10, Rokubacteria, Aminicenantes, Acidobacteria

Planctomycetes Chlamydiae

Lentisphaerae Verrucomicrobia

Verrucomicrobia

RBX-1 WOR-1

Firmicutes, Tenericutes, Armatimonadetes, Chloroflexi, Actinobacteria Fusobacteria, Synergistetes

Uncultured bacteria (CP RIF32)

Zixibacteria, Marinimicrobia, Caldithrix, Chlorobi, Ignavibacteria, Bacteroidetes Fibrobacteres

Cloacamonetes

Atribacteria (OP9) BRC1, Poribacteria

Latescibacteria WS3 Gemmatimonadetes, WOR-3, TA06

ElusimicrobiaUncultured bacteria


Aigarchaeota, Cand. Caldiarchaeum subterraneum

Unclassified archaea

Parcubacteria

Candidate Phyla Radiation



Caldiserica, Dictyoglomiq ,q ,

ThermotogaeA ifi C


pp

Spirochaetes SpirochaetesS i h t


H d d t N

Epsilonproteobacteriab

TM6Alphaproteobacteria, Zetaproteobacteria, Betaproteobacteria, Gammaproteobacteria Chrysiogenetes, Deferribacteres

Modulibacteria, Tectomicrobia, Nitrospinae, Nitrospirae, Dadabacteria, Thermodesulfobacteria, Deltaprot. NC10, Rokubacteria, Aminicenantes, Acidobacteria

D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey

LentisphaeraeC a yd Ch

Verrucomicrobia Verrucomicrobia

pp

RBX-1 WOR-1


Uncultured bacteria (CP RIF32), y g, y g


Cloacamonetes


( )Latescibacteria WS3

Gemmatimonadetes, WOR-3, TA06b M


Uncultured bacteria (CP RIF1)O h




MicrogenomatesMicrogenomates Curtissbacteria

ggMicrogenomates Daviesbacteria

gg


Microgenomates Woesebacteria Microgenomates AmesbacteriaMi t L b t i

Microgenomates ShapirobacteriaMi t W bMi t

Microgenomates Beckwithbacteria, Pacebacteria, CollierbacteriaMi Sh i b i

Microgenomates Gottesmanbacteriat R i b t i

g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria

Parcubacteria Kuenenbacteria, Falkowbacteria, Uhrbacteria, Magasanikbacteriate a

ParcubacteriaParcubacteria

Parcubacteria

Parcubacteria AbscAbs

Parcubacteria Azambacteria, Jorgensenbacteria, Wolfebacteria, Giovannonibacteria, Nomurabacteria, Campbellbacteria, Adlerbacteria, Kaiserbacteria

ggParcubacteriaParcubacteria Moranbacteria


P b i




Pacearchaeota


Woesearchaeota


Methanopyri, Methanococci, Methanobacteria, Hadesarchaea, ThermococciE43

Archaeoglobi, Methanomicrobia, Halobacteria, , ,, , ,

Aciduliprofundum, Thermoplasmatagg

Uncultured Thermoplasmatap ,p ,

Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA

Cand. Caldiarchaeum subterraneum

C b t i M l i b t i

Opisthokonta, Excavata, Archaeplastida Chromalveolata, Amoebozoa

Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3

Bootstrap ≥ 85% 85% > Bootstrap ≥ 50%


Figure 2 | A reformatted view of the tree in Fig. 1 in which each major lineage represents the same amount of evolutionary distance. The threshold forgroups (coloured wedges) was an average branch length of <0.65 substitutions per site. Notably, some well-accepted phyla become single groups andothers are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resultinggroups to have special taxonomic status. The massive scale of diversity in the CPR and the large fraction of major lineages that lack isolated representatives(red dots) are apparent from this analysis. Bootstrap support values are indicated by circles on nodes—black for support of 85% and above, grey for supportfrom 50 to 84%. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. 1 and in Newickformat in Supplementary Dataset 2.

NATURE MICROBIOLOGY DOI: 10.1038/NMICROBIOL.2016.48 LETTERS

NATURE MICROBIOLOGY | www.nature.com/naturemicrobiology 3

© 2016 Macmillan Publishers Limited. All rights reserved

0.2

Korarchaeota




Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







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ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







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pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

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pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

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SM2F11Parcubacteria



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P b i




Pacearchaeota


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Thermoplasmatap


Korarchaeota

,



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b l b

Aigarchaeota,FFA


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Th h,

Th h tEukaryotes

Bacteria

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Cloacamonetes







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ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

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pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



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P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

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Berkelbacteria

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RBX-1 WOR-1




Cloacamonetes







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ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



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P b i




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Thermoplasmatap


Korarchaeota

,



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b l b

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Th h,

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Bacteria

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Cloacamonetes







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ThermotogaeA ifi C


pp



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D f bD f b, , p ,, , p ,

Planctomycetespp

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pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



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SM2F11Parcubacteria



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P b i




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Thermoplasmatap


Korarchaeota

,



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b l b

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Th h,

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Bacteria

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SM2F11Parcubacteria


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Cloacamonetes







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ThermotogaeA ifi C


pp



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Planctomycetespp

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pp

RBX-1 WOR-1




Cloacamonetes











gg






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Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



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P b i




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Thermoplasmatap


Korarchaeota

,



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b l b

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Th h,

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Bacteria

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SM2F11Parcubacteria


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ThermotogaeA ifi C


pp



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pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

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Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




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Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


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Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







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Peregrinibacteria


SM2F11Parcubacteria


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RBX-1 WOR-1




Cloacamonetes







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ThermotogaeA ifi C


pp



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pp

RBX-1 WOR-1




Cloacamonetes











gg






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Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





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Thermoplasmatap


Korarchaeota

,



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b l b

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C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

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0.2

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Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














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RBX-1 WOR-1




Cloacamonetes







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ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

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pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







0.2

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Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







Parcubacteria





ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







0.2

Korarchaeota




Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







Parcubacteria





ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







0.2

Korarchaeota




Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







Parcubacteria





ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3







0.2

Korarchaeota




Woesearchaeota







YNPFFA












Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria


Parcubacteria














Verrucomicrobia

RBX-1 WOR-1




Cloacamonetes







Parcubacteria





ThermotogaeA ifi C


pp



H d d t N




D f bD f b, , p ,, , p ,

Planctomycetespp

Chlamydiaey



pp

RBX-1 WOR-1




Cloacamonetes











gg






g yg y


Berkelbacteria

Berkelbacteria



Peregrinibacteria


SM2F11Parcubacteria



Parcubacteria





P b i




Pacearchaeota


Woesearchaeota






Thermoplasmatap


Korarchaeota

,



YNPFFA


b l b

Aigarchaeota,FFA


C b t i M l i b t i


Th h,

Th h tEukaryotes

Bacteria

Archaea

Katanobacteria WWE3








Also many uncultured eukaryotic groups

5353


Details

• Dowloaded 10,000+ genomes from various databases (including many I generated)

• 1000+ new genomes

• Searched these genomes for a set universal homologous genes (ribosomal proteins) (based on AMPHORA)

• Aligned the sequences of these genes between species

• Maximum likelihood tree

54


Details

• If you want to do things like this

• Learn biology but also

• Bioinformatics

• Programming

• Data science

• Quantitative biology

• Statistics55


Reminder

These trees are based on analysis of ribosomal proteins. They represent only a small subset of all the genes in a genome.

56


Microbial Diversity

• We do not have time to cover all of these groups of microbes in lecture

• These groups barely scratch the surface of the true diversity

• Examples of Biological Diversity of Microbes

• Focus on the Big Picture Patterns of This Diversity

57


Clicker

58


Clicker

Which of the following is an example of universal homology

A: Ether-linked lipids

B: Peptidoglycan

C: Ester-linked lipids D: Transcription of DNA into RNA

E: Translation of RNA in the nucleus

59


Clicker

Which of the following is an example of universal homology

A: Ether-linked lipids

B: Peptidoglycan

C: Ester-linked lipids D: Transcription of DNA into RNA

E: Translation of RNA in the nucleus

60

Bacterial Diversity: Gram Positive vs. Negative

61

Outside of cell

Outside of cell

Inside of cell

Inside of cell

Cell envelope

Cell wall (peptidoglycan)

Plasma membrane

Outer membrane of cell envelope

Periplasmic space

Peptidoglycan layer

Periplasmic space

Plasma membrane

5 µm

5 µm

Gram Positive

Gram Negative

Bacterial and Archaeal Shapes

Archaea cell membranes have lipids with fatty acids linked to glycerol by ether linkages (a synapomorphy of archaea):

62

Ester Linkages

Bacterial and eukaryotic cell membranes have lipids with fatty acids connected to glycerol by ester linkages:

63


Diversity of Form

• Bacteria and archaea way more diverse in morphology (e.g., size, shape) than many appreciate

• Morphological diversity in NPAF eukaryotes also immense (NPAF = non plant, animal, or fungal)

• Diversity of movement connected to diversity of form

• Many examples of convergent evolution in morphology, related features

64


Bacteria: Major Cell Forms

• Among the Bacteria and Archaea, three shapes are common: ! Sphere or coccus (plural cocci), occur

singly or in plates, blocks, or clusters. ! Rod—bacillus (plural bacilli) ! Helical

• Rods and helical shapes may form chains or clusters.

65


Bacteria: Other Forms

66


Archaea: Examples of Forms

67


Motility of Vibrio (a member of the Proteobacteria phylum)

68


Corkscrew Movement of Spiraling (A Cyanobacterium)

69


•Most are marine and are important photoautotrophic primary producers

•Mixture of pigments give them a golden brown color.

•Have two flagella, one in an equatorial groove, the other in a longitudinal groove.

Alveolates: Dinoflagellates

70

Certium tenue

Coral symbiont


Chromalveolates: Haptophytes

• Haptophytes

71

Coccolithophores (haptophytes) can also form immense blooms in the ocean.

Blooms can reduce the amount of sunlight that penetrates deeper waters.

Emiliania huxleyi—one of smallest unicellular eukaryotes. May contribute to global warming through its metabolism.


Alveolates: Ciliates

72 Movement in a ciliate from the gut of a termite

• All have numerous cilia, • Most are heterotrophic; very diverse

group. • Have complex body forms and two

types of nuclei.


Stramenopiles: Diatoms•Unicellular, but many associate in filaments. •Have carotenoids and appear yellow or brown. •Excellent fossil record •Most are photoautotrophic •Responsible for 20% of all carbon fixation. •Oil, gas source

73

A colony of the diatom, Bacillaria paradoxa

Rhizaria: Foraminiferans

Sand beaches in the tropics

• Secrete shells of calcium carbonate. • Discarded shells make up limestone. • Create some beach sands • Used to date & characterize sedimentary

rocks. • Some live as plankton, others at sea bottom. • Thread-like, branched pseudopods extend

through pores in the shell and form a sticky net that captures smaller plankton.

74


Rhizaria: Radiolarians

• Have thin, stiff pseudopods reinforced by microtubules.

• The pseudopods increase surface area for exchange of materials; and help the cell float.

• Exclusively marine, most secrete glassy endoskeletons, many with elaborate designs.

75


Unikonts: Opisthokonts: Choanoflagellates

•Choanoflagellates are sister to the animals.

•Some are colonial and resemble a type of cell found in sponges.

76

The choanoflagellate Salpingoeca sp. feeding

Convergent Evolution

• Look Like Fungi

77


Figure 30.14 Sexual Life Cycles of Chytrids and Zygospore Fungi (Part 1)

78

Stramenopiles: Oomcyetes

Phytophthora

Potato Late Blight

• Non-photosynthetic. • Are absorptive heterotrophs • Once were classed as fungi, but

are unrelated.

79Sudden Oak Death

Amoebozoans: Plasmodial Slime Molds

• Individual motile cells can form single, multinucleate cell (plasmodium)

• Ingest food by endocytosis

• Form spores on stalks called fruiting bodies.

• Found in cool, moist habitats

80

Amoebozoans: Cellular Slime Molds• Life cycle consists of individual motile cells that

ingest food by endocytosis • This is followed by the formation of single,

multicellular fruiting structure • Each cell retains its own plasma membrane

and individuality

81

Karyo

Multicellularity

• Many lineages, not just PAF (plants, animals and fungi) include multicellular representatives

• Mechanisms responsible for multicellularity different in different groups (why might that be)?

82


Many Fungi Multicellular

83


Animals

84


Plants

85

Amoebozoans: Cellular Slime Molds• Life cycle consists of individual motile cells that

ingest food by endocytosis • This is followed by the formation of single,

multicellular fruiting structure • Each cell retains its own plasma membrane

and individuality

86

Karyo

•All are multicellular; some get very large (e.g., giant kelp). •The carotenoid fucoxanthin imparts the brown color. •Almost exclusively marine.

Stramenopiles: Brown Algae

87

A community of brown algae: The marine kelp forest

Amoebozoans: Plasmodial Slime Molds

• Individual motile cells can form single, multinucleate cell (plasmodium)

• Ingest food by endocytosis

• Form spores on stalks called fruiting bodies.

• Found in cool, moist habitats

88

Plantae: Red Algae

89

• Most red algae are marine and multicellular. • Red pigment is phycoerythrin. •Many reproduce with spores

Motile spores from Purpureofilum

Audouinella pacifica

Spyridia


The chlorophytes are the sister group to charophytes and land plants.

Synapomorphies include chlorophyll a and b, and starch as a storage product.

More than 17,000 species; marine, freshwater, and terrestrial. Unicellular to large

Chlamydomonas

90

Plantae: Chlorophytes

Movement in the green alga Volvox

Micrasterias

Multicellular Bacteria (Stigmatella, a Proteobacterium)

Photo 26.24 Fruiting body of gliding bacterium Stigmatella aurantiaca. SEM.91

Biofilms are common in bacteria

92


Photo 26.4 Filaments of photoautotrophic cyanobacteria,

93


More on Multicellularity Later in BIS2C

94

Diversity of Processes

• Microbes are able to make use of or alter just about any chemical bond found on Earth

• This allows a wide range of niches, and a wide diversity of roles in ecosystems

• Also diverse mechanisms for surviving and thriving in “harsh” conditions

• Humans and other organisms have taken advantage of this diversity in many ways

95


The Unusual

105°C CH3

CO, 80°CH2S, pH 0, 95°C High salt

CO2 4°Clow pH

96

The Influential

Carbon cycle Nitrogen cycle

97

The Consumable

• =

98

Feed microbes a little carbon and they can make some nice things


Functional Diversity Covered in

Labs 2 and 3 and Lecture 11-13

99

Interactions

• Microbes have diverse interactions with other organisms (both microbes and macrobes)

• Symbiosis is an intimate association between at least two different organisms in which at least one of them benefits

100

The Bad

101

Alveolates: Apicomplexans• All parasitic

• Have a mass of organelles at one tip—the apical complex that help the parasite enter the host’s cells.

102

Apical complex • Plasmodium falciparum- Malaria kills 700,000-2,000,000 people per year—75% of them are African children


Red tide caused by dinoflagellates (Gonyaulax sp.).

103

Excavates: Diplomonads and Parabisalids

• Unicellular

• Lack mitochondria and most are anaerobic. This is a derived condition

• Giardia lamblia - a diplomonad - is a human parasite

• Trichomonas vaginalis - parabasalid - STD

104

Excavates: Heteroloboseans

• Amoeboid body form.

• Naegleria can enter humans and cause a fatal nervous system disease - “brain eating”

• Some can transform between amoeboid and flagellated stages.

105

Excavates: Kinetoplastids

• Unicellular parasites with two flagella and a single mitochondrion.

• Mitochondrion contains a kinetoplast - structure with multiple, circular DNA molecules

• Includes trypanosomes and agents of chagas, sleeping sickness, Leishmaniasis

Trypanosoma sp.mixed with blood cells

106

The Good

Nitrogen Fixation

Carbon Fixation

Animal Nutrition

107

The Unknown

108


Interactions Covered in

Lecture 12-13 and Labs 3 and 3

109

Organelle Diversity

• A key feature of eukaryotes is the possession of diverse organelles

• Two key ones we will focus on are mitochondria and chloroplasts

• Pay particular attention to where (what organisms) they are found or not found in eukaryotes

110

Diverse Organelles

111

Mitochondrion Chloroplast

Nucleus

Excavates: Diplomonads and Parabisalids

• Unicellular

• Lack mitochondria and most are anaerobic. This is a derived condition

• Giardia lamblia - a diplomonad - is a human parasite

• Trichomonas vaginalis - parabasalid - STD

112

Excavates: Euglenids

• Have flagella. • Some are

photosynthetic, some always heterotrophic, and some can switch.

113

Movement in the euglenoid Eutreptia

•All are multicellular; some get very large (e.g., giant kelp). •The carotenoid fucoxanthin imparts the brown color. •Almost exclusively marine.

Stramenopiles: Brown Algae

114

A community of brown algae: The marine kelp forest

•Most are marine and are important photoautotrophic primary producers

•Mixture of pigments give them a golden brown color.

•Have two flagella, one in an equatorial groove, the other in a longitudinal groove.

Alveolates: Dinoflagellates

115

Certium tenue

Coral symbiont

Stramenopiles: Diatoms

116

A colony of the diatom, Bacillaria paradoxa

•Unicellular, but many associate in filaments. •Have carotenoids and appear yellow or brown. •Excellent fossil record •Most are photoautotrophic •Responsible for 20% of all carbon fixation. •Oil, gas source

Rhizaria: Cercozoans

Some cercozoans are aquatic, others live in soil.

They have diverse forms and habitats.

One group has chloroplasts derived from a green alga by secondary endosymbiosis.

Euglyphid

117

Chlorarachnion reptans

Plantae: Red Algae

118

• Most red algae are marine and multicellular. • Red pigment is phycoerythrin. •Many reproduce with spores

Motile spores from Purpureofilum

Audouinella pacifica

Spyridia

Plantae: Chlorophytes• Sister group to charophytes and land plants.

• Synapomorphies include chlorophyll a and b, and starch as a storage product.

• >17,000 species; marine, freshwater, and terrestrial. Unicellular to large multicellular forms.

Chlamydomonas

119

Movement in the green alga Volvox

Micrasterias

Plantae: Glaucophytes

• Unicellular, freshwater organisms

• The chloroplast retains a bit of peptidoglycan between the inner and outer membrane.

120


Scattered distribution of chloroplasts

121121

bis2c: lecture 9: microbial diversity

Science