The CURE for Cultivating Fastidious Microbes

Abstract

Course-Based Undergraduate Research Experiences (CUREs) expand the scientific educational benefits of research to large groups of students in a course setting. As part of an ongoing effort to integrate CUREs into first-year biology labs, we developed a microbiology CURE (mCURE) that uses a modified dilution-to-extinction high throughput culturing protocol for isolating abundant yet fastidious aquatic bacterioplankton during one semester. Students learn common molecular biology techniques like nucleic acid extraction, PCR, and molecular characterization; read and evaluate scientific literature; and receive training in scientific communication through written and oral exercises that incorporate social media elements. In the first three semesters, the mCUREs achieved similar cultivability success as implementation of the protocol in a standard laboratory setting. Our modular framework facilitates customization of the curriculum for use in multiple settings and we provide classroom exercises, assignments, assessment tools, and examples of student output to assist with implementation.

FIGURE 1

Flowchart of the mCURE background and experimental design. Using this flowchart, students are guided through the scientific process to gain an understanding of the relevance and importance of the project. Various segments of the course are color-coded (grey, orange, green, blue, and yellow), corresponding to Table 1, where the week-by-week activities for each of these segments are described. This flowchart may be modified as needed to suit alternative projects using a similar protocol.

FIGURE 2

Grade distributions for two sections of mCURE students during each of two semesters in the 2015–2016 school year. Fall 2015 consisted of ~50 Honors college students majoring in biology. The topics for the five quizzes (Q1–Q5) were as follows: Q1 = Safety, Controls; Q2 = Experimental design, Scientific writing; Q3 = DNA extraction; Q4 = PCR; Q5 = Gel electrophoresis, Purpose of sequencing, Primer design. Spring 2016 consisted of ~60 mostly nonbiology major students. The topics for the five quizzes (Q1–Q5) were as follows: Q1 = Dilutions, Pipetting, Safety, Controls, Scientific writing; Q2 = Experimental design, Dilution, Pipetting, Controls; Q3 = DNA extraction; Q4 = PCR, Primer selection/design, Gel electrophoresis; Q5 = Purpose of sequencing, Sequence analysis. The grades for both semesters were assigned based on the following score criteria: A = 90%–100%; B = 80%–90%; C = 70%–80%; D = 60%–70%; F = <60%.

FIGURE 3

Example gel electrophoresis image of a successful 16S rRNA gene PCR amplification from fall 2015. Lanes labeled according to contents: “Sample A11–22” is the amplicon from isolate DNA (expected size 1,466 bp); “Ladder” is Lambda HindIII digest ladder (NEB N3012S), with the lowest visible band at 2,027 bp; “Control” is the negative control (water).