Development of Analytical Protocols & Optimization of a Capillary Waveguide Biosensor for Marine Microbial Process Studies

P.I. Paul Kemp (SUNY-SB) Proposal #: 0352252 The PIs have developed a Capillary Waveguide Biosensor system to study microbial populations and processes in aquatic systems, particularly coastal and estuarine waters and sediments. The biosensor system employs fluorescence detection to measure the hybridization of nucleic acids to probe molecules bound to the interior surface of a capillary tube. The tube walls serve as an optical waveguide, while the capillary interior serves as a flow cell and hybridization chamber. By targeting DNA, rRNA and mRNA sequences appropriately, the fiber-optic biosensor system can be used to assay for the abundance of specific genes (DNA target), the expression of those genes (mRNA target), or the physiological status of cells (rRNA target) within mixed microbial communities. The goals of this proposal are to 1) develop and test the analytical protocols required to apply the instrument, using model biological systems representative of different research problems; 2) test alternative analytical protocols that show promise for increased sensitivity; and 3) conduct theoretical analyses leading to practical refinements in instrument design. During the course of this research, two graduate students will be supported and other high school, undergraduate and graduate students will be involved. The biosensor will be tested with pathogens of direct interest to human health and the seafood industry. It can be used not only for detection of pathogens in seawater, but human pathogens in processed seafood, fish pathogens in aquaculture facilities, and other harmful and nuisance species in a diverse range of environments. The capacity to examine microbial abundance and population dynamics, biomass production and gene expression in marine environments has enormous potential benefit for water quality management and the seafood industry, both economically and with respect to food safety. Other potential applications beyond ecological research include detection and quantification of microbial contaminants for estuary management, shellfish aquaculture, and water quality for public health purposes. The biosensor also has implications for homeland security issues, particularly monitoring for the presence of potentially harmful organisms in recreational waters and reservoirs, and in coastal waters.