Application of sequence-specific labeled 16S rRNA gene oligonucleotide probes for genetic profiling of cyanobacterial abundance and diversity by array hybridization

DNA sequence information for the small-subunit rRNA gene (16S rDNA) obtaine d from cyanobacterial cultures was used to investigate the presence of cyan obacteria and their abundance in natural habitats. Eight planktonic communi ties developing in lakes characterized by relatively low algal biomass (mes otrophic) and in lakes with correspondingly high biomass (eutrophic) were s elected for the study. The organismal compositions of the water samples wer e analyzed genetically, using multiplex sequence-specific labeling of oligo nucleotide probes targeted to 16S rDNA and subsequent hybridization of the labeled probes to their respective complements spotted onto a solid support (DNA array). Ten probes were established to determine the relative abundan ces of the discernible cyanobacteria encountered in the selected lakes, The probes were generally specific for their targets, as determined through an alyses of clone cultures. Reproducible abundance profiles were established for the lakes investigated in the subsequent analyses of natural cyanobacte rial communities. The results from the genetic analyses were then compared with information obtained from standard hydrobiological and hydrochemical a nalyses. Qualitatively, there were relatively good correlations among the g roups of organisms (Nostoc, Microcystis, and Planktothrix species) found in the different lakes. The levels of correlation were lower for the quantita tive data. This may, however, be due to differences in sample processing te chnique. The conclusions from these comparisons are that the genetic abunda nce profiles may provide a foundation for separating and quantifying geneti cally distinct groups of cyanobacteria in their natural habitats.