I had the good fortune to attend a PIRE/PASI field course this past summer in the Peruvian Amazon. It was incredible! My first taste of tropical forest research. The course was split between cloud forest at ~3,500m in the Andes and lowland forest at ~sea level. In the cloud forest we stayed at Wayquecha, a fantastic field station with delicious traditional Peruvian food. Highlights include quinoa porridge with chunks of sugarcane and pasta casseroles.
I was part of the “A-team”, sampling microbes. In addition to taking “real” samples (i.e. preserving leaf samples and air samples in Lifeguard for chemical analysis in the U.S.), we took culturable samples using a high-tech microbe flux sampling device. We hung it from the meteorological boom another group installed on cabin 2B (right). They had wind sensors, temperature and humidity probes, light intensity sensors, and would have been taking water isotope measurements if their very expensive laser had arrived in Peru intact. We built our microbe sampler out of popsicle sticks, gorrila tape, and duct tape. The petri dishes were of the miniature variety, with malt agar to embed and foster the growth of bacteria and fungi. The up/down design was largely due to Kerton Victory, with confirmation from the atmospheric scientists on the course, to separate microbes falling down from those being wafted up.
We sampled with 30 minute exposures multiple times per day. In addition to sampling at the station, where there was a lot of air flow up and down the valley over the course of a day, we hiked out to the canopy walkway to sample a vertical gradient through the cloud forest. This involved dangling our high-tech sampling device off the walkway at different heights. Some misty times of day, the dishes would be wet after sampling from all the fog deposition. Not a problem, Parafilm! Rachel Gallery, whom we have to thank for bring the petri dishes to Peru in the first place, has a trick for Parafilming: rub your hands together first. (The heat softens the plastic.)
Rachel’s expertise was also key in storing our precious dishes. Her work with culturable fungi in other tropical places alerted her to a key source of microbiological failure: mites and other insects that eat through the Parafilm and mess up the sample. This actually happened to me in my current lab—most of the lab works on Drosophila and the last time they had a mite outbreak some nice plates I had just poured and was letting dry on my bench acquired suspicious trails of assorted bacteria.
You may be suspicious, as we were, that everything would be horribly contaminated. But it wasn’t! A large number of plates didn’t grow anything. Nothing. Zip. Zero. Zilch. Nada. Rinsing our hands in ethanol apparently worked. I had a very difficult time doing microbiology without a sterile hood and built a little area in my room enclosed in plastic that I could wipe down with ethanol… Ziploc bags are apparently pretty darn clean. Go A-team!