A collaboration with Dan Beiting at University of Pennsylvania
20" x 30" plexiglass frame with removable face (Dave Perry, Precision Plastics)
A collaboration is born! 2017
As a judge for the MoMA sponsored Biodesign Summit in summer 2017, I sat next to Dan Beiting (we both are Cornell alumni). When I learned about his Host+Microbe lab at University of Pennsylvania (https://hostmicrobe.org/), I had to ask if he wanted to collaborate. He said Yes!
With Dan's kids, we collected this mud in playgrounds, fishing ponds, and streams around Moorestown, NJ. Then the samples were placed in a special container designed by Precision Plastics in Maryland. The goal: to be able to remove the 'face' of the painting and collect DNA samples to speciate colorful bacteria along an oxygen gradient (anaerobic at the bottom, aerobic at the top). This is a contemporary application of Winogradsky's soil column to identify species that are typically hard to identify in traditional landscapes.
Samples were taken by swab from the plexiglass face and frozen; DNA was later extracted using a bead-beating method; DNA underwent PCR for a region of the 16s gene; PCR products were sequenced on Illumina MiSeq sequencer (250bp chemistry). The resulting data was run through the full QIIME2 bioinformatics pipeline.
This is the final image I took before Dan and I deconstructed the frame and took samples. I mapped the sampling sites with the estimate color from that site. Look closely!
Of the 40 samples taken, 29 had sufficient DNA for sequencing results.
- Swabbing 1 color is a community of organisms
- Different colors have a similar community of organisms! Is it the who that is there or the what they do together that is important to creating the pigment?
- Two of the most abundant organisms at each site were Bosea and Rhodospirillium, both known to make purple pigments, but maybe they make more than purple pigments!