Module 1 Flashcards
What is microbial biomass
Microbial biomass (bacteria and fungi) is a measure of the mass of the living component of soil organic matter. The microbial biomass decompose plant and animal residues and soil organic matter to release carbon dioxide and plant available nutrients.
What is organic matter content
Soil organic matter is the organic matter component of soil, consisting of plant and animal detritus at various stages of decomposition, cells and tissues of soil microbes, and substances that soil microbes synthesize.
What is oven dried weight
Remaining weight of a soil once moisture and OM have been accounted for.
List the basics of soil genesis
Soil genesis is a function of climate, organisms, relief, parent material, and time
Where are soil bacteria found
Attached to surface of soil particles, few are found free in soil solution.
List soil particle size of textural classes
Sand 2.0 to 0.05 mm
Silt 0.05 to 0.002 mm
Clay <0.002 mm
0.001 mm = 1 um
1 mm = 1000 um
What is soil anion and cation exchange capacity + microbes?
Microorganisms bind to negatively charged clay and OM through areas of pos charge (protiens).
Cation exchange capacity (CEC) represents the quantity of negative charge available to attract cations. Anion exchange capacity (AEC) represents the positive charge available to attract anions in solution.
What are the three states of soil water potential?
- Saturation soil pores are full of water.
- Field capacity majority of water is gone, esp large pore water
- Wilting point critical point for plants, can no longer extract water
Soil water potential - energy required to pull water from soil. The above describe water content across diff potentials.
Which soil solution components affect pH?
Water, dissolved OM, inorganic constituents, O2 and CO2.
Describe microbial activity as a function of temperature
Microbial activity increases as the optimal temperature is reached as governed by the laws of thermodynamics. The rate of chemical reactions is a direct function of temp.
What is Q10
A measure of the change in enzyme activity (reaction rate) caused by a 10C rise in temp.
Most microbial enzymes have a Q10 of 2.
Direct and indirect ways macro, meso, and microfauna interact?
Grazing - decreases microbial biomass
Selective grazing - changes in composition
Nutrient cycling
Habitat engineering - primary production and transport of smaller fauna
Difference between detritivores and decomposers
Decomposers subsist on dead plant debris via saprotrophic feeding (fungi and bacteria perform extracellular digestion). Detritivores also subsist on dead plant debris but involves macroscopic swallowing of material.
List the 4 classes of soil organisms and an associated type
- Microflora/orgs - bacteria
- Microfauna - protozoa
- Mesofauna - mites
- Macrofauna - earthworm
Photoorganotrophs
Use light as energy source. Use organic compounds as electron donors. Many organic compounds used, depends on functional group of microbe. Eg. bacteria.
Photolithotrophs
Use light as energy source. Use inorganic compound (CO2, H2S) as electron donor. Eg. Bacteria
Have oxygenic or anoxygenic photosynthesis.
Chemolithotrophs
- Use chemicals for energy (hydrogen gas, ammonia)
- Use inorganic substances for electron donors
- Eg. Archaea
What is metabolic classification based on?
- Source of energy (photo or chemo)
- Source of reducing equivalents (i.e. electron donor/acceptor)
- Source of carbon (autotroph or heterotroph)
Chemoorganotrophs
- Use chemicals as source of energy (sugars, fats)
- Use organic substances for electron donors
- Eg. most animals and bacteria
List 4 methods to measure soil microbial biomass (quantitative)
- Chloroform-fumigation incubation
- Chloroform-fumigation extraction
- Glucose-stimulated respiration
- Phospholipid fatty acids
List life attributes of soil bacteria
-Rapid growth/reproduction
-Min number of 1000 enzymes
-Nutrient uptake optimized by high surface area/volume ratio
-Can outgrow predators
List 3 points on composition of bacterial cells
-Water makes most of weight (70-90%)
-Remaining ~30% is ions, molecules, phospholipids, DNA, RNA, proteins and carbs
-Some trace elements
List 4 classes of biomolecules
- Proteins (amino acids)
- Carbs (sugars)
- Nucleic acid (DNA)
- Lipids
List the functions of a cell wall
- Protect bacteria from osmotic lysis (bursting)
- Determines and maintains cell shape
- Provides platform for appendages like flagellum
- Does not protect against toxicants
What is the structure of a cell wall made of and what two types are there
- Contains peptidoglycan
- May be gram+ or gram-
Describe the structure and composition of peptidoglycan
Composed of repeating NAG and NAM chains that are linked together by tetrapeptide chains. The links make peptidoglycan a rigid sheet.
Define gram positive
Gram+ cell wall is composed of numerous dense layers of peptidoglycan sheets and teichoic acid, lipoteichoic acid, and surface proteins.
Define gram negative
Gram- wall is composed of a thin wall of peptidoglycan and an outer membrane as well as a periplasmic space between the outer and inner membrane.
Which type of cell wall contains teichoic acid? What is the peptido, and lipid/lipoprotein content of each?
- Gram+ has teichoic acid
- Gram+ is >50% and 0-3% for lipids
- Gram- is 10-20% and up to 10% lipids
Which solutions will identify a gram+ and gram- cell wall after crystal violet and iodine stain the wall violet?
Alcohol will decrease permeability so the pores will trap crystal violet thus remaining violet for gram+. Lipids in gram- will retain permeability and thus the CV will be washed out.
After safranin is applied, the gram+ will still be violet but gram- will stain red.
Which qualities give gram- a competitive advantage
The outer membrane and the periplasmic space. The outer membrane can defend against toxicants.
Why does the periplasmic space give gram- a competitive advantage
This space concentrates the zone of enzyme activity unlike gram+ where enzymes are secreted.
What two types of enzymes are in the periplasmic space
Detoxifying enzymes - alter harmful agents before entering the cell
Hydrolytic enzymes - part of initial degradation of food molecules
When does the charge increase or decrease in redox equations
Oxidation is the loss of electrons (charge increases).
Reduction is the gain of electrons (charge decreases).
*Remember electrons are negatively charged
