BIS2C. Biodiversity and the Tree of Life. 2014. L7. Intro to Microbial Diversity

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014

Lecture 7

!

Lecture 7 !

Introduction to Microbial Diversity !!!

BIS 002C Biodiversity & the Tree of Life

Spring 2014 !

Prof. Jonathan Eisen

1


Where we are going and where we have been

• Previous Lecture: !6: The Tree of Life

• Current Lecture: !7: Microbial Diversity

• Next Lecture: !8: Microbial Diversity

2


Weeks 2-3: Microbial Diversity

3

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 4

Bacteria Archaea Eukaryotes

Diversity Within Each Domain


Unrooted Tree of Life

5adapted from Baldauf, et al., in Assembling the Tree of Life, 2004




PWeeks 4-5




F AWeeks 6-9

P




Weeks 2-3 The Rest




Weeks 2-3 The Rest




Weeks 2-3 Mostly Microbes


The Bad

11


The Good

Nitrogen Fixation

Carbon Fixation

Animal Nutrition

12


The Unusual

• Extremophiles

105°C CH3

CO, 80°CH2S, pH 0, 95°C High salt

CO2 4°Clow pH

13


The Influential

Carbon cycle Nitrogen cycle

14


The Unknown

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The Consumable

• =

16

Feed microbes a little carbon and they can make some nice things


Weeks 2-3

• 7: Intro to diversity of microbes

• 8: Microbial diversity II

• 9: Physiological diversity

• 10: Symbioses

• 11: Human microbiome

• 12: The microbes among us

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!18

Biochemical and metabolic Diversity

Component Different FormsEnergy source Light

Photo

Chemical

Chemo

Electron source (reducing equivalent)

Inorganic

Litho

Organic

Organo

Carbon source Carbon from C1 compounds

Auto

Carbon from organics

Hetero

Forms of nutrition (trophy)

• Three main components to “trophy”


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero




Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero




Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero




Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero




Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero




Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero




Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero




Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero




Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero




Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero




Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero




Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• E. coli


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• E. coli


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• E. coli


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• E. coli


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• E. coli • Chemo organo hetero trophy


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• E. coli • Chemo organo hetero trophy• Chemo hetero trophy


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• Cyanobacteria


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• Cyanobacteria


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• Cyanobacteria


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• Cyanobacteria


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• Cyanobacteria • Photo litho auto trophy


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• Cyanobacteria • Photo litho auto trophy• Photo auto trophy


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• Humans?


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• Humans?


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• Humans?


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• Humans?


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• Humans? • Chemo organo hetero trophy


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• Humans? • Chemo organo hetero trophy• Chemo hetero trophy

Incredible diversity in forms of nutrition in bacteria and archaea

• Amazing thing about bacteria and archaea is that every type of “trophy” is seen

• Also there are many distinct mechanisms to carry out each form of “trophy”

• Also great deal of diversity in microbial eukaryotes

!23

!24

Diversity of bacteria, archaea, and eukaryotes

• You should learn the names of the major groups

• You should be able to give some examples of key properties of the groups

• Much more about these groups is in Chapter 26-27. You should read these Chapters.

• We are going to do a VERY quick tour today ...


The Bacteria

25


Bacterial Diversity: Form

• 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.

26

A giant bacterium

!27


Bacterial Diversity: Multicellularity

Photo 26.24 Fruiting body of gliding bacterium Stigmatella aurantiaca. SEM.28


Bacterial Diversity: Biofilms

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Bacterial Diversity: Gram Positive vs. Negative

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Outside of cell

Outside of cell

Inside of cell

Inside of cell

Cell envelope

Cell wall (peptidoglycan)

Plasma membrane

Outer membrane of cell envelope

Periplasmic space

Peptidoglycan layer

Periplasmic space

Plasma membrane

5 µm

5 µm

Gram Positive

Gram Negative


Bacterial Diversity: Motility

Flagella

31


Figure 4.5 Prokaryotic Flagella (Part 2)

Rotor

Inside of cell

Outside of cell

Transport apparatus

Drive shaft

Filament of flagellum

Plasma membrane

Outer membrane

Peptidoglycan

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Vibrio motility

!33

Vibrio motility

!33


Woese Tree of Life

34

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

EukaryotesBacteria ?????Archaebacteria


The Bacteria


The Bacteria


Major Phyla of Bacteria and Archaea (2013)

37C Rinke et al. Nature 000, 1-7 (2013) doi:10.1038/nature12352


Spirochetes

• Gram-negative

• Motile

• Chemoheterotrophic

• Unique rotating, axial filaments (modified flagella)

• Many are pathogens: !Syphilis !Lyme disease

• Others free-living38


Spirochetes

• Gram-negative

• Motile

• Chemoheterotrophic

• Unique rotating, axial filaments (modified flagella)

• Many are pathogens: !Syphilis !Lyme disease

• Others free-living38


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

39

C. trachomatis

http://upload.wikimedia.org/wikipedia/commons/a/aa/ChlamydiaTrachomatisEinschlussk%25C3%25B6rperchen.jpg


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

39

C. trachomatis

http://upload.wikimedia.org/wikipedia/commons/a/aa/ChlamydiaTrachomatisEinschlussk%25C3%25B6rperchen.jpg


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

40


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

40


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

41

Mycoplasmas


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

41

Mycoplasmas


Cyanobacteria

• Photolithoautotrophic

• Contain internal membrane system for photosynthesis

• Chloroplasts are derived from endosymbiotic cyanobacteria

• Colonies can differentiate into vegetative cells, spores, & heterocysts

42


Cyanobacteria

• Photolithoautotrophic

• Contain internal membrane system for photosynthesis

• Chloroplasts are derived from endosymbiotic cyanobacteria

• Colonies can differentiate into vegetative cells, spores, & heterocysts

42


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

43


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

43


Archaeal Diversity

44


Bacterial and Archaeal Shapes

Archaea cell membranes have lipids with fatty acids linked to glycerol by ether linkages (a synapomorphy of archaea):

45


Ester Linkages

Bacterial and eukaryotic cell membranes have lipids with fatty acids connected to glycerol by ester linkages:

46


Woese Tree of Life

47

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

EukaryotesBacteria ?????Archaebacteria


Figure 26.1 The Three Domains of the Living World

48


Major Phyla of Bacteria and Archaea (2013)

49C Rinke et al. Nature 000, 1-7 (2013) doi:10.1038/nature12352


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

50


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

51


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)

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Eukaryotic Diversity

53


Diverse Organelles

54

Mitochondrion Chloroplast

Nucleus


The Bacteria


Oversimplification of eukaryotic phylogeny

56


Oversimplification of eukaryotic phylogeny

57


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)

58


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.

Coral symbiont

Alveolates: Dinoflagellates

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Certium tenue


Alveolates: Apicomplexans

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Apical complex

Apicomplexans are all parasites. They have a mass of organelles at one tip—the apical complex that help the parasite enter the host’s cells.

Plasmodium falciparum- Malaria kills 700,000-2,000,000 people per year—75% of them are African children.


Chromalveolates: Alveolates: Ciliates

Ciliates have numerous cilia, the structure is identical to flagella.

Most are heterotrophic; very diverse group.

Have complex body form; two types of nuclei (and in most species, very active telomerase)

62 Movement in a ciliate from the gut of a termite

Science

BIS2C. Biodiversity and the Tree of Life. 2014. L7. Intro to Microbial Diversity