Lecture 4: Soil Flashcards
List the 3 types of microbial habitats.
- Air
- Aquatic
- Terrestrial
What are the types of aquatic habitats?
- Freshwater
- Marine
- Brackish
- Hypersaline
What are the types of terrestrial habitats?
- Hard rock
- Soil
Which of the following habitats has the most diverse communities of microbes?
A. Soils/sediments
B. Freshwater
C. Seawater
D. Atmostphere
E. Deep subsurface
A. Soils/sediments
B. Freshwater - stable
C. Seawater - nutrient poor
D. Atmostphere - nutrient poor?
E. Deep subsurface - stable
What does allochthonous mean?
Foreign
What does autochthonous mean?
Local
What are the stresses of rock surfaces as a habitat?
- Desiccation
- Low water potential
- High UV
What types of organisms live on rock surfaces?
- Cyanobacteria
- Lichens (fungi and algae)
What are hypoliths?
Microbial communities that live on the underside of rocks or at the rock-soil surface
What are endoliths?
Microorganisms that live inside rocks or in pores between mineral grains
List and describe the 3 types of endoliths.
- Cryptoendoliths: live in rock on Earth’s crust
- Subsurface endoliths: found in groundwater aquifers or caves
- Deep-biosphere endoliths: found in deep, extremely hot or cold rock, miles beneath the ocean floor
Pseudomonas aeruginosa is a common bacteria found in _____.
soil
What does P. aeruginosa do?
- Breaks up the toxic compounds that are a major concern of oil spills
Soil is a _____ medium.
porous
What is the composition of soil in terms of solids vs. pore space?
50/50
What is in the solid portion of soil?
- Minerals
- Organics only
What is in the pore space portion of soil?
- Liquids (water)
- Gases (air)
- Flooding can reduce gas content
Soil has 3 “horizons”. List and describe each.
- A horizon
- Topsoil: minerals, humus - B horizon
- Less broken down - C horizon
- Solid or partially broken-down rock
How do soil particles form?
By the breakdown of parent rock by weathering
List and describe the 2 types of refractory compounds.
- Humic substances: decayed organic monomers that polymerize into complex molecules
- Lignin: vegetation above affects soil type
List the 3 soil texture types from biggest to smallest particle size.
- Sand
- Silt
- Clay
_____ is the most fertile soil type.
Loam
Why is loam so fertile?
It has a good balance of clay, silt, and sand
Why are sand and clay not good for plant growth?
- Sand won’t retain enough water
- Clay retains too much water
Define humus.
Decayed organic matter
How does humus form?
Plant and animal matter decompose
How is humus important for plant nutrition?
Contains lots of nutrients form the decaying organic matter
What is topsoil composed of?
Inorganics
Most soil particles are negative aka _____.
anions
Plant soil nutrients (NO3-, H2PO4-, SO42-) are also _____.
anions
_____ attached to _____ soil particles.
- Cations
- negative
What does soil pH affect?
The solubility of chemicals in soil (ionization)
What affects soil pH?
Rainfall
- Leaches basic cations and promotes high organics –> acidic (low pH)
- Low rainfall –> higher pH –> neutral or alkaline
What are the 3 general categories of soil fauna?
- Macro and megafauna
- Mesofauna
- Microfiora and microfauna
What are soil animals (macro and megafauna) important for?
- Decomposition (shredding tissues)
- Mixing soil (aeration)
List some examples of soil animals (macro and megafauna).
- Termites
- Pseudoscorpions
- Earthworms
- Centipedes
- Snails
- Voles
What are soil mesofauna imporant for?
- Decomposition
- Predation
List some examples of soil mesofauna.
- Nematodes
- Rotifers
- Tardigrade
- Springtails
Describe soil microbes.
- Most diverse group
- Mostly bacteria
- Exopolysaccharides involved in soil aggregation
- 80-90% are sorbed onto particles
Describe the type of bacteria found in soil.
- Small
- Mostly gram-negative
- But above average % of gram-positive spore formers
What type of archaea are found in soil?
- Crenarchaeota
- Thaumarchaeota
Describe the type of fungi found in soil.
- Less per gram than bacteria, but can compose more biomass
- Saprophytes: decompose plant matter
- Mycorrhizae: mutualistic association with plants
What types of protists are found in soil?
- Protozoa
- Algae
What is a slime mold?
A single-celled amoeboid-like protist
_____ obtain carbon from producers passively from dead biomass, excretions and secretions.
Saprotrophs
_____ and _____ obtain carbon from producers actively.
- Necrotrophs
- Biotrophs
Necrotrophs actively obtain carbon by _____.
attacking and decaying biomass
Biotrophs actively obtain carbon _____.
from plants in exchange for a microbe-supplied nutrient
Explain the agricultural implications of soil microbes.
- Role of microbes in decomposition and nutrient cycling is very important in soil
- Humus generation
- Nitrogen cycle (N fixation and denitrification)
Nitrogen fixation converts _____ to _____.
N2 –> NH3
Denitrification converts _____ to _____.
NO3 –> N2
Define rhizobacteria.
Root-associated bacteria
Define rhizosphere.
Thin layer of soil closely surrounding the plant’s roots
What types of effect(s) do rhizobacteria have on the plant?
Can be detrimental, neutral, or beneficial
Rhizobacteria can be _____ (free-living) or _____ (living between cells of the plant itself).
- Free-living
- Endophytic
Both depend on nutrients secreted by plant cells and, in return, help to enhance plant growth by _____, _____, and _____.
- producing chemicals that stimulate plant growth
- producing antibiotics that protect roots
- increasing nutrient availability
What element is often the limiting factor?
Nitrogen
In what forms can plants absorb nitrogen? What form of nitrogen can they NOT use?
- Nitrate (NO3) and ammonium (NH4+
- Atmospheric nitrogen (N2)
Nitrogen is needed for the synthesis of _____ that produce _____ and _____ that produce _____.
- Amino acids
- Nucleic acids
4.
Soil nitrate is formed through a 2-step process called _____.
nitrification
What is the order of nitrification (i.e. what gets converted to what)?
ammonia –> nitrite –> nitrate
What are the steps of acquiring soil ammonium (NH4+)?
- Nitrogen fixation: nitrogen-fixing bacteria convert atmospheric nitrogen to ammonia
- Ammonia can pick up an H+ in the soil solution and forms ammonium
What enzyme facilitates nitrogen fixation?
Nitrogenase
What do the plant and fungi provide for each other?
- Plant provides sugars
- Fungi provide more surface area (get water and minerals)
What are the 2 major types of mycorrhizae?
- Ectomycorrhizae
- Arbuscular micorrhizae
Which of the following habitats has the greatest abundance of microbes?
A. Soils/sediments
B. Freshwater
C. Seawater
D. Atmosphere
E. Deep subsurface
A. Soils/sediments
B. Freshwater
C. Seawater
D. Atmosphere
E. Deep subsurface
Describe deep subsurface environments.
- Huge area: large total global biomass possibilities
- Fissures are important for water
What are the implications of deep subsurface environments?
Possible early Earth evolution
- Protects from bombardment
List the types of studies in deep drilling operations. What are the concerns for these?
- Waste disposal
- Gold mines
- Seafloor drilling projects
- Concerns: contamination (use rigorous sterile sampling processes)
Describe the types of microbes in deep subsurface environments.
- Diverse: autotrophic and heterotrophic pathways
- Anaerobic and aerobic respiration
