MOLECULAR-IDENTIFICATION OF NANOPLANKTONIC PROTISTS BASED ON SMALL-SUBUNIT RIBOSOMAL-RNA GENE-SEQUENCES FOR ECOLOGICAL-STUDIES

Nanoplanktonic protists are comprised of a diverse assemblage of speci es which are responsible for a variety of trophic processes in marine and freshwater ecosystems. Current methods for identifying small proti sts by electron microscopy do not readily permit both identification a nd enumeration of nanoplanktonic protists in field samples. Thus, one major goal in the application of molecular approaches in protistan eco logy has been the detection and quantification of individual species i n natural water samples. Sequences of small subunit ribosomal RNA (SSU rRNA) genes have proven to be useful towards achieving this goal. Com parison of sequences from clone libraries of protistan SSU rRNA genes amplified from natural assemblages of protists by the polymerase chain reaction (PCR) can be used to examine protistan diversity. Furthermor e, oligonucleotide probes complementary to short sequence regions uniq ue to species of small protists can be designed by comparative analysi s of rRNA gene sequences. These probes may be used to either detect th e RNA of particular species of protists in total nucleic acid extracts immobilized on membranes, or the presence of target species in water samples via in situ hybridization of whole cells. Oligonucleotide prob es may also serve as primers for the selective amplification of target sequences from total population DNA by PCR. Thus, molecular sequence information is becoming increasingly useful for identifying and enumer ating protists, and for studying their spatial and temporal distributi on in nature. Knowledge of protistan species composition, abundance an d variability in an environment can ultimately be used to relate commu nity structure to various aspects of community function and biogeochem ical activity.