The protozoan fauna and species richness in the pelagic zone of 15 Japanese lakes were investigated in 1996 using polyurethane foam (PF) substrates. The most common species were flagellates, such as Cryptomonas erosa, Oikomonas termo, and Pleuromonas jaculans. Cinetochilum margaritaceum and Actinophrys sol were the most common species of the Ciliata and Sarcodina, respectively. The similarity of species occurrence was calculated from presence/absence data, but this revealed no clear trend with respect to the influence of lake properties such as trophic state, surface area, or mean depth. The occurrence pattern of Protozoa was most similar in L. Chuzenji and L. Biwa (north basin), two oligomesotrophic natural lakes. Log species richness was positively correlated with log total phosphorus (r = 0.54, P < 0.05) and negatively with log mean depth (r = −0.58, P < 0.05). The diversity index (Margalef's formula), highly correlated with the total species number (r = 0.85, P < 0.01), was negatively correlated with log lake area (r = −0.71, P < 0.01). The logarithm of Phytomastigophora number was positively correlated with log total nitrogen (r = 0.53, P < 0.05), and the logarithm of Ciliata number was negatively correlated with log lake area (r = −0.55, P < 0.05). The species richness of Protozoa on PF substrates was determined by both the nutrient status of the lake and the distance from the location of the suspended PF substrate to the lake bottom or shore.
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