Omics-Enabled Microbial Sensors on Ocean Platforms

In order to assess the diversity and function of microbial communities most effectively, molecular assays need to be designed that target the phylogenetic markers and functional genes that are key to major ecological processes and microorganisms. A streamlined design process is presented here that designs probes for microarray and quantitative PCR (qPCR) assays, for application on the lab bench or on remote instrumentation. These assays can be used for DNA (genome) and RNA (gene transcription) studies. The pipeline described here establishes a database of environmental sequences, which is then used for the design of molecular probes for microarrays and to inform the design of qPCR assays, which is detailed here along with the assay optimization process. Finally, the process for the design of high-density microarrays is described. The qPCR protocol is currently used for assay optimization on the Environmental Sample Processor, a deployable robotic “genosensor” (http://www.mbari.org/esp ). The protocols described here should advance applications in microbial oceanography using robotic instrumentation as well as traditional sampling methods.