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A laboratory unit investigating 2,4dichlorophenoxyacetic acid degradation in soils
Teresa Johnson, College of Wooster
Amy Treonis, University of Richmond
Diuto Esiobu, Florida Atlantic University
Sample 2,4-D
degradation pathway
Who degrades 2,4-D in soils?
Pseudomonas spp.
Arthrobacter spp.
Audience:
Biology Majors in a Microbiology course (intermediate to
upper level)
Objectives:
Students who complete these activities will:
•Explore environmental problems using bioinformatics tools.
•Appreciate metabolic flexibility of microbes through study of their ability to
use novel chemicals (xenobiotics) as energy sources.
•Integrate concepts in functional genomics, phylogenetics, and ecology.
Step 1: Finding 2,4-D degraders
•Challenge students to develop an appropriate
enrichment culture technique & isolate a 2,4-D
degrader in pure culture.
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
Quick Time™a nd a
TIFF ( Unco mpre ssed ) dec ompr esso r
ar e nee ded to see this pictur e.
Step 2: Identification of isolate
•16S rDNA sequencing from pure culture
•BLAST search to identify microbe
Step 3: Functional genomics
•BLAST search for tfdA amino acid sequences (Pseudomonas)
•Use aa sequence from BLAST to perform a JGI search
for sequenced bacteria that contain the gene to determine
whether our isolate has been identified as having tfdA genes.
•Design primers to attempt to amplify tfdA genes from isolate
for sequencing.
•If tfdA genes aren’t present, propose alternative mechanism
for degradation.
•If tfdA genes are present, compare aa or nucleotide sequence
similarity between known degraders and our isolate.