The characteristics of micro-scale vertical heterogeneity of physicochemical parameters, photosynthetic pigments’ content and populations of phototrophic microbial plankton in four karst lakes of the Mari-Chodra NP (rep. Mari El), the Bolshoy Kichier, Cherny Kichier, Shungaldan and the Blue Oxbow, are presented on the basis of summer surveys of 2006, 2007 and 2009. According to our data, two lakes, Shungaldan and Cherny Kichier are, meromictic waterbodies of crenogenic type; the Lake Bolshoy Kichier is holomictic with stable summer stratification and anoxic hypolimnion. The Lake Blue Oxbow occupies an intermediate position, and, apparently, is irregularly mixing. The physicochemical conditions and composition of the phototrophic plankton communities of the chemocline zone of the two previously studied lakes, Bolshoy and Cherny Kichier, have remained stable over the past 20-35 years. Significant development of anoxygenic phototrophic bacteria was found in two lakes in which data on their development were previously absent. In the bacterial plates of meromictic lakes, the concentration of bacteriochlorophyll d, the pigment of green phototrophic bacteria, reaches some mg per liter.

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“Filamentous anoxygenic phototrophs” or “green non-sulfur bacteria” form a distinct lineage, order Chloroflexales (Chloroflexia: Chloroflexi) in broad polyphyletic group of anoxygenic phototrophic bacteria. Filamentous anoxygenic phototrophic bacteria have apparently important, though not fully understood functions in contemporary ecosystems and perhaps were much more significant in the Archaean. However, since their discovery in hot spring mats in the late 1960s, the extremophilic species of thermal, hypersaline and/or hyperalcaline habitats remain the most studied representatives of the lineage. In this overview, we show our representation of the history of finding and research of filamentous anoxygenic phototrophs, and current situation with their taxonomy, phylogeny and diversity. Some problems and uncertainties in these fields are also discussed. The special section is dedicated to the discovery and research of this group in the Volga River basin. Due to the small number of studies, the exact distribution of filamentous anoxygenic phototrophic bacteria in the region is unknown. For example, in small stratified lakes with high humic and/or ferruginous water in the basins of the Oka and the Upper Volga the development of planktonic filamentous anoxygenic phototrophs is very likely. Besides, the development of Chloroflexales, including new species, is quite expected in the microbial mats of saline rivers and hypersaline lakes of the Lower Volga region. Further progress in the field will be possible only with the use of molecular methods along or preferably in combination with traditional methods (polyphasic approach). Since their role in communities is far from elucidated, further studies of FAP may also provide new opportunities in the field of microbial biotechnology.