Microbial species diversity, both global and local, is still poorly understood. In this study all species of ciliated protozoa were recorded microscopically from ∼ 1 cm² sediment collected from a small lake and from a marine shallow-water bay. Additional adjacent sediment samples (together representing < 50 cm²) were then incubated under a variety of culture conditions to reveal "cryptic species" that are present as resting cysts or are too rare to be found microscopically. About 85 and 57% of the total number of observed species from the limnic and marine sediment, respectively, were such cryptic species. In both cases the number of species found in < 50 cm² of sediment represented about 75% of all ciliate species ever recorded from these two previously well-studied habitats, and about 8% of all named free-living ciliates. These observations support the assumption that in the case of microorganisms "everything is everywhere" and that their global species diversity is relatively limited.

Microbial diversity and activity were studied in a stratified basin of Mariager Fjord, Denmark in August 1994. The basin is about 30 m deep and the lower half of the water column is anoxic and sulphidic. The hydrographical and biological features of the system are described. Based on chemical gradient profiles and measurements of process rates, we found that the relative importance of sulphate reduction, denitrification and methanogenesis in terms of anaerobic terminal mineralisation was about 5:1:0.4. It is possible, however, that methanogenesis is underestimated because an unknown fraction of the methane production escaped by ebullition. It was estimated that 10–15 % of the net primary production is mineralised anaerobically. The mean residence time of methane, sulphide and ammonia beneath the chemocline is within the range 1.6–2.3 yrs. Chemolithotrophic production in the chemocline (sulphide oxidation and nitrification) accounted for about 3% of the net primary production of the system. Methane was oxidised (anaerobically or aerobically) throughout a large part of the water column, but most escaped to the atmosphere. The fjord has an impoverished zooplankton. This may be due to the sulphidic deep water which will be lethal to sedimenting eggs. The protozoan biota were studied quantitatively and qualitatively. Eighty-one species of protozoa were identified in the water column; of these, 37 were ciliates and the remainder were flagellates or rhizopods. Only one new species of ciliate was found. All flagellates from the aerobic zone could be assigned a generic name. In contrast, the microaerobic and especially the anaerobic parts of the water column revealed about ten undescribed flagellates (three of which are formally described), suggesting that the smaller protists of anaerobic habitats are still poorly known. Three relatively distinct protistan assemblages could be identified, being associated with the oxic water column, the microaerobic zone around the chemocline, and the anoxic zone, respectively.