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Additional file 1: Table S1. Number of intracellular bacteria.

Previously, in the first part of publication (Goodkov et al., 2014) we had presented and described the collection of free living freshwater amoeba strains of Amoeba proteus-type (family Amoebidae), the collection being for a long time maintained in the Institute of Cytology RAS, Saint-Petersburg, Russia. This collection is named Amoebae Culture Collection at the Institute of Cytology (ACCIC). In the second part of collection description (the present publication) we quote the full list of amoebae strains maintaining today in the Collection with their passports containing the date of the strain acceptance, whom it was received from, when and where the strain was isolated from, notes, and the full register of articles where these strains were used as research objects (bibliography).

Amoebae Culture Collection at the Institute of Cytology RAS in St. Petersburg (Russia) ACCIC (SPb) was founded in 1960; it includes strains (clones) of large free living freshwater amoebae of Amoeba proteus -type (family Amoebidae). These protists have been extensively used as model organisms in cell biology for almost two centuries. The amoebae strains were originally received from a number of laboratories and collections of cell cultures in many countries; some strains were raised from the samples isolated directly from nature in various regions of the world. Many of the strains in the ACCIC have been thoroughly characterized. In this paper, history of the Collection and its application in different scientific research fields are briefly presented.

A method to synchronize cell cycle in the culture of Amoeba proteus is proposed. Amoeba cells were kept in quail egg albumen and thus having been fed by the pinocytosis, then thoroughly washed from the protein and examined at stained slides in different periods of time after washing. It appeared that practically all the cells on the slide corresponding to certain time after feeding/washing underwent the same stage of cell cycle either interphase or one of the phases of mitosis depending on time. The method of amoebae feeding by the pinocytosis also allows avoiding negative effect of food remains in the cell cytoplasm, thus providing the higher quality of stained slides.

The general morphology, ultrastructure, and development of a new pelobiont protist, Pelomyxa gruberi, have been described. The entire life cycle of this eukaryotic microbe involves an alteration of uni and multinucleate stages and is commonly completed within a year. Reproduction occurs by plasmotomy of multinucleate amoebae: they form division rosettes or divide unequally. Various surface parts of this slowly moving organism characteristically form finger shaped hyaline protrusions. Besides, during the directed monopodial movement, a broad zone of hyaline cytoplasm with slender finger shaped hyaline protrusions is formed at the anterior part of the cell. In multinucleate stages up to 16 or even 32 nuclei of a vesicular type may be counted. Individuals with the highest numbers of nuclei were reported from the southernmost part of the investigated area: the North West Russia. Each nucleus of all life cycle stages is surrounded with microtubules. The structure of the flagellar apparatus differs in individuals of different age. Small uninucleate forms have considerably fewer flagella per cell than do larger or multinucleate amoebae but these may have aflagellated basal bodies submerged into the cytoplasm. In young individuals, undulipodia, where available, emerge from a characteristic flagellar pocket or tunnel. The basal bodies and associated rootlet microtubular derivatives (one radial and one basal) are organized similarly at all life cycle stages. There is a thin walled cylinder in the flagellar transition zone, and an electron dense column above that zone. In the separate non motile undulipodia the arrangement of axoneme microtubules deviates from the typical 9+2 eukaryotic pattern. In the cytoplasm of P. gruberi two types of rod shaped endocytobionts are present: (1) large bacteria with a pronounced longitudinal cleft, and (2) smaller methanogen like bacteria.

Morphology of a pelobiont Pelomyxa binucleata (Gruber, 1884) has been studied using light and electron microscopy. The organisation of P. binucleata has been shown to differ from that of P. palustris, P. prima and P. corona. The cell surface of P. binucleata is represented by the plasma membrane with a thin but distinct layer of non structured glycocalyx. The ectoplasm, containing a network of fine fibrils, is separated from the endoplasm with a boundary layer of cisterns and reticulum channels. The flagella are poorly motile. The axoneme has a non stable set of microtubules. A short kinetosome is about 200 nm long; the transition zone, also about 200 nm long, is situated above the cell border and contains a transition cylinder. Microtubular rootlet and microtubular cone are absent. From the kinetosome, almost in parallel to its longitudinal axis, 35 40 microtubules arranged in 3 4 rows start. Right below the kinetosome base they bend at a right angle to its longitudinal axis and pass further as a bundle in the ectoplasm below the cell surface. These microtubules do not penetrate into the endoplasm. The system of structural vacuoles is poorly developed. Glycogen bodies are rounded, smooth and surrounded with flattened reticulum cisterns. The set of endocytobionts includes two kinds of rod like bacteria: thick bacteria with a poorly developed cleft and thin Gram positive ones. The length of both kinds of bacteria may be 30 μm and more. The nuclear envelope bears a multilaminar layer on its outer surface. The nucleolus is fragmented and situated at the centre of the nucleus. The species composition of the genus Pelomyxa Greeff, 1874 is discussed in the context of revision of outdated ideas about its monotypy. Morphology of its representatives is considered in comparative aspect.

A new species of multinucleate pelobionts, Pelomyxa corona, is described. Morphology of the amoebae has been studied with the use of the light and the transmission electron microscope. The cells of P. corona are rounded. The cytoplasm is clearly differentiated into the marginal hyaloplasm and the endoplasm. Numerous hyaline pseudopodia of approximately equal length make the amoeba look like a crown, which is reflected in the specific name. Ultrastructurally P. corona is rather similar to P. palustris, but a number of unique characters allows a reliable differentiation of these two species. The study of P. corona revealed a well developed structured glycocalyx, the dictyosomes of the Golgi apparatus and fine pseudopodia armoured with bundles of microtubules. One species out of the set of the symbiotic bacteria characteristic of P. palustris is lacking in P. corona, but another bacterial species is present which has not been reported from pelobionts so far. Flagella have not been found.

Detailed analyses of the diversity of locomotive forms among naked lobose amoebae (Lobosea, Gymnamoebia) allow us to construct a typology consisting of 19 morphotypes encompassing all known species of the subclass Gymnamoebia. We identify a morphotype as a general pattern of the morphodynamic organisation of the locomotive form of an amoeba. This system of morphotypes is not a taxonomical one and does not duplicate existing systematic classifications of the respective taxa, although some morphotypes correspond well to the systematic groups of gymnamoebae. Morphotypes are illustrated with schematic drawings and accompanied with brief diagnoses. Selected representatives of different morphotypes are illustrated with photomicrographs. The proposed system of morphotypes seems to be a useful tool for description of gymnamoebae and for elaboration of an iconographic key to gymnamoebae. It can be a helpful tool for preliminary determination of naked amoebae (especially in ecological studies).

A large freshwater multinucleate amoeba Chaos illinoisense (Amoebidae), previously only recorded in natural collection by Kudo (1950, 1951) from a small pond in Illinois, Central North America, has been rediscovered in backwaters of the River Luga, North-West Russia. Amoebae were cultured, cloned, and studied using lightand electron-microscopic techniques. This species is the only currently known cyst-forming representative of the genus. Numerous cytoplasmic crystals is a conspicuous characteristic of the species; they appear in two forms: platelike and bipyramidal. Trophozoites contain several hundred spherical nuclei of granular type. The fibrous inner nuclear lamina with loosely organised honeycomb-like structure was revealed as well as distinct mitochondrial heteromorphism. Two-layered cell surface coat with filamentous appearance is demonstrated. Current justification of the specific diagnosis is presented.