Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
BIS2C
Biodiversity & the Tree of Life
Spring 2020
Lecture 8:
Phylogenetic Diversity of Microbes
Prof. Jonathan Eisen
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Anna’s Hummingbird in Davis, CA April 8, 2020
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Learning Goals
1. Understand what type of data has been used to infer
the overall major structures in the Tree of Life
2. Understand the great plate count anomaly and how it
has impacted our view of the phylogenetic diversity of
life
3. Understand and be able to give examples of key
features present in key ancestors of major branches
in the tree of life (e.g., LUCA, BCA, ECA)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
!7: The Domains of Life
!8: Phylogenetic Diversity of Microbes
!9: Functional Diversity of Microbes
Lecture 8 Context
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
• Bonus Tours
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
• Bonus Tours
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Background: Lab Connections
• Lab 2 - Intro to Bacteria and Archaea
• Lab 2 - Station A - classification
• Lab 3 - Intro to microbial eukaryotes
• Lab 2 - Great plate count anomaly
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Background: Review of Lecture 7
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Cell Structure Observations
L7: Prokaryotes vs. Eukaryotes
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
L7: Prokaryotes vs. Eukaryotes
EukaryotesProkaryotes
No Nucleus Nucleus
Two Main Kinds of Structures
What Other Differences Are There?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
L7: Prokaryotes vs. Eukaryotes
EukaryotesProkaryotes
No Nucleus Nucleus
Two Main Kinds of Structures
What Other Differences Are There?
Mitochondria
Endoplasmic
Reticulum
Diploid
MeiosisBinary
Fission
Mitosis
Golgi
Linear DNACircular DNA
Haploid
Chromatin
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Prokaryotic
Eukaryotic
P1 P2 P3 E1 E2 E3P4
L7: Prokaryotes vs. Eukaryotes
Interpreted as
implying this tree
because this would
require only one event
for the nucleus origin
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Prokaryotic
Eukaryotic
P1 P2 P3 E1 E2 E3P4
L7: Prokaryotes vs. Eukaryotes
Interpreted as
implying this tree
because this would
require only one event
for the nucleus origin
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Prokaryotic
Eukaryotic
P1 P2 P3 E1 E2 E3P4
L7: Prokaryotes vs. Eukaryotes
Interpreted as
implying this tree
because this would
require only one event
for the nucleus origin
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
P1 P2 P3 E1 E2 E3P4
Prokaryotic
Eukaryotic
L7: Prokaryotes vs. Eukaryotes
Interpreted As Implying This Tree Because That Would
Require Only One Event For Nucleus Origin
But this is a mistake
since this tree, also
only requires one
event for origin of
the nucleus
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Prokaryotic
Eukaryotic
P1 P2 P3 E1 E2 E3P4
L7: Prokaryotes vs. Eukaryotes
So no reason to
assume this is the
correct tree, even
though many did
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
L7: Woese rRNA Tree of Life
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
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
L7: Woese rRNA Tree of Life
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
L7: Rooted Woese rRNA Tree of Life
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
B1 B2 B3 E1 E2 E3B4 A1 A2 A3
Prokaryotic
Eukaryotic
L7: The Three Domain Tree of Life
EukaryaBacteria Archaea
Three Domains
Re-labelled
individual taxa
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
L7: Loki’s Castle
• Loki’s Castle
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
B1 B2 B3 E1 E2 E3B4 A1 A2 Loki
Prokaryotic
Eukaryotic
EukaryaBacteria Archaea
Phylogenetic Trees
Using Genomes from
Lokiarchaea Look Like
This
L7: Alternative to Three Domain Tree of Life
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard
Prokaryotic
Eukaryotic
Bacteria
L7: Two Domain Tree of Life
Two Domain Tree of Life
Archaea
Eukarya
“Prokaryotic
Archaea”
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard
Prokaryotic
Eukaryotic
Bacteria
L7: Three Domain Tree of Life
Three Domain Tree of Life
Archaea Eukarya
Note Position of Asgard Archaea
New Slide
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
• Method developments
!Same data, with different methods,
sometimes gives different results
!Some methods are more prone to artifacts
and errors than others
• Differences between genes
• Better taxonomic sampling
!Can improve resolution in trees
!Can help get around some method problems
Reasons for Changes in the Tree of Life
L7: Two Domain Tree of Life
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard
Prokaryotic
Eukaryotic
Bacteria
L7: Two Domain Tree of Life
Two Domain Tree of Life
Archaea
Eukarya
“Prokaryotic
Archaea”
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard
Prokaryotic
Eukaryotic
Bacteria
L7: Three Domain Tree of Life
Three Domain Tree of Life
Archaea Eukarya
Note Position of Asgard Archaea
New Slide
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background and Context
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
• Bonus tours
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard
Prokaryotic
Eukaryotic
Bacteria
Two Domain Tree of Life
Two Domain Tree of Life
Archaea
Eukarya
“Prokaryotic
Archaea”
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Key Lesson #1
• The overall structure of the tree of life has
been determined by analysis of molecular
sequence data
• Molecular data particularly important for
placing most microbes into the tree of life
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Woese rRNA Tree of Life
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
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
Woese rRNA Tree of Life
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
genome genomegenome
ACUGCACCUAU
CGUUCGACUGCACC
UAUCGUUCGACUGC
ACCUAUCGUUCGAC
UGCACCUAUCGUUC
GACCUAUCGUUCGA
CUGCACCUAUCGUU
CGACCUAUCGUUCG
ACUGCACCUAUCGU
UCG
ACUGCACCUAU
CGUUCGACUGCACCU
AUCGUUCGACUGCAC
CUAUCGUUCGACUGC
ACCUAUCGUUCGACC
UAUCGUUCGACUGCA
CCUAUCGUUCGACCU
AUCGUUCGACUGCAC
ACUGCACCUAU
CGUUCGACUGCACCU
AUCGUUCGACUGCAC
CUAUCGUUCGACUGC
ACCUAUCGUUCGACC
UAUCGUUCGACUGCA
CCUAUCGUUCGACCU
AUCGUUCGACUGCAC
CUAUCGUUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
Woese rRNA Tree of Life
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard
Prokaryotic
Eukaryotic
Bacteria
Two Domain Tree of Life
Two Domain Tree of Life
Archaea
Eukarya
“Prokaryotic
Archaea”
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Two Domain Tree of Life
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Two Domain Tree of Life
B1
B2
B3
E1
E2
E3
B4
A1
A2
Asgard
Bacteria
Archaea
Eukarya
“Prokaryotic
Archaea”
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Two Domain Tree of
Life with Some Major
Subbranches Shown
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Key Lesson #2
• Most microbes were only included in the tree
of life if they could be grown in the lab
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
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
Woese rRNA Tree of Life
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Great Plate Count Anomaly
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Great Plate Count Anomaly
<<<<
Culturing Observation
CountCount
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Great Plate Count Anomaly
<<<<
Culturing Observation
CountCount
http://www.google.com/url?
sa=i&rct=j&q=&esrc=s&source=images&cd
=&docid=rLu5sL207WlE1M&tbnid=CRLQYP
7d9d_TcM:&ved=0CAUQjRw&url=http%3A%
2F%2Fwww.biol.unt.edu%2F~jajohnson%2F
DNA_sequencing_process&ei=hFu7U_TyCtO
qsQSu9YGwBg&psig=AFQjCNG-8EBdEljE7-
yHFG2KPuBZt8kIPw&ust=140487395121142
4
DNA
Lab 2:
“Culture Independent
DNA Studies”
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
Environmental Sampling
genome genomegenome
ACUGCACCUAU
CGUUCGACUGCACC
UAUCGUUCGACUGC
ACCUAUCGUUCGAC
UGCACCUAUCGUUC
GACCUAUCGUUCGA
CUGCACCUAUCGUU
CGACCUAUCGUUCG
ACUGCACCUAUCGU
UCG
ACUGCACCUAU
CGUUCGACUGCACCU
AUCGUUCGACUGCAC
CUAUCGUUCGACUGC
ACCUAUCGUUCGACC
UAUCGUUCGACUGCA
CCUAUCGUUCGACCU
AUCGUUCGACUGCAC
ACUGCACCUAU
CGUUCGACUGCACCU
AUCGUUCGACUGCAC
CUAUCGUUCGACUGC
ACCUAUCGUUCGACC
UAUCGUUCGACUGCA
CCUAUCGUUCGACCU
AUCGUUCGACUGCAC
CUAUCGUUCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Most of the
phylogenetic diversity
of bacteria only known
through DNA from
environmental
samples
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Most of the
phylogenetic diversity
of bacteria only known
through DNA from
environmental
samples
Same is true for
Archaea
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Most of the
phylogenetic diversity
of bacteria only known
through DNA from
environmental
samples
Same is true for
Archaea
Also true for the
microbial lineages in
eukaryotes
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Most of the
phylogenetic diversity
of bacteria only known
through DNA from
environmental
samples
Same is true for
Archaea
Also true for the
microbial lineages in
eukaryotes
No way to cover all
this diversity in this
class
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Focus on this reduced
subset of the full
phylogenetic diversity
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Plants: L14-21
Fungi L 22-23
Animals L 25-36
Choanos: L 24
Everything Else L 8-13
NOOP
Not Opisthokonts or Plants
Focus on this reduced
subset of the full
phylogenetic diversity
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
L8: Features and
Innovations of Major
Groups
L9: Functional Diversity
L10: Parasites and
Pathogens
L11: Viruses and Gene
Transfer
L12: Mutualisms and
Microbiomes
L13: Endosymbioses and
Organelles
Everything Else L 8-13
NOOP
Not Opisthokonts or Plants
Focus on this reduced
subset of the full
phylogenetic diversity
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background and Context
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
• Bonus Tours
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background and Context
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
!LUCA
• Bonus Tours
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
LUCA
LUCA
Last
Universal
Common
Ancestor
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
LUCA
LUCA
Last
Universal
Common
Ancestor
Can infer
traits using
character
state
reconstruction
methods
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
• Made up of cells
• Use of DNA as a genetic material
• Use of ACTG in DNA
• Use of ACUG in RNA
• Three letter genetic code
• Central dogma (DNA » RNA » protein)
• Use water as a solvent
• Lipoprotein cell envelope
• 20 core amino acids in proteins
• Live on Earth
• Ribosome for translation
• RNA polymerase proteins
• Acquires energy from environment
• Store energy in chemicals
Universal Traits
• Made up of cells
• Use of DNA as a genetic material
• Use of ACTG in DNA
• Use of ACUG in RNA
• Three letter genetic code
• Central dogma (DNA » RNA » protein)
• Use water as a solvent
• Lipoprotein cell envelope
• 20 core amino acids in proteins
• Live on Earth
• Ribosome for translation
• RNA polymerase proteins
• Acquires energy from environment
• Store energy in chemicals
Universal Traits
Infer that
LUCA had all
of these
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Prokaryotes vs. Eukaryotes
EukaryotesProkaryotes
No Nucleus Nucleus
Two Main Kinds of Structures
What Other Differences Are There?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Prokaryotes vs. Eukaryotes
EukaryotesProkaryotes
No Nucleus Nucleus
Two Main Kinds of Structures
What Other Differences Are There?
Mitochondria
Endoplasmic
Reticulum
Diploid
MeiosisBinary
Fission
Mitosis
Golgi
Linear DNACircular DNA
Haploid
Chromatin
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Circular DNA
Linear DNA
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Circular DNA
Linear DNA
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Traits of LUCA = Last Universal Common Ancestor
• For characters that differ between prokaryotes
and eukaryotes, LUCA likely had the
character / character state found in
prokaryotes
!Circular DNA genome with plasmids
!No nucleus or membrane bound organelles
!Operons
!Binary fission reproduction
!Haploid
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background and Context
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
!LUCA
!BCA
• Bonus Tours
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
BCA
BCA
Bacterial
Common
Ancestor
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
BCA = Bacterial Common Ancestor
• Likely inherited most of the traits inferred to
be in LUCA
• A few other key innovations, we are just going
to discuss one today
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Peptidoglycan
• Unique to bacteria
• Polymer that provides a
firm, mesh like structure
around the cell
• Key component of cell
wall
• Is the target for many
antibiotics
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Peptidoglycan
• Unique to bacteria
• Polymer that provides a
firm, mesh like structure
around the cell
• Key component of cell
wall
• Is the target for many
antibiotics
• Why?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
PG
Peptidoglycan
is a key
innovation of
bacteria
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Peptidoglycan variation in bacteria
• Two major ways it is
used in bacteria
• Gram-positive bacteria -
thick peptidoglycan layer
outside 1 cell membrane
• Gram-negative bacteria
- thin peptidoglycan
layer outside between
two cell membranes
• This has many impacts
on biology, including
sensitivity to antibiotics
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background and Context
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
!LUCA
!BCA
!ECA
• Bonus Tours
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
ECA
Eukaryote
Common
Ancestor
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Prokaryotes vs. Eukaryotes
EukaryotesProkaryotes
No Nucleus Nucleus
Two Main Kinds of Structures
What Other Differences Are There?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Prokaryotes vs. Eukaryotes
EukaryotesProkaryotes
No Nucleus Nucleus
Two Main Kinds of Structures
What Other Differences Are There?
Mitochondria
Endoplasmic
Reticulum
Diploid
MeiosisBinary
Fission
Mitosis
Golgi
Linear DNACircular DNA
Haploid
Chromatin
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
ECA
Eukaryote
Common
Ancestor
Tons of
innovations
thought to have
happened here
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Many Other Innovations Associated w/ Origin of Euks
• Cell Structure
!Cytoskeleton
!Phagocytosis
!Diverse organelles and compartments
• Molecular Processes
!Mitosis (vs. binary fission)
!Sexual reproduction (vs. gene transfer)
" Meiosis
" Haploidy vs. Diploidy
" Fertilization
!Linear chromosomes & telomeres
!Chromosomes packaged into chromatin
!Decoupling of transcription and translation
!Introns and splicing
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background and Context
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
!LUCA
!BCA
!ECA
!Asgard Archaea and Eukaryotes
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lokiarchaea named after Loki’s Castle Vent Site
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Many Other Innovations Associated w/ Origin of Euks
• Cell Structure
!Cytoskeleton
!Phagocytosis
!Diverse organelles and compartments
• Molecular Processes
!Mitosis (vs. binary fission)
!Sexual reproduction (vs. gene transfer)
" Meiosis
" Haploidy vs. Diploidy
" Fertilization
!Linear chromosomes & telomeres
!Chromosomes packaged into chromatin
!Decoupling of transcription and translation
!Introns and splicing
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Found in Asgard Archaea
• Cell Structure
!Cytoskeleton
!Phagocytosis
!Diverse organelles and compartments
• Molecular Processes
!Mitosis (vs. binary fission)
!Sexual reproduction (vs. gene transfer)
" Meiosis
" Haploidy vs. Diploidy
" Fertilization
!Linear chromosomes & telomeres
!Chromosomes packaged into chromatin
!Decoupling of transcription and translation
!Introns and splicing
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Some features
previously
thought to be
“Eukaryotic”
innovations
were likely
present in the
Eukaryote-
Asgard
ancestor
Cytoskeleton
Chromatin
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background and Context
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
• Bonus Tours
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Tour of Major Clades
• You Do Not Need to Know These Details
• Really
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Bacteria
Tour
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Spirochetes
• Gram-negative
• Motile
• Chemoheterotrophic
• Unique rotating, axial
filaments (modified flagella)
• Many are pathogens:
!Syphilis
!Lyme disease
• Others free-living
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Chlamydias
• Gram-negative
• Cocci or rod-shaped
• Extremely small
• Live only as parasites
inside cells of
eukaryotes & cause
various diseases
!Trachoma
!Multiple sexually
transmitted diseases
!Pneumonia
C. trachomatis
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Cyanobacteria
• Photolithoautotrophic
• Contain internal
membrane system
for photosynthesis
• Chloroplasts are
derived from
endosymbiotic
cyanobacteria
• Colonies can
differentiate into
vegetative cells,
spores, & heterocysts
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Proteobacteria
• Gram-negative
• Escherichia coli: model
organism and human gut
commensal and
pathogen
• Mitochondria evolved
from this group
• Includes many human
and animal pathogens:
plague, cholera, typhoid
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Low-GC Gram Positives (Firmicutes)
• Low G+C/A+T ratio in DNA
• Some produce endospores
which are resistant “seeds”
that germinate when
conditions are good
• Many agents of diseases
(e.g., anthrax, MRSA,
Streptococcus, botulism,
tetanus)
• Many of agricultural and
industrial use (e.g., Lactic
acid bacteria)
• Some (Mycoplasmas) have
no cell wall and are
extremely small
Mycoplasmas
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
High-GC Gram Positives (Actinobacteria)
• High G+C/A+T ratio in DNA
• Elaborate branching
• Some reproduce by forming
chains of spores at tips of
filaments
• Most antibiotics are from
this group
• Causative agents of many
diseases such as
tuberculosis and leprosy
• Many originally misclassified
as fungi
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Prokaryotic
Archaea
Tour
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Crenarchaeota
• Most are both
thermophilic (heat
loving) & acidophilic
(acid-loving)
• Sulfolobus lives in
hot sulfur springs
(70–75°C, pH 2-3)
• One species of
Ferroplasma lives at
pH near 0
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Euryarchaeota: Methanogens
• Only known methanogens
(produce methane (CH4)
by reducing CO2 ) - a form
of chemoautotrophy
• Methanogens release 2
billion tons of methane per
year
• Many live in the guts of
grazing mammals
• Many such as
Methanopyrus live in deep-
ocean hydrothermal vents
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Euryarchaeota: Halophiles (Salt lovers)
• Pink carotenoid
pigments – very visible
• Have been found at
pH up to 11.5.
• Unusual adaptations
to high salt,
desiccation
• Many have
bacteriorhodopsin
which uses energy of
light to synthesize ATP
(photoheterotrophs)
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Eukarya
Tour
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Plantae
The Plantae consist of
several clades; all
chloroplasts trace back to a
single incidence of
endosymbiosis.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Plantae: Glaucophytes
• Unicellular, freshwater
organisms
• The chloroplast retains a bit
of peptidoglycan between the
inner and outer membrane.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Plantae: Red Algae
• Most red algae are marine and
multicellular.
• Red pigment is phycoerythrin.
•Many reproduce with spores
Motile spores from
Purpureofilum
Audouinella pacifica
Spyridia
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
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.
Movement in the green alga
Volvox
Micrasterias
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Plantae: Charophytes and Land Plants
STAY
TUNED
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
•Choanoflagellates are sister to the
animals.
•Some are colonial and resemble a type
of cell found in sponges.
The choanoflagellate Salpingoeca sp. feeding
Opisthokonts: Choanoflagellates
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts: Fungi and Animals
STAY
TUNED
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Alveolates
Alveolates
Have alveoli or
sacs beneath
surface of
plasma
membrane.
All are unicellular;
many are
photosynthetic.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
•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
Certium
tenue
Coral symbiont
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Alveolates: Apicomplexans
• All parasitic
• Have a mass of organelles at one tip—the
apical complex that help the parasite enter
the host’s cells.
Apical complex • Plasmodium falciparum-
Malaria kills 700,000-2,000,000
people per year—75% of them
are African children
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Alveolates: Ciliates
Movement in a ciliate from the gut of a termite
• All have numerous cilia, the structure is
identical to flagella.
• Most are heterotrophic; very diverse group.
• Have complex body forms and two types of
nuclei.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Stramenopiles
Stramenopiles
Two flagella, with rows of tubular hairs
on the longer one.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
•All are multicellular; some get very large (e.g., giant
kelp).
•The carotenoid fucoxanthin imparts the brown color.
•Almost exclusively marine.
Stramenopiles: Brown Algae
A community of brown algae: The marine kelp forest
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Stramenopiles: Diatoms
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Stramenopiles: Oomcyetes
Phytophthora
Potato Late Blight
• Non-photosynthetic.
• Are absorptive heterotrophs
• Once were classed as fungi, but are
unrelated.
Sudden Oak Death
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Rhizaria
Rhizaria
Unicellular, aquatic, with long, thin pseudopods.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
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
Chlorarachnion reptans
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
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.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
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.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Excavates
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
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.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Excavates: Euglenids
• Have flagella.
• Some are
photosynthetic,
some always
heterotrophic, and
some can switch.
Movement in the euglenoid Eutreptia
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Amoebozoans
Amoebozoans
Lobe-shaped pseudopods are used for
locomotion.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
• Not colonial; live as single cells
• Some secrete shells or glue sand
grains together to form a casing.
• Many pathogens
Amoebozoans: Loboseans
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Entamoeba histolytica
http://www.npr.org/blogs/health/2014/04/09/300991364/gut-eating-amoeba-
caught-on-film
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
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
Karyog
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
End of The Tours
• End of the Tours
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
!7: The Domains of Life
!8: Phylogenetic Diversity of Microbes
!9: Functional Diversity of Microbes
Lecture 8 Context
• See you Monday for Functional Diversity of
Microbes

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BIS2C_2020. Lecture 8. Phylogenetic Diversity of Microbes

  • 1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 BIS2C Biodiversity & the Tree of Life Spring 2020 Lecture 8: Phylogenetic Diversity of Microbes Prof. Jonathan Eisen
  • 2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Anna’s Hummingbird in Davis, CA April 8, 2020
  • 3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Learning Goals 1. Understand what type of data has been used to infer the overall major structures in the Tree of Life 2. Understand the great plate count anomaly and how it has impacted our view of the phylogenetic diversity of life 3. Understand and be able to give examples of key features present in key ancestors of major branches in the tree of life (e.g., LUCA, BCA, ECA)
  • 4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 !7: The Domains of Life !8: Phylogenetic Diversity of Microbes !9: Functional Diversity of Microbes Lecture 8 Context
  • 5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 8 Outline • Background • Phylogenetic Diversity of Life • Features and Innovations of Major Groups • Bonus Tours
  • 6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 8 Outline • Background • Phylogenetic Diversity of Life • Features and Innovations of Major Groups • Bonus Tours
  • 7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Background: Lab Connections • Lab 2 - Intro to Bacteria and Archaea • Lab 2 - Station A - classification • Lab 3 - Intro to microbial eukaryotes • Lab 2 - Great plate count anomaly
  • 8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Background: Review of Lecture 7
  • 9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Cell Structure Observations L7: Prokaryotes vs. Eukaryotes
  • 10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 L7: Prokaryotes vs. Eukaryotes EukaryotesProkaryotes No Nucleus Nucleus Two Main Kinds of Structures What Other Differences Are There?
  • 11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 L7: Prokaryotes vs. Eukaryotes EukaryotesProkaryotes No Nucleus Nucleus Two Main Kinds of Structures What Other Differences Are There? Mitochondria Endoplasmic Reticulum Diploid MeiosisBinary Fission Mitosis Golgi Linear DNACircular DNA Haploid Chromatin
  • 12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotic Eukaryotic P1 P2 P3 E1 E2 E3P4 L7: Prokaryotes vs. Eukaryotes Interpreted as implying this tree because this would require only one event for the nucleus origin
  • 13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotic Eukaryotic P1 P2 P3 E1 E2 E3P4 L7: Prokaryotes vs. Eukaryotes Interpreted as implying this tree because this would require only one event for the nucleus origin
  • 14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotic Eukaryotic P1 P2 P3 E1 E2 E3P4 L7: Prokaryotes vs. Eukaryotes Interpreted as implying this tree because this would require only one event for the nucleus origin
  • 15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 Prokaryotic Eukaryotic L7: Prokaryotes vs. Eukaryotes Interpreted As Implying This Tree Because That Would Require Only One Event For Nucleus Origin But this is a mistake since this tree, also only requires one event for origin of the nucleus
  • 16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotic Eukaryotic P1 P2 P3 E1 E2 E3P4 L7: Prokaryotes vs. Eukaryotes So no reason to assume this is the correct tree, even though many did
  • 17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 L7: Woese rRNA Tree of Life
  • 18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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 L7: Woese rRNA Tree of Life
  • 19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 P1 P2 P3 E1 E2 E3P4 P5 P6 P7 Prokaryotic Eukaryotic L7: Rooted Woese rRNA Tree of Life
  • 20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 A3 Prokaryotic Eukaryotic L7: The Three Domain Tree of Life EukaryaBacteria Archaea Three Domains Re-labelled individual taxa
  • 21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 L7: Loki’s Castle • Loki’s Castle
  • 22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Loki Prokaryotic Eukaryotic EukaryaBacteria Archaea Phylogenetic Trees Using Genomes from Lokiarchaea Look Like This L7: Alternative to Three Domain Tree of Life
  • 23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic Bacteria L7: Two Domain Tree of Life Two Domain Tree of Life Archaea Eukarya “Prokaryotic Archaea”
  • 24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic Bacteria L7: Three Domain Tree of Life Three Domain Tree of Life Archaea Eukarya Note Position of Asgard Archaea New Slide
  • 25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Method developments !Same data, with different methods, sometimes gives different results !Some methods are more prone to artifacts and errors than others • Differences between genes • Better taxonomic sampling !Can improve resolution in trees !Can help get around some method problems Reasons for Changes in the Tree of Life L7: Two Domain Tree of Life
  • 26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic Bacteria L7: Two Domain Tree of Life Two Domain Tree of Life Archaea Eukarya “Prokaryotic Archaea”
  • 27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic Bacteria L7: Three Domain Tree of Life Three Domain Tree of Life Archaea Eukarya Note Position of Asgard Archaea New Slide
  • 28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 8 Outline • Background and Context • Phylogenetic Diversity of Life • Features and Innovations of Major Groups • Bonus tours
  • 29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic Bacteria Two Domain Tree of Life Two Domain Tree of Life Archaea Eukarya “Prokaryotic Archaea”
  • 30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Key Lesson #1 • The overall structure of the tree of life has been determined by analysis of molecular sequence data • Molecular data particularly important for placing most microbes into the tree of life
  • 31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Woese rRNA Tree of Life
  • 32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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 Woese rRNA Tree of Life
  • 33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 genome genomegenome ACUGCACCUAU CGUUCGACUGCACC UAUCGUUCGACUGC ACCUAUCGUUCGAC UGCACCUAUCGUUC GACCUAUCGUUCGA CUGCACCUAUCGUU CGACCUAUCGUUCG ACUGCACCUAUCGU UCG ACUGCACCUAU CGUUCGACUGCACCU AUCGUUCGACUGCAC CUAUCGUUCGACUGC ACCUAUCGUUCGACC UAUCGUUCGACUGCA CCUAUCGUUCGACCU AUCGUUCGACUGCAC ACUGCACCUAU CGUUCGACUGCACCU AUCGUUCGACUGCAC CUAUCGUUCGACUGC ACCUAUCGUUCGACC UAUCGUUCGACUGCA CCUAUCGUUCGACCU AUCGUUCGACUGCAC CUAUCGUUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG Woese rRNA Tree of Life
  • 34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard Prokaryotic Eukaryotic Bacteria Two Domain Tree of Life Two Domain Tree of Life Archaea Eukarya “Prokaryotic Archaea”
  • 35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Two Domain Tree of Life
  • 36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Two Domain Tree of Life B1 B2 B3 E1 E2 E3 B4 A1 A2 Asgard Bacteria Archaea Eukarya “Prokaryotic Archaea”
  • 37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Two Domain Tree of Life with Some Major Subbranches Shown
  • 38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Key Lesson #2 • Most microbes were only included in the tree of life if they could be grown in the lab
  • 39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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 Woese rRNA Tree of Life
  • 40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Great Plate Count Anomaly
  • 41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Great Plate Count Anomaly <<<< Culturing Observation CountCount
  • 42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Great Plate Count Anomaly <<<< Culturing Observation CountCount http://www.google.com/url? sa=i&rct=j&q=&esrc=s&source=images&cd =&docid=rLu5sL207WlE1M&tbnid=CRLQYP 7d9d_TcM:&ved=0CAUQjRw&url=http%3A% 2F%2Fwww.biol.unt.edu%2F~jajohnson%2F DNA_sequencing_process&ei=hFu7U_TyCtO qsQSu9YGwBg&psig=AFQjCNG-8EBdEljE7- yHFG2KPuBZt8kIPw&ust=140487395121142 4 DNA Lab 2: “Culture Independent DNA Studies”
  • 43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG Environmental Sampling genome genomegenome ACUGCACCUAU CGUUCGACUGCACC UAUCGUUCGACUGC ACCUAUCGUUCGAC UGCACCUAUCGUUC GACCUAUCGUUCGA CUGCACCUAUCGUU CGACCUAUCGUUCG ACUGCACCUAUCGU UCG ACUGCACCUAU CGUUCGACUGCACCU AUCGUUCGACUGCAC CUAUCGUUCGACUGC ACCUAUCGUUCGACC UAUCGUUCGACUGCA CCUAUCGUUCGACCU AUCGUUCGACUGCAC ACUGCACCUAU CGUUCGACUGCACCU AUCGUUCGACUGCAC CUAUCGUUCGACUGC ACCUAUCGUUCGACC UAUCGUUCGACUGCA CCUAUCGUUCGACCU AUCGUUCGACUGCAC CUAUCGUUCG
  • 44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates
  • 45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Most of the phylogenetic diversity of bacteria only known through DNA from environmental samples
  • 46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Most of the phylogenetic diversity of bacteria only known through DNA from environmental samples Same is true for Archaea
  • 47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Most of the phylogenetic diversity of bacteria only known through DNA from environmental samples Same is true for Archaea Also true for the microbial lineages in eukaryotes
  • 48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Most of the phylogenetic diversity of bacteria only known through DNA from environmental samples Same is true for Archaea Also true for the microbial lineages in eukaryotes No way to cover all this diversity in this class
  • 49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Focus on this reduced subset of the full phylogenetic diversity
  • 50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Plants: L14-21 Fungi L 22-23 Animals L 25-36 Choanos: L 24 Everything Else L 8-13 NOOP Not Opisthokonts or Plants Focus on this reduced subset of the full phylogenetic diversity
  • 51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates L8: Features and Innovations of Major Groups L9: Functional Diversity L10: Parasites and Pathogens L11: Viruses and Gene Transfer L12: Mutualisms and Microbiomes L13: Endosymbioses and Organelles Everything Else L 8-13 NOOP Not Opisthokonts or Plants Focus on this reduced subset of the full phylogenetic diversity
  • 52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 8 Outline • Background and Context • Phylogenetic Diversity of Life • Features and Innovations of Major Groups • Bonus Tours
  • 53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 8 Outline • Background and Context • Phylogenetic Diversity of Life • Features and Innovations of Major Groups !LUCA • Bonus Tours
  • 54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates LUCA LUCA Last Universal Common Ancestor
  • 55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates LUCA LUCA Last Universal Common Ancestor Can infer traits using character state reconstruction methods
  • 56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  • 57. • Made up of cells • Use of DNA as a genetic material • Use of ACTG in DNA • Use of ACUG in RNA • Three letter genetic code • Central dogma (DNA » RNA » protein) • Use water as a solvent • Lipoprotein cell envelope • 20 core amino acids in proteins • Live on Earth • Ribosome for translation • RNA polymerase proteins • Acquires energy from environment • Store energy in chemicals Universal Traits
  • 58. • Made up of cells • Use of DNA as a genetic material • Use of ACTG in DNA • Use of ACUG in RNA • Three letter genetic code • Central dogma (DNA » RNA » protein) • Use water as a solvent • Lipoprotein cell envelope • 20 core amino acids in proteins • Live on Earth • Ribosome for translation • RNA polymerase proteins • Acquires energy from environment • Store energy in chemicals Universal Traits Infer that LUCA had all of these
  • 59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotes vs. Eukaryotes EukaryotesProkaryotes No Nucleus Nucleus Two Main Kinds of Structures What Other Differences Are There?
  • 60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotes vs. Eukaryotes EukaryotesProkaryotes No Nucleus Nucleus Two Main Kinds of Structures What Other Differences Are There? Mitochondria Endoplasmic Reticulum Diploid MeiosisBinary Fission Mitosis Golgi Linear DNACircular DNA Haploid Chromatin
  • 61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Circular DNA Linear DNA
  • 62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Circular DNA Linear DNA
  • 63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Traits of LUCA = Last Universal Common Ancestor • For characters that differ between prokaryotes and eukaryotes, LUCA likely had the character / character state found in prokaryotes !Circular DNA genome with plasmids !No nucleus or membrane bound organelles !Operons !Binary fission reproduction !Haploid
  • 64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 8 Outline • Background and Context • Phylogenetic Diversity of Life • Features and Innovations of Major Groups !LUCA !BCA • Bonus Tours
  • 65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates BCA BCA Bacterial Common Ancestor
  • 66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 BCA = Bacterial Common Ancestor • Likely inherited most of the traits inferred to be in LUCA • A few other key innovations, we are just going to discuss one today
  • 67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Peptidoglycan • Unique to bacteria • Polymer that provides a firm, mesh like structure around the cell • Key component of cell wall • Is the target for many antibiotics
  • 68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Peptidoglycan • Unique to bacteria • Polymer that provides a firm, mesh like structure around the cell • Key component of cell wall • Is the target for many antibiotics • Why?
  • 69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates PG Peptidoglycan is a key innovation of bacteria
  • 70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Peptidoglycan variation in bacteria • Two major ways it is used in bacteria • Gram-positive bacteria - thick peptidoglycan layer outside 1 cell membrane • Gram-negative bacteria - thin peptidoglycan layer outside between two cell membranes • This has many impacts on biology, including sensitivity to antibiotics
  • 71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 8 Outline • Background and Context • Phylogenetic Diversity of Life • Features and Innovations of Major Groups !LUCA !BCA !ECA • Bonus Tours
  • 72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates ECA Eukaryote Common Ancestor
  • 73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotes vs. Eukaryotes EukaryotesProkaryotes No Nucleus Nucleus Two Main Kinds of Structures What Other Differences Are There?
  • 74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Prokaryotes vs. Eukaryotes EukaryotesProkaryotes No Nucleus Nucleus Two Main Kinds of Structures What Other Differences Are There? Mitochondria Endoplasmic Reticulum Diploid MeiosisBinary Fission Mitosis Golgi Linear DNACircular DNA Haploid Chromatin
  • 75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates ECA Eukaryote Common Ancestor Tons of innovations thought to have happened here
  • 76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Many Other Innovations Associated w/ Origin of Euks • Cell Structure !Cytoskeleton !Phagocytosis !Diverse organelles and compartments • Molecular Processes !Mitosis (vs. binary fission) !Sexual reproduction (vs. gene transfer) " Meiosis " Haploidy vs. Diploidy " Fertilization !Linear chromosomes & telomeres !Chromosomes packaged into chromatin !Decoupling of transcription and translation !Introns and splicing
  • 77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 8 Outline • Background and Context • Phylogenetic Diversity of Life • Features and Innovations of Major Groups !LUCA !BCA !ECA !Asgard Archaea and Eukaryotes
  • 78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lokiarchaea named after Loki’s Castle Vent Site
  • 79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Many Other Innovations Associated w/ Origin of Euks • Cell Structure !Cytoskeleton !Phagocytosis !Diverse organelles and compartments • Molecular Processes !Mitosis (vs. binary fission) !Sexual reproduction (vs. gene transfer) " Meiosis " Haploidy vs. Diploidy " Fertilization !Linear chromosomes & telomeres !Chromosomes packaged into chromatin !Decoupling of transcription and translation !Introns and splicing
  • 80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Found in Asgard Archaea • Cell Structure !Cytoskeleton !Phagocytosis !Diverse organelles and compartments • Molecular Processes !Mitosis (vs. binary fission) !Sexual reproduction (vs. gene transfer) " Meiosis " Haploidy vs. Diploidy " Fertilization !Linear chromosomes & telomeres !Chromosomes packaged into chromatin !Decoupling of transcription and translation !Introns and splicing
  • 81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates
  • 82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates
  • 83. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Some features previously thought to be “Eukaryotic” innovations were likely present in the Eukaryote- Asgard ancestor Cytoskeleton Chromatin
  • 84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 8 Outline • Background and Context • Phylogenetic Diversity of Life • Features and Innovations of Major Groups • Bonus Tours
  • 85. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Tour of Major Clades • You Do Not Need to Know These Details • Really
  • 86. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Bacteria Tour
  • 87. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Spirochetes • Gram-negative • Motile • Chemoheterotrophic • Unique rotating, axial filaments (modified flagella) • Many are pathogens: !Syphilis !Lyme disease • Others free-living
  • 88. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Chlamydias • Gram-negative • Cocci or rod-shaped • Extremely small • Live only as parasites inside cells of eukaryotes & cause various diseases !Trachoma !Multiple sexually transmitted diseases !Pneumonia C. trachomatis
  • 89. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Cyanobacteria • Photolithoautotrophic • Contain internal membrane system for photosynthesis • Chloroplasts are derived from endosymbiotic cyanobacteria • Colonies can differentiate into vegetative cells, spores, & heterocysts
  • 90. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Proteobacteria • Gram-negative • Escherichia coli: model organism and human gut commensal and pathogen • Mitochondria evolved from this group • Includes many human and animal pathogens: plague, cholera, typhoid
  • 91. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Low-GC Gram Positives (Firmicutes) • Low G+C/A+T ratio in DNA • Some produce endospores which are resistant “seeds” that germinate when conditions are good • Many agents of diseases (e.g., anthrax, MRSA, Streptococcus, botulism, tetanus) • Many of agricultural and industrial use (e.g., Lactic acid bacteria) • Some (Mycoplasmas) have no cell wall and are extremely small Mycoplasmas
  • 92. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 High-GC Gram Positives (Actinobacteria) • High G+C/A+T ratio in DNA • Elaborate branching • Some reproduce by forming chains of spores at tips of filaments • Most antibiotics are from this group • Causative agents of many diseases such as tuberculosis and leprosy • Many originally misclassified as fungi
  • 93. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Prokaryotic Archaea Tour
  • 94. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Crenarchaeota • Most are both thermophilic (heat loving) & acidophilic (acid-loving) • Sulfolobus lives in hot sulfur springs (70–75°C, pH 2-3) • One species of Ferroplasma lives at pH near 0
  • 95. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Euryarchaeota: Methanogens • Only known methanogens (produce methane (CH4) by reducing CO2 ) - a form of chemoautotrophy • Methanogens release 2 billion tons of methane per year • Many live in the guts of grazing mammals • Many such as Methanopyrus live in deep- ocean hydrothermal vents
  • 96. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Euryarchaeota: Halophiles (Salt lovers) • Pink carotenoid pigments – very visible • Have been found at pH up to 11.5. • Unusual adaptations to high salt, desiccation • Many have bacteriorhodopsin which uses energy of light to synthesize ATP (photoheterotrophs)
  • 97. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts Amoebozoans Excavates Plantae Rhizaria Stramenopiles Alveolates Eukarya Tour
  • 98. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Plantae The Plantae consist of several clades; all chloroplasts trace back to a single incidence of endosymbiosis.
  • 99. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Plantae: Glaucophytes • Unicellular, freshwater organisms • The chloroplast retains a bit of peptidoglycan between the inner and outer membrane.
  • 100. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Plantae: Red Algae • Most red algae are marine and multicellular. • Red pigment is phycoerythrin. •Many reproduce with spores Motile spores from Purpureofilum Audouinella pacifica Spyridia
  • 101. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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. Movement in the green alga Volvox Micrasterias
  • 102. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Plantae: Charophytes and Land Plants STAY TUNED
  • 103. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts
  • 104. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 •Choanoflagellates are sister to the animals. •Some are colonial and resemble a type of cell found in sponges. The choanoflagellate Salpingoeca sp. feeding Opisthokonts: Choanoflagellates
  • 105. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Opisthokonts: Fungi and Animals STAY TUNED
  • 106. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Alveolates Alveolates Have alveoli or sacs beneath surface of plasma membrane. All are unicellular; many are photosynthetic.
  • 107. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 •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 Certium tenue Coral symbiont
  • 108. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Alveolates: Apicomplexans • All parasitic • Have a mass of organelles at one tip—the apical complex that help the parasite enter the host’s cells. Apical complex • Plasmodium falciparum- Malaria kills 700,000-2,000,000 people per year—75% of them are African children
  • 109. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Alveolates: Ciliates Movement in a ciliate from the gut of a termite • All have numerous cilia, the structure is identical to flagella. • Most are heterotrophic; very diverse group. • Have complex body forms and two types of nuclei.
  • 110. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Stramenopiles Stramenopiles Two flagella, with rows of tubular hairs on the longer one.
  • 111. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 •All are multicellular; some get very large (e.g., giant kelp). •The carotenoid fucoxanthin imparts the brown color. •Almost exclusively marine. Stramenopiles: Brown Algae A community of brown algae: The marine kelp forest
  • 112. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Stramenopiles: Diatoms 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
  • 113. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Stramenopiles: Oomcyetes Phytophthora Potato Late Blight • Non-photosynthetic. • Are absorptive heterotrophs • Once were classed as fungi, but are unrelated. Sudden Oak Death
  • 114. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Rhizaria Rhizaria Unicellular, aquatic, with long, thin pseudopods.
  • 115. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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 Chlorarachnion reptans
  • 116. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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.
  • 117. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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.
  • 118. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Excavates
  • 119. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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
  • 120. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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.
  • 121. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Excavates: Euglenids • Have flagella. • Some are photosynthetic, some always heterotrophic, and some can switch. Movement in the euglenoid Eutreptia
  • 122. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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
  • 123. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Amoebozoans Amoebozoans Lobe-shaped pseudopods are used for locomotion.
  • 124. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Not colonial; live as single cells • Some secrete shells or glue sand grains together to form a casing. • Many pathogens Amoebozoans: Loboseans
  • 125. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Entamoeba histolytica http://www.npr.org/blogs/health/2014/04/09/300991364/gut-eating-amoeba- caught-on-film
  • 126. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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
  • 127. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 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 Karyog
  • 128. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 End of The Tours • End of the Tours
  • 129. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 !7: The Domains of Life !8: Phylogenetic Diversity of Microbes !9: Functional Diversity of Microbes Lecture 8 Context • See you Monday for Functional Diversity of Microbes