Characterization of diatom (Bacillariophyceae) nitrate reductase genes and their detection in marine phytoplankton communities

The complete assimilatory nitrate reductase (NR) gene from the pennate diatom Phaeodactylum triconutum Bohlin was sequenced from cDNA and compared with NR sequences from fungi, green algae, vascular plants, and the recently sequenced genome of the centric diatom Thalassiosira pseudonana Hasle and Heimdal CCMP1335. In all the major eukaryotic nitrate reductase (Euk-NR) functional domains, diatom NR gene sequences are generally 50%-60% identical to plant and alga sequences at the amino acid level. In the less conserved N-terminal, hinge 1, and hinge 2 regions, homology to other NR sequences is weak, generally<30%. Two PCR primer sets capable of amplifying Euk-NR from plants, algae, and diatoms were designed. One primer set was used to amplify a 750-base pair (bp) NR fragment from the cDNA of five additional diatom strains. The PCR amplicon spans part of the well-conserved dimer interface region, the more variable hinge 1 region, and part of the conserved cytochrome b heme binding region. The second primer set, targeted to the dimer region, was used to amplify an approximately 400-bp fragment of the NR gene from DNA samples collected in Monterey Bay, California and in central New Jersey inner continental shelf (LEO-15 site) waters. Only diatom-like NR sequences were recovered from Monterey Bay samples, whereas LEO-15 samples yielded NR sequences from a range of photosynthetic eukaryotes. The prospect of using DNA- and RNA-based methods to target the NR genes of diatoms specifically is a promising approach for future physiological and ecological experiments.