This revision of the classification of eukaryotes follows that of Adl et al., 2012 [ J. Euk. Microbiol . 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.

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In this work, we present reisolation and redescription of Balantidium duodeni Stein, 1867 from the European common brown frog Rana temporaria Linnaeus, 1758 using light and electron microscopy. This species has a unique morphological feature--its cells are flattened along the dorsoventral axis. Because of its unique morphology and localization (duodenum) in the gastrointestinal tract of the host, it has been proposed to recognize B. duodeni as a member of separate genus, Balantidiopsis Penard, 1922. Molecular phylogenetic analysis demonstrates it to be close to the type species Balantidium entozoon (Ehrenberg, 1838). We argue that its placement into separate genus is not substantiated. We also propose to reinstate the genus Balantioides Alexeieff, 1931 with the type species Paramecium coli (Malmstein, 1857). The recently proposed generic name for this taxon, Neobalantidium Pomajbíková et al., 2013, is a junior synonym of the previously recognized name.

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In this chapter, a novel technique for investigation of natural and laboratory cyanobacterial cultures is presented. The technique is based on a strict relation between the intrinsic singlecell fluorescence emission spectra of cyanobacteria and the physiological state of the whole culture. It will be shown else that the single-cell fluorescence spectra for different species are steady enough to conduct a taxonomic analysis of cyanobacterial cultures based on a common statistical data evaluation among the parameters extracted from a set of such spectra. Several examples are given to illustrate the power and simplicity of a new technique, which can become a promising tool for automation of production in the cyanobacterial biotechnology, as well as give a valuable contribution to the development of innovative approaches in environmental monitoring of harmful algal blooms.