The potential of genomic approaches to rotifer ecology

Rotifers are a key component of many freshwater ecosystems, but surveys of the composition of rotifer communities are limited by the labor-intensiveness of sample processing, particularly of non-planktonic taxa, and by the shortage of investigators qualified to identify a broad range of rotifer species. Additional problems are posed by species that must be identified from living specimens, and by members of cryptic species complexes. As DNA sequencing becomes easier and cheaper, it has become practical to obtain representative DNA sequences from identified rotifer species for use in genome-based surveys to determine which rotifers are present in a new sample, avoiding the difficulties of traditional surveys. Here we discuss two genome-based tools used in surveys of microbial communities: serial analysis of gene tags (SAGT) and microarray hybridization. SAGT is a method for inexpensively obtaining characteristic short DNA sequences from a sample that can both identify taxa for which the tag sequence is known and signal the presence of additional uncharacterized species. Microarray hybridization allows detection of DNA sequences in the sample that are identical or similar to sequences present on the microarray. We also report the construction and hybridization of a small microarray of rotifer sequences, demonstrating that this method can discriminate among bdelloid families, and is likely to make much finer discriminations if appropriate sequences are present on the microarray. These techniques are most powerful when combined with traditional systematics in collaborative efforts, which may be fostered through the data base of rotifer biology, WheelBase (http://jbpc.mbl.edu/wheelbase).