Soil Microbiology

Question 1

Ecosystem vs. habitat

Answer 1

Ecosystem: sum of all organisms and abiotic factors interacting as a functioning unit

Habitat: Portion of an ecosystem where a community could reside

Many habitats have only microbes - 50% of world’s biomass

Question 2

Population vs. community

Answer 2

Population: group of microorganisms of the same species

Community: a group of populations

Question 3

Species richness vs abundance

Answer 3

Richness: total number of different species present

Abundance: proportion of a species in an ecosystem

Question 4

Guilds vs. Niche

Prime niche

Answer 4

Guild: metabolically related microbial populations - sets of guilds form communities

Niche: habitats which provide nutrients and conditions for growth that are shared by a guild
Ex. photic zone, oxic zone, anoxic zone

Prime niche: niche in which an organism would be most successful

Question 5

Microenvironment

Answer 5

The immediate environmental surroundings of a microbial cell or group of cells such as soil particles

Soil particles have reducing O2 as you get closer to center of particle

Question 6

Parasitism vs. mutualism vs. commensalism

Answer 6

Parasitism: one organism is harmed while the other benefits

Mutualism: both species benefit (symbiosis)

Commensalism: one species benefits and the other is neither harmed nor helped

Question 7

Biogeochemistry

Examples

Answer 7

Study of biologically mediated chemical transformations

Often proceeded by redox rxn

Microbes involved in energy transformation - recycling of elements to living systems
- Carbon cycle CO2 –> organic compounds –> CO2
- Nitrogen cycle N2 –> NH3 –> NO2- –> NO3- –> NO2- –> NO –> N2O –> N2
- Sulfur cycle H2S –> SO4^2- –> H2S

Question 8

Soil definition and types

Answer 8

Definition: loose outer material of Earth’s surface

Composed of: inorganic matter (40%), organic matter (5%), air and water (50%) and living organisms

Mineral soil: derived from rock weathering and other inorganic materials

Organic soil: derived from sedimentation of bogs and marshes

Question 9

Soil layers

Answer 9

O horizon: layer of un-decomposed plant materials

A horizon: surface soil - high in organic matter, tiled for agriculture
- high microbial activity

B horizon: subsoil full of minerals, humus (dead plant material resistant to decomposition but keeps water and nutrients in the soil), little organic material
- lower microbial activity

C horizon: soil base, develops from underlying bedrock weathering
- minimal microbial activity

Question 10

What is the most important factor in determining microbial activity in soils?

Answer 10

Availability of water is most important factor in microbial activity in surface soils - where activity mostly is

Nutrient availability is most important factor in subsurface environments

Sand: water drains quickly
Silt: retains water to right extent
Clay: retains water too well and becomes anoxic

Question 11

Rhizosphere vs. Rhizobium vs. mycorrhizae

Answer 11

Rhizosphere: soil that surrounds plant roots and receives plant secretions

Rhizobium: N fixing bacteria symbiosis with plant roots in nodules

Mycorrhizae: association of fungi with plant roots

Question 12

Top few centimeters of soil contains

Answer 12

Archaea and bacteria - largest percentage
- production of humus, release of minerals from soil, nutrient cycling, nitrogen fixation

Fungi: next highest %

Protozoa and algae smallest percentages

Question 13

Nitrogen fixation importance:

Nitrogen fixation catalyzed by:

Source of energy:

Answer 13

70% of nitrogen is in the atmosphere and is inaccessible without nitrogen fixers
- Point of nitrogen fixation - makes low nutrient and low oxygen environments possible to live in (niche)

Nitrogenase complex catalyzes rxn
- dinitrogenase reductase is inhibited by the presence of O2

8 electrons from pyruvate –> 2 lost in the process with H2 –> NH3 as final product used for AA synth, etc
- ATP $$$ process to break triple bond using 16-24 ATP

Question 14

Free-living nitrogen fixers

Answer 14

Azotobacter: strict aerobe which does anaerobic respiration
- protected by high rate of O2 consumption keeping intracellular environment anoxic

Clostridium: strict anaerobe

Cyanobacteria (some): MAJOR nitrogen fixing organism in nature - produce energy by oxygenic photosynthesis

Notes:
- Organic matter fuels N fixation
- Produce NH3 which dissolves in water to form NH4

Question 15

Cyanobacteria N fixation mechanism

Answer 15

Live in filaments

N fixation inside special anaerobic cells called heterocyts lacking PSII

Heterocysts have thick cell wall to slow down O2 diffusion

Regular/vegetative cells do oxygenic photosynthesis and provide heterocysts with pyruvate CHO fuel for N-fixation

Question 16

Rhizobium N fixation mechanism

Answer 16

Mutualistic relationship between legumes and N-fixing bacteria
Ex. soybeans, clover, alfalfa, beans and peas

Nodule formed on roots of plants to house nitrogen fixing bacteria

Question 17

Root nodule formation

Answer 17

1) Rhizobial cells recognize and attach to plant root hairs

2) Nod factors excreted by bacterium cause root hair curling if plant is N-starved

3) Rhizobia invade root hairs and multiply in an infection thread (cellulose tube) and spread into the root cells themselves

4) nearby root cells are stimulated to divide (early nodule development)

5) Formation within plant cells to form bacteroid state: swollen and misshapen bacteria which fix N2
- terminal state - non reversible

6) Continuous plant and bacterial division forms root nodules
- plants provide organic acids as fuel to produce ATP for N fixation

Question 18

Leghemoglobin

Answer 18

Produced by plant cells to control oxygen levels for N fixing symbiotic bacteroids

1) Leghemoglobin sequesters O2 by binding it
2) Manages release of O2 to ensure no O2 inhibition of nitrogen fixation (limits amount of O2 for bacteria)
3) releases O2 to produce H2O in the bacteroid

Question 19

N-fixation agricultural implications

Answer 19

Most plants rely on free-living N-fixers or ammonia produced by organisms (ex. urine from cows)

GOOD for agriculture: NO3- is more soluble than NH3 and more available to plants
- Nitrifying bacteria convert NH3 –> NO3- very helpful

BAD for agriculture: Water logged soil becomes anaerobic and favors denitrifying bacteria which convert NO3- –> N2
- anaerobic soil promote sulfur and sulfate reduction –> H2S which is toxic for plants