Functional Gene Arrays for Analysis of Microbial Communities on Ocean Platform

Recently there has been an increased use of microarray technology as a tool to determine the presence of functional genes in a population of hard to culture communities (e.g., soil, extreme environments). A functional gene array (FGA), or GeoChip, uses probes to screen for specific functional genes vital in biological systems such as nitrogen and carbon cycling, and has even been expanded to include aquatic conditions. However, the time delay from when the sample is taken from the ocean to evaluating the test results back in the lab still posed a problem. The Environmental Sample Processor (ESP) minimizes this time difference by housing a robotic system placed in the ocean for a long period of time that can collect a small sample, concentrate the DNA, run a microarray, and take a picture of the array before sending the data ashore to be evaluated by a researcher. The included protocol and reagents list goes through both lab microarray procedures as well as the procedures list for the ESP, which briefly mentions deployment and data acquisition. The protocols described here should advance applications in microbial oceanography using robotic instrumentation.