Evaluation of DNA methodologies in identifying Brachionus species used in European hatcheries

Few efforts have dealt with the genetic make up of the Brachionus plicatilis rotifers which are often used as live feed in the larviculture of many marine fish. Recent results have demonstrated that the B. plicatilis species is actually a species complex. In this study a number of molecular markers (Restriction Fragment Length Polymorphism (RFLP) analysis of mitochondrial COI gene, Single-Stranded Conformation Polymorphism (SSCP) analysis and Denaturing Gradient Gel Electrophoresis (DGGE) of mitochondrial 16S rRNA gene as well as microsatellite genotyping of nuclear loci) have been developed and applied to identify genetically rotifer strains used in European hatcheries. All methods have proven highly efficient for the reliable diagnosis of the genetic variability within hatchery strains at bulk or individual level. Results point towards an absence of the typical B. plicatilis and Brachionus rotundiformis species and a predominance of the Brachionus sp. Cayman biotype (Brachionus SM morphological type). All the other biotypes/species were either rarely found or were coexistent with B. sp. Cayman. These biotypes were B. plicatilis sensu stricto, B. sp. Nevada and B. sp. Austria, all belonging to the Brachionus L group. Minimal genetic variability was detected within strains. The above results have important implications for rotifer cultures, with respect to the different temperature and salinity optima of each biotype/species. Caution is needed regarding the common practice used by hatcheries around the world of exchanging samples based solely on morphological criteria.