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 transfer3


Microbial Diversity


• Alveolates

• Stramenopiles

• Rhizaria

• Excavates

• Amoebozoans

• Plantae

• Opisthokonts




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.

17Sudden 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.

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• Not colonial; live as single cells

• Some secrete shells or glue sand grains together to form a casing.

• Many pathogens

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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





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





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.

Chlamydomonas

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




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



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


Endosymbioses


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

Endosymbioses


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

Internal membranes studded with ribosomes formed.

Endosymbioses


Endosymbioses


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.


Endosymbioses


Microtubules from the cytoskeleton formed eukaryotic flagellum, enabling propulsion.

Early digestive vacuoles evolved into lysosomes using enzymes from the early endoplasmic reticulum.


Endosymbioses


Endosymbioses


Endosymbioses


Proteobacteria

Endosymbioses


Proteobacteria

Endosymbioses


Mitochondria formed through endosymbiosis with a proteo-bacterium.

Proteobacteria

Endosymbioses


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



Bacteria



Bacteria Archaea



Bacteria Archaea Eukaryotes














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

Science