Chapter 26: Microbial Ecology nad Microbiomes

Review

Chemoheterotrpohs acquire carbon for organic molecules from other organisms and use chemical componds as a source of energy
Microbes in biofilm formation communicate via quorum sensing
Archaea use Hami to attach to surfaces

Levels of Microbial Associations in the Environment

population: all the members of a single species in a location
guilds: populations of microorganisms that perform metabolically related processes
- example: anaerobic fermenters
microbiome: all microbes in one location, which includes sets of guilds
microhabitats: specific small spaces where conditions are optimal for survival
ecosystem: groups of microhabitats form habitats in which microorganisms interact with larger organisms and the environment

The role of adaption in microbial survival

Extremophiles: microbes adapted to harsh temperatures, pH levels, or salt concentrations
Competition can hold microbial growth in check
Antagonism: microbe makes some products that actively inhibits the growth of another
Cooperation: networks that are created when one organism uses the waste producing of another for their own metabolism

methanogens (which are archaea) degrade organic molecules to methane
soil microbes anaerobically break down biodegradable wastes
to prevent leaching of potentially hazardous materials, land fill pits are line with clay or plastic.
- sand and drainage pipes line the bottom filter
Bioremediation: the use of microorganisms to clean up toxic, hazardous, or recalcitrant compounds by degrading them to harmless compounds

Acid mine drainage: serious environmental problem resulting from the exposure of certain metal ores to oxygen and microbial action
coal deposits are often found associated with reduced metal compounds such as pyrite
Thiobacillus oxidize the sulfur
Rainwater leaches the oxidized compounds from the soil to form sulfuric acid which is carried into streams and rivers, reducing the pH enough that it kills fish, plants, and other organisms
Ferroplasma acidarmanus: unique archael species found in mine drainage that lives at a pH near zero and obtains its energy from oxidizing pyrite in mine sediments

most elements are tied up in chemical and physical forms therefore unavailable to organisms
biogeochemical cycles: the processes by which organisms convert elements from one form to another, typically between oxidized and reduced forms

The carbon cycle

cycling oc carbon in the form of organic molecules
carbon in rocks and sediments has a low turnover rate
The start of the cycle is autotrophy
- photoautotrophic primary produces covert carbon dioxide to organic molecules (carbon fixation)
  - they use the calvin benson cycle to fix carbon
phototrophs are restricted to surfaces of soil and water systems bc of light
chemoautotrophs have more freedom but do not fix as much carbon as autotrophs and are not as important
heterotrophsplay a crucial role in terrestrial and aquatic ecosystems by decomposing organic matter and recycling nutrients, making them essential for maintaining the balance within microbial communities.

The Nitrogen Cycle

majority of organisms aquire nitrogen as part of organic molecules or from soluble inorganic nitrogen compounds found in limited quantities in soil and water
microbes cycle nitrogen atoms from dead organic materials and animal wastes
nitrogen fixation: gaseous nitrogen is reduced to ammonia
- energy expensive process
- nitrogenase
  - functions only in the complete abscence of oxygen
Ammonification: amino groups are converted to ammonia
Nitrification: ammonium is oxidized to nitrate
Denitrification: nitrate is oxidized to nitrogen by anaerobic respiration
Anammox: anaerobic ammonium oxidation

Th Sulfur cycle

involves moving sulfer between several oxidation states
sulfate is the most readily usable form of sulfire for plants and algae, which animals eat

The phosphorus cycle

involves the movement of phosphorus from insoluble to soluble forms available for uptake by organisms and the conversion of phosphorous from organic to inorganic forms by pH dependent processes
eutrophication: overgrowth of microorganisms in nutrient rich waters (bloom) which depletes oxygen from the water and in turn kills aerobic organisms such as fish

The cycling of metals

biomining: process in which microbes (mostly archaea) dissolve more readily than reduced ions of the same metal

The nature of soils

soil arises from the weathering of rocks and through the actions of microorganisms, which produce wastes and organic materials needed to support more complex life forms such as plants
Two layers
- topsoil: rich in humus (organic chemicals)
- subsoil: inorganic materials
most microorganisms are found in topsoil

Factors affecting microbial abundance in soils

amount of water, availability of oxygen and other electron acceptors, acidity, temperature, and availability of nutrients
moisture is essential for microbial survival
high acidic and high basic soil favors fungi, but fungi does prefer acidic
moist soil organisms are mesophiles
psychotriles cannot survive in soils that experience spring thawing
thermophiles cannot survive in harsh winters

Microbial population in soilds

some algae and protoza live in soils
- algae live near the surface for light
- protoza are mobile throughout soil

Soilborn disease of humans and plants

Bacillus Anthracis
- causative agent of anthrax
- produces endospores shed from skins of infected livestock
Histoplasma capsulatum
- fungi that cause severe respiratory tract infection
- spores in droppings of infected birds and bats
Hantavirus
- life threatening pulmonary syndrome respiratory disease inherited from inhalation of soil contaminated with mouse droppings

Types of aquatic habitats

freshwater systems
- littoral zone: area along the shoreline where nutrients enter the lake
- limnetic zone: upper layer of water away from the shore
- profundal zone: deeper water beneath the limnetic zone
- benthic zone: deeper lake water and sediments
marine environments
- abyssal zone: deep trenches
- Hydrothermal vents: unique ecosystems located on the ocean floor, where superheated water rich in minerals supports diverse microbial communities.
domestic water
- halobacterium salinarum

bioterrorism: use of microbes or their toxins to terrorize human populations
agroterrorism: bioterrorist use of microbes to destroy food supply

Criteria for assesing biological threats to humans