Effects of some environmental factors on the shell morphology of testate amoebae (Rhizopoda, Protozoa)

Does microhabitat influence the testate amoebae communities in the Nameri National Park, northeastern India? A tropical forest perspective

The community structure of testate amoebae inhabiting different microhabitats (soil and tree-moss) within a tropical forest biome in Nameri National Park, northeastern India, was investigated. A total of 33 testate amoebae species belonging to 13 genera were identified. Species belonging to the class Lobosea constituted 73% of total testate amoebae density in the soil habitat, whereas the class Filosea constituted the most dominant forms (58%) in the moist tree-moss habitat. The relative abundance of species was higher in the tree-moss habitat compared to the soil habitats of the forest. Although multivariate analysis suggested a significant difference in assemblage patterns between the habitats, the turnover in species (i.e., beta diversity) was insignificant. Species accumulation curves (SAC) constructed using both parametric and non-parametric species richness estimators revealed that the asymptote of species richness was achieved by a low number of sample replicates in both habitats. The temperature and pH of the substratum on testate amoebae distribution patterns suggest the importance of additional background factors on testate amoebae community structure. Further studies involving more biotopes, seasons, and trophic interactions are recommended to document a complete record of testate amoebae diversity and their interactions with environmental gradients in the tropical forest biomes of northeastern India.

Are soil testate amoebae and diatoms useful for forensics?

Two of the main goals of forensic science are (1) to estimate the time since death, or post mortem interval (PMI) and (2) to find the site where a dead body was buried. Soil testate amoebae and diatoms may be useful indicators for these goals. However, the structure and patchiness of the habitat appears to be a main driver for the amoeba and diatom soil communities (e.g., individual density). In case the soil substrate is very dry and nutrient-poor (as in our study), the influence of a dead body on the soil microfaunal community may be superimposed by natural environmental heterogeneity, especially soil moisture content. Further studies are necessary to clarify if protist abundance data are helpful for forensic investigations.

Evaluation of Morphological Characteristics to Delineate Taxa of the Genus Trigonopyxis (Amoebozoa, Arcellinida)

Morphological features are often the only characteristics suitable for identification of taxa in testate amoebae, especially in ecological and palaeoecological studies. However, whereas the morphology of some species is rather stable it may vary considerably in others. Within the order Arcellinida the genus Trigonopyxis with the type species Trigonopyxis arcula is morphologically highly variable. To identify reliable characteristics for morphology-based taxon delineation we investigated variations in shell size, pseudostome diameter and pseudostome form in T. arcula from three different sites of the Ecuadorian Andes, where these characteristics vary even more than previously described. Further, we investigated if morphological characteristics in Trigonopyxis varied with changes in environmental factors. We studied 951 shells of Trigonopyxis collected along an altitudinal gradient with varying abiotic factors. We established a method for characterization of the pseudostome form, which lead to five different morphotypes. Our results suggest that shell size alone is not an appropriate character for taxon delineation but can be used as an indicator for changes in environmental conditions. In contrast, the pseudostome form might be used for taxon delineation, but likely also varies considerably within taxa. Overall, the study provides an overview of the morphological variability of the genus Trigonopyxis.

Taxonomic Implications of Morphological Complexity Within the Testate Amoeba Genus Corythion from the Antarctic Peninsula

Precise and sufficiently detailed morphological taxonomy is vital in biology, for example in the accurate interpretation of ecological and palaeoecological datasets, especially in polar regions, where biodiversity is poor. Testate amoebae on the Antarctic Peninsula (AP) are well-documented and variations in their population size have recently been interpreted as a proxy for microbial productivity changes in response to recent regional climate change. AP testate amoeba assemblages are dominated by a small number of globally ubiquitous taxa. We examine morphological variation in Corythion spp. across the AP, finding clear evidence supporting the presence of two morphospecies. Corythion constricta (Certes 1889) was identified on the AP for the first time and has potentially been previously misidentified. Furthermore, a southerly trend of decreasing average test size in Corythion dubium (Taránek 1881) along the AP suggests adaptive polymorphism, although the precise drivers of this remain unclear, with analysis hindered by limited environmental data. Further work into morphological variation in Corythion is needed elsewhere, alongside molecular analyses, to evaluate the potential for (pseudo)cryptic diversity within the genus. We advocate a parsimonious taxonomical approach that recognises genetic diversity but also examines and develops accurate morphological divisions and descriptions suitable for light microscopy-based ecological and palaeoecological studies.

A contribution to the phylogeny of agglutinating Arcellinida (Amoebozoa) based on SSU rRNA gene sequences

Arcellinid testate amoebae include a wide variety of amoeboid organisms whose test (shell) varies in shape, composition and size. A decade ago, we initiated molecular phylogenetic analyses based on SSU rRNA gene sequences and a taxonomic revision of Arcellinida. However, many lineages within Arcellinida still lack molecular data, and the phylogeny of this group is largely incomplete. In this study, we obtained SSU rRNA gene sequences from seven taxa, of which six have agglutinated shell (Difflugia oblonga, D. labiosa, D. gramen, Mediolus corona, Netzelia wailesi, and N. tuberculata), and one has an entirely proteinaceous shell (Arcella intermedia). All species but Difflugia oblonga branched within the recently erected suborder Sphaerothecina, confirming the synapomorphic value of an oviform or discoid shell. Thus, we propose that species with an oviform or discoid shell currently classified within genus Difflugia must be transferred to other genera, thus continuing the process of taxonomic revision of genus Difflugia, the largest Arcellinida genus. We therefore transferred the current and the previously sequenced oviform Difflugia spp. to Netzelia spp., based on the shared globular/oviform shell shape and their monophyly. Another species, D. labiosa, formed an independent lineage that branched as a sister clade to Arcella spp.; based on the shell morphology and their phylogenetic position, we considered D. labiosa as incertae sedis.

Culture growth of testate amoebae under different silicon concentrations

Testate amoebae with self-secreted siliceous shell platelets ("idiosomes") play an important role in terrestrial silicon (Si) cycles. In this context, Si-dependent culture growth dynamics of idiosomic testate amoebae are of interest. Clonal cultures of idiosomic testate amoebae were analyzed under three different Si concentrations: low (50μmolL^-1), moderate/site-specific (150μmolL^-1) and high Si supply (500μmolL^-1). Food (Saccharomyces cerevisiae) was provided in surplus. (i) Shell size of four different clones of idiosomic testate amoebae either decreased (Trinema galeata, Euglypha filifera cf.), increased (E. rotunda cf.), or did not change (E. rotunda) under the lowest Si concentration (50μmolSiL^-1). (ii) Culture growth of idiosomic Euglypha rotunda was dependent on Si concentration. The more Si available in the culture medium, the earlier the entry into exponential growth phase. (iii) Culture growth of idiosomic Euglypha rotunda was dependent on origin of inoculum. Amoebae previously cultured under a moderate Si concentration revealed highest sustainability in consecutive cultures. Amoebae derived from cultures with high Si concentrations showed rapid culture growth which finished early in consecutive cultures. (iv) Si (diluted in the culture medium) was absorbed by amoebae and fixed in the amoeba shells resulting in decreased Si concentrations.

How discordant morphological and molecular evolution among microorganisms can revise our notions of biodiversity on Earth

Microscopy has revealed tremendous diversity of bacterial and eukaryotic forms. Recent molecular analyses show discordance in estimates of biodiversity between morphological and molecular analyses. Moreover, phylogenetic analyses of the diversity of microbial forms reveal evidence of convergence at scales as deep as interdomain: morphologies shared between bacteria and eukaryotes. Here, we highlight examples of such discordance, focusing on exemplary lineages such as testate amoebae, ciliates, and cyanobacteria. These have long histories of morphological study, enabling deeper analyses on both the molecular and morphological sides. We discuss examples in two main categories: (i) morphologically identical (or highly similar) individuals that are genetically distinct and (ii) morphologically distinct individuals that are genetically the same. We argue that hypotheses about discordance can be tested using the concept of neutral morphologies, or more broadly neutral phenotypes, as a null hypothesis.

Distribution and phylogenetic relationships of freshwater Thaumatomonads with a description of the new species Thaumatomonas coloniensis n. sp

The order Thaumatomonadida includes biflagellated heterotrophic flagellates that form filopodia and typically possess siliceous surface scales. We found thaumatomonads to contribute on average about 5%-10% to flagellate abundance in different benthic habitats. A new species of thaumatomonads, Thaumatomonas coloniensis n. sp., is described on the basis of morphological and molecular biological features. This new species was isolated both from groundwater at Appeldorn near Rees (Germany) and from the Rhine River at Cologne (Germany). We have sequenced the small subunit rRNA (ssu rRNA) gene and a fragment of the large subunit rRNA (lsu rRNA) gene (D3-D5 region) from the isolates of the new species, including the first sequence of a representative of the thaumatomonad genus Gyromitus. In agreement with previous studies, the differences in ribosomal genes of different thaumatomonad species are very small. For understanding the phylogenetic relationships of Thaumatomonadida and to explore their sister group relationships, we have created three sequence data sets (ssu rRNA, partial lsu rRNA, concatenated alignment of both) with the same composition of isolates (from Thaumatomonadida, Euglyphida, Cercomonadidae, and Heteromitidae). According to a Kishino-Hasegawa test, Thaumatomonadida evolved within the Cercozoa as a sister taxon to the Heteromitidae. A possibly close relationship to the Euglyphida, recently grouped together with the Thaumatomonadida in the class Imbricatea/Silicofilosea based on the rRNA data sets was not supported by our analyses.

Phylogenetic analyses of small subunit ribosomal RNA coding regions reveal a monophyletic lineage of euglyphid testate amoebae (Order Euglyphida)

The Testaceafilosia includes amoebae with filopodia and with a proteinaceous, agglutinated or siliceous test. To explore the deeper phylogeny of this group, we sequenced the small subunit ribosomal RNA coding region of 13 species, including the first sequence of an amoeba with an agglutinated test, Pseudodifflugia sp. Phylogenetic analyses using maximum parsimony and maximum likelihood methods as well as neighbor joining method yielded the following results: the order Euglyphida forms a monophyletic lineage with the sarcomonads as sister group. The next related taxa are the Chlorarachnea and the unidentified filose strain N-Por. In agreement with the previous studies the Phytomyxea branch off at the base of this lineage. The Monadofilosa (Testaceafilosia and Sarcomonadea) appear monophyletic. The Testaceafilosia are polyphyletic, because Pseudodifflugia sp. is positioned as the sister taxon to the sarcomonads. Within the order Euglyphida Paulinella branches off first, together with Cyphoderia followed by Tracheleuglypha. In maximum likelihood and neighbor joining analyses, the genus Euglypha is monophyletic. The branching pattern within the order Euglyphida reflects the evolution of shell morphology from simple to complex built test.

Ecology of testate amoebae (Protozoa: Rhizopoda) on peatlands in western Russia with special attention to niche separation in closely related taxa

Testate amoebae (Protozoa: Rhizopoda) are frequently used as indicators of past environmental changes, and the interpretation of fossil assemblages depends upon our knowledge of ecological affinities of taxa in modern environments. A variety of taxonomic approaches have been used in fossil studies, mostly involving grouping of closely related taxa. This paper presents data from peatlands in western Russia relating surface wetness parameters to species occurrence. Relationships between species abundance, water table depth and soil moisture are modelled using weighted averaging, and species niches are calculated as optima and tolerance for these parameters. Niche separation of closely related taxa is examined in detail and it is shown that there is often a gradient of hydrological preference within each group of taxa. Wet to dry gradients include those found in the Trigonopyxis arcula group (T. arcula var. major > T. arcula > T. minuta), the Assulina-Valkanovia group (A. seminulum > A. muscorum > V. elegans), and the Trinema lineare group (T. lineare var. truncatum/ T. lineare > T. lineare var. terricola), all of which are associated with a large to small size gradient. In addition, spined forms within the Euglypha and Placocista genera are shown to consistently occur in wetter habitats than glabrous forms or those with shorter spines. It is concluded that palaeoecological studies should attempt the lowest taxonomic divisions possible within these groups, to maximise the ecological indicator value of the assemblages recorded.