2. Microbiology 101

Question 1

Types of organic pollutant degradation (2)

Answer 1

• abiotic
• biological mechanisms

Question 2

Types of abiotic mechanisms (3 + examples)

Answer 2

• photochemical
• chemical (e.g. oxidation, reduction, …)
• mechanical (e.g. wind, water, mixing, dilution)

Question 3

Types of biological mechanisms done by plants and animals (2)

Answer 3

• direct consumption
• indirect degradation via compounds secreted by organisms, associated with microbes biodegrade contaminants

Question 4

How do microorganisms degrade pollutants? (3)

Answer 4

• diverse metabolism
• mineralization
• modification or transformation (product may be more or less of a pollution problem)

Question 5

What is mineralization?

Answer 5

Conversion of organic compounds to CO2

Question 6

What are microbes? (6)

Answer 6

Microsocopic:
- plants
- animals (including protozoa)
- bacteria
- fungi
- archaea
- viruses

Question 7

Are visible bacteria still microbes?

Answer 7

Yes e.g. cyanobacteria

Question 8

Main morphologies of prokaryotes (shapes) (2)

Answer 8

• rods / bacili = rectangular boxes
• cocci = spheres

Question 9

What is hegemony?

Answer 9

Leadership, predominant influence, or domination of, esp. as exercised by one nation over others

Question 10

Microbial hegemony? (3 points)

Answer 10

• domination = 50% of the global biomass is microbial
• predominant influence = global biogeochemical cycling
• leadership, supremacy = extraordinary metabolic capacity

Question 11

Why is microbiological evolution important to biodegradation? (6 points)

Answer 11

• microbes have been around for 3-4 billion years
• over that time they have become exposed to every single imaginable organic compound and environment
• they evolved complex processes
• any niche or source of energy and carbon has been exploited meaning that they can live almost anywhere on the planet
• but most microbial species have never been cultured (99%)!
• we do not know much about their metabolic pathway, etc

Question 12

Can bacteria and archaea be grown in culture?

Answer 12

The vast majority cannot be grown in culture.
Some may be viable-but-not-culturable (VBNC)

Question 13

If they are not culturable, how do we know they exist? (3)

Answer 13

• Microscopy: direct microscopic counts can exceed viable counts by several orders of magnitude
• Respiration tests
• Molecular biology: 16S rRNA sequences, the molecular clock, position on tree of life

Question 14

What are Haeckel and Whittaker’s trees of life based on? And why doesn’t that work well for bacteria, prokaryotes?

Answer 14

• Morphology (shape)
• because most are all rods or spheres

Question 15

What is the tree of life based off of?

Answer 15

The comparison of 16S rRNA sequences (phylogeny)

Question 16

Where is there the greatest diversity according to the tree of life?

Answer 16

The microbial world

Question 17

What are the 3 forms of life?

Answer 17

• bacteria
• archaea
• eukaryotes

Question 18

Bacteria (3 points)

Answer 18

• include pathogens
• but the majority of species have never been characterized
• are found in every niche on the planet

Question 19

Archaea (2 points)

Answer 19

• previously thought to be limited to extreme environments, like anaerobic sediments and hot springs
• although they do dominate some of these niches, they are found everywhere

Question 20

How many branches did the last common ancestor give rise to?

Answer 20

2 branches: Bacteria & Archaea/Eucarya
- Archaea and Eucarya split later

Question 21

what is anaerobic?

Answer 21

without oxygen

Question 22

What is the central dogma of life?

Answer 22

Genetic information flows from DNA, to RNA, to protein.

Question 23

Relating the central dogma to evolution of metabolic capacities in microbes

Answer 23

genetics → physiology → ecological niche → genetics

Question 24

What is the ecological niche the site of? (2)

Answer 24

• competition / predation
• change in conditions (physical and environmental conditions)

So these factors are part of the selective pressure that stimulates the evolution of metabolic capacities in microbes

Question 25

What does it mean for biodegradation that microbes have been around since the atmosphere was harsher? (3)

Answer 25

• They have evolved many different and complex metabolic strategies
• So, they can be used to degrade many types of pollutants that are toxic to us
• This also means that the probability that we find a species that can bioremediate a particular problem is high

Question 26

How can we find what microbes would be useful for specific bioremediation?

Answer 26

Culture based and/or molecular based methods

Question 27

Where do we look for pollution biodegraders? (2 places and why)

Answer 27

Soil and water in contaminated sites

This is because biodegraders should be enriched and selected for in these environments