Targeted microarray analysis of two symbiotic cyanobacterial diazotroph strains in the western tropical North Atlantic

We designed a new specific mRNA microarray targeting a subset of genes (956) of the diazotrophs Richelia intracellularis and Calothrix rhizosoleniae (genomes RintRC01, RintHH01, RintHM01 and CalSC01) which associate with diatom hosts. The aim was to be able to describe the gene expressions of genes related to several metabolic pathways, specifically nitrogen fixation and how they possibly differed between the closely related strains based on environment and host association. In this study we focused on the RintRC01 and RintHH01. To better understand how the gene expression of nitrogen fixation genes relates to nitrogen fixation rates both gene expression and rate measurements were done in parallell. In total 7 samples from 2 stations were collected during daytime, and in 2 depth profiles (2-36 m). The microarray was designed with one probe for each target gene, which some had cross-hybridization with a cultured and closely related strain. Therefore, the final number of probes included in the study decreased to 750. An updated Agilent microarray design, without cross-hybridization, has been applied elsewhere (ID: Agilent-085960). The microarray was printed with a total of 15 probe replicates.