Soil Microbiology Flashcards
Ecosystem vs. habitat
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
Population vs. community
Population: group of microorganisms of the same species
Community: a group of populations
Species richness vs abundance
Richness: total number of different species present
Abundance: proportion of a species in an ecosystem
Guilds vs. Niche
Prime niche
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
Microenvironment
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
Parasitism vs. mutualism vs. commensalism
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
Biogeochemistry
Examples
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
Soil definition and types
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
Soil layers
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
What is the most important factor in determining microbial activity in soils?
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
Rhizosphere vs. Rhizobium vs. mycorrhizae
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
Top few centimeters of soil contains
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
Nitrogen fixation importance:
Nitrogen fixation catalyzed by:
Source of energy:
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
Free-living nitrogen fixers
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
Cyanobacteria N fixation mechanism
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
Rhizobium N fixation mechanism
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
Root nodule formation
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
Leghemoglobin
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
N-fixation agricultural implications
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
