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The starting point for Tom Fenchel’s scientific career was the ecology of protozoa in marine sediments. That in turn drew his attention to the vertical chemical gradients and the zonation and rates of different microbial processes in sediments. Later he worked on the microbial food chains of the marine water column which contributed to the concept of the microbial loop that fundamentally changed the view of the role of microbes in the sea. Tom Fenchel has also studied the physiology of anaerobic protozoa and their bacterial symbionts, protozoa with endosymbiotic phototrophs, motile behaviour of prokaryotic as well as eukaryotic microbes, and biodiversity and biogeography of protozoa.