BiS2C: Lecture 11: Microbial Growth and Functions

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016

Lecture 11: Microbial Growth and Functions

BIS 002C Biodiversity & the Tree of Life

Spring 2016

Prof. Jonathan Eisen

1


Where we are going and where we have been

• Previous Lecture: !10: Not a Tree

• Current Lecture: !11: Microbial Growth and Functions

• Next Lecture: !12: Symbiosis

2


Thought Questions & Main Topics

• What are the ranges of conditions in which life on Earth lives?

• What are the ranges of conditions in which life on Earth prefers to live?

• What are the key ways that living systems acquire carbon and energy?

3


Key Concepts and Topics

• Culturing

• Extremophily !Thermophiles !Halophiles

• Trophies

• Oxygen

• More on organelles

4

Culturing

• Culturing (or cultivation) is the growth of microorganisms in controlled or defined conditions.

• A pure culture (which is the ideal if possible) is one in which only one type of microbe is present

!5

General approach to culturing

! Collect sample ! Make an environment with specific growth conditions

" Energy " Electrons " Carbon " Other conditions (e.g., O2, temperature, salt, etc)

! Dilution/passaging until one obtains a “pure” sample with just a single clone

!6

Culturing

!7


Prokaryotic Cell Division (Part 1)

8

Mitosis

!9

Binary fission and Mitosis Clonal Growth

10

Examples of Benefits of Culturing:

• Allows one to connect processes and properties to single types of organisms

• Enhances ability to do experiments from genetics, to physiology to genomics

• Provides possibility of large volumes of uniform material for study

• Can supplement appearance based classification with other types of data.

!11

Function Example I: Extremophily

!12

Example 1: Thermophiles

!13

Figure 26.16 Some Crenarchaeotes Like It Hot

!14

Figure 26.14 What Is the Highest Temperature Compatible with Life?

!15

Some prokaryotes can survive at temperatures above the 120°C threshold of sterilization.

1. Seal samples of unidentified, iron-reducing, thermal vent prokaryotes in tubes with a medium containing Fe3+ as an electron acceptor. Control tubes contain Fe3+ but no organisms.

2. Hold both tubes in a sterilizer at 121°C for 10 hours. if the iron-reducing organisms are metabolically active, they will reduce the Fe3+ to Fe2+ (as magnetite, which can be detected with a magnet).

Archaea of “Strain 121” can survive at temperatures above the previously defined sterilization limit.

Set up some flasks with growth media

60° 70° 80° 90°1 2 3 4 Use different

flasks for different conditions

Determining Optimal Growth Temperature

!1633

Grow starter culture

Add a small portion of the starter culture to flasks

Monitor growth over time


60° 70° 80° 90°1 2 3 4 Use different


1 2 3 460° 70° 80° 90°1h 1h 1h 1h


!1633





60° 70° 80° 90°1 2 3 4 Use different


1 2 3 460° 70° 80° 90°1h 1h 1h 1h

1 2 3 460° 70° 80° 90°2h 2h 2h 2h


!1633





60° 70° 80° 90°1 2 3 4 Use different


1 2 3 460° 70° 80° 90°1h 1h 1h 1h

1 2 3 460° 70° 80° 90°2h 2h 2h 2h

1 2 3 460° 70° 80° 90°3h 3h 3h 3h


!1633




Growth vs. Time

!17

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

Den

sity

of G

row

th

Growth Rate

!18

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

Gro

wth

Rat

e

Optimal growth temperature (OGT) for Different Species

!19

Optimal growth temperature (OGT) for Different Species

!21

A > B >> E

Mesophile Optimum at 15-45 °C Thermophile Optimum at 45-80°C Hyperthermophile Optimum at > 80°C

Hug et al 2016

!22

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

http://dx.doi.org/10.1038/nmicrobiol.2016.48

Hug et al 2016

!24

Thermophiles Across the Tree


What are some possible evolutionary scenarios that would account for this pattern of presence of thermophily across the Tree of Life?


Thermophile Adaptations

!30

Stresses of High Temperature

Examples of common adaptations

Denatures proteins, RNA and DNA

Make proteins more stable

Speeds up reactions Slow down enzyme rates

Liquifies membranes Decrease fluidity of membranes


Example 1: Extreme Halophiles

31

Determining Optimal Salt Concentrations

!3233




1 2 3 4 Use different flasks for different conditions

1M 2M 3M 4M



!3233





1M 2M 3M 4M


1 2 3 41M 2M 3M 4M1h 1h 1h 1h


!3233





1M 2M 3M 4M


1 2 3 41M 2M 3M 4M1h 1h 1h 1h

1 2 3 41M 2M 3M 4M2h 2h 2h 2h


!3233





1M 2M 3M 4M


1 2 3 41M 2M 3M 4M1h 1h 1h 1h

1 2 3 41M 2M 3M 4M2h 2h 2h 2h

1 2 3 41M 2M 3M 4M3h 3h 3h 3h

Growth vs. Time

Plot Growth vs. Time for Each Condition

!33

0.0

20.0

40.0

60.0

80.0

0h 1h 2h 3h

1M 2M 3M 4M

Time Elapsed

Den

sity

of G

row

th

Growth Rate

!34

0.0

12.5

25.0

37.5

50.0

1M 2M 3M 4M

Calculate and Plot Growth Rate vs. Conditions

Salinity

Gro

wth

Rat

e

Optimal salt concentration for different species

!35


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)

36

Hug et al 2016

!38

Extreme Halophiles Across the Tree


What are some possible evolutionary scenarios that would account for this pattern of presence of halophily across the Tree of Life?


• Some stresses of high salt ! Osmotic pressure on cells ! Desiccation

Halophile adaptations

!39

H20


• Halophile adaptations ! Increased osmolarity inside cell

" Proteins " Carbohydrates " Salts

! Membrane pumps ! Desiccation resistance


!40

H20

H20


• Halophile adaptations ! Increased osmolarity inside cell

" Proteins " Carbohydrates " Salts - only done in extremely halophilic archaea

! Membrane pumps ! Desiccation resistance


!42

High internal salt requires ALL cellular components to be adapted to salt, charge. For example, all proteins must change surface charge and other properties.


Uses of extremophiles

!43

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

44

Function Example I: Trophies

!45

Incredible diversity in forms of nutrition in bacteria and archaea

• Bacteria and archaea 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.

• Examples: ! autotrophy ! chemotrophy ! phototrophy ! heterotrophy

!46

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


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


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


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


Photo

Chemical

Chemo


Inorganic

Litho

Organic

Organo


Auto


Hetero


• Cyanobacteria • Photo litho auto trophy• Photo auto trophy

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 51

αProteo

Genome

Bacterial cell envelope

Cell membrane

Genome

A Symbiosis with a Proteobacterium


Engulfment

52

αProteo

Cell membrane

Genome

Genome

Bacterial cell envelope


What Does This Provide Host?

53


Symbiosis with Free Living Cyanobacterium

54

N

Mitochondrion

Mitochondrial Genome

MNucleus

Cell membrane

Nuclear Genome

Cyanobacterial Cell envelope

Cyanobacterial Genome Cyano


Engulfment

55

N

Mitochondrion

Mitochondrial Genome

MNucleus

Cell membrane

Nuclear Genome

Cyanobacterial Cell envelope

Cyanobacterial Genome Cyano


What Does This Provide Host?

56


Clicker Question

57


Clicker Question

What is the different between chemoautolithotrophy and chemoheterolithotrophy?

• A: The source of electrons

• B: The source of energy

• C: The source of carbon

• D: A and B

• E: All of the above

58


Clicker Question

What is the different between chemoautolithotrophy and chemoheterolithotrophy?

• A: The source of electrons

• B: The source of energy

• C: The source of carbon

• D: A and B

• E: A, B and C

59


Growth vs. Oxygen

60

Aerobes vs. AnaerobesMicrobes differ in their use and tolerance of oxygen.

1. Aerobes- Require oxygen 2. Anaerobes- Vary in their tolerance/ use of oxygen

Obligate anaerobes – oxygen is toxic.

Aerotolerant anaerobes – can’t use oxygen, but are not damaged by it.

Facultative anaerobes – don’t need oxygen, but use it when available.

Organelle Evolution

61

Simple Species Tree for Three Domains

62

Archaea Eukaryotes Bacteria

63

Archaea Euks BacteriaTACK

Eocyte Species Tree for Three Domains

Acquisition of Mitochondria At Base of Eukaryotic Branch

64


Endosymbiosis Shown on Species Tree

65


Continued Evolution After Endosymbiosis

66


Simple Model Showing Some Diversification within Eukaryotes

67

A2 E1 PBT E2 B2 B3 B4A1 A3

68

Suppose we built phylogenetic trees with different genes from each of these species


Simple Model Showing Some Diversification within Eukaryotes

Gene Set 1

69


Some Genes with Show This Pattern with Eukaryotes Sister to TACK

Gene Set 2: Organellar Genes

70


Some Genes with Show Alternative Pattern With “Eukaryotes” Branching within Bacteria

After Additional Speciation in the Eukaryote Portion of the Tree

71

A2 E1 PBT E2 B2 B3 B4A1 A3 E3

Gene transfer model

72



Nuclear Genes

73


Some Genes with Show This Pattern with Eukaryotes Sister to TACK

Nuclear Genes

74


Note - Branching of E2 sister to E3

Mitochondrial Genes

76


Some Genes with Show Alternative Pattern With “Eukaryotes” Branching within Bacteria

Mitochondrial Genes

77


Note - Branching of E2 sister to E3

Mitochondrial Genes

78


The topology of the tree within Eukaryotes is the same regardless of which genes. They differ in where eukaryotes placed in the tree.

Another Symbioses - with a CB - Cyanobacterium

79

Archaea T PBEukaryotes CB B3 B4

80

Another Symbioses - with a CB - Cyanobacterium

Archaea T PBEukaryotes CB B3 B4

81

Continued Evolution - Diversification of Plants

Archaea T PBE1 CB B3 B4E2 Plants


Science

BiS2C: Lecture 11: Microbial Growth and Functions