BIS2C_2020. Lecture 9. Form and function

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
BIS2C
Biodiversity & the Tree of Life
Spring 2020
Lecture 9:
Diversity of Form and Function
Prof. Jonathan Eisen

Some insects from my yard in Davis Western HoneyBee

Some insects from my yard in Davis Argentine ant

Some insects from my yard in Davis Tiger ﬂy?

Some insects from my yard in Davis Carpenter bee

iNaturalist
• Take pictures
• Upload them
!http://iNaturalist.org
!Inaturalist App
!Seek App (real time identification)
• Use their AI system and also community to
help with identification
• My observations here: https://
www.inaturalist.org/observations/
phylogenomics

Learning Goals
• Understand general patterns of diversity of form
seen in Bacteria, “Prokaryotic Archaea” and
Eukarya
• Understand key ways that organisms acquire
carbon and use energy and electrons
• Understand how one can use culturing to study
extremophiles in the lab
• Understand example patterns of the evolution of
extremophily

!8: Phylogenetic Diversity
!9: Diversity of Form and Function
!10: Pathogens and Parasites
Lecture 9 Context

Lecture 9 Outline
• Background and Context
• Diversity of Form and Function
!Form
!Trophy
!Extremophily

Background: Lab Connections
• Lab 2 Station B: Microbial Metabolic
Diversity
• Lab 2 & 3 Microscopy
• Lab 2 Station F: Winogradsky columns

Background: Review Lecture 8

Lecture 8 Outline
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
• Bonus tours

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

Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Two Domain Tree of
Life with Some Major
Subbranches Shown

Key Lesson #2
• Most microbes were only included in the tree
of life if they could be grown in the lab

Great Plate Count Anomaly
<<<<
Culturing Observation
CountCount

Great Plate Count Anomaly
<<<<
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
“Culture Independent
DNA Studies”

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

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

Lecture 8 Outline
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
• Bonus Tours

Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
LUCA
LUCA
Last
Universal
Common
Ancestor
Can infer
traits using
character
state
reconstruction
methods

Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
BCA
BCA
Bacterial
Common
Ancestor

Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
ECA
Eukaryote
Common
Ancestor

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

Unicellularity & Multicellularity continuum
• Unicellular: one cell does
everything
R
• Colonial: collections of many
attached cells (usually of the
same genotype); no
differentiation or division of
labor or reproduction capabilities
• Multicellular: collection of many
attached cells (usually of same
genotype); differentiation and
division of labor and
reproductive capabilities

Bacteria & “Prokaryotic Archaea” : 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.
Cocci = Spheres Bacilli = Rods Spirilla = Curved

Bacteria & “Prokaryotic Archaea” : 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.
Cocci = Spheres Bacilli = Rods Spirilla = Curved
These are the most common forms seen but
there are all sorts of other forms
What follows is a brief tour of this diversity. You do
not have to know the details unless presented
elsewhere in class

TOUR BEGINS
Diversity of Form in Bacteria and “Prokaryotic Archaea”

Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
“Full Tree”

TOUR
Compressed
Tree
Compressed Tree of Life

• Many are single celled but not all have the
“simple” sphere, rod, or spiral shapes
TOUR

TOUR
Endospores: Only
Seen in Firmicutes
Phylum
Resistant to
Everything

TOUR
Heterocysts Unique
to Cyanobacteria
Used for N2 fixation

TOUR
“Spiral” shape
comes in many
kinds

TOUR
Some Chlamydia
species change forms
during life cycle

Thiomargarita
Epulopiscium
TOUR
Some Bacteria are
not microbial (can
see with eyes
without aids)

TOUR
Square Archaea

• Some are colonial
TOUR

TOUR
Clumps of
Cocci Seen
in Many
Phyla

TOURFilaments Seen in Many Phyla

• A few may be truly multicellular
TOUR

TOUR
More Complex
Structure in Some
Taxa
Fruiting body of gliding bacterium
Stigmatella aurantiaca. SEM.

Vibrio
Cyanobacterium
Many are Motile
TOUR

TOUR ENDS
Need to Know Material not in the “Tours”

• More than just cocci, bacilli, and spirals but
these are common
• Most are single celled but some are colonial and
a few may be multicellular
• Many are motile
• Some can be identified from morphology
• In most cases morphology does not match
phylogeny and is more related to ecology or
functions
• Most phylogenetic studies are based on
sequence data

Eukaryotic Diversity of Form

TOUR BEGINS

• Many are single celled
TOUR

Alveolates: Dinoflagellates
TOUR

Alveolates: Apicomplexans
Apical complex
TOUR

Alveolates: Ciliates
TOUR

Rhizarians: Cercozoans
TOUR

Rhizarians: Foraminiferans
TOUR

Rhizarians: Radiolarians
TOUR

Amoebozoans: Loboseans
TOUR

Trypanosoma sp.
mixed with blood cells
Excavates: Kinetoplastids
TOUR

Excavates: Euglenids
TOUR
Movement in the euglenoid Eutreptia
TOUR

Excavates: Diplomonads and Parabasalids
TOURTOUR

Excavates: Heteroloboseans
TOUR

• Many are colonial
TOUR

Stramenopiles: Diatoms
TOUR

Opisthokonts: Choanoflagellates
The choanoﬂagellate Salpingoeca sp. feeding
TOUR

• Many are multicellular
TOUR

Multicellular Eukaryotes
TOUR
Plants, Animals, Many Fungi

Stramenopiles: Brown Algae
A community of brown algae: The marine kelp forest
TOUR

Amoebozoans: Plasmodial Slime Molds
TOUR

Kary
Amoebozoans: Cellular Slime Molds
TOUR

Plantae: Red Algae
Motile spores from
Purpureoﬁlum
Audouinella paciﬁcaSpyridia
TOUR

Plantae: Chlorophytes
Movement in the green
alga Volvox
Micrasterias
TOUR

TOUR ENDS

• Range from single celled to colonial to
multicellular
• Incredible diversity in form & motility among
Eukaryotes
• For many, but not all taxa, morphology (aka
form) is a valuable trait for identification and
phylogeny
Eukaryotic Diversity of Form (Need to Know This)

Lesson: Convergence of Form is Common

Fungal Hyphae

Stramenopiles: Oomycetes
Phytophthora
Sudden Oak Death
Potato Late Blight

Actinobacterial Branching Filaments

Thought Question
The similarity in appearance of ooymcetes to
fungi is an example of _______
• A. Homology
• B. Homoplasy
• C. Divergent evolution
• D. Monophyly
• E. Synapomorphy

Trophy

Trophy
• Organisms exhibit incredible diversity in how
they obtain nutrition (i.e., the processes by
which an they assimilates chemicals and
energy and uses them for growth)
• Generally referred to with the suffix “trophy”
• Origin: Greek -trophiā, from trophē, from
trephein, to nourish.

Component Different Forms
Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
Organic
Organo
Carbon source Carbon from C1
compounds
Auto
Carbon from
organics
Hetero
Trophy
• Three main components to “trophy”

Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
Organic
Organo
Carbon source Carbon from
inorganics
Auto
Carbon from
organics
Hetero
• E. coli • Chemo organo hetero trophy
• Chemo hetero trophy
Trophy

Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
Organic
Organo
inorganics
Auto
Carbon from
organics
Hetero
• Humans? • Chemo organo hetero trophy
• Chemo hetero trophy
Trophy

Energy source Light
Photo
Chemical
Chemo
Electron source
(reducing
equivalent)
Inorganic
Litho
Organic
Organo
inorganics
Auto
Carbon from
organics
Hetero
Cyanobacteria
• Photo litho auto trophy
• Photo auto trophy
Trophy

Trophy
• Bacteria and “prokaryotic archaea” are very diverse in
types of trophy
• There are many distinct mechanisms to carry out each
form of “trophy”
• Also a great deal of diversity in some eukaryotes groups

Thought Question
What is the difference between
chemolithoautotrophy and
chemolithoheterotrophy?
• A: The source of electrons
• B: The source of energy
• C: The source of carbon
• D: A and B
• E: All of the above

Clicker Question
What is the difference between
chemolithoautotrophy and
chemolithoheterotrophy?
• A: The source of electrons
• B: The source of energy
• C: The source of carbon
• D: A and B
• E: All of the above

Extremophiles
Extremophile:
Organism that survives and thrives extreme
conditions
(as compared to conditions where other forms
of life survive and thrive).

Extreme Environments
105°C
CH3
CO, 80°CH2S, pH 0, 95°C High salt
CO2 4°Clow pH

Methods for Studying Microbes
Observation
What Next?
Collect Sample
Look in Microscope
See Cells

What Next?
Collect Sample
Look in Microscope
See Cells

<<<<
What Next?
The Great Plate Count
Anomaly
Collect Sample
Look in Microscope
See Cells

<<<<
DNA
What Next?
Anomaly
Culture independent
DNA studies
Collect Sample
Look in Microscope
See Cells

<<<<
DNA
What Next?
Anomaly
Culturing can work,
and this allows all
sorts of studies
Culture independent
DNA studies
Collect Sample
Look in Microscope
See Cells

Culturing Microbes

Example 1: Thermophiles

Determining Optimal Growth Temperature
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33

Grow starter culture

Set up some
flasks with
growth media

Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks

Set up some
flasks with
growth media
1 2 3 4 Use different
flasks for
different
conditions
Add a small
portion of the
starter culture
to flasks

Set up some
flasks with
growth media
60° 70° 80° 90°
flasks for
different
conditions
Add a small
portion of the
starter culture
to flasks

Set up some
flasks with
growth media
60° 70° 80° 90°
flasks for
different
conditions
Add a small
portion of the
starter culture
to flasks
Monitor growth over time

Set up some
flasks with
growth media
60° 70° 80° 90°
flasks for
different
conditions
1 2 3 4
60° 70° 80° 90°
1h 1h 1h 1h
Add a small
portion of the
starter culture
to flasks

Set up some
flasks with
growth media
60° 70° 80° 90°
flasks for
different
conditions
1 2 3 4
60° 70° 80° 90°
1h 1h 1h 1h
1 2 3 4
60° 70° 80° 90°
2h 2h 2h 2h
Add a small
portion of the
starter culture
to flasks

Set up some
flasks with
growth media
60° 70° 80° 90°
flasks for
different
conditions
1 2 3 4
60° 70° 80° 90°
1h 1h 1h 1h
1 2 3 4
60° 70° 80° 90°
2h 2h 2h 2h
1 2 3 4
60° 70° 80° 90°
3h 3h 3h 3h
Add a small
portion of the
starter culture
to flasks

Growth vs. Time
0.0
20.0
40.0
60.0
80.0
0h 1h 2h 3h
60° 70° 80° 90°
Plot Growth vs. Time for Each Condition
Time Elapsed
DensityofGrowth

Growth Rate
0.0
12.5
25.0
37.5
50.0
60 °C 70 °C 80 °C 90° C
Calculate and Plot Growth Rate vs. Conditions
Temperature
GrowthRate

Optimal growth temperature (OGT) for Different Species

Optimal growth temperature (OGT) for Different Species
Extremophile Type Low High
Psychrophile -20 °C 10 °C
Mesophile 11 °C 40 °C
Thermophile 41 °C 80 °C
Hyperthermophile 81 °C 122 °C

Hug et al 2016
Hug et al. 2016 Tree of Life
Hug et al. Nature Microbiology. A new view of the tree of life.
http://dx.doi.org/10.1038/nmicrobiol.2016.48
Two Domain Tree of
Life with Some Major
Subbranches Shown
Laura Hug
U. Waterloo
Jill Banﬁeld
UC Berkeley

Hug et al 2016
Thermophiles Across the Tree
41 - 80 °C
Thermophiles Across
Tree of Life

Hug et al 2016Thermophiles Across the Tree
What are some possible
evolutionary scenarios that
would account for this
pattern of presence of
thermophily across the Tree
of Life?

Hug et al 2016
Hyperthermophiles Across the Tree
Hyperthermophiles
Across Tree of Life
No Eukaryotes
Only a few Bacteria
81 - 122 °C

Example 2: Halophiles

Determining Optimal Salt Concentrations

Set up some
flasks with
growth media

Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks

Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
flasks for
different
conditions

Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
flasks for
different
conditions
1M 2M 3M 4M

Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
flasks for
different
conditions
1M 2M 3M 4M
1 2 3 4
1M 2M 3M 4M
1h 1h 1h 1h

Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
flasks for
different
conditions
1M 2M 3M 4M
1 2 3 4
1M 2M 3M 4M
1h 1h 1h 1h
1 2 3 4
1M 2M 3M 4M
2h 2h 2h 2h

Set up some
flasks with
growth media
Add a small
portion of the
starter culture
to flasks
flasks for
different
conditions
1M 2M 3M 4M
1 2 3 4
1M 2M 3M 4M
1h 1h 1h 1h
1 2 3 4
1M 2M 3M 4M
2h 2h 2h 2h
1 2 3 4
1M 2M 3M 4M
3h 3h 3h 3h

Growth vs. Time
Plot Growth vs. Time for Each Condition
0.0
20.0
40.0
60.0
80.0
0h 1h 2h 3h
1M 2M 3M 4M
Time Elapsed
DensityofGrowth

Growth Rate
0.0
12.5
25.0
37.5
50.0
1M 2M 3M 4M
Calculate and Plot Growth Rate vs. Conditions
Salinity
GrowthRate

Optimal salt concentration for different species

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)

Hug et al 2016
Extreme Halophiles Across the Tree
Most extreme
halophiles are from a
single clade of
“prokaryotic
Archaea”

Hug et al 2016Extreme Halophiles Across the Tree
What are some possible
evolutionary scenarios that
would account for this
pattern across the Tree of
Life?

Uses of extremophiles
Type of
environment
Examples Example of
mechanism of
survival
Practical Uses
High temp
(thermophiles)
Deep sea vents,
hotsprings
Amino acid
changes
Heat stable enzymes
Low temp
(psychrophile)
Antarctic ocean,
glaciers
Antifreeze
proteins
Enhancing cold
tolerance of crops
High pressure
(barophile)
Deep sea vents,
hotsprings
Solute changes Industrial processes
High salt
(halophiles)
Evaporating
pools
Incr. internal
osmolarity
Soy sauce production
High pH
(alkaliphiles)
Soda lakes Transporters Detergents
Low pH
(acidophiles)
Mine tailings Transporters Bioremediation
Desiccation
(xerophiles)
Deserts Spore formation Freeze-drying
additives
High radiation
(radiophiles)
Nuclear reactor
waste sites
Absorption, repair
damage
Bioremediation,
space travel

Novozymes in Davis

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BIS2C_2020. Lecture 9. Form and function