High diversity of the ‘Spumella‐like’ flagellates: an investigation based on the SSU rRNA gene sequences of isolates from habitats located in six different geographic regions

Abstract

We isolated 28 strains of 'Spumella-like' flagellates from different freshwater and soil habitats in Austria, People's Republic of China, Nepal, New Zealand, Uganda, Kenya, Tanzania and Hawaii by use of a modified filtration-acclimatization method. 'Spumella-like' flagellates were found in all of the samples and were often among the dominant bacterivorous flagellates in the respective environments. The small subunit ribosomal RNA (SSU rRNA) gene sequence of the isolates was determined and aligned with previously published sequences of members belonging to the Chrysophyceae sensu stricto. Phylogenetic analysis of the 28 new sequences confirmed their position within the Chrysophyceae sensu stricto and positioned them within different clades. Most of the sequences grouped within clade C and formed several subclusters separated from each other by green taxa including flagellates belonging to Ochromonas, Dinobryon, Poterioochromonas and others. All soil isolates clustered together (subcluster C1) with the soil strain Spumella elongata and the undescribed soil strain 'Spumella danica'. Aquatic isolates were affiliated with at least two branches (C2 and C3). Sequence similarity to the closest related member of the Chrysophyceae ranged between 92% and 99.6%, sequence divergence among the 'Spumella-like' flagellates was as high as 10%. We conclude that (i) the 'Spumella-like' flagellates are a diverse group both in terms of sequence dissimilarity between isolates and in terms of the number of genotypes, (ii) Spumella and Ochromonas are polyphyletic, and (iii) based on the SSU rRNA gene no biogeographical restriction of certain branches could be observed even though different ecotypes may be represented by the same genotype.

Genetic diversity in chrysophytes: Comparison of different gene markers

“…Most strains were isolated during sampling campaigns in 2002 and 2006. Isolation and maintenance of strains were conducted as already described in Boenigk et al (2005). For details on origin of the isolates see table S1.…”

“…Molecular analyses revealed that some morphotypes are in fact polyphyletic and form separate clusters within the chrysophytes, showing that classification solely based on morphology is sometimes misleading (grossmann et al 2016). One good example are colorless, nonscaled chrysophytes which are genetically far more diverse than morphology reflects (Boenigk et al 2005;Pfandl et al 2009;findenig et al 2010). Several new genera were recently erected mainly based on molecular identification, since light microscopy could not distinguish between isolates belonging to different phylogenetic lineages (grossmann et al 2016).…”

Cellular identity of an 18S rRNA gene sequence clade within the class Kinetoplastea: the novel genus Actuariola gen. nov. (Neobodonida) with description of the type species Actuariola framvarensis sp. nov.

“…The basal medium for the cultivation and isolation of the flagellate strain was an inorganic basal medium containing (g l O,3?857;KCl,0?469;and NaCl,19?705. The isolation protocol followed the approach of Boenigk et al (2005). The original sample was diluted to an abundance of 0?5 flagellates ml 21 , transferred to 24-well cell culture plates (1 ml per well) and supplemented with various food sources, i.e.…”

Improved Methodology for Identification of Protists and Microalgae from Plankton Samples Preserved in Lugol's Iodine Solution: Combining Microscopic Analysis with Single-Cell PCR

“…The proposed method is particularly well suited to detect minute genotypic differences between individuals of the same morphospecies. Genotypic variation within nominal protist taxa is of special interest with respect to the debate on microbial distribution and biogeographies (3,22,23,33). We applied our method to check for differences in the dominant genotypes in protist taxa affiliated with the same morphospecies but originating from different habitats or seasons.…”