BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 8
!
Lecture 8
!
Introduction to Microbial Diversity
Part 2
!
!
BIS 002C
Biodiversity & the Tree of Life
Spring 2014
!
Prof. Jonathan Eisen
1

Where we are going and where we have been
• Previous Lecture:
!7: Microbial Diversity
• Current Lecture:
!8: Microbial Diversity part 2
• Next Lecture:
!9: Symbioses
2

Microbial Diversity
• Seven major lineages of eukaryotes
• Alveolates
• Stramenopiles
• Rhizaria
• Excavates
• Amoebozoans
• Plantae
• Opisthokonts
• Complications 1: Endosymbioses
• Complications 2: Lateral gene transfer
3

Microbial Diversity
• Alveolates
• Stramenopiles
• Rhizaria
• Excavates
• Amoebozoans
• Plantae
• Opisthokonts
4

Oversimplification of eukaryotic phylogeny
5

Phylogenetic diversity of eukaryotes
• As with bacteria and archaea, phylogeny of major groups
based largely on molecular data.
• However, non-molecular data more useful for studies of
eukaryotic phylogeny
• Major groupings, and the relationships among groups, still
being resolved
• All organisms other than plants, animals and fungi are
sometimes referred to as protists or microbial
eukaryotes (note - paraphyletic)
6

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 7
Alveolates
Alveolates
Have alveoli or
sacs beneath
surface of
plasma
membrane.
All are
unicellular;
many are
photosynthetic.

•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
8
Certium
tenue
Coral symbiont

Clicker Question
9

Clicker Question
What is the different between
photoautotrophy and photoheterotrophy?
!
• A: The source of electrons
• B: The source of carbon
• C: The source of energy
• D: All of the above
10

Clicker Question
What is the different between
photoautotrophy and photoheterotrophy?
!
• A: The source of electrons
• B: The source of carbon
• C: The source of energy
• D: All of the above
11

Alveolates: Apicomplexans
• All parasitic
• Have a mass of organelles at one tip
—the apical complex that help the
parasite enter the host’s cells.
12
Apical complex • Plasmodium falciparum-
Malaria kills 700,000-2,000,000
people per year—75% of them
are African children

Alveolates: Ciliates
13
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.

Stramenopiles
Stramenopiles
Two flagella, with rows of tubular
hairs on the longer one.

•All are multicellular; some get very large
(e.g., giant kelp).
•The carotenoid fucoxanthin imparts the
brown color.
•Almost exclusively marine.
Stramenopiles: Brown Algae
15
A community of brown algae: The marine kelp forest

Stramenopiles: Diatoms
16
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

Stramenopiles: Oomcyetes
Phytophthora
Potato Late Blight
• Non-photosynthetic.
• Are absorptive heterotrophs
• Once were classed as fungi, but
are unrelated.
17
Sudden Oak Death

Clicker Question
18

Clicker Question
The similarity in appearance of ooymcetes to
fungi is an example of _______
!
• A. Homology
• B. Homoplasy
• C. Divergent evolution
• D. Monophyly
19

Clicker Question
The similarity in appearance of ooymcetes to
fungi is an example of _______
!
• A. Homology
• B. Homoplasy
• C. Divergent evolution
• D. Monophyly
20

Rhizaria
Rhizaria
Unicellular, aquatic, with long, thin
pseudopods.
21

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
22
Chlorarachnion reptans

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.
23

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.
24

Excavates
25

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
26

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.
27

Excavates: Euglenids
• Have flagella.
• Some are
photosynthetic,
some always
heterotrophic, and
some can switch.
28
Movement in the euglenoid Eutreptia

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
29

Amoebozoans
Amoebozoans
Lobe-shaped pseudopods are used for
locomotion.
30

• Not colonial; live as single cells
• Some secrete shells or glue sand
grains together to form a casing.
• Many pathogens
31
Amoebozoans: Loboseans

Entamoeba histolytica
32
http://www.npr.org/blogs/health/2014/04/09/300991364/gut-
eating-amoeba-caught-on-ﬁlm

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
33

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
34
Karyo

Plantae
35
The Plantae consist of
several clades; all
chloroplasts trace back
to a single incidence of
endosymbiosis.

Plantae: Glaucophytes
• Unicellular, freshwater
organisms
• The chloroplast retains a bit
of peptidoglycan between the
inner and outer membrane.
36

Clicker Question
37

organisms
38
Which of the following groups do
not have peptidoglycan in their
cell envelopes?
•A: Gram positive bacteria
•B: Gram negative bacteria
•C: Cyanobacteria
•D: Crenarchaeota

organisms
39
Which of the following groups do
not have peptidoglycan in their
cell envelopes?
•A: Gram positive bacteria
•B: Gram negative bacteria
•C: Cyanobacteria
•D: Crenarchaeota

Plantae: Red Algae
40
• 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.
41
Movement in the green
alga Volvox
Micrasterias

Plantae: Charophytes and Land Plants
STAY
TUNED
42

Opisthokonts

•Choanoflagellates are sister to the
animals.
•Some are colonial and resemble a
type of cell found in sponges.
44
The choanoﬂagellate Salpingoeca sp. feeding
Opisthokonts: Choanoflagellates

Opisthokonts: Fungi and Animals
STAY
TUNED

Eukaryotic Diversity
• Alveolates
• Stramenopiles
• Rhizaria
• Excavates
• Amoebozoans
• Plantae
• Opisthokonts
46

The Bacteria

Oversimplification of eukaryotic phylogeny
48

Diverse Organelles
49
Mitochondrion Chloroplast
Nucleus

Endosymbioses in eukaryotic evolution
50
Prokaryotic cell

50
Cell wall
Prokaryotic cell

50
DNA
Cell wall
Prokaryotic cell

50
DNA
Cell wall
Prokaryotic cell
The protective cell
wall was lost.

50
DNA
Cell wall
Prokaryotic cell
Infolding of the
plasma membrane
added surface area
without increasing
the cell’s volume.
The protective cell
wall was lost.

50

Endosymbioses

Cytoskeleton (micro-
filament and micro-
tubules) formed.
Endosymbioses

Cytoskeleton (micro-
filament and micro-
tubules) formed.
Internal membranes
studded with
ribosomes formed.
Endosymbioses

Endosymbioses

As regions of the infolded
plasma membrane enclosed
the cell’s DNA, a precursor of
a nucleus formed.
Endosymbioses

Early digestive vacuoles evolved
into lysosomes using enzymes from
the early endoplasmic reticulum.
a nucleus formed.
Endosymbioses

Microtubules from the
cytoskeleton formed
eukaryotic flagellum,
enabling propulsion.
Early digestive vacuoles evolved
into lysosomes using enzymes from
the early endoplasmic reticulum.
a nucleus formed.
Endosymbioses

Endosymbioses

Proteobacteria
Endosymbioses

Mitochondria
formed through
endosymbiosis
with a proteo-
bacterium.
Proteobacteria
Endosymbioses

Endosymbioses

Cyanobacteria
Endosymbioses

Endosymbiosis with
cyanobacteria led to
the development of
chloroplasts.
Endosymbioses

Flagellum
Eukaryotic cell
Chloroplast
Mitochondria
Nucleus
Endosymbiosis with
cyanobacteria led to
the development of
chloroplasts.
Endosymbioses

Mitochondrial Symbiosis

Bacteria

Bacteria Archaea

Bacteria Archaea Eukaryotes

BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.

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