Microbial Ecology


Microbial Ecology

• Microbes in their Environment

• Microbe-Microbe Interactions

• Biogeochemistry (Cycling of Elements)

• Microbe-Higher Organism Interactions

• Environmental Pollution Control

Positive Population Interactions




Negative Population Interactions




Actinomycete amensalism of parasitic fungi



Carbon Biogeochemistry

Aerobic Carbon Use

Anaerobic Carbon Use

(No Oxygen)

Carbon Biogeochemistry


• Oxygen supply limited by mineral particle size, organic matter content and water content.

• Plant roots may also add oxygen to deeper soils or anaerobic soils.

• Water saturation leads to anaerobic conditions and increased denitrification.

• Distribution of microbes depends on organic matter supply and source (humus and root exudates)

Soil Close-Up

Geosmin = “earthy smell”

= Cyanobacteria

= Actinomycetes



Ectomycorrhizal association between

Douglas Fir

( Pseuditsuga menziesii ) and a boletus-like mushroom

( Suillus caerulescens).

Legume Root

Nodule formed by

Rhizobium spp.

Bovine Rumen

It’s a 100+ liter cellulose-degrading methane-producing microbial incubation.

There are only a few manned submersibles in the world that can explore hydrothermal vent communities (e.g. Alvin )

Control Point Sources

Wastewater Treatment

• Raw Sewage (99.9% water to 0.1% waste)

• Pollutants in sewage are:

– Debris and grit

– Particulate organic material

– Colloidal and dissolved organic material

– Dissolved inorganic material

– Human Pathogens

– Toxic Chemicals

– Pharmaceuticals

Wastewater Treatment

• Preliminary (physical screening)

• Primary (physically settle solids)

• Secondary (biological)

– Remove organics aerobicaly (lower BOD)

– Solids production (separate water and “sludge”)

– Sludge Treatment (solids reduced)

• Tertiary (biological or chemical “polishing”)

– Biological nutrient removal systems

– Pathogen removal by chlorine or ozone

– Chemical nutrient removal (costly)

Wastewater Treatment

Secondary Treatment:

Activated Sludge (aerobic)

Trickle Filters (aerobic)

Anaerobic Sludge Digesters

Trickle Filter Biofilms

What da Floc?

• Bacterial growth in activated sludge digested (aerobic) will aggregate (floc).

• Dissolved organics aggregate with bacterial growth and removed from the water.

• Imbalances may cause growth of filamentous bacteria or fungi; prevents settling; called “bulking”.

Anaerobic Sludge Digester

(Methane Production)

What’s a coliform? Why test them? How can we test for them?