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A contribution to the phylogeny of agglutinating Arcellinida (Amoebozoa) based on SSU rRNA gene sequences
Abstract
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.
... The cluster analysis further divides the basal process shape group between the Elongate (30%) and Ovoid (69%) clusters. This distinction of taxa based on a simplified morphological descriptor reliably represented the cluster assignment (e.g., elongatetype taxa were assigned to the Elongate cluster); however, several exceptions exist: D. acuminata, D. capreolata, Netzelia gramen (Penard 1902) Gomaa et al. (2017), D. globulosa and Difflugia angulostoma Gauthier-Lièvre and Thomas (1958) (Figure 7). Cluster analysis divides these taxa into several clusters. ...
... Wiik et al. (2015) also observed coincident increases in C. tricuspis (i.e., N. gramen), planktic diatoms and Daphnia sp., in response to increasing eutrophication of a small marl lake, Cunswick Tarn (United Kingdom). Interestingly, Han et al. (2008Han et al. ( , 2011 described the feeding agility and wide prey range of several planktic Arcellinida taxa including N. tuberspinifera, which is morphologically and phylogenetically related to N. corona (Gomaa et al., 2017) which is assigned to the spherical cluster (Figure 7). Taking these points together, it is likely that the observed increase in the spherical cluster in our study reflects the expansion of planktic and epibiotic life strategies, both for Arcellinida and their prey, driven by the expansion of canopy forming macrophyte forming denser stands in the shallower waters. ...
... The existence of an ecological separation between taxa in the spherical (i.e., planktic or epibiotic) and elongate cluster (i.e., benthic) is mirrored by differences in their phylogenetic placement. Molecular barcoding results demonstrate that spherical cluster taxa (e.g., Netzelia sp.) previously classified as part of the genus Difflugia in fact belong to the family Netzellidae and were assigned to the genus Netzelia (Kosakyan et al., 2016;Blandenier et al., 2017;Gomaa et al., 2017). The genetic divergence between these two groups could reflect a speciation event related to divergent life habits (i.e., planktic/epibiotic vs. benthic; Weisse, 2008). ...
We review the potential for applying traits-based approaches to freshwater testate amoeba, a diverse protist group that are abundant in lakes and are valuable ecological indicators. We investigated the efficacy of geometric morphometric analysis to define Arcellinida test size and shape indices that could summarize freshwater testate amoeba community dynamics along a temporal gradient of eutrophication in Loch Leven, Scotland (United Kingdom). A cluster analysis of test size and shape indices yielded three clusters, each dominated by a single shape: elongate, spherical and ovoid. When plotted stratigraphically, we observed increases in spherical tests, decreases in elongate tests and shrinking of test size coeval with eutrophication in Loch Leven. Decreases in the elongate cluster may reflect benthic conditions with reduced oxygen levels, while increases in the spherical cluster are likely associated with an expanding macrophyte community that promoted pelagic and epibiotic life habits. Shrinking of test size may be a stress response to eutrophication and/or warming temperatures. Tracking community dynamics using test size and shape indices was found to be as effective as using species-based approaches to summarize key palaeolimnological changes, with the added benefits of being free from taxonomic bias and error. The approach thus shows significant potential for future studies of aquatic community change in nutrient impacted lakes.
... Mulot et al. (2017) demonstrated that test shape and pore numbers varied with environmental conditions in wild and cultured populations of Hyalosphenia papilio Leidy, 1874. Jennings (1916, in an early study of a clonal culture of Difflugia corona (now Netzelia corona (Wallich, 1864) Gomaa et al., 2017), observed a variation in both number and placement of spines that was independent of environmental conditions. Porfírio-Sousa et al. (2017) observed very little variability in the test or aperture diameter in clonal cultures of Arcella intermedia, but found that wild populations occupied a distinct morphometric space compared to clonal populations, corroborating previous studies (Wanner, 1999). ...
... Centroid size can also be used to characterise members of the "Lanceolate" clade as D. lanceolata has a smaller average centroid size (centroid size < 300; Appendix C Table C.1; Fig. 3). We note that the sequenced specimen of D. oblonga (small morphotype) from Gomaa et al. (2017) and Lahr et al. (2019) falls within the centroid size and PC1 score ranges of the "Lanceolate" clade rather than the "Pyriform" clade (Fig. 3). ...
... Our NADH phylogenetic tree replicates the global topology of the 18S rRNA phylogenetic reconstruction of Gomaa et al. (2017) and Lahr et al. (2019) and the NADH phylogenetic reconstruction of Blandenier et al. (2017). They all show Arcellinida as monophyletic containing three well resolved infraorders: Sphaerothecina, Hyalospheniformes and Longithecina. ...
Arcellinida (lobose testate amoebae) are abundant and diverse in many ecosystems, especially in moist to aquatic environments. Molecular phylogeny has shown that overall test morphology (e.g., spherical or elongate) is generally conserved in Arcellinida lineages, but the taxonomic value of other traits (e.g., size, ornamentation, mixotrophy/heterotrophy metabolism type) has not been systematically evaluated. Morphological and physiological traits that correspond to genetic differences likely represent adaptive traits of ecological significance. We combined high-resolution phylogenetics (NAD9-NAD7 genes) and advanced morphometrics to assess the phylogenetic signal of morphological traits of a group of elongate Difflugia species (Arcellinida). The phylogenetic analyses revealed two clades which could be reliably separated by test size and the presence/absence of mixotrophy. Differences in test size may reflect trophic level, with smaller organisms occupying lower trophic levels. In addition to having larger tests, elongate mixotrophic Difflugia are characterised by wide, flat bases and an inflation of the lower two thirds of their test. These morphological traits may provide additional volume for endosymbionts and/or increased surface area to aid light transmission. Our results showcase greater diversity within the elongate Difflugia and highlight morphological traits of ecological and evolutionary significance.
... Mulot et al. (2017) demonstrated that test shape and pore numbers varied with environmental conditions in wild and cultured populations of Hyalosphenia papilio Leidy, 1874. Jennings (1916, in an early study of a clonal culture of Difflugia corona (now Netzelia corona (Wallich, 1864) Gomaa et al., 2017), observed a variation in both number and placement of spines that was independent of environmental conditions. Porfírio-Sousa et al. (2017) observed very little variability in the test or aperture diameter in clonal cultures of Arcella intermedia, but found that wild populations occupied a distinct morphometric space compared to clonal populations, corroborating previous studies (Wanner, 1999). ...
... Centroid size can also be used to characterise members of the "Lanceolate" clade as D. lanceolata has a smaller average centroid size (centroid size < 300; Appendix C Table C.1; Fig. 3). We note that the sequenced specimen of D. oblonga (small morphotype) from Gomaa et al. (2017) and Lahr et al. (2019) falls within the centroid size and PC1 score ranges of the "Lanceolate" clade rather than the "Pyriform" clade (Fig. 3). ...
... Our NADH phylogenetic tree replicates the global topology of the 18S rRNA phylogenetic reconstruction of Gomaa et al. (2017) and Lahr et al. (2019) and the NADH phylogenetic reconstruction of Blandenier et al. (2017). They all show Arcellinida as monophyletic containing three well resolved infraorders: Sphaerothecina, Hyalospheniformes and Longithecina. ...
Recent molecular phylogenies of the Arcellinida have demonstrated significant issues with morphology-based taxonomies and the need to incorporate insights from their ecology and evolutionary history. We summarize our current understanding of the relationship between freshwater Arcellinida test morphology, ecology and phylogenetic placement. We draw on the insights from two studies of the ‘ECOTRAIT’ project – an EU funded project examining the association between lobose testate amoebae ecology and morphology on both temporal and spatial scales.
The excellent preservation potential of Arcellinida tests in lake sediments provides researchers with an effective tool to characterize a range of environmental changes (e.g., nutrient enrichment) on the scale of decades to millennia. Biometric tools (e.g., geometric morphometrics) can be used to quantify morphological variability independent of size variability, whilst multivariate statistical techniques can be used to test for relationships between morphology and ecological change. We combine paleoecological approaches with biometric analysis to illustrate a potential link between life habit (e.g., benthic, epibiotic, planktic) and Arcellinida test morphology.
Recent results of molecular phylogenies have demonstrated that the genus Difflugia is paraphyletic. Taxa with spherical tests form a distinct branch from elongated taxa. We present new molecular barcoding results using the NAD9/NAD7 (mitochondrial nicotinamide adenine dinucleotidedehydrogenase gene) gene marker on elongated Difflugia taxa. The resulting phylogeny demonstrates there might exist another distinct branch within the difflugids. We support this inference with the results from test morphological analysis.
... Testate amoebae were already described in Neoproterozoic rocks from Brazil (Morais et al., 2017), however, no similar specimen was described until now. Additionally, tests in Netzelia muriformis and N. tuberculata are constructed of autogenous siliceous elements and possess a lobate opening with 3-8 indentations (Gomaa et al., 2017). Despite these discrepancies, phylogenomic reconstructions suggest that major lineages of testate amoebae were already diversified during the Neoproterozoic, which may suggest that the specimens reported here could be related to hypothetical ancestors for Netzelia (Lahr et al., 2019). ...
... The two larger specimens are reminiscent of the small hollow aperturate spherical tests of the extant species of testate amoebae Netzelia muriformis and N. tuberculata (Gauthier-Lièvre and Thomas, 1960;Owen and Jones, 1976), which have small regular rounded protuberances giving them a raspberry-like outline. The extant organisms differ, however, in being composed of endogenous siliceous elements (Gomaa et al., 2017) and having lobate openings with three to eight indentations (Gauthier-Lièvre and Thomas, 1960). ...
Acritarchs, a polyphyletic group of acid-resistant organic-walled microfossils, dominate the eukaryotic microfossil record in the Proterozoic (2500–541 Ma) yet exhibit significant reduction in diversity and size at the transition to the Phanerozoic (541–520 Ma). Despite the difficulty of tracing phylogenetic relationships among acritarchs, changes in their complexity and diversity through time have allowed their use in paleoecological and biostratigraphic schemes. The Doushantuo-Pertatataka Ediacaran acritarch assemblage, for example, is usually considered as restricted to the early Ediacaran between 635 and 580 Ma. But similar, diverse acritarchs have been recovered from younger rocks in Mongolia and Arctic Siberia and are now reported here from phosphatized horizons of the upper Bocaina Formation (ca. 555 Ma), Corumbá Group, SW Brazil. In the overlying black limestones and shales of the latest Ediacaran Tamengo Formation (542 Ma) acritarch diversity is low, but the skeletal metazoans Cloudina and Corumbella are abundant. The Bocaina acritarch assemblage shares forms referable to the genera Leiosphaeridia, Tanarium, Asseserium and Megasphaera with the Doushantuo-Pertatataka assemblage, but also includes specimens similar to the Phanerozoic genus Archaeodiscina in addition to two new complex acritarchs. The first is covered by rounded low conical bumps, similar to Eotylotopalla but differs in having a distinct opening suggestive of greater (multicellular?) complexity. The second, identified here as Morphotype 1, is a double-walled acanthomorph acritarch with scattered cylindrical processes between the walls. The contrast in acritarch diversity and abundance between the Bocaina and Tamengo formations is likely due in part to paleoenvironmental and taphonomic differences (absence of the phosphatization window in the latter), as well as to the appearance of both suspension-feeding skeletal metazoans (Cloudina and Corumbella). The occurrence of Doushantuo-Pertatataka acritarchs in SW Brazil, northern Mongolia, and Arctic Siberia extend the biostratigraphic range of this assemblage up to the terminal Ediacaran Cloudina biozone.
... Recently, Ndayishimiye et al. (2019) developed temperature transfer functions of testate amoebae on freshwater ecosystems across China to gain insight into the ecological integrity and vulnerability to global warming. Netzelia tuberspinifera (basionym Difflugia tuberspinifera) is an endemic sensitive species of East Asia (Yang et al., 2004;Gomaa et al., 2017) and played an important role in the temperature transfer functions (Ndayishimiye et al., 2019). From datasets of 88 lakes and reservoirs in China, we found that the occurrence and distribution of N. tuberspinifera were significantly related to latitude, elevation and temperature (Yang et al., 2006;Liu et al., 2010;Ju et al., 2014;Ndayishimiye et al., 2019;Wang et al., 2021), indicating it is mainly distributed in subtropical and tropical waterbodies with relatively low latitude, low elevation and high temperature (Fig. S1). ...
... However, mucins are upregulated again from 25 to 35°C, as biomineralization is again required to build new shells for daughter-cells. Like other members of genus Netzelia, N. tuberspinifera builds its test at least in part with selfsecreted mineral elements, unlike the genus Difflugia (Netzel, 1972;Gomaa et al., 2017). Here, our results may contain only part of mucins involved in life-related activities of N. tuberspinifera. ...
With the effects of global warming becoming ever more obvious, biodiversity conservation is facing severe challenges. Currently, a deeper understanding the mechanisms of the effects of warming on sensitive species has become an important topic in aquatic biodiversity and ecological management. Our study first overcame the “challenge” for a sensitive indicator species (Netzelia tuberspinifera, an endemic testate amoeba species in East Asia) of culturing under laboratory conditions, and then explored its molecular response mechanisms to warming using transcriptomic analysis. Our data indicate that temperature mainly drove the geographical and seasonal variation of N. tuberspinifera populations. Transcriptomic results indicate that when the temperature is <25 °C, rising temperature triggers the biosynthesis of ribosomes; while the temperature is >25 °C, it triggers molecular processes related with cell division, test formation and general biomass increase. However, once the temperature exceeds 40 °C, N. tuberspinifera is unable to survive. Following from these results, the distribution of N. tuberspinifera might expand towards higher altitude or latitude regions under global warming. For the first time, our study showed direct evidence for sensitive protozoa species that presents a very narrow adaptation mechanism to local climate. Our work provides fundamental data for regional biodiversity conservation and scientific reference in subtropical and tropical waterbodies.
... Phylogenetic reconstruction using single cell transcriptomic data has also provided evidence that the shape of the test is a key element to determine and characterize the relation between higher taxonomic ranks (Lahr et al., 2019). In an analysis of the SSU rRNA gene in species attributed to the genus Difflugia, Gomaa et al. (2012Gomaa et al. ( , 2017 showed that the group is polyphyletic. Other phylogenetic reconstructions based on the NAD9/NAD7 gene have also shown that Difflugia species can be definitively separated in different clades that correspond closely to morphologic features . ...
... Most specimens observed had two spines on the fundus, which was why the type species as named 'bidens', although specimens with zero, one, and three spines were also observed. It is likely that the presence or absence of spines is due to phenotypic plasticity and is not a suitable classification criterion (Jennings, 1916;Lahr et al., 2008;Gomaa et al., 2017). ...
Testate lobose amoebae of the order Arcellinida are a diverse, cosmopolitan group of shelled protists found in many environments, including freshwater habitats, peatlands, and soils. Their decay-resistant tests make them an important fossil group for reconstructing Quaternary environments. Within the family Difflugidae Stein, 1859 more than 300 species and 200 sub-species have been attributed to the genus Difflugia Leclerc, 1815. Although carried out on only a few taxa, molecular evidence has demonstrated that test morphology is more important than test composition in categorizing distinct taxa within the Arcellinida. The type species of Difflugia, D. proteiformis Lamarck, 1816, is characterized by a terminal aperture and an elongate acuminate test. The morphology of D. proteiformis is vastly different from most species assigned to Difflugia, explaining its polyphyletic status. We reclassify Difflugia bidens Penard, 1902 as type species of Erugomicula, a new genus within the Difflugidae, which is distinguished from other taxa within Difflugia by its broad, ovoid test, and distinct compression. Based on the compressed morphology of the test, which is not a characteristic of the Difflugiidae, we tentatively assign Erugomicula to the family Hyalospheniidae.
... The Arcellinida accommodate the major part of amoebozoan testate amoebae, but still many testate amoeba taxa have yet to be characterized by molecular means (Kang et al. 2017). For example, single gene phylogenies challenged meanwhile the monophyly of the most species rich genera Difflugia and Nebela (Gomaa et al. 2012;Gomaa et al. 2017;Kosakyan et al. 2016b;Lara et al. 2008) further confirming the need for a molecular characterization of the diversity of testate amoebae. ...
... The maximum likelihood tree (Fig. 8) positions Phryganella in the the Arcellinida; the Tubulinida were used as outgroup. Similar to other studies using SSU rDNA sequences, the lobosan families Hyalospheniidae, Netzeliidae and Arcelliidae were monophyletic while the Difflugiidae were polyphyletic and internal relationships could not be fully resolved (Gomaa et al. 2017). The newly obtained sequences of Phryganella paradoxa branch with full support next to the Cryptodifflugiidae. ...
A major drawback in testate amoeba research is a general lack of scientific studies combining molecular approaches and classical laboratory experiments. We isolated five yet uncultured testate amoebae of the genus Phryganella Penard, 1902 from three different rivers and one pond in Germany. Based on established cultures we show their morphology, which we studied by light and electron microscopy, and present their unique feeding mode on abundant and common pennate diatoms like Nitzschia spp. and Synedra spp., whose frustules are bent and frequently, but not always, broken during the feeding process. We further obtained the first SSU rDNA sequences of strains of the family Phryganellidae, all of which contain introns. We used the sequences to confirm the taxonomic placement of the Phryganellidae in the Arcellinida (Amoebozoa), branching as a sister group to the Cryptodifflugiidae.
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... При разработването на настоящата дисертация е възприета класификацията на висшите таксони според Аdl et al. (2019). Таксономичните ревизии на някои родове и семейства, както и множество таксономични и номенклатурни промени, основаващи се на скорошни молекулярни изследвания и последващите филогенетични реконструкции, също са взети под внимание (Tsiganov & Mazei 2006;Lara et al. 2007;Mazei & Warren 2012, 2014Kosakyan et al. 2012Kosakyan et al. , 2016aKosakyan et al. , 2016bChatelain et al. 2013;Gomaa et al. 2013Gomaa et al. , 2017Lahr et al. 2013Lahr et al. , 2019Bobrov 2016, Blandenier et al. 2017Duckert et al. 2018 Genus Antarcella Deflandre, 1928 Genus Arcella Ehrenberg, 1830 Family Netzeliidae Kosakyan et al. 2016 Genus Cyclopyxis Deflandre, 1929 Genus Netzelia Ogden, 1979 Incertae sedis Sphaerothecina, Genera: Cornuapyxis Coûteaux et Chardez, 1981;Cucurbitella Penard, 1902;Distomatopyxis Bonnet, 1964;Ellipsopyxella Bonnet, 1975;Ellipsopyxis Bonnet, 1965;Geopyxella Bonnet et Thomas, 1955;Lamtopyxis Bonnet, 1974;Protocucurbitella Gauthier-Lièvre et Thomas, 1960;Suiadifflugia Green, 1975;Trigonopyxis Penard, 1912. Infraorder Longithecina Lahr et al. 2019 Family Difflugiidae Wallich, 1864 ...
The thesis contains summarized data about the composition, distribution and ecology of Sphagnum-dwelling testate amoebae from Bulgaria. The materials were collected from Vitosha and Stara Planina Mountains in 2016, Rila and Pirin Mountains in 2017 and Rhodopes Mountains in 2018. A total of 266 samples (one qualitative and one quantitative) from 133 localities of 17 Sphagnum species were examined. As a result of the present study we established 148 species from 41 genera and 17 families
There is a high degree of similarity between the different mountains, as the number of species varies within narrow limits (between 110 in Stara Planina and 116 species in Pirin). Most of the registered testate amoebae are typical sphagnophilic representatives belonging to the genera Assulina, Cyphoderia, Gibbocarina, Hyalosphenia, Longinebela, Nebela, Playfairina, Quadrulella and Sphenoderia. A large percent of the commonly found species are eurybionts (Argynnia dentistoma, Centropyxis aerophila, Centropyxis aculeata, Corythion dubium, Trachelocorythion pulchellum, Euglypha spp. and Trinema spp.). Among the accidentally imported as a result of meteorological conditions (wind and/or running water) are testaceans characteristic of aerophilous mosses (Awerintzewia cyclostoma and Bullinularia indica), as well as typical freshwater (Arcella spp., Difflugia spp. and Netzelia spp.) and soil (Centropyxis spp., Plagiopyxis spp. and Phryganella spp.) representatives.
The analysis of the data from testate amoebae communities from different mountain shows that in general, they are characterized by extremely high similarity (82.88% – 88.70%). The small differences in the fauna of these mountains can be explained mainly by the presence of a relatively large number of rare species found in only one of the mountains (27 species in total, 18.2% of all found). When comparing different regions, the results clearly show that relatively distant areas from different mountains form well-separated clusters. A decisive role for the development of similar fauna has the presence of similar ecological conditions.
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In the quantitative studies genera showing the largest numbers in the testacean communities in Vitosha, Stara Planina, Rila and Pirin are Hyalosphenia, Trinema, Euglypha, Assulina and Nebela. An exception is the Rhodopes Mountains, where as dominant genus is registered Archerella. In all mountains the structural parameters vary in a relatively narrow range. High values of the Shannon-Weaver, Margalef and Pielu’s indices are observed, and at the same time very low for the Simpson’s dominance index. These values show in general, that the ecological conditions in Sphagnum mosses are very favorable and the testate amoebae communities are characterized by high species diversity and high degree of species uniformity.
The relationship between testate amoebae communities and environmental factors has been studied through ordinal analysis. Environmental factors with highest impact on the distribution and community structure are the type of substrate (Sphagnum moss), groundwater level, oxygen content and pH.
... The phylogenetic tree presented here shows a monophyletic Arcellinida, with full support for all except three nodes that received high support ( Figure 2, see also Figure S3). While Arcellinida have been treated as monophyletic in the majority of morphology-based works (e.g., [29]), and has been shown as monophyletic in wider-scope Amoebozoa molecular reconstructions [2,[22][23][24], most previous reconstructions focusing on the Arcellinida point either to a non-monophyletic or poorly supported clade while additionally showing unsupported branching of deep lineages within the group [26,30]. The current tree presents 8 well-defined and robustly supported major lineages in the Arcellinida, of which only three had been previously identified (Sphaerothecina, Hyalospheniidae, and Phryganellina [5]). ...
Life was microbial for the majority of Earth's history, but as very few microbial lineages leave a fossil record, the Precambrian evolution of life remains shrouded in mystery. Shelled (testate) amoebae stand out as an exception with rich documented diversity in the Neoproterozoic as vase-shaped microfossils (VSMs). While there is general consensus that most of these can be attributed to the Arcellinida lineage in Amoebozoa, it is still unclear whether they can be used as key fossils for interpretation of early eukaryotic evolution. Here, we present a well-resolved phylogenomic reconstruction based on 250 genes, obtained using single-cell transcriptomic techniques from a representative selection of 19 Arcellinid testate amoeba taxa. The robust phylogenetic framework enables deeper interpretations of evolution in this lineage and demanded an updated classification of the group. Additionally, we performed reconstruction of ancestral morphologies, yielding hypothetical ancestors remarkably similar to existing Neoproterozoic VSMs. We demonstrate that major lineages of testate amoebae were already diversified before the Sturtian glaciation (720 mya), supporting the hypothesis that massive eukaryotic diversification took place in the early Neoproterozoic and congruent with the interpretation that VSM are arcellinid testate amoebae.
... The higher classification used here follows Adl SM et al. 2012 andMeisterfeld (2002a), Meisterfeld (2002b). Taxonomic revision of some genera and Checklist of Sphagnum-dwelling testate amoebae in Bulgariafamilies, as well as numerous taxonomic and nomenclature changes, based on recent molecular studies and subsequent phylogenetic reconstructions, have also been taken into account (Blandenier et al. 2017, Chatelain et al. 2013, Gomaa et al. 2013, Gomaa et al. 2017, Kosakyan et al. 2016a, Kosakyan et al. 2012, Kosakyan et al. 2016b, Lahr et al. 2013, Mazei and Warren 2012, Mazei and Warren 2014, Mazei and Warren 2015. ...
Until now, a complete checklist of Sphagnum -dwelling testate amoebae in Bulgaria has never been published. Records for species diversity and distribution in the country were scattered in many faunistic and ecological publications. The aim of the present study is to summarise all data for the species distribution at the level of country by reviewing the existing literature and by additional data obtained in our research over the past two years.
The checklist comprises 171 species, classified into 43 genera, 20 families, three orders, three classes and three phyla. We present data for 16 new Sphagnum -dwelling testate amoebae in Bulgaria and new distribution data for 134 species. Of them, 99 species are recorded from Stara Planina Mt., for which there was no available data to date. Additionally are recorded 69 new species for Pirin Mt., 21 for Vitosha Mt. and 18 for Rila Mt. Thirty six species are synonymised according to the latest taxonomic changes. Two misidentified taxa ( Euglyphabrachiata Penard, 1902 and Difflugiacompressavar.africana Gauthier-Lièvre et Thomas, 1958) are transferred into valid species E.acanthophora and Zivkoviciacompressa , respectively. Three of the recorded species have not been included in the checklist, because they are currently not refering to testate amoebae ( Cochliopodiumbilimbosum (Auerbach 1856) and Cochliopodiumechinatum Korotneef, 1879 are gymnamoebae (naked amoebae) and Microgromiaelegantula (Penard 1904) = Paralieberkuehniaelegantula (Penard 1904) is freshwater foraminifera).
... The close evolutionary relationship between cluster A LLAB and LLAP8 is noteworthy. LLAP8 was isolated from a hospital shower head biofilm in Leeds, UK and can be cocultured with Vermamoebae vermiformis but not with Acanthamoebae (Adeleke et al. 1996;Gomaa et al. 2017;Rowbotham 1993). Previous analysis of the 16S showed that LLAP8, LLAP1, and LLAP10 are phylogenetically divergent from other LLAPs (Adeleke et al. 1996(Adeleke et al. , 2001Birtles et al. 1996) and probably form distinct species. ...
Diverse species of Legionella and Legionella-like amoebal pathogens (LLAPs) have been identified as intracellular bacteria in many amoeboid protists. There are, however, other amoeboid groups such as testate amoeba for which we know little about their potential to host such bacteria. In this study we assessed the occurrence and diversity of Legionella spp. in cultures and environmental isolates of freshwater arcellinid testate amoebae species, Arcella hemispherica, Arcella intermedia, and Arcella vulgaris, via 16S rRNA gene sequence analyses and fluorescent in situ hybridization (FISH).
Protists, the micro-eukaryotes that are neither plants, animals nor fungi build up the greatest part of eukaryotic diversity on Earth. Yet, their evolutionary histories and patterns are still mostly ignored, and their complexity overlooked. Protists are often assumed to keep stable morphologies for long periods of time (morphological stasis). In this work, we test this paradigm taking Arcellinida testate amoebae as a model. We build a taxon-rich phylogeny based on two mitochondrial (COI and NADH) and one nuclear (SSU) gene, and reconstruct morphological evolution among clades. In addition, we prove the existence of mitochondrial mRNA editing for the COI gene. The trees show a lack of conservatism of shell outlines within the main clades, as well as a widespread occurrence of morphological convergences between far-related taxa. Our results refute, therefore, a widespread morphological stasis, which may be an artefact resulting from low taxon coverage. As a corollary, we also revise the groups systematics, notably by emending the large and highly polyphyletic genus Difflugia. These results lead, amongst others, to the erection of a new infraorder Cylindrothecina, as well as two new genera Cylindrifflugia and Golemanskia.
Data on the distribution and species-environment relationships of rare and endemic species of protists in Asian tropical waterbodies could provide valuable information for better understanding of auto- and synecology of microbes in tropical ecosystems. We studied the morphology, abundance and distribution of two rare endemic species of testate amoebae Netzelia tuberspinifera and Netzelia mulanensis co-existing in Ba Be Lake (Bac Kan province), the largest natural lake of Vietnam. The results of NMDS and ANOSIM analyses showed insignificant difference by measured physicochemical parameters of water between nearshore and open water areas of the lake. Difference of abundances of each studied species between nearshore and open water areas of Ba Be Lake was not statistically significant. Additionally, abundances of N. tuberspinifera and N. mulanensis were weakly and insignificantly correlated at the time of investigation. The relation between environmental parameters and species distribution was investigated using a redundancy analysis (RDA) following forward selection procedure. The first and second RDA axes explained together 67% of the total variance in the data. Forward selection identified that water temperature and turbidity should be retained for the parsimonious RDA model. It is suggested that water turbidity should be considered in the next studies of relation between environmental variables and testate amoeba data. There were statistically significant differences in morphology between Vietnamese and Chinese populations of both investigated species.
Protists are probably the most species-rich eukaryotes, yet their systematics are inaccurate, leading to an underestimation of their actual diversity. Arcellinida (= lobose testate amoebae) are amoebozoans that build a test (a hard shell) whose shape and composition are taxonomically informative. One of the most successful groups is Arcellidae, a family found worldwide in many freshwater and terrestrial environments where they are indicators of environmental quality. However, the systematics of the family is based on works published nearly a century ago. We re-evaluated the systematics based on single-cell barcoding, morphological and ecological data. Overall, test shape appears to be more related to environmental characteristics than to the species’ phylogenetic position. We show several convergences in organisms with similar ecology, some traditionally described species being paraphyletic. Based on conservative traits, we review the synapomorphies of the infraorder Sphaerothecina, compile a list of synonyms and describe a new genus Galeripora, with five new combinations. Seven new species: Arcella guadarramensis sp. nov., Galeripora balari sp. nov., Galeripora bufonipellita sp. nov., Galeripora galeriformis sp. nov., Galeripora naiadis sp. nov., Galeripora sitiens sp. nov. andGaleripora succelli sp. nov. are also described here.
Southern Spain is currently under threat of desertification as a consequence of global climate change, which pressures on fragile ecosystems such as caves. The organisms living in these extremely stable environments are particularly sensitive and prone to extinction, therefore they can be used as bioindicators for climate change. Cyanobacterial mats form peculiar and vulnerable micro-ecosystems at the entrance of caves and house a diversity of protists. Amongst them, Arcellinida testate amoebae have been traditionally used as bioindicators for environmental quality, notably because their narrow ecological tolerance and their key ecological position as top predators of the microbial foodwebs. We report here two new species of Arcellinida found in the cyanobacterial mats of cave Hundidero, in Sierra de Grazalema, Malaga province, whose traits suggest a narrow tolerance for changes in humidity. We provide a formal description for Difflugia alhadiqa and Heleopera baetica based on morphometrics and 18S rRNA gene data, and propose using the presence of these species to indicate the good health of the cyanobacterial mats, like miner’s canaries for local climate.
New Zealand (NZ) is a well-known hotspot of biodiversity and endemism for macroscopic organisms, but its microbial diversity is comparatively poorly documented. We assembled all records on NZ testate amoebae published since the early 20th century and present a comprehensive taxonomic checklist for NZ. Testate amoebae are reported from six major habitat types across both the North and South Islands of NZ, but the sampling effort is ecologically and geographically biased in favour of wetlands and the South Island. As a result, 93% of all 128 morphotypes recorded in NZ occur in wetlands, 28% are restricted to the South Island, and diversity is greater at higher latitudes. Around 50% of morphotypes have a broad latitudinal distribution across the NZ mainland, whereas 15% have narrow latitudinal ranges. Future research should aim to broaden the geographical and ecological ranges. We predict that our list of NZ testate amoebae will expand substantially with future work, and that the latitudinal diversity gradient will be inverted. We also introduce an interactive, fully illustrated, online Lucid key for the rapid identification of NZ testate amoebae. As many morphospecies are cosmopolitan, this key provides a useful tool for testate amoebae identification in other parts of the world.
Difflugia australis, first described by Playfair (1918), has a unique morphotype. However, in the absence of morphometric data, it has not yet been reliably classified within the largest testate amoeba genus Difflugia. In this study D. australis collected from a subtropical reservoir in southeast China was investigated by means of light and scanning electron microscopy. Basing on biometrical data, we provide an improved diagnosis of this little known species. Difflugia australis is different from other similar congeners (i.e., D. bacillariarum Perty, 1849 and D. elegans Penard, 1890) mainly by the combination of the following features: the shell is broadly ovate, with rounded dome and convex sides converging down to a very short distance from the aperture and diverging suddenly into a short rim (collar). It is usually more or less asymmetrical, with one side being more dilated than the other. The shell surface is slightly smooth, composed of flat siliceous plates of irregular shape and size, mixed with fine grains; microbial spores of comparable forms are spread on the shell surface; particles are often interspersed with a network of organic cement with unique mesh pattern; one (sometimes two) slanting spine-like posterior end of the shell is variable in form; collar is mainly formed by small plates of equal size. The dimensions of the shell are: total shell length 88–106 µm; shell width 53–88 µm; aperture diameter 19–28 µm; collar height 3–6 µm; spine length 3‒23 µm. The size frequency distributions of both total shell length and shell width indicate that it is a size-monomorphic species with low variability.
Amoeboid protists are extremely abundant and diverse in natural systems where they often play outstanding ecological roles. They can be found in almost all major eukaryotic divisions, and genomic approaches are bringing major changes in our perception of their deep evolutionary relationships. At fine taxonomic levels, the generalization of barcoding is revealing a considerable and unsuspected specific diversity that can be appreciated with careful morphometric analyses based on light and electron microscopic observations. We provide examples on the difficulties and advances in amoeboid protists systematics in a selection of groups that were presented at the VIIIth ECOP/ISOP meeting in Rome, 2019. We conclude that, in all studied groups, important taxonomical rearrangements will certainly take place in the next few years, and systematics must be adapted to incorporate these changes. Notably, nomenclature should be flexible enough to integrate many new high level taxa, and a unified policy must be adopted to species description and to the establishment of types.
Testate amoebae are a polyphyletic assemblage of at least three major, unrelated taxonomic groups of free-living unicellular eukaryotes (Amoebozoa, Stramenopiles and Cercozoa) which ameboid cell is covered by an extracellular shell (test). They are worldwide distributed and occur in most terrestrial and freshwater environments, as well as in brackish and marine habitats, from the tropics to polar regions. The studies on this group have significantly increased over the past two decades due to their increasing use in different applied aspects. Testate amoebae are considered as valuable bioindicators for ecological and environmental monitoring studies, in particular, as proxies for hydrological changes and for paleoclimate reconstruction in peatlands. The fact that different species have distinct ecological requirements and after death of the amoebae their shells remain well preserved in peat and sediment makes them excellent microfossils and extremely valuable in micro-paleontological studies for palaeoenvironmental reconstructions. Testate amoebae are very sensitive and quickly respond to environmental changes, such as water table depth, dryness, atmospheric pollution, deforestation and other human activities, and this makes them valuable biomonitors for current environmental health.
A total of 120 species are described in the atlas, including the majority of recorded Sphagnum-dwelling testate amoebae in Bulgaria. The following information is given for each species: description; ecology; geographical distribution; distribution in Sphagnum mosses in Bulgaria and relevant literature sources; morphometric characterisation; taxonomic notes; synonymous names; original publication and publication where last revision is made. Each species is illustrated by nine micrographs, primarily on scanning electron microscope (SEM), to receive information about the shell ultrastructure. Micrographs taken on light microscope (LM) are additionally given for most of them to illustrate the cytoplasm and pseudopodia of live individuals.
Since most of the described species appear to be widely distributed in Europe, as well as in many other regions of the world, the atlas may be of interest to all researchers on testate amoebae and can also be used by specialists in ecology, hydrobiology, palaeoecology, environmental monitoring, as well as by lecturers and students in biology.
Molecular phylogeny is an indispensable tool for assessing evolutionary relationships among protists. The most commonly used marker is the small subunit ribosomal RNA gene, a conserved gene present in many copies in the nuclear genomes. However, this marker is not variable enough at a fine-level taxonomic scale, and intra-genomic polymorphism has already been reported. Finding a marker that could be useful at both deep and fine taxonomic resolution levels seemed like a utopic dream. We designed Amoebozoa-specific primers to amplify a region including partial sequences of two subunits of the mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene (NAD9/NAD7). We applied them to arcellinids belonging to distantly related genera (Arcella, Difflugia, Netzelia and Hyalosphenia) and to Arcellinid-rich environmental samples to obtain additional Amoebozoa sequences. Tree topology was congruent with previous phylogenies, all nodes being highly supported, suggesting that this marker is well-suited for deep phylogenies in Arcellinida and perhaps Amoebozoa. Furthermore, it enabled discrimination of close-related taxa. This short genetic marker (ca. 250 bp) can therefore be used at different taxonomic levels, due to a fast-varying intergenic region presenting either a small intergenic sequence or an overlap, depending on the species.
A new method of total RNA isolation by a single extraction with an acid guanidinium thiocyanate-phenol-chloroform mixture is described. The method provides a pure preparation of undegraded RNA in high yield and can be completed within 4 h. It is particularly useful for processing large numbers of samples and for isolation of RNA from minute quantities of cells or tissue samples.
One explanation for the Early Neoproterozoic expansion of eukaryotes is the appearance of eukaryovorous predators-i.e. protists that preyed on other protists. Evidence for eukaryovory at this time, however, is indirect, based on inferences from character state reconstructions and molecular clocks, and on the presence of possible defensive structures in some protistan fossils. Here I describe 0.1-3.4 µm circular holes in seven species of organic-walled microfossils from the 780-740 million-year-old Chuar Group, Grand Canyon, Arizona, USA, that are similar to those formed today by predatory protists that perforate the walls of their prey to consume the contents inside. Although best known in the vampyrellid amoebae, this ‘vampire-like’ behaviour is widespread among eukaryotes, making it difficult to infer confidently the identity of the predator. Nonetheless, the identity of the prey is clear: some-and perhaps all-of the fossils are eukaryotes. These holes thus provide the oldest direct evidence for predation on eukaryotes. Larger circular and half-moon-shaped holes in vase-shaped microfossils from the upper part of the unit may also be the work of ‘tiny vampires’, suggesting a diversity of eukaryovorous predators lived in the ancient Chuar sea. © 2016 The Author(s) Published by the Royal Society. All rights reserved.
Mediolus, a new arcellacean genus of the Difflugidae (informally known as the-camoebia, testate rhizopods, or testate lobose amoebae) differs from other genera of the family in having distinctive tooth-like inward oriented apertural crenulations and tests generally characterized by a variable number of hollow basal spines.
The morphological variability and morphometry of the freshwater testate amoeba Diffl ugia urceolata
CARTER, isolated from the benthic samples of the tectonic Lake Doiran (Macedonia) were studied. Based
on the morphometrical data of 248 specimens, high variability of the main shell characters in D. urceolata
was emphasized and was concluded that it is a size-polymorphic species. Besides, the taxonomical status
of the two varieties of D. urceolata, namely D. urceolata var. olla LEIDY and D. urceolata var. sphaerica
PLAYFAIR, found in the same population, is discussed. Many intermediate forms between the nominant
species and these two varieties were established and it was not possible to distinguish them clearly. Based
on the obtained data, it is concluded that two varieties – D. urceolata var. olla LEIDY and D. urceolata var.
sphaerica PLAYFAIR, should be considered synonyms of D. urceolata CARTER.
Arcellacean (thecamoebian) assemblages recovered from Lake Sentani, a large tropical lake southwest of Jayapura, Irian Jaya, Indonesia, are characterized by low diversity and low abundances. Dominated by Cen- tropyxis aculeata and Arcella vulgaris, this fauna is sim- ilar to those indicative of stressed environments (brack- ish conditions, high levels of industrial contaminants) in temperate regions. However, neither condition exists in Lake Sentani. Previous work has determined that the lake is oligomictic, characterized by weak circulation with turnover occurring only every few years. Prolonged isolation of the lake bottom produces progressively re- duced oxygen levels and results in reduced productivity among benthic organisms. The feeble stratification that exists here creates reduced oxygen levels at depth pro- viding a likely explanation of the stressed arcellacean fauna. The oligomictic conditions observed here and the resultant fauna are widespread and are characteristic of a large proportion of tropical lakes around the world. As the low bottom water oxygen conditions will have a serious impact on most benthic organisms in these lakes, other limnological signals including anthropogenic con- tamination will be masked. This is a disappointing result as the utility that has been developed for the group as a limnological indicator in temperate lakes does not ap- pear to apply in a significant proportion of low latitude lakes.
Thousands of exceptionally well-preserved Arcellaceans (Thecamoebians) have been recovered from a Late Albian (Cretaceous)
deposit. Sedimentary samples were obtained from a clayey-silt leaf bed in the Dakota Formation, outcropping in a clay pit
excavated by the Yankee Hill Brick Company, located near Lincoln, Nebraska. Based on recovered freshwater macrophyte spore
and fossil remains, the leaf bed is a lagerstätten of paleobotanical remains in which the paleoenvironment has been interpreted
as a quiescent freshwater setting. The large number of recovered thecamoebians revealed a high intraspecific variability in
test morphology that is comparable to Holocene thecamoebian populations. Consequently, we employ the thecamoebian strain taxonomic
framework, a first for ancient thecamoebians. Extant species contained in this collection include Difflugia oblonga, Difflugia protaeiformis, Difflugia urens, Pontigulasia compressa, Lagenodifflugia vas, Cucurbitella tricuspis, Lesquereusia spiralis and the cysts of environmentally stressed protozoans—with only one new species reported, Difflugia baukalabastron. The well-preserved nature of the taxa, suggesting little taphonomic bias, and the lack of significant new species supports
the current hypothesis of minimal evolution in thecamoebian lineages through geologic time.
The program MRBAYES performs Bayesian inference of
phylogeny using a variant of Markov chain Monte Carlo.
Availability: MRBAYES, including the source code, documentation,
sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
Contact: johnh{at}brahms.biology.rochester.edu
Vase-shaped microfossil (VSM) assemblages front early diagenetic carbonate nodules in >742 +/- 6 Ma black shales of the Chuar Group, Grand Canyon, provide evidence for affinities with testate amoebae. Not only are VSMs exceptionally preserved in Chuar rocks, they exhibit a much higher degree of morphological diversity than was previously known. Using the taxonomy of modern testate amoebae as a guide, nine new species and eight new genera of VSMs are described, augmenting the eight species and two genera already recognized. Taxa described here are Melanocyrillium hexodiadema Bloeser, 1985, Trigonocyrillium horodyskii (Bloeser, 1985) n. comb., T. fimbriatian (Bloeser, 1985) n. comb., Cycliocyrillium simplex n. sp., C. torquata n. sp., Bonniea dacruchares n. sp., B. pytinaia n. sp., Trachycyrillium pudens n. sp., Palaeoarcella athanata n. sp., Hemisphaeriella ornata n. sp., Bombycion micron n. sp., and Melicerion poikilon n. sp. All of the test characters observed in VSM taxa (e.g., collars; indentations; hexagonal symmetry; lobed, triangular or invaginated apertures, curved necks) occur in modern testate amoeban taxa, though not always in the same combinations. Some VSM species have characters found today in diverse extant taxa, making it difficult to assess their relationships. A few species, however, have character combinations that closely approximate those found in specific genera of both lobose and filose testate amoebae, suggesting that at least stem group, and possibly crown group, representatives of these taxa were present similar to ~742 Ma. These fossils indicate that ecosystems were diverse and complex, that eukaryotic biomineralization had already evolved, and that the last common ancestor of animals+fungi had already appeared by similar to ~750 Ma. Organismic and Evolutionary Biology
Morphological identification of naked lobose amoebae has always been a problem, hence the development of reliable molecular tools for species distinction is a priority for amoebae systematics. Previous studies based on SSU rDNA sequences provided a backbone for the phylogeny of Amoebozoa but were of little help for the species distinctions in this group. On one hand, the SSU rDNA sequences were rather conserved between closely related species; on the other hand, the intra-strain polymorphism of the SSU gene obscured species identification. In the present study, a 3' fragment of the SSU, a complete ITS1-5.8S-ITS2 block and a 5' fragment of COI gene were cloned and sequenced for six Vannella morphospecies, of which V. simplex was represented by six different isolates. SSU rDNA and ITS were found to be inappropriate for species differentiation, while distinctive and homogenous COI sequences were obtained for each well-defined morphospecies. Moreover, a number of distinct COI genotypes have been identified among V. simplex isolates. This suggests that COI may be a good candidate for DNA barcoding of amoebae, but further studies are necessary to confirm the accurateness of the COI gene as a barcode in other gymnamoebae, and to understand the taxonomic meaning of COI variations.
Unlabelled:
RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively.
Availability:
icwww.epfl.ch/~stamatak
To date only five partial and two complete SSU rRNA gene sequences are available for the lobose testate amoebae (Arcellinida). Consequently, the phylogenetic relationships among taxa and the definition of species are still largely dependant on morphological characters of uncertain value, which causes confusion in the phylogeny, taxonomy and the debate on cosmopolitanism of free-living protists. Here we present a SSU rRNA-based phylogeny of the Hyalospheniidae including the most common species. Similar to the filose testate amoebae of the order Euglyphida the most basal clades have a terminal aperture; the ventral position of the pseudostome appears to be a derived character. Family Hyalospheniidae appears paraphyletic and is separated into three clades: (1) Heleopera sphagni, (2) Heleopera rosea and Argynnia dentistoma and (3) the rest of the species from genera Apodera, Hyalosphenia, Porosia and Nebela. Our data support the validity of morphological characters used to define species among the Hyalospheniidae and even suggest that taxa described as varieties may deserve the rank of species (e.g. N. penardiana var. minor). Finally our results suggest that the genera Hyalosphenia and Nebela are paraphyletic, and that Porosia bigibbosa branches inside the main Nebela clade.
Using scanning electron micrographs, this book illustrates most of the common species of testate amoebae found in freshwater habitats. Information on the biology, ecology, geographical distribution, and classification is followed by descriptions of 95 species, each illustrated by several views of the shell. The text serves both as an identification guide and as an introduction to the biology and taxonomy of these freshwater protozoa. Readership: protozoologists, ecologists, limnologists, water tyreatment specialists, and micropaleontologists interested in recent sediments.
Species diversity in most protistan groups has been underestimated. Many morpho-species are in fact complexes that require detailed morphometric studies to be discriminated. However, which traits can be used for species descriptions remains in many cases unclear. The testate amoeba genus Quadrulella produces self-secreted, siliceous plates with a very characteristic square shape-such plates were assumed to be synapomorphic of the genus. Here we demonstrate that Quadrulella symmetrica (the most common Holarctic species) is not monophyletic. Square plate size and arrangement, test size and general shape are efficient criteria for species discrimination. Based on morphology and sequence data, we describe Quadrulella variabilis sp. nov. from Switzerland, and Quadrulella madibai sp. nov. from South Africa, and confirm the validity of Q. alata. The former species Q. subcarinata does not belong to the genus Quadrulella. We therefore transfer this species to the new genus Mrabella gen. nov. Our results show that hyalosphenids presenting siliceous square shell plates do not form a monophyletic clade. Several possible hypotheses about the origins of square plates are discussed. Additionally, this comprehensive phylogenetic analysis of the family Hyalospheniidae confirms that the genus Nebela is paraphyletic and needs to be divided into genera based on general shell shape: Nebela sensu stricto, Longinebela gen. nov., Planocarina gen. nov., Gibbocarina gen. nov., Cornutheca gen. nov. and Mrabella gen. nov.
Planktonic arcellinid testate amoebae exhibit a broad-range of morphological
variability but it is currently unclear to what extent this variability represents
phenotypic plasticity or if it is genetically determined. We investigated the
morphology and phylogenetic relationships of three endemic east-asian
Difflugia taxa 1) the vase-shaped D. mulanensis, 2) and a spinose and a
spineless morphotypes of D. tuberspinifera using scanning electron
microscopy and two ribosomal genetic markers (SSU rDNA and ITS sequences).
Our phylogenetic analysis shows that all three taxa are genetically distinct and
closely related to D. achlora and Netzelia oviformis. The genetic variations
between the spineless and spinose morphotypes of D. tuberspinifera were low
at the SSU rRNA level (0.4%), but ten times higher at the ITS level (4.5-6%). Our
data suggest that the two forms of D. tuberspinifera are sufficiently
differentiated in terms of morphology and genetic characteristics to constitute
two separate entities and that the presence of spines does not result from
phenotypic plasticity due to environmental selective pressure. However further
observational and experimental data are needed to determine if these two
forms constitute different biological species.
Cultures were used to test the impact of environmental factors on clones of testate amoebae. Morphological changes in the shell are of particular interest in this field of research. An image-analysis system was used to measure shells of Trinema lineare and Cyclopyxis kahli. Application of lime or mineral fertilizer, used in forestal restabilization, caused — directly or indirectly — significant changes in shell morphology of C. kahli (ANOVA, P < 0.05). In fertilized cultures the largest mean shell diameter was observed. Pseudostome diameter was significantly affected, too, but inversely, with the largest openings in the control group. Changes in shell dimensions (length, width, pseudostome diameter) were also observed in T. lineare. Although the observed differences were statistically significant, the actual differences were very small. Different temperatures and food caused significant changes in shell and pseudostome diameter of Cyclopyxis kahli. It was demonstrated that temperature and food interact significantly. Changes in shell morphology, depending on environmental factors, imply new feasibilities in bioindication. However, it should be kept in mind that the broad variability in shape caused, e.g., by climatic factors, makes taxonomical separation of closely related taxa difficult.
Construction of an organic shell casing by a species of Difflugia in culture is described from examination by electron microscopyChemical analysis shows that it is composed mainly of calcium, manganese, iron and phosphorusExperiments to show the modifications induced in the organic matrix by the inclusion of agglutinate particles are included.
1.Während der etwa 1–1½ h dauernden Zweiteilung der Thekamöbe Netzelia oviformis werden etwa 20 min für die Herstellung der Gehäusewand benötigt.2.Die cytoplasmatische Gehäuseanlage überzieht sich mit einem dünnen Häutchen — wahrscheinlich um einen Verlust von Baumaterial zu verhindern.3.Die anorganischen Bausteine, kieselige Idiosomen verschiedenster Form und Größe, werden in ihren Vesikeln unter die Oberfläche transportiert, in einer Lage so angeordnet, daß die lange Achse oberflächenparallel gestellt ist, und nahezu gleichzeitig abgeschieden (1. Exocytosephase).4.Die organischen Bauteile, 2 Typen thekagener Grana mit komplexer Ultrastruktur (525 to 810 nm lange Siebplatten-Grana, 625–750 nm lange tropfenförmige Grana), werden im Golgi-Apparat gebildet.5.Die Siebplatten-Grana gelangen nach den Idiosomen in den Kortex der Anlage und werden zu einer Schicht angeordnet. Sie werden in ihren Golgi-Vesikeln an der Basis von Cytoplasma-Lamellen, die zwischen die Idiosomen ragen, gleichsinnig so ausgerichtet, daß die Siebplatte ins Zellinnere weist, und ungefähr gleichzeitig in die Idiosomenfugen abgeschieden (2. Exocytosephase). Zur Erklärung des resultierenden Mosaik- bzw. Netzmusters wird angenommen, daß Vesikelmembran nur mit Plasmalemma zur Exocytose fusionieren kann.6.Der nach außen orientierte, exzentrische Hohlraum der Siebplatten-Grana öffnet sich, so daß die Siebplatte an Außenmedium grenzt ; die seitliche Matrix der Grana lockert sich auf und legt sich an bzw. teilweise unter die angrenzenden Idiosomen, welche damit über den entstandenen Kitt verbunden sind (“granular-cement”-Theorie).7.Während dieses Auflockerungs- und Umformungsvorganges haften die Grana mit ihrer Bodenplatte an der Spitze von Cytoplasma-Zotten.8.Anschließend werden die tropfenförmigen Grana vor allem in enge Fugen hinein abgeschieden und dort zu Kitt umgewandelt (3. Exocytose-Phase) ; dabei formt sich das zellwärts orientierte, schüsseiförmige Lumen dieser Grana in einen ± kugelförmigen Hohlraum im Kitt um. (Die in diese Räume zentripetal eingelagerten, wandständigen Flocken und Fransen sind wahrscheinlich das fein strukturelle Substrat der mit dem Alter des Gehäuses zunehmenden Braunfärbung.)9.Nach der Ausformung der arttypischen Gestalt des neuen Gehäuses erhärtet der Kitt unter Wiederverdichtung der Matrix.10.Die bisher als Difflugia tuberculata bekannte Spezies wird wegen weitgehender ultrastruktureller übereinstimmungen mit Netzelia oviformis als N. tuberculata in das Genus Netzelia eingereiht.11.Hinweise auf das Vorkommen von granulärem Kitt bzw. von thekagenen Grana bei anderen Thekamöben werden zusammengestellt. Die Verwendung von thekagenen Grana scheint innerhalb der Lobosa ein weit verbreitetes Prinzip zu sein.
The varieties of the soil-inhabiting testate species Trinema complanatum Penard, 1890, and Euglypha laevis Perty, 1849 (including Euglypha rotunda Wailes & Penard, 1911) are shown to be adaptive morphs of an extreme polymorphism. The morphs represent adaptations in the (upper) litter and the underlying humus horizon in raw humus soils. The morphs of the litter horizon also occur in Sphagnum where the microhabitat structure is similar to that of litter.
In clonal cultures the features of the morphs remain relatively constant. Nevertheless, over the course of several months other morphs occur.
The morphs could be transformed into each other by selection. In nature these species have a high ability to manoeuvre ecologically. With the help of known genetic mechanisms this paper proposes a genetic interpretation of the polymorphism of asexual protozoan species, which simultaneously gives understanding of the delimitation and evolution of asexual species.
Difflugia geosphaira sp. nov. is only the second agglutinate member of the genus Difflugia to be examined by transmission electron microscopy. Significant features of the cytoplasm are numerous dictyosomes, peroxisomes, endocellular bacteria and a nucleus with distinct nucleoli. The fine structure of the nucleus serves to distinguish these SPecimens from several other species having a similar size and globose shape.
A critical examination of the biology and morphology of two species of Cucurbitella, six species of Difflugia and three species of Netzelia is presented. A new term 'necklace' is given to species of Difflugia which have an apertural rim, but lack a distinct collar like those of Cucurbitella. Details of the shell surface composition is used to differentiate some species, and a knowledge of the general biology assists the interpretation of these results. Biometrical data is also shown to be useful in separating morphologically similar species. Cytoplasmic features such as the size and structure of the nucleus and nucleolus is used to further distinguish species. As a consequence of our investigation one new species is erected and several synonyms proposed.
Species identification by means of morphology is often problematic in protists. Nebela tincta-collaris-bohemica (Arcellinida) is a species complex of small to medium-sized (ca.100μm) testate amoebae common in peat bogs and forest soils. The taxonomic validity of characters used to define species within this group is debated and causes confusion in studies of biogeography, and applications in palaeoecology. We examined the relationship between morphological and genetic diversity within this species complex by combined analyses of light microscopy imaging and Cytochrome Oxidase Subunit 1(COI) sequences obtained from the same individual amoeba cells. Our goals were (1) to clarify the taxonomy and the phylogenetic relationships within this group, and (2) to evaluate if individual genotypes corresponded to specific morphotypes and the extent of phenotypic plasticity. We show here that small variations in test morphology that have been often overlooked by traditional taxonomy correspond to distinct haplotypes. We therefore revise the taxonomy of the group. We redefine Nebela tincta (Leidy) Kosakyan et Lara and N. collaris (Ehrenberg 1848) Kosakyan et Gomaa, change N. tincta var. rotunda Penard to N. rotunda (Penard 1890), describe three new species: N. guttata n. sp. Kosakyan et Lara, N. pechorensis n. sp. Kosakyan et Mitchell, and N. aliciae n. sp. Mitchell et Lara.
The taxonomic identity in microbial eukaryotes remains an impediment to discussing ecology, biogeography and phylogeny, mainly due to a lack of standards in organism descriptions and few comparative works. The lobose testate amoebae (Arcellinida) present an ideal study system, as progress is severely hindered due to taxonomic confusion. In the present survey, we have examined the morphology, biometry and ecology of 2400 individuals in the genus Arcella Ehrenberg, 1832, collected from the Tiete River in Sao Paulo, Brazil. We then contrasted these new data with 26 previously described species, varieties and forms, looking for consistencies and trying to establish distinct entities. Using a combination of morphology and multivariate statistics we were able to determine 4 distinct taxa (Arcella hemisphaerica, Arcella discoides, Arcella gibbosa and Arcella brasiliensis), each of them encompassing a number of other non-distinct nominal taxa. We describe in detail each of the 4 taxa with notes on ecology and biogeography, and list the indistinguishable names in an effort to make iden-tification and taxonomy in the testate amoebae a more objective and precise exercise by clarifying the taxonomic identity.
Testate amoebae are an important and abundant component of aquatic ecosystems. Our knowledge of their distribution and the species inventory in Asia is still limited. This paper describes a new planktonic Difflugia from Lake Mulan, province of Hubei, China. These findings are of taxonomic, as well as biogeographic significance because Difflugia mulanensis nov. spec. is a rare and perhaps the only locally distributed member of the well-known urceolate division within this most species-rich genus of lobose testate amoebae. We have studied its morphology and biometry with light and scanning electron microscopical methods. D. mulanensis differs from related species by its very large wide funnel-shaped apertural collar which normally exceeds the width of the test, a relatively long neck, its rounded apical end and the presence of only one nucleus. All shell parameters are normally distributed with low variability. Only the collar height is more variable. This shows that D. mulanensis is a size-monomorphic species.
The biological species concept as coined by Ernst Mayr is not applicable to many protists which reproduce by inbreeding or asexually. An extended concept supplementing the biological species concept was suggested by T. M. Sonneborn after intensive studies on differently reproducing species of the Paramecium aurelia complex. In his concept based on the hypothesis that inbreeding or asexually reproducing taxa also evolve as discrete units, he suggested that a species should be recognized as an evolving entity that has undergone a threshold of minimum evolutionary divergence. However, Sonneborns idea was poorly received. We examine different morphological and molecular characters discovered and applied in taxonomy since Sonneborn developed his hypothesis. We conclude that there is now an abundance of objective characters to arrive at sound judgement about the complexity of the genetic differences necessary to delimit species in Sonneborns sense when the biological species concept is not applicable. In addition, combined morphological and molecular studies reveal that, although many free-living protists may be globally distributed, geographical patterns and local distribution also occur.
We used Cytochrome Oxidase Subunit 1 (COI) to assess the phylogenetic relationships and taxonomy of Nebela sensu stricto and similar taxa (Nebela group, Arcellinida) in order to clarify the taxonomic validity of morphological characters. The COI data not only successfully separated all studied morphospecies but also revealed the existence of several potential cryptic species. The taxonomic implications of the results are: (1) Genus Nebela is paraphyletic and will need to be split into at least two monophyletic assemblages when taxon sampling is further expanded. (2) Genus Quadrulella, one of the few arcellinid genera building its shell from self-secreted siliceous elements, and the mixotrophic Hyalosphenia papilio branch within the Nebela group in agreement with the general morphology of their shell and the presence of an organic rim around the aperture (synapomorphy for Hyalospheniidae). We thus synonymise Hyalospheniidae and Nebelidae. Hyalospheniidae takes precedence and now includes Hyalosphenia, Quadrulella (previously in the Lesquereusiidae) and all Nebelidae with the exception of Argynnia and Physochila. Leptochlamys is Arcellinida incertae sedis. We describe a new genus Padaungiella Lara et Todorov and a new species Nebela meisterfeldi n. sp. Heger et Mitchell and revise the taxonomic position (and rank) of several taxa. These results show that the traditional morphology-based taxonomy underestimates the diversity within the Nebela group, and that phylogenetic relationships are best inferred from shell shape rather than from the material used to build the shell.
Amber-preserved shells of testate amoebae often provide as many diagnostic features as the tests of modern taxa. Most of these well-preserved microfossils are morphologically assignable to modern species indicating either evolutionary stasis or convergent evolution. Here we describe two Lower Cretaceous testate amoebae that are clearly distinguishable from modern species. Centropyxis perforata n. sp. and Leptochlamys galippei n. sp. possessed perforate shells that were previously unknown in these genera. They are preserved in highly fossiliferous amber pieces from the Upper Albian (ca. 100 million years old) of Archingeay/Les Nouillers (Charente-Maritime, southwestern France). Syninclusions of soil and litter dwelling arthropods and microorganisms indicate a limnetic-terrestrial microhabitat at the floor of a coastal conifer forest.
Spumochlamys perforata n. sp. and Spumochlamys bryora n. sp. were isolated and described from dry epiphytic moss. The morphology and ultrastructure of both species clearly demonstrate that they belong to the genus Spumochlamys (family Microchlamyiidae). They differ from its only described member, Spumochlamys iliensis (as well as from species of Microchlamys), in the relief of the dorsal surface of the test, revealed by scanning electron microscopy, which can represent a good characteristic for species identification. They also differ in the structure of the dorsal part of the test wall (especially S. perforata). Small subunit ribosomal DNA-based molecular phylogenetic analyses show that Spumochlamys is a deeply branching lineage of the Arcellinida, without any close affinities. Actin gene sequence analysis places this genus within the Tubulinea, close to two other arcellinid lineages but without forming a monophyletic group with them. These data together strongly suggest that the lack of resolution in the arcellinid molecular phylogenies is due to serious undersampling of taxa, a limited number of sequence data, and high divergence rates in most of the species.
We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm
include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log‐expectation score, and refinement using tree‐dependent
restricted partitioning. The speed and accuracy of MUSCLE are compared with T‐Coffee, MAFFT and CLUSTALW on four test sets
of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest,
rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable
from T‐Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences
of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely
available at http://www.drive5. com/muscle.
Testate amoebae (classes: Lobosea and Filosea)
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New species and new records of protozoa from Wuling Mountains Area
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A survey of the testate amoeba genus Difflugia Leclerc, 1815 based on specimens in the E. Penard and CG Ogden collections of the Natural History Museum, London. Part 2: species with shells that are spherical or ovoid
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