CHAPTER 25

ENVIRONMENTAL MICROBIOLOGY

FChapter Overview

Microbes play a fundamental role in the ecology of all living systems. Without them, in the words of the famous microbiologist Hans Zinsser, ". . . the physical world would become a storehouse of well-preserved specimens of its past flora and fauna . . . useless for the nourishment of the bodies of posterity. . . ." A review of the biogeochemical cycles immediately reveals their essential presence in the conversion of many components of each cycle.

Although the emphasis of this chapter is to provide a description of the role and importance of microbes in our environment, there are still several opportunities to emphasize their medical importance as they relate to the air, soil, water, and sewage. Upon completion of this chapter, it should be clear that as long as life exists on this planet, microbes will continually be an integral part of every aspect of our lives.

FChapter Objectives

  • Define ecology, and describe how energy flows in ecosystems.
  • Describe the importance of recycling, and note how water and carbon are recycled.
  • List and describe three other major biogeochemical cycles, and indicate what roles microorganisms play.
  • Describe the kinds of microorganisms found in air, and indicate how they are detected and controlled.
  • List and describe several kinds of microorganisms found in soil, and indicate their roles in biogeochemical cycles and as potential pathogens.
  • Describe how microorganisms found in freshwater and marine environments differ.
  • Describe how water pollution and waterborne pathogens affect humans.
  • Describe how water is purified and how it is tested to determine purity.
  • Describe the term sewage, and list the processes involved in primary, secondary, and tertiary sewage treatment.
  1. Animations and videos – online
  2. Flash animations on Living Things in their Environment at the BBC website - Once there, click on Carbon cycle or Nitrogen cycle
  3. Simple soil animation -
  4. NASA site of microbes riding the dust with a few good animations -

Web Destinations


  • The Center for Microbial Ecology web site

  • Digital learning center for microbial ecology

  • Oak Ridge National Laboratory Microbial Genomics and Ecology Group web site

  • U.S. Geological Survey bioremediation web site

  • Cornell bioremediation web site

  • Ocean explorations web site - marine vents

Discussion Topics

  • Farmers often use fertilizer to improve their crop yields. Excessive fertilization can lead to runoff into our rivers and streams. Why is this important?
  • New bacterial species have been discovered around deep-sea volcanic vents. Since the pressures there are enormous, temperatures exceedingly high, and nutrient source very primitive, what role do these microbes play in this type of ecology?

Track It Down

  • Identify the organisms that have been genetically designed to degrade waste oils. How useful have these organisms been in cleaning up actual oil spills? When and where have they been used?
  • Some of the rivers in India, such as the Ganges, are badly polluted. What is the government trying to do to solve this problem? Why is the river so polluted?
  • What changes have occurred in the microbial population following a major oil spill? What effect would these have on higher life forms?

FChapter Outline

I. Fundamentals of Ecology

A.Basic Terms

1.Ecology

2.Abiotic factors

3.Biotic factors

4. Ecosystems

B.The nature of ecosystems

1.Biosphere

a.Hydrosphere

b.Lithosphere

c.Atmosphere

2.Community

a.Indigenous organisms

b.Nonindigenous organisms

3.Population

4.Organism

a.Habitat

b.Microenvironment

c.Niche

C.The flow of energy in ecosystems

1.Role of energy

2.Producers

3.Consumers

4.Decomposers

II.Biogeochemical Cycles

A.General characteristics

B.The water cycle

C.The carbon cycle

D.The nitrogen cycle and nitrogen bacteria

1.Nitrogen cycle

2.Nitrogen-fixing bacteria

a.Energy source

b.Examples

c.Symbiotic relationships

(1.)Mechanism

(2.)Nitrogenase

3.Nitrifying bacteria

a.Nitrification

b.Examples

4.Denitrifying bacteria

a.Denitrification

b.Examples

c.Detriments of process

E.The sulfur cycle and sulfur bacteria

1.Sulfur cycle

2.Sulfate-reducing bacteria

3.Sulfur-reducing bacteria

4.Sulfur-oxidizing bacteria

F.Other biogeochemical cycles

1.Phosphorus cycle

2.Other elements

G.The deep hot biosphere

III.Air

A.Microorganisms found in air

1.Examples of organisms

2.Determining the microbial content of air

B.Methods for controlling microorganisms in air

1.Chemical agents

2.Radiation

3.Filtration

4.Laminar airflow

IV.Soil

A.Components of soil

1.Soil horizons

2.Inorganic components

a.Rocks and minerals

b.Water and gases

3.Organic components

a.Humus

b.Living organisms

B.Microorganisms in soil

1.Types of microbes

2.Factors affecting soil microorganisms

a.Physical factors

b.Microbial interactions

3.Importance of decomposers in soil

a.Decomposition

b.Anaerobes

C.Soil pathogens

1.Plant pathogens

2.Animal pathogens

D.Caves

1.Cave formation

2.Snottites

V.Water

A.Freshwater environments

1.Zonation

2.Algal blooms

3.Effect of oxygen

4.Effect of depth

B.Marine environments

1.Effect of depth

2.Importance of sunlight

3.Nutrient concentrations

4.Producers of the oceans

5.Heterotrophs

C.Deep ocean vents

1.Hydrothermal vents

2.Cold seeps

D.Water pollution

1.Basic problems

2.Pollutants

a.Biological oxygen demand

b.Industrial wastes

c.Eutrophication

d.Heat

e.Effects of water pollution

3.Pathogens in water

E.Water purification

1.Purification procedures

a.Settling

b.Flocculation

c.Filtration

d.Chlorination

2.Tests for water purity

a.Coliform bacteria

b.Multiple-tube fermentation method

(1.)Presumptive test

(2.)Confirmed test

(3.)Completed test

c.Membrane filter method

d.ONPG and MUG tests

e.Nuisance organisms

f.Other contaminants

VI.Sewage Treatment

A.Definition

B.Treatment facilities

C.Primary treatment

D.Secondary treatment

1.Trickling filter system

2.Activated sludge system

3.Sludge digesters

E.Tertiary treatment

F.Septic tanks

VII. Bioremediation

A.Basic concepts

B.Cleanup enhancements

C.Advantages and disadvantages

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