Summer workshop in metagenomics: one week plus eight students equals gigabases of cloned DNA

Abstract

We designed a week-long laboratory workshop in metagenomics for a cohort of undergraduate student researchers. During this course, students learned and utilized molecular biology and microbiology techniques to construct a metagenomic library from Puerto Rican soil. Pre-and postworkshop assessments indicated student learning gains in technical knowledge, skills, and confidence in a research environment. Postworkshop construction of additional libraries demonstrated retention of research techniques by the students.

FIG. 1

Students’ perception of knowledge and skills proficiency before (A) and after (B) library school. Skills specifically addressed during library school are listed in bold type. Students were asked to rate their knowledge and skills in: 1) generation of small insert (<10kbp) metagenomic libraries; 2) generation of large inset (> 20 kbp) metagenomic libraries; 3) direct DNA extraction from soil; 4) indirect DNA extraction from soil; 5) cloning DNA fragments using the TOPO TA system; 6) cloning DNA fragments via traditional methods; 7) using fosmids to build metagenomic libraries; 8) using BACs to generate metagenomic libraries; 9) transformation of E. coli by electroporation; 10) transformation of E. coli by chemical methods; 11) restriction endonuclease digestion of DNA; 12) determination of optimal endonuclease concentration to generate small genomic fragments by incomplete digestion; 13) amplification of DNA fragments by PCR; 14) analysis of DNA by standard gel electrophoresis; 15) analysis of DNA by pulse-field gel electrophoresis; 16) detection of activities in metagenomic clones; 17) generation of recombinant DNA libraries from metagenomic libraries; 18) in silico analysis of nucleotide and amino acid sequences; 19) plasmid extraction from transformed E. coli cells; and 20) DNA sequencing. The scale used by the students to assess their level of knowledge or proficiency was high, intermediate, or low.

FIG. 2

Dry forest library characterization. Eighteen clones were chosen randomly to determine the presence of an insert via fosmid DNA purification, restriction endonuclease digestion, and gel electrophoresis. All but one clone contained insert DNA. Two molecular markers were used: 1 kb ladder (Promega Corporation, Madison WI) (lane 1) and Yeast Chromosome PFG Marker (New England BioLabs, Ipswich MA) (lane 2). The arrow indicates where linearized vector runs (approximately 7.5 kbp).