Application of bead array technology to community dynamics of marine phytoplankton

Studies of the dynamics of marine microplanktonic systems have been hampered by a lack of high-throughput technologies for the simultaneous identification and quantification of the many taxa comprising such communities. To address this problem, we describe a DNA-hybridization-based method of analysis employing bead array technology. Species- and/or genus-specific probes for 8 phytoplankton taxa were designed and applied to the microplankton community sampled from coastal waters off La Jolla, California, over an exploratory time series 10 d in length. Bulk DNA extractions from 1 l of seawater were used without PCR amplification. Taxa analyzed comprised 4 dinoflagellates, 3 diatoms, and 1 coccolithophorid. The results demonstrated that specifically targeted oligonucleotide probes can be used in this fashion with a high degree of binding-specificity, dependent on hybridization temperature, and that standard curves relative to target-cell concentration can be constructed. The use of 2 different probes for each taxon can provide added confidence that probes are taxon-specific. Further, single-species assays and multiplexed assays were generally in good agreement, as were assays of replicate seawater samples. Once sets of probes are developed for particular groups of taxa, the bead array system appears to provide a technological platform with great promise for high-throughput analyses of microplanktonic communities.