Heterotrophic Flagellates from Freshwater and Soil Habitats in Subtropical China (Wuhan Area, Hubei Province)

We studied the diversity of heterotrophic flagellates from the sandy sediments of the Yangtze River, sandy and silty sediments of Donghu Lake, soil, moss and litter from the Luojiashan and Moshan hills as well as litter from the floodplain near Donghu Lake in April 2010. Sixty-seven heterotrophic flagellate species were identified by means of phase and interference contrast light microscopy and transmission electron microscopy. The majority of the observed flagellates were bacterivorous. Local species richness of river sediment communities was significantly lower than that of lake sediments and terrestrial habitats. The communities from the terrestrial habitats were more heterogeneous than those from freshwater sediments. Common species for the aquatic habitats were Rhynchomonas nasuta, Paraphysomonas sp., Neobodo designis, N. curvifilis, Bodo saltans and Spumella spp. In the soils only Spumella spp. was found in the majority of samples. Most characteristic taxa for the lake sediments were Helkesimastix faecicola, Petalomonas minuta, P. pusilla, Diphylleia rotans, Amastigomonas caudata. Amoeboflagellates such as Cercomonas angustus, C. granulifera, Paracercomonas crassicauda were specific for the terrestrial habitats. There were no specific taxa in the river sediments. The majority of the heterotrophic flagellates identified in this survey have been noted in China earlier. They are common (and usually predominant) for other regions in both freshwater and soil habitats

Evolutionary Relationship of the Scale-Bearing Kraken (incertae sedis, Monadofilosa, Cercozoa, Rhizaria): Combining Ultrastructure Data and a Two-Gene Phylogeny

The genus Kraken represents a distinct lineage of filose amoebae within the Cercozoa. Currently a single species, Kraken carinae, has been described. SSU rDNA phylogeny showed an affiliation to the Cercomonadida, branching with weak support at its base, close to Paracercomonas, Metabolomonas, and Brevimastigomonas. Light microscopical analyses showed several unique features of the genus Kraken, but ultrastructure data were lacking. In this study, K. carinae has been studied by electron microscopy, these data conjoined with a two-gene phylogeny were used to give more insight into the evolutionary relationship of the genus Kraken within Cercozoa. The data confirmed the absence of flagella, but also showed novel characteristics, such as the presence of extrusomes, osmiophilic bodies, and mitochondria with flat cristae. Surprising was the presence of single-tier scales which are carried by cell outgrowths, much of what is expected of the last common ancestor of the class Imbricatea. The phylogenetic analyses however confirmed previous results, indicating Kraken as a sister group to Paracercomonas in Sarcomonadea with an increased but still low support of 0.98 PP/63 BP. Based on the unique features of Kraken we establish the Krakenidae fam. nov. that we, due to contradictory results in morphology and phylogeny, assign incertae sedis, Monadofilosa. (C) 2017 Elsevier GmbH. All rights reserved

Molecular Comparisons of Freshwater and Marine Isolates of the Same Morphospecies of Heterotrophic Flagellates

Heterotrophic flagellates are key components of all ecosystems. Understanding the patterns of biodiversity of these organisms is thus particularly important. Here we analyzed the intraspecific diversity of 10 morphospecies of heterotrophic flagellates comprising representatives of the Apusozoa (2 morphospecies) and Kinetoplastea (8 morphospecies), all belonging to the most common flagellates with worldwide distribution. Most morphospecies showed a mixing of lineages isolated from diverse habitats, indicating that some lineages of these morphospecies had been able to colonize different habitats several times. Furthermore, our results revealed remarkable levels of genetic divergence within most of the morphospecies studied, underlining the difficulty of correctly determining species by means of morphology alone. Many cryptic or pseudocryptic species seem to occur. Our results revealed clear divergence between marine and freshwater lineages of the morphospecies Ancyromonas sigmoides, showing that freshwater lineages have not been able to colonize marine environments and marine lineages have not been able to colonize freshwater environments for a long time

An evaluation of the use of the LSU rRNA D1-D5 domain for DNA-based taxonomy of eukaryotic protists

Diagnostic signature DNA sequences are important tools for the identification of species. There is an active debate in the literature on the choice of the best markers applicable for a broad range of organisms. Protists have seldom been included in these evaluations. Mitochondrial gene sequences are inappropriate for protists since several groups do not possess mitochondria. Here we studied the application of the large subunit (LSU) rRNA gene fragments (D1-D5) regarding their usefulness to discriminate between a wide range of heterotrophic nanoflagellates. Phylogenetic analyses based on the LSU rRNA fragments showed similar results compared to phylogenetic trees based on the small subunit (SSU) rRNA. The data set indicates the power of the use of the D1-D5 region as a marker for a DNA-based taxonomy. Our results, together with the available sequences in Genbank, form a comprehensive database for unicellular eukaryotes, especially heterotrophic flagellates. It is now possible to assign new sequences to the different groups of heterotrophic flagellates which we have tested for different closely related Cercomonas and Paracercomonas strains from groundwater

Ecologically relevant choanoflagellates collected from hypoxic water masses of the Baltic Sea have untypical mitochondrial cristae

Abstract Background Protist communities inhabiting oxygen depleted waters have so far been characterized through both microscopical observations and sequence based techniques. However, the lack of cultures for abundant taxa severely hampers our knowledge on the morphology, ecology and energy metabolism of hypoxic protists. Cultivation of such protists has been unsuccessful in most cases, and has never yet succeeded for choanoflagellates, even though these small bacterivorous flagellates are known to be ecologically relevant components of aquatic protist communities. Results Quantitative data for choanoflagellates and the vertical distribution of Codosiga spp. at Gotland and Landsort Deep (Baltic Sea) indicate its preference for oxygen-depleted zones. Strains isolated and cultivated from these habitats revealed ultrastructural peculiarities such as mitochondria showing tubular cristae never seen before for choanoflagellates, and the first observation of intracellular prokaryotes in choanoflagellates. Analysis of their partial 28S rRNA gene sequence complements the description of two new species, Codosiga minima n. sp. and C. balthica n. sp. These are closely related with but well separated from C. gracilis (C. balthica and C. minima p-distance to C. gracilis 4.8% and 11.6%, respectively). In phylogenetic analyses the 18S rRNA gene sequences branch off together with environmental sequences from hypoxic habitats resulting in a wide cluster of hypoxic Codosiga relatives so far only known from environmental sequencing approaches. Conclusions Here, we establish the morphological and ultrastructural identity of an environmental choanoflagellate lineage. Data from microscopical observations, supplemented by findings from previous culture-independent methods, indicate that C. balthica is likely an ecologically relevant player of Baltic Sea hypoxic waters. The possession of derived mitochondria could be an adaptation to life in hypoxic environments periodically influenced by small-scale mixing events and changing oxygen content allowing the reduction of oxygen consuming components. In view of the intricacy of isolating and cultivating choanoflagellates, the two new cultured species represent an important advance to the understanding of the ecology of this group, and mechanisms of adaptations to hypoxia in protists in general.</p

First finding of free-living representatives of Prokinetoplastina and their nuclear and mitochondrial genomes

Abstract Kinetoplastids are heterotrophic flagellated protists, including important parasites of humans and animals (trypanosomatids), and ecologically important free-living bacterial consumers (bodonids). Phylogenies have shown that the earliest-branching kinetoplastids are all parasites or obligate endosymbionts, whose highly-derived state makes reconstructing the ancestral state of the group challenging. We have isolated new strains of unusual free-living flagellates that molecular phylogeny shows to be most closely related to endosymbiotic and parasitic Perkinsela and Ichthyobodo species that, together with unidentified environmental sequences, form the clade at the base of kinetoplastids. These strains are therefore the first described free-living prokinetoplastids, and potentially very informative in understanding the evolution and ancestral states of morphological and molecular characteristics described in other kinetoplastids. Overall, we find that these organisms morphologically and ultrastructurally resemble some free-living bodonids and diplonemids, and possess nuclear genomes with few introns, polycistronic mRNA expression, high coding density, and derived traits shared with other kinetoplastids. Their genetic repertoires are more diverse than the best-studied free-living kinetoplastids, which is likely a reflection of their higher metabolic potential. Mitochondrial RNAs of these new species undergo the most extensive U insertion/deletion editing reported so far, and limited deaminative C-to-U and A-to-I editing, but we find no evidence for mitochondrial trans-splicing

Heterotrophic Flagellates from Freshwater and Soil Habitats in Subtropical China (Wuhan Area, Hubei Province)

We studied the diversity of heterotrophic flagellates from the sandy sediments of the Yangtze River, sandy and silty sediments of Donghu Lake, soil, moss and litter from the Luojiashan and Moshan hills as well as litter from the floodplain near Donghu Lake in April 2010. Sixty-seven heterotrophic flagellate species were identified by means of phase and interference contrast light microscopy and transmission electron microscopy. The majority of the observed flagellates were bacterivorous. Local species richness of river sediment communities was significantly lower than that of lake sediments and terrestrial habitats. The communities from the terrestrial habitats were more heterogeneous than those from freshwater sediments. Common species for the aquatic habitats were Rhynchomonas nasuta, Paraphysomonas sp., Neobodo designis, N. curvifilis, Bodo saltans and Spumella spp. In the soils only Spumella spp. was found in the majority of samples. Most characteristic taxa for the lake sediments were Helkesimastix faecicola, Petalomonas minuta, P. pusilla, Diphylleia rotans, Amastigomonas caudata. Amoeboflagellates such as Cercomonas angustus, C. granulifera, Paracercomonas crassicauda were specific for the terrestrial habitats. There were no specific taxa in the river sediments. The majority of the heterotrophic flagellates identified in this survey have been noted in China earlier. They are common (and usually predominant) for other regions in both freshwater and soil habitats