High resolution microarray assay for rapid taxonomic assessment of Pseudo-nitzschia spp. (Bacillariophyceae) in the field

Deployable methods facilitating rapid microbial identification provide opportunities to respond quickly when pathogenic or toxin-producing organisms threaten water quality. We developed a microarray assay to streamline identification of microorganisms in the field, focusing on the harmful algal bloom diatom Pseudo-nitzschia. The assay employed electrochemical signal detection and a simplified protocol, allowing identification of specific taxa onboard research vessels within 7 h of water collection. Microarrays targeted the internal transcribed spacer (ITS1) region between the 18S and 28S ribosomal RNA genes using 307 oligonucleotide probes. The probes, ranging from broadly specific to unique, represented 118 Pseudo-nitzschia ribotypes from 15 species available at the time of assay development. Hybridization signals from multiple probes for each target strain were integrated using a novel algorithm for data analysis. Designated the ‘integrated sumscore data analysis’ (ISDA), the algorithm used probe specificity metrics for signal integration, with uniqueness corresponding to higher probe weight values. The integrated signals provided a ‘sumscore’ for each ribotype represented on the array, indicating its presence or absence in the sample. The algorithm was ‘trained’ by comparison with data from scanning electron microscopy, and cloning and sequence analysis of Pseudo-nitzschia ITS1 ribotypes from 7 laboratory cultures and a complex environmental sample. The ISDA provided correct identification and target sequences for all tested strains. Through design of custom probes (up to 12,000 on a microarray chip), this approach may be used to identify additional microbial taxa of interest and provides rapid, reliable shipboard assays for basic research or water quality monitoring.