Chapter 27: Microbial Ecology and Microbiomes

Define environmental microbiology.

The study of microorganisms as they occur in their natural habitats

Define habitats.

The physical localities in which organisms are found 

Define microbial ecology.

The study of the interactions of microorganisms among themselves and their environment 

Define biodiversity.

The number of species living in a given ecosystem 

Define biomass

The quantity of all organisms in a given ecosystem 

Define population.

All the members of a single species in a location 

• Populations of microorganisms performing metabolically related processes make up groups called guilds 

Define microbiome (community).

All the microbes in a particular environment 

Define microhabitats.

Specific small spaces where conditions are optimal for survival 

• Populations and guilds within a community reside in their own distinct microhabitats 

• Groups of microhabitats form habitats where microorganisms interact with larger organism and the environment 

Define ecosystem.

All of the organisms living in a particular habitat and the relationships between the two 

Define biosphere.

The region of Earth inhabited by living organisms 

• All ecosystems together make up biosphere 

What is an example of competition?

• Microbial growth can be held in check by competition 

• The best-adapted microorganisms have traits that provide them advantages in nutrient uptake, reproduction, response to environmental changes, or some other factors 

What is an example of antagonism?

A microbe makes some product that actively inhibits the growth of another microbe 

What is an example of cooperation?

Microbes use the waste products of other microbes for their own metabolism which results in networks of cooperation 

What is bioremediation?

The use of microorganisms to metabolize toxins in the environment to reclaim soils and waterways 

What type of compounds asre harder for microbes to remove from the environment

Synthetic

• Petroleum, pesticides, munitions, herbicides, and industrial chemicals

  • Biodegradability of these molecules relates to chemical structure

How does acid mine drainage occur?

Results from the exposure of certain metal ores to oxygen and microbial action

•  Strip-mining for coal exposes pyrite to oxygen in the air, which oxidizes the iron, and bacteria oxidize the sulfur

• Rainwater then leaches oxidized compounds from the soil to form sulfuric acid which ends up in rivers and streams

  • lowers the pH of these environments enough to kill fish, plants, and other organisms

Define biogeochemical cycling.

The movement of elements and nutrients from unusable forms to usable forms because of the activities of microorganisms 

Describe the Carbon cycle.

1. Photoautotrophic primary producers convert CO2 to organic molecules in a process known as carbon fixation

2. Heterotrophs catabolize some organic molecules for energy in respiration, resulting in the release of CO2 

3. Other organic molecules made by autotrophs are incorporated into the tissues of heterotrophs where they remain until the organism dies 

   • Decomposers then catabolize the organic materials, releasing CO2 

4. The release of CO2 starts the cycle over as primary producers fix CO2 once more into organic material 

Describe the Nitrogen cycle.

1. Gaseous nitrogen (N2) is reduced to ammonia through nitrogen fixation

   • Only certain prokaryotes can fix nitrogen; no eukaryotes

2. When nitrogen fixers die, they release fixed nitrogen into the soil or water where it becomes available to other organisms, notably plants

3. Bacteria and fungi in soil decompose wastes and dead organisms, disassembling proteins into amino acids which then undergo deamination (removal of their amino groups) 

4. The amino groups are then converted to ammonia through process called ammonification 

   • In dry or alkaline soils, NH3 escapes as gas into atmosphere 

   • In moist soils, NH3 converted to ammonium ion which organism absorb, or ammonium is oxidized (nitrification)

5. In nitrification, ammonium is oxidized to nitrate (NO3-) via two-step process requiring autotrophic archaea and bacteria

   1.  Bacteria convert ammonium to nitrite (NO2-) which is toxic to plants

   2. Bacterium, then convert nitrite to nitrate which is soluble and can be used. by plants

6. Nitrate is leached from soil by water and accumulates in groundwater, lakes, and rivers

7. Certain microbes in waterlogged souls perform denitrification wher nitrate is oxidized to N2 gas by anaerobic respiration

8. N2 gas then escapes into the atmosphere!!!!

Describe the Sulfur cycle.

1. Bacteria decompose dead organisms, releasing sulfur-containing amino acids into the environment 

2. Sulfur released from amino acids then converted to hydrogen sulfide (H2S) by microorganisms via process called sulfur dissimilation 

3. H2S then oxidized to elemental sulfur and then to sulfate under various conditions and by various organisms 

4. Anaerobic respiration reduces sulfate back to H2S 

Describe the Phosphorus cycle.

• Involves the movement of phosphorus from insoluble to soluble forms available for uptake by organisms and the conversion of phosphorus from organic to inorganic forms by pH-dependent process 

• Dissolved phosphates accumulate in water and organic forms of phosphorus are deposited in surface soils following decomposition of dead animals and plants  

Describe the Trace Metals cycle

• Cycling of metal ions involves a transition from an insoluble to a soluble form, allowing them to be used by organisms and move through the environment 

• Fe2+, Zn2+, Cu2+, Cd2+, Mg2+ 

Define eutrophication.

The overgrowth of microorganisms in aquatic systems 

How does eutrophication occur and what effect does it have?

• Occurs when too much phosphorus runs off into rivers and lakes which causes overgrowth of microbes (cyanobacteria and algae) in nutrient-rich waters

• Overgrowth (bloom) depletes oxygen fromw water, killing aerobic organisms

• Anaerobic organisms then take over the water system, leading to increased production of H2S and the release of foul odors

Define biomining

The use of microbes to convert metals to soluble forms that can be more easily extracted  

What are the five factors that affect microbial abundance in soils?

1. Amount of water

2. Availibility of oxygen and other electron acceptors

3. Acidity

4. Temperature

5. Availibility of nutrients

What soil pH do fungi favor?

Highly acidic and highy basic

What soil pH do bacteria favor?

pH closer to 7

What soil temperature do soil microbes prefer?

• Temperature between 20°C - 50°C

• Live well in areas where winters and summers and not too extreme

How do humans contact soilborne infections?

Direct contact with, ingestion of, or inhalation of microorganisms deposited in soil in animal or human feces or urine

Describe the soil microbe Bacillus anthracis.

• Bacterium that causes anthrax which produces endospores shed from the skins of infected livestock 

• Endospores remain dormant in soil for decades or centuries until disturbed 

• Disturbing soil can lead to infection is endospores enter cuts or abrasions on skin, or are inhaled into the lungs 

Describe the soil microbe Histoplasma capsulatum.

• Fungus that causes histoplasmosis which is a serious respiratory infection 

• Grows in soil and is also deposited there as spores in droppings of infected birds and bats 

• Spores can be inhaled by humans when contaminated soil is disturbed 

Describe the soil microbe Hantavirus.

• Virus that causes Hantavirus pulmonary syndrome

• Acquired via the inhalation of soil contaminated by mouse droppings and urine containing virus  

How are freshwater ecosystems characterized?

• Low salt content (~0.05%) 

• Include groundwater, water from deep wells and springs, and water from lakes, streams, rivers, shallow wells, and springs 

• Surface waters are high in oxygen, well lighted, and warmer than deeper water 

• In large lakes, wave action continually mixes nutrients, oxygen, and organisms, which allow for efficient use of resources 

• In stagnant waters, oxygen is depleted resulting in more anaerobic metabolism and poorer water quality 

What are the four zones of a deep lake?

• Littoral zone

• Limnetic zone

• Profundal zone

• Benthic zone

Describe the Littoral zone.

Area along the shoreline where nutrients enter body of water

• most microbes live here

Describe the Limnetic zone.

The upper layer of water away from the shore 

• Photoautotrophs reside here and in littoral zone 

Describe the Profundal zone.

The deeper water beneath the limnetic zone 

• Lesser oxygen content and more diffuse light than littoral and limnetic zones

• Some photosynthetic organisms, such as purple and green sulfur bacteria, perform anaerobic photosynthesis here 

Describe the Benthic zone.

Encompasses deeper lake water and sediments, and the majority of the marine environment

• Anaerobic bacteria in sediments produce H2S which is used by organisms nearer to the surface 

How are marine ecosytems characterized?

• Salt content of about 3.5%

• Include open ocean and coastal waters such as bays, estuaries, and lagoons 

• Typically nutrient poor, dark, cold, and subject to great pressure 

• Photoautotrophic prokaryotes, diatoms, dinoflagellates, and algae are found near surface 

• Most marine waters are extreme environments inhabited by highly specialized microorganisms 

What are the 5 zones of oceans?

• Littoral zone

• Limnetic zone

• Profundal zone

• Benthic zone

• Abyssal

Describe the Abyssal zone.

Encompasses deep ocean trenches 

• Few nutrients but can still support microbial growth, especially around hydrothermal vents 

  • Vents spew superheated, nutrient-rich water which provides nutrients and energy source for thermophilic chemoautotrophic anaerobes 

  • Anaerobes support variets of invertebrate and vertebrate animals

What are the criteria used to assess microorganisms for potential use as biological weapons or agents of bioterrorism?

• Public health impact

• Delivery potential

• Public perception

• Public health preparedness

Define the criteria of pulic health impact.

The ability of hospitals and clinics to deal effectively with numerous casualties 

Define the criteria of delivery potential.

How easily an agent can be introduced into a population 

Define the criteria of delivery potential.

The effect of public fear on the ability of response personnel to control a disease outbreak following an attack.

Define the criteria of delivery potential.

The existing response measures and attempts to identify improvements needed in the health care infrastructure to prepare for biological attack