MICR601 TEST 1

Define ecology

Study of relationships between organisms and their environment.

Define ecosystem

Community of organisms interacting with each other and abiotic factors.

Define microbiota vs microbiome

Microbiota: All microorganisms in an environment
Microbiome: Their genetic material

Levels of ecological organisation (in order)

Cell → Population → Community → Ecosystem → Biome → Biosphere

Define population

Same species in the same area.

Define community

Multiple species living together.

Define ecosystem (exam wording)

Community + abiotic environment interactions.

What is microbial adaptation?

Ability to survive environmental stress (UV, antibiotics, temp, etc.)

Two genetic mechanisms of adaptation

Mutation
Genetic recombination

Why is microbial evolution fast?

Rapid reproduction + large populations

Define natural selection (microbial)

Environment selects organisms with beneficial traits → they survive & reproduce.

What are culture-dependent methods?

Growing microbes in lab.

Advantages of culture-dependent methods

Study metabolism
Count living cells

Limitation of culture-dependent methods

Most microbes cannot be cultured (Great Plate Count Anomaly)

What is the Great Plate Count Anomaly?

Microbes seen under microscope don’t grow in lab.

Why do microbes fail to grow in culture? (key list)

Wrong nutrients
Wrong pH/temp/O₂
Need symbiotic partners
Slow growth
Competition/inhibitors

What are culture-independent methods?

DNA-based methods (e.g., sequencing, metagenomics)

Advantages of culture-independent methods

Detects unculturable microbes → higher diversity

Limitations of culture-independent methods

Detects dead cells
May overestimate diversity

Best modern approach?

Combine culture + molecular methods

Baas Becking hypothesis

“Everything is everywhere, but the environment selects.”

Meaning of Baas Becking hypothesis

Microbes are widespread, but environment determines survival.

Why is the atmosphere not ideal for microbial growth?

Low nutrients
High UV
Unstable conditions
No surfaces

Where do airborne microbes come from?

Soil, water, plants, humans

Are microbes growing in air?

No — they are mostly transported

Effect of UV radiation on microbes

Damages DNA → kills cells

Effect of moisture

Vegetative cells need moisture
Spores resist drying

Which bacteria survive better in air and why?

Gram-positive → thicker cell walls

Role of dust/pollution

Protect microbes from UV

Gravity (agar exposure) method

Microbes settle onto plates by gravity

Gravity method advantage

Simple, cheap

Gravity method limitation

Not quantitative

Filtration method

Air passed through filter trapping microbes

Filtration advantage

Large volume sampling + DNA analysis

Filtration limitation

May damage/kill cells

Liquid impingement method

Air bubbled through liquid to trap microbes

Liquid impingement advantage

High volume + maintains viability

Liquid impingement limitation

Requires power + extra processing

What dominates air microbiomes?

Bacteria > fungi

Key feature of atmospheric microbes

Many are unknown species

What affects air microbiome variation?

Time of day (diel cycles)

Night vs day microbial diversity

Lower diversity at night

Main driver of diel changes

Temperature (affects humidity)

What is the indoor microbiome?

Microbial community in built environments

Key feature of indoor microbiomes

Each building is unique

Main source of indoor bacteria

Humans

Main source of indoor fungi

Outdoor environment (soil/plants)

Two main transmission routes indoors

Aerosols
Fomites

What are aerosols?

Airborne droplets (coughing, sneezing, talking)

What are fomites?

Contaminated surfaces/objects

What is soil?

A mixture of minerals, organic matter, water, air, and living organisms.

Why is soil considered a living system?

Contains diverse organisms that drive nutrient cycling and ecosystem functions.

4 main functions of soil

Nutrient supply
Water supply
Root anchoring
Habitat for microbes

Soil horizons (top → bottom)

O → A → B → C → R

O horizon

Organic layer with decomposing plant material

A horizon (topsoil)

Most biologically active; rich in humus and microbes

B horizon

Subsoil; more clay, less organic matter

C horizon

Weathered parent material

R horizon

Bedrock

Typical soil composition (%)

Minerals: 45%
Water: 25%
Air: 25%
Organic matter: 5%

Why is organic matter important despite being only 5%?

Controls fertility, water retention, and microbial activity

What is humus?

Stable, decomposed organic matter formed by microbes

Functions of organic matter (3 key)

Nutrient source
Improves water retention
Energy source for microbes

Where are microbes most abundant in soil?

Near surface and in rhizosphere

What is the rhizosphere?

Soil region around plant roots with high microbial activity

Key roles of soil microbes

Decomposition
Nutrient cycling
Plant growth promotion

6 factors affecting soil microbial communities

pH
Nutrients
Moisture/O₂
Soil texture
Land use
Plant diversity

Effect of soil pH

Determines which microbes can survive

Effect of moisture

Controls oxygen availability and metabolism

Effect of plant diversity

Increases microbial diversity

What are biogeochemical cycles?

Movement of elements through ecosystems via biological + chemical processes

Role of microbes in cycles

Act as catalysts for chemical transformations

4 key cycles to know

Nitrogen, Carbon, Sulfur, Phosphorus

Why is nitrogen important?

Needed for amino acids, proteins, DNA

Why can’t most organisms use N₂?

It is chemically inert

Nitrogen fixation

N₂ → NH₃

Key nitrogen-fixing microbes

Rhizobium
Azotobacter
Cyanobacteria

Enzyme for nitrogen fixation

Nitrogenase

Symbiotic nitrogen fixation

Occurs in plant root nodules (e.g., legumes + Rhizobium)

Ammonification (mineralisation)

Organic N → NH₃/NH₄⁺

Nitrification

NH₃ → NO₂⁻ → NO₃⁻

Nitrification step 1 microbes

Nitrosomonas, Nitrosospira

Nitrification step 2 microbes

Nitrobacter, Nitrospira

Denitrification

NO₃⁻ → N₂ (anaerobic)

Denitrification microbes

Pseudomonas, Bacillus

Why is denitrification important?

Returns nitrogen to atmosphere

Main carbon reservoir in soil?

Soil organic matter

Carbon fixation

CO₂ → organic carbon (photosynthesis)

Respiration

Organic carbon → CO₂

Decomposition

Breakdown of organic matter by microbes

Key decomposers

Bacillus, Pseudomonas, fungi

Why is sulfur important?

Component of proteins and enzymes

Sulfur oxidation

Sulfur → sulfate

Sulfur oxidation microbe

Acidithiobacillus

Dissimilatory sulfate reduction

SO₄²⁻ → H₂S (anaerobic)

Sulfate-reducing bacteria

Desulfovibrio

Assimilatory sulfate reduction

Sulfur incorporated into biomass

Key difference of phosphorus cycle

No gaseous phase

Why is phosphorus important?

ATP, DNA, membranes

Main phosphorus reservoir

Rocks and sediments