BIS2C. Biodiversity and the Tree of Life. 2014. L8. Intro to Microbial Diversity 2.
-
Upload
jonathan-eisen -
Category
Science
-
view
462 -
download
1
Transcript of 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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Microbial Diversity
• Seven major lineages of eukaryotes
• Alveolates
• Stramenopiles
• Rhizaria
• Excavates
• Amoebozoans
• Plantae
• Opisthokonts
• Complications 1: Endosymbioses
• Complications 2: Lateral gene transfer3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Microbial Diversity
• Seven major lineages of eukaryotes
• Alveolates
• Stramenopiles
• Rhizaria
• Excavates
• Amoebozoans
• Plantae
• Opisthokonts
• Complications 1: Endosymbioses
• Complications 2: Lateral gene transfer4
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Oversimplification of eukaryotic phylogeny
5
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
•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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 14
Stramenopiles
Stramenopiles Two flagella, with rows of tubular
hairs on the longer one.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
•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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Stramenopiles: Oomcyetes
Phytophthora
Potato Late Blight
• Non-photosynthetic. • Are absorptive heterotrophs • Once were classed as fungi, but
are unrelated.
17Sudden Oak Death
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Clicker Question
The similarity in appearance of ooymcetes to fungi is an example of _______
!
• A. Homology
• B. Homoplasy
• C. Divergent evolution
• D. Monophyly
19
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Clicker Question
The similarity in appearance of ooymcetes to fungi is an example of _______
!
• A. Homology
• B. Homoplasy
• C. Divergent evolution
• D. Monophyly
20
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Rhizaria
Rhizaria Unicellular, aquatic, with long, thin
pseudopods.21
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Excavates: Euglenids
• Have flagella. • Some are
photosynthetic, some always heterotrophic, and some can switch.
28
Movement in the euglenoid Eutreptia
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Amoebozoans
Amoebozoans Lobe-shaped pseudopods are used for
locomotion.
30
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
• Not colonial; live as single cells
• Some secrete shells or glue sand grains together to form a casing.
• Many pathogens
31
Amoebozoans: Loboseans
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Entamoeba histolytica
32
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 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Plantae
35
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 2014
Plantae: Glaucophytes
• Unicellular, freshwater organisms
• The chloroplast retains a bit of peptidoglycan between the inner and outer membrane.
36
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Plantae: Glaucophytes
• Unicellular, freshwater organisms
• The chloroplast retains a bit of peptidoglycan between the inner and outer membrane.
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Plantae: Glaucophytes
• Unicellular, freshwater organisms
• The chloroplast retains a bit of peptidoglycan between the inner and outer membrane.
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Plantae: Charophytes and Land Plants
STAY TUNED
42
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
•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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 45
Opisthokonts: Fungi and Animals
STAY TUNED
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Eukaryotic Diversity
• Seven major lineages of eukaryotes
• Alveolates
• Stramenopiles
• Rhizaria
• Excavates
• Amoebozoans
• Plantae
• Opisthokonts
• Complications 1: Endosymbioses
• Complications 2: Lateral gene transfer46
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Oversimplification of eukaryotic phylogeny
48
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Diverse Organelles
49
Mitochondrion Chloroplast
Nucleus
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Endosymbioses in eukaryotic evolution
50
Prokaryotic cell
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Endosymbioses in eukaryotic evolution
50
Cell wall
Prokaryotic cell
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Endosymbioses in eukaryotic evolution
50
DNA
Cell wall
Prokaryotic cell
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Endosymbioses in eukaryotic evolution
50
DNA
Cell wall
Prokaryotic cell
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Endosymbioses in eukaryotic evolution
50
DNA
Cell wall
Prokaryotic cell
The protective cell wall was lost.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Endosymbioses in eukaryotic evolution
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.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 51
Cytoskeleton (micro-filament and micro-tubules) formed.
Endosymbioses
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 51
Cytoskeleton (micro-filament and micro-tubules) formed.
Internal membranes studded with ribosomes formed.
Endosymbioses
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 52
As regions of the infolded plasma membrane enclosed the cell’s DNA, a precursor of a nucleus formed.
Endosymbioses
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 52
Early digestive vacuoles evolved into lysosomes using enzymes from the early endoplasmic reticulum.
As regions of the infolded plasma membrane enclosed the cell’s DNA, a precursor of a nucleus formed.
Endosymbioses
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 52
Microtubules from the cytoskeleton formed eukaryotic flagellum, enabling propulsion.
Early digestive vacuoles evolved into lysosomes using enzymes from the early endoplasmic reticulum.
As regions of the infolded plasma membrane enclosed the cell’s DNA, a precursor of a nucleus formed.
Endosymbioses
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 53
Mitochondria formed through endosymbiosis with a proteo-bacterium.
Proteobacteria
Endosymbioses
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 54
Endosymbiosis with cyanobacteria led to the development of chloroplasts.
Endosymbioses
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 54
Flagellum
Eukaryotic cell
Chloroplast
Mitochondria
Nucleus
Endosymbiosis with cyanobacteria led to the development of chloroplasts.
Endosymbioses
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 55
Bacteria Archaea
Mitochondrial Symbiosis
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 55
Bacteria Archaea Eukaryotes
Mitochondrial Symbiosis
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 55
Bacteria Archaea Eukaryotes
Mitochondrial Symbiosis
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 55
Bacteria Archaea Eukaryotes
Mitochondrial Symbiosis
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 55
Bacteria Archaea Eukaryotes
Mitochondrial Symbiosis