Towards a Genome-Enabled Sensor for In Situ Monitoring of Microbial Communities in Hydrothermal Vent Fields

We report the progress towards a genome-enabled instrument to monitor variations in microbial community in hydrothermal vent fields for long durations. Our long-term goal is to deploy an in situ microarray device embedded in a lab-on-a-chip device. The microarray detects both the 16S rRNA to identify prokaryotic species and cDNA (converted from mRNA) of selected functional genes to understand activities and dynamics of ocean microbial communities. Each automated, self-contained instrument contains a stack of disposable lab-on-a-chip devices. All measurements are performed on individual chips, starting with pumping seawater through on-chip filter to collect microbes, lysing cells to release nucleic acids, and then analyzing their genomic information. To aid the effort of building the first functional microarray, we participated in the TN-221 cruise funded by the National Science Foundation's Ocean Observatories Initiative to map the seafloor in areas of high scientific interest. During the cruise, multiple deep-sea water samples were collected. The microbes were filtered, frozen and shipped to our laboratory for molecular analysis. The DNA was isolated from these samples and a detailed metagenomic analysis is ongoing for samples of one site (80 km offshore of Oregon coast, 380 km away from the Axial Seamount vent field, and 5 meters above the 780- meter deep seafloor). From the isolated chromosomal DNA the 16S rRNA clone library was constructed and resultant clones were sequenced. Although the fluorescence microscopic analyses showed the density of biomass is relatively low, phylogenetic results suggested high diversity in these microbial communities. In addition, efforts were made to isolate mRNA directly from these deep-sea ocean samples. The information obtained from these analyses will be essential for development of oligonucleotide probes for the microarray device. First two authors contributed equally.