Short Course Outline

Lecture Schedule by Dr. Mary Ann Bruns, Meetings on Tues, Wed, Thurs
Period Morning Session (9:00-12:00)
Afternoon (14:00-17:00)
Week 1
(24-28 Jan)
Introduction to research by MA Bruns
Mon, 24/1: Higher education and research in the U.S.—my experiences
Tues, 25/1: Introduction to National Center for Biotechnology Information (NCBI) Web site
Wed, 26/1: Culture media for microorganisms and the "Great Plate Count Anomaly"
Thurs, 27/1: Serial dilutions of soil inocula, microbial enumeration, and gravimetric moisture content determination of soils
Mon: Lab planning by instructors
Tues: Lab planning by instructors
Wed: Lab preparation by instructors
Thurs: Lab preparation by instructors
Week 2
(31 Jan - 4 Feb)
General introduction to the soil ecosystem
Tues, 1/2: Soil as habitat for life: soil components and microbial distribution, r- and k-selected organisms
Wed, 2/2: Major groups of soil organisms and their classification by rRNA genes in the “tree of life”
Thurs, 3/2: Cultural, process, and molecular methods for studying soil and rhizosphere microorganisms
Mon: Instructors collect soils
Tues: Dilution and plate counting of soils on non-selective media
Wed: Demonstration on obtaining rhizosphere soil samples
Thurs: Two-day enumeration of soil organisms on non-selective media
Week 3
(7-11 Feb)
Biogeochemical cycling in soil, emphasizing nitrogen
Tues, 8/2: Organic matter decomposition, C/N ratios and N mineralization and immobilization
Wed, 9/2: Biological vs industrial N fixation, symbiotic, associative, free-living N fixers
Thurs, 10/2: Nitrification and denitrification as mechanisms for N loss
Tues: Soil respiration demonstration and discussion
Wed: Plating of organisms on selective media
Thurs: Nine-day enumeration of soil organisms on non-selective media
Week 4
(14-18 Feb)
Molecular techniques in microbiology I
Tues, 15/2: DNA and RNA isolation from soils and isolates; design of PCR primers
Wed, 16/2: Quantitation of genomic DNA; polymerase chain reaction: components and steps
Thurs, 17/2: Considerations and exercises in setting up PCR reactions for ribosomal RNA intergenic spacers
Tues: Extraction of metagenomic (community) DNA from soils with kits
Wed: Estimation of DNA yields using agarose gel electrophoresis
Thurs: PCR of community DNA with ribosomal intergenic primers
Week 5
(21-25 Feb)
Molecular techniques in microbiology II
Tues, 22/2: Gel electrophoresis analysis of PCR products; ribosomal RNA intergenic spacer analysis
Wed, 23/2: Restriction fragment length polymorphism (RFLP) fingerprinting
Thurs, 24/2: Whole genome fingerprinting of genomic DNA from individual strains
Tues: analysis of RISA fingerprints; genomic DNA extraction from isolates
Wed: PCR of DNA from isolates
Thurs: Analysis of PCR products from isolates
Week 6
(28 Feb - 4 Mar)
Biodegradation of xenobiotic compounds
Tues, 1/3: Biodegradation of organic pollutants Wed, 2/3: Excursion to ABU water treatment plant
Thurs, 3/3: Excursion to Galma/Kubanni streams and irrigation site
Tues: Review of molecular results
Wed: Workshop on proposal development
Thurs: Discussion of excursions
Week 7
(7-11 Mar)
Soil science attendees: Travel to Soil Science Society of Nigeria Annual Meeting in Minna Microbiology attendees: No meetings  
Week 8
(14-18 Mar)
Bioremediation of contaminated soils
Tues, 15/3: Oxidation-reduction and heavy metals
Wed, 16/3: Excursion to Challawa industrial estate and irrigation site in Kano
Thurs, 17/3: Bioremediation approaches
Tues: Group work, proposals
Wed: excursion
Thurs: Proposal development
Week 9
(21-24 Mar)
Continue with proposal development
Interaction with undergraduate students and staff
Group work and evaluation of instructors and attendees
Week 10
(28-30 Mar)
Student Presentations
Public lecture on 29 March