CHAPTER
26
Microbial Ecology and
Microbiomes
Chapter Outline
Environmental Microbiology (pp. 802–812)
Microbial Ecology
Bioremediation
The Problem of Acid Mine Drainage
The Roles of Microorganisms in Biogeochemical Cycles
Soil Microbiology
Aquatic Microbiology
Biological Warfare and Bioterrorism (pp. 812–816)
Assessing Microorganisms as Potential Agents of Warfare or Terror
Chapter Summary
Environmental microbiology involves the study of microorganisms found in nature.
Environmental Microbiology (pp. 802–812)
Environmental microbiology is the study of microorganisms as they occur in their natural
habitats—the location in which they live.
Microbial Ecology
Microorganisms grow and adapt to a variety of habitats. The study of the interrelationships
among microorganisms and the environment is called microbial ecology. There are different
levels of microbial associations: populations include all the members of a single species; guilds
are groups of microorganisms performing metabolically related processes; communities are sets
Instructor’s Manual for Microbiology with Diseases by Body System, 5e
Bioremediation
Humans produce waste products in huge quantities in industrialized nations. Soil microbes
break down biodegradable wastes in landfills, while methanogens degrade organic molecules to
The Problem of Acid Mine Drainage
Acid mine drainage is a serious environmental problem resulting from exposure of certain metal
ores to oxygen and microbial action. Rainwater leaches oxidized compounds from the soil to
form sulfuric acid (H2SO4) and iron hydroxide compounds that kill plants, fish, and other organ-
isms and make local waterways unfit for drinking or recreational use. Strip mines are supposed
to be refilled to reduce damage. An excellent example of microbial diversity is the archaea Fer-
roplasma acidarmanus found thriving in acid mine drainage at a pH near zero.
The Roles of Microorganisms in Biogeochemical Cycles
Six elements make up most macromolecules: hydrogen, oxygen, carbon, nitrogen, sulfur, and
phosphorus. These elements must be recycled in the biosphere. Biogeochemical cycles are pro-
cesses by which organisms (mostly microbes) convert elements from one form to another, typi-
cally between oxidized and reduced forms. These cycles include production, in which producers
convert inorganic compounds into organic ones; consumption, in which consumers eat produc-
ers and other consumers; and decomposition, in which decomposers convert the components of
dead organisms back into inorganic compounds.
The carbon cycle involves the cycling of carbon in the form of organic molecules, the start of
Chapter 26 Microbial Ecology and Microbiomes
In the nitrogen cycle, microbes cycle nitrogen atoms from dead organic materials and wastes
to soluble forms for use by other organisms. The process involves nitrogen fixation, in
which gaseous nitrogen is reduced to ammonia; ammonification, in which amino groups
In the sulfur cycle, microorganisms decompose dead organisms, releasing amino acids,
which can be converted to hydrogen sulfide through sulfur dissimulation and then oxidized to
Soil Microbiology
Soil or terrestrial microbiology examines the roles played by organisms in soil, which is com-
posed of topsoil rich in humus (organic chemicals) and subsoil or mineral soil, which is made up
primarily of inorganic materials. Factors that affect the microbial populations living within soil
include availability of water, oxygen content, acidity, temperature, and nutrient availability. The
majority of organisms are found in topsoil. Bacteria and fungi are both numerous in soil; soil al-
Aquatic Microbiology
Aquatic ecosystems support fewer organisms than soil habitats because nutrients are diluted.
Many organisms live in biofilms attached to surfaces that concentrate nutrients to sustain
growth. Freshwater systems have low salt content; marine environments have a salt content of
Instructor’s Manual for Microbiology with Diseases by Body System, 5e
Biological Warfare and Bioterrorism (pp. 812–816)
Bioterrorism is the use of microbes or their toxins as biological weapons to terrorize human
populations. Agroterrorism is aimed at destroying the food supply.
Assessing Microorganisms as Potential Agents of Warfare or Terror
Not all pathogens have biological weapon potential. A potential biological threat to humans is
based on four criteria: public health impact, delivery potential, public perception, and public
health preparedness.
The same criteria can be used to assess the risk to livestock plus plausible deniability. The an-
Known Microbial Threats
Biological agents are categorized from highest to lowest (or unknown) weapons potential as cat-
egory A, category B, and category C agents. Smallpox is currently considered the greatest threat
to humans, but is difficult to obtain and work with, and an effective vaccine is available. Animal
Defense Against Bioterrorism
Defense involves surveillance combined with effective response protocols to an attack. Category
A diseases are reportable, allowing effective monitoring of unusual outbreaks and providing for
Chapter 26 Microbial Ecology and Microbiomes
The Roles of Recombinant Genetic Technology in Bioterrorism
Recombinant genetic technology could be used to create modified or new biological threats. Re-