Detection and mapping of species and strains from the diatom genus Pseudo-nitzchia (Bacillariophyceae) along the Oregon and Washington coast using microarray-based, field-deployable, rapid, high-resolution assay

ABSTRACT: DNA oligonucleotide microarrays were designed with 307 probes for 96 internal transcribed spacer (ITS1, located between 18S and 26S rRNA genes) sequences of known species and strains from the genus Pseudo-nitzschia (Bacillariophyceae). In addition, microarrays also carried 1893 probes targeting ITS1 aequences of marine Crenarchaeota and Alphaproteobacteria of SAR11 clade. In order to assign microarray profiles to Pseudo-nitzschia ribotypes and species and to 'train' the data analysis system, we grew cultures of Pseudo-nitzschia in the laboratory with identities confirmed through rDNA sequence analysis. In total, 9 cultures and 35 environmental water samples were hybridized to microarrays, in some cases, in duplicate or triplicate. Analysis of microarray data allowed us to identify and map Pseudo-nitzschia spp. in the coastal waters along Washington and Oregon coast of the Eastern Pacific Ocean, and to observe seasonal changes in diatom community composition.

ORGANISM(S): Skeletonema Pseudo-nitzschia uncultured Pelagibacterales bacterium uncultured marine crenarchaeote Bradyrhizobium Thalassiosira Mesorhizobium Rhizobium environmental samples Roseovarius

PROVIDER: GSE27141 | GEO | 2012/06/01

SECONDARY ACCESSION(S): PRJNA137575

REPOSITORIES: GEO