Environmental Microbiology

1. Introduction

• History of environmental microbiology

• Survey of organisms (prokaryotes, eukaryotes, viruses and other microbiological entities)

• Review of microbial growth (batch culture, continuous cultures, growth in the environment)

2. Earth environments

• Environmental conditions

• Factors affecting survival

• Survey of environments (surface, deep soil and sediments)

3. Aeromicrobiology

• Environmental conditions

• Factors affecting survival

• Survey of environments (external and internal aerial environments)

• Controls of bioaerosols

4. Aquatic microbiology

• Environmental conditions

• Factors affecting survival

• Survey of environments (marine, freshwater, groundwater)

5. Microbiology of extreme environments

• Environmental conditions

• Factors affecting survival

• Survey of environments (low and high temperature, desiccation, UV light, aphotic environments with chemolithoautotrophy)

6. Methods for detection, enumeration and identification of microbes

• Sample collection and processing (soil, sediments, water and air)

• Microscopy (light, fluorescence, transmission electron, scanning electron)

• Culturing (isolation, plating, methods specific for bacteria, fungi, cyanobacteria, algae and viruses)

• Physiological methods (measuring microbial activity, carbon respiration, radiolabeled tracers, enzyme assays, stable isotopes)

• Immunological methods (fluorescent immunolabeling, enzyme-linked immunosorbent assay, western immunoblotting)

• Nucleic acids (obtaining nucleic acids, hybridization, amplification, fingerprinting, recombinant DNA and sequence analysis)

7. Bioinformatics and genomics

• Metagenomics

• Transcriptomics

• Proteomics

• Metabolomics

• Bioinformatics

8. Biogeochemical cycling

9. Microbial food webs dynamics

10. Microbial communities and communication (quorum sensing, etc.)

11. Applications of environmental microbiology (some of the following topics will be covered)

• Environmentally transmitted pathogens

• Indicator microorganisms

• Wastewater treatment/disinfection

• Remediation of organic and metal pollutants

• Agricultural uses of microbes

• Emerging microbial uses

12. Laboratory techniques

• Laboratory operations and safety

• Laboratory reporting techniques

• Aseptic techniques

• Isolation of environmental microbes from soil, water and air (sampling, collecting, culturing)

• Enumeration of environmental microbes from soil, water and air (e.g. microscopy, plating, enzyme-linked immunosorbent assay, coliforms as indicator organisms)

• Identification of environmental microbes from soil, water and air (biochemical tests, polymerase chain reaction, sequence analysis)

• Determination of  environmental microbial function (analysis of carbon metabolism, enzyme assays)

• Assessment of degradation of hydrocarbons