Diversity of rDNA in Chilostomella: Molecular differentiation patterns and putative hermit types

We present new data on nuclear DNA sequences coding for the 3′ region of the small subunit ribosomal RNA (SSU rDNA), the 5.8 subunit and the internal transcribed spacers (ITS1 and ITS2). 56 SSU rDNA and 23 ITS clones were obtained from 12 specimens of the genus Chilostomella collected in the Pacific Ocean, the Atlantic Ocean and the Mediterranean at depth between 600 and 1500 m. Surprisingly, the sequences could be attributed to a number of highly divergent SSU genotypes which cluster in different parts of the foraminiferal SSU rDNA phylogeny. One genetic type, found in most Chilostomella individuals, shows affinity to calcareous foraminifera and its phylogenetic position is consistent with the morphological classification of the genus. We call this genetic type “domestic”, to highlight the anomalous nature of the other obtained SSU rDNA types. The “domestic” sequences (SSU rDNA and ITS) indicate the presence of three distinct genetic types within Chilostomella of which one is limited to the Atlantic–Mediterranean and the other two were found in the Pacific Ocean, both co-occurring at one locality in the Sagami Bay. Albeit limited in size, our dataset provides the first indication for ocean-wide dispersal in bathyal benthic foraminifera. Five other foraminiferal SSU rDNA types were identified among the cloned sequences, all clustering outside the well-supported calcareous clade. The presence of these “contaminant” or “hermit” sequences indicates that calcareous tests of bathyal foraminifera may be inhabited or invaded by other non-calcareous taxa. This has implications for the recognition of standing stocks of individual benthic foraminiferal species in the deep-sea. Using cytoplasm staining techniques, these tests would be considered representative of a living individual of the species that produced the test.