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.

Background The family Trypanosomatidae encompasses parasitic flagellates, some of which cause serious vector-transmitted diseases of humans and domestic animals. However, insect-restricted parasites represent the ancestral and most diverse group within the family. They display a range of unusual features and their study can provide insights into the biology of human pathogens. Here we describe Vickermania, a new genus of fly midgut-dwelling parasites that bear two flagella in contrast to other trypanosomatids, which are unambiguously uniflagellate. Results Vickermania has an odd cell cycle, in which shortly after the division the uniflagellate cell starts growing a new flagellum attached to the old one and preserves their contact until the late cytokinesis. The flagella connect to each other throughout their whole length and carry a peculiar seizing structure with a paddle-like apex and two lateral extensions at their tip. In contrast to typical trypanosomatids, which attach to the insect host’s intestinal wall, Vickermania is separated from it by a continuous peritrophic membrane and resides freely in the fly midgut lumen. Conclusions We propose that Vickermania developed a survival strategy that relies on constant movement preventing discharge from the host gut due to intestinal peristalsis. Since these parasites cannot attach to the midgut wall, they were forced to shorten the period of impaired motility when two separate flagella in dividing cells interfere with each other. The connection between the flagella ensures their coordinate movement until the separation of the daughter cells. We propose that Trypanosoma brucei, a severe human pathogen, during its development in the tsetse fly midgut faces the same conditions and follows the same strategy as Vickermania by employing an analogous adaptation, the flagellar connector.

Self-fluorescence of light-harvesting complex is a powerful tool for investigation of living photosynthetic microorganisms. As the physiological state of single cells of such microorganisms is closely related to the operation and activity of photosynthetic system, any variations in spectroscopic properties of their self-fluorescence indicate the changes in their physiological state. In this chapter, we present several applications of confocal laser scanning microscopy (CLSM) for investigation of living photosynthetic cells. A set of ordinary CLSM techniques will be applied for studying of cyanobacteria (or blue-green algae) such as 3D imaging, spectral imaging, microscopic spectroscopy, and fluorescence recovery after photobleaching (FRAP). Cyanobacteria were chosen as a model microorganism due to their great importance for different scientific and biotechnological applications. Cyanobacteria are the most ancient photosynthetic microorganisms on Earth. Nowadays, cyanobacteria are one of the most wide-spreaded organisms in nature, and the ecological aspect in their investigation is quite valuable. On the other hand, thousand strains belonging to different species are cultivated in biolaboratories all over the world for different biotechnological applications such as biofuel cells, food production, pharmaceuticals, fertilizers, etc. Thus, the noninvasive spectroscopic methods are quite important for monitoring of physiological state of cyanobacterial cultures and other photosynthetic microorganisms.

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