Abstract
Summary The presence of aerobic anoxygenic phototrophs (AAPs) was recently reported from various marine environments; however, there is little information regarding their distribution in fresh waters. We surveyed a number of freshwater systems in central Europe, by infra‐red fluorometry, infra‐red epifluorescence microscopy, fluorescence emission spectroscopy and pigment analyses. AAPs were found to be abundant in several oligotrophic and mesotrophic lakes (50–400 ng of bacteriochlorophyll a l −1 , 10–80% of bacterial biomass), while in more eutrophized water bodies they represented a negligible part of the total microbial community (