What are the rhizosphere and rhizoplane?
Rhizosphere: The soil region influenced by roots—rich in exudates, elevated microbial activity and diversity compared with bulk soil.
Rhizoplane: The root surface itself (immediate interface), often densely colonized biofilm‑like communities.
Different opinions on what rhizosphere is
The “Rhizosphere effect”
Where is microbial growth most extensive?
The most extensive microbial growth takes place on the surfaces of soil particles (usually within the rhizosphere)
Why can a single soil particle support many different microorganisms?
A soil particle (aggregate) contains multiple contrasting microenvironments—varying in O₂, moisture, pH, and organic substrates—so it supports several physiologically distinct microbial groups in close proximity.
What factors primarily regulate microbial activity in soils?
Water availability (controls diffusion and activity).
Air penetration (oxygenation/porosity)—determines oxic vs anoxic niches.
Nutrient status (type/amount of utilizable substrates and minerals).
Describe the soil horizons (O, A, B, C).
O horizon: Surface organic layer (litter → humus), site of active decomposition.
A horizon: Surface soil (high in organic matter) Plants and large numbers of microorganisms grow here
B horizon: Subsoil—accumulation zone (clays, iron, etc.); less organic matter.
C horizon: Parent material—weathered rock/mineral fragments; minimal biology.
How deep can the deep soil subsurface extend, and who dominates there?
The deep subsurface can extend hundreds to thousands of meters below the surface (varies by geology).
Prokaryotes dominate: anaerobes, aerobes, and facultative aerobes adapted to low nutrients, often using groundwater‑delivered substrates.
Why is the open ocean often nutrient‑poor, and where does open‑ocean primary productivity typically come from?
The open ocean is typically oligotrophic (low nutrients) because nutrient inputs are limited and rapid recycling/grazing keep concentrations low → low heterotrophic activity.
How do in‑shore marine areas differ from the open ocean, and how do prokaryote numbers vary with depth?
In‑shore regions are more nutrient‑rich (runoff, upwelling, inputs) → greater productivity.
Prokaryote numbers generally decrease with depth as light and fresh organic inputs decline; some deep layers may show a slight predominance of Archaea.
What environmental extremes define the deep sea, and what pressure must microbes tolerate?
Extremes: Low temperature, high hydrostatic pressure, and low nutrients.
Pressure increases ~1 atm per 10 m of depth (e.g., 5000 m → ~500 atm); specialized barotolerant/barophilic microbes thrive there.
Define hydrothermal vents and distinguish warm vents vs black smokers.
Hydrothermal vents: Underwater hot springs at mid‑ocean rifts.
Warm vents: 6–23 °C, 0.5–2 cm s⁻¹ flow.
Black smokers (hot vents): 270–380 °C, 1–2 m s⁻¹ flow; fluids laden with reduced chemicals.
What fuels vent ecosystems?
Biological communities in these ecosystems are dependent on chemolithtropic activity
What animal–microbe symbiosis is typical at vents?
Tube worms possess an internal organ (trophosome) densely packed with S‑oxidizing bacteria that fix CO₂ using reduced sulfur from vent fluids—supporting the worm’s nutrition without a digestive tract
In freshwater, where is O₂ produced and how does it change with depth?
Photosynthesis in surface layers produces O₂.
Because O₂ has low solubility in water and is consumed by respiration, it is rapidly depleted with depth, especially if stratification reduces mixing.
O₂ profiles depend on the degree of mixing (wind, turnover) in lakes/rivers.
Define the lake zones used in the lecture: littoral, limnetic, profundal, benthic.
Littoral: Shallow near‑shore zone with light to the bottom; rooted plants and periphyton abundant.
Limnetic: Open‑water photic zone away from shore; phytoplankton‑dominated.
Profundal: Deep aphotic water below light penetration; colder, often lower O₂. (transition zone)
Benthic: Sediment interface; high microbial activity, steep redox gradients.
What is BOD and how is it measured in this course?
BOD (Biochemical Oxygen Demand): the amount of dissolved O₂ in water that can be consumed by microorganisms during oxidation of organic matter.
Measured as O₂ depletion after 5 days at 20 °C (BOD₅). Higher BOD indicates higher organic pollution.
Define wetlands ecologically and list the sub‑types highlighted.
Wetlands: Shallow aquatic systems dominated by emergent plants
What is known about microbial communities in wetlands?
Profiles vary with local conditions and climate.
Wetlands support abundant heterotrophic aerobes and anaerobes wherever anoxia prevails (e.g., sediments/peat).
They are better studied in association with treatment wetlands
Define biodegradation
Biodegradation is the breakdown of a complex chemical through biological processes:
- Minor loss of functional groups
- Fragmentation into larger constituents
- Complete breakdown to CO₂ and minerals
What is the Principle of Microbial Infallibility (Alexander, 1965)?
It is the observation that no natural organic compound is totally resistant to biodegradation as long as environmental conditions are favorable (nutrients, electron acceptors, temperature, etc.).
What environmental and molecular factors influence decomposition of organic substrates?
- Elemental composition (C/H/O/N content)
- Structure of basic repeating units
- Types of linkages (e.g., ester, ether, amide)
- Nutrient availability in the environment
- Abiotic factors (pH, temp, O₂, moisture)
- Microbial community composition
Define bioremediation
Bioremediation is the use of biologically mediated processes to remove or degrade pollutants from specific environments.
It can include modifying the environment to accelerate biological activity, with or without adding microorganisms
What are hydrocarbons, and what are their general properties?
Hydrocarbons are organic molecules containing only carbon and hydrogen.
They are typically hydrophobic and poorly soluble in water, meaning biodegradation depends on microbial ability to access non‑aqueous phases.
Hydrocarbon‑degrading microbes are widespread in the environment (terrestrial + aquatic).
How does hydrocarbon chain length affect biodegradation?
C10–C24: Most readily degraded
< C9: toxic to microorganisms
> C24: branching decreases biodegradation
