Time to regulate microbial eukaryote nomenclature

Expansion of the cytochrome C oxidase subunit I database and description of four new lobose testate amoebae species (Amoebozoa; Arcellinida)

Arcellinida is ascending in importance in protistology, but description of their diversity still presents multiple challenges. Furthermore, applicable tools for surveillance of these organisms are still in developing stages. Importantly, a good database that sets a correspondence between molecular barcodes and species morphology is lacking. Cytochrome oxidase (COI) has been suggested as the most relevant marker for species discrimination in Arcellinida. However, some major groups of Arcellinida are still lacking a COI sequence. Here we expand the database of COI marker sequences for Arcellinids, using single-cell PCR, transcriptomics, and database scavenging. In the present work, we added 24 new Arcellinida COI sequences to the database, covering all unsampled infra- and suborders. Additionally, we added six new SSUrRNA sequences and described four new species using morphological, morphometrical, and molecular evidence: Heleopera steppica, Centropyxis blatta, Arcella uspiensis, and Cylindrifflugia periurbana. This new database will provide a new starting point to address new research questions from shell evolution, biogeography, and systematics of arcellinids.

Deconstructing Difflugia: The tangled evolution of lobose testate amoebae shells (Amoebozoa: Arcellinida) illustrates the importance of convergent evolution in protist phylogeny

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.

Transitional and small aquatic cave habitats diversification based on protist assemblages in the Veternica cave (Medvednica Mt., Croatia)

Protists in caves are scarcely researched. Most cave studies address the diversity of protists, but very little is known about their habitats and spatio-temporal dynamics. The aim of this study was to investigate the diversity and abundance of protists in the Veternica cave in the Medvednica mountain in Croatia on hygropetric and sinter and clay pools during six months. During this study, 47 protists taxa were distinguished belonging to the groups of heterotrophic flagellates, ciliates, heliozoans, stramenopiles and testate and naked amoebae. The highest taxon richness was found at the sinter pool site richest in bats guano (36 taxa). Most diverse were testate amoebae and ciliates. The number of taxa and their abundance differed significantly between the sampling sites. The prospected habitats supported different protist assemblages, proved by ordination analysis. The most distinctive habitat was the hygropetric. Habitat heterogeneity could be attributed to the presence of inorganic and organic sediments at the sites and habitat microhydrology (lotic or lentic system). Kendall’s concordance coefficient showed a good synchronicity between the habitats in the Veternica cave, based on taxon richness and abundance of protists indicating similar seasonal trends. Seasonality in the studied habitats is attributed to the hydro-meteorological conditions in the Veternica cave drainage area. This study is one of the few studies of spatio-temporal diversity and abundance of protists in caves. Despite the similar appearance of small transitional and aquatic habitats in caves, an example of this study showed specific habitat diversification.

Multiple convergences in the evolutionary history of the testate amoeba family Arcellidae (Amoebozoa: Arcellinida: Sphaerothecina): when the ecology rules the morphology

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.

An emerging paradigm for the origin and evolution of shelled amoebae, integrating advances from molecular phylogenetics, morphology and paleontology

The phylogenetic paradigm of eukaryotic evolution has changed dramatically over the past two decades, with profound reflections on the understanding of life on earth. Arcellinida testate (shelled) amoebae lineages represent some of the oldest fossils of eukaryotes, and the elucidation of their phylogenetic relationships opened a window to the distant past, with important implications for understanding the evolution of life on earth. This four-part essay summarises advances made in the past 20 years regarding: (i) the phylogenetic relationships among amoebae with shells evolving in concert with the advances made in the phylogeny of eukaryotes; (ii) paleobiological studies unraveling the biological affinities of Neoproterozoic vase-shaped microfossils (VSMs); (iii) the interwoven interpretation of these different sets of data concluding that the Neoproterozoic contains a surprising diversity of organisms, in turn demanding a reinterpretation of the most profound events we know in the history of eukaryotes, and; (iv) a synthesis of the current knowledge about the evolution of Arcellinida, together with the possibilities and pitfalls of their interpretation.

Amoeboid protist systematics: A report on the "Systematics of amoeboid protists" symposium at the VIIIth ECOP/ISOP meeting in Rome, 2019

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.

Unmasking "The Eldest Son of The Father of Protozoology": Charles King

In 1703 two articles appeared in the Transactions of the Royal Society, authored by an unnamed gentleman. The articles, with deference to Leeuwenhoeck, described recent observations made with a microscope. Clifford Dobell, in his biography of Leeuwenhoeck, remarked at length on the extraordinary quality of the illustrations and descriptions of "animalcules". He declared the anonymous author to be the scion and master draughtsman of Leeuwenhoeck's followers. Still today, one of the illustrations is credited with being the first unambiguous depiction of a diatom. Here I present evidence that the anonymous author was Charles King of Staffordshire and evidence of his talent. John Hill is often credited for the first naming and illustrating Paramecium and other ciliates in his 1752 book, but it has been claimed repeatedly that he copied the anonymous 1703 illustrations without attribution. Here, the illustrations from 1703 and 1752 are given, and casual examination suffices to show not only that the illustrations were copied, but also that the 1703 illustrations (and text descriptions) of Charles King are of a far higher quality than those of John Hill. Although very little is known about Charles King, he deserves recognition as a pioneer of protistology.

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.

Is Myxomycetes (Amoebozoa) a Truly Ambiregnal Group? A Major Issue in Protist Nomenclature

Myxomycetes is one of the largest groups of protists belonging to Amoebozoa, with ca 1,000 species recognised and more than 4,000 names in use. Historically, myxomycetes were considered fungi or protozoans which, however, fell under the provisions of the former International Code of Botanical Nomenclature (ICBN), currently the International Code of Nomenclature for algae, fungi, and plants (ICN). Attempts to apply the International Code of Zoological Nomenclature (ICZN) to myxomycetes were rare and inconsistent; thus, we argue that Myxomycetes is not a truly ambiregnal group (i.e. one falling under both Codes). Recently, nomenclatural novelties within Myxomycetes have been proposed using ICZN rules, and the application of zoological orthography to myxomycete higher-level taxa in the recent amoebozoan phylogenies is increasingly common. We summarise the consequences of application of either ICN or ICZN to Myxomycetes. In our opinion, nomenclatural stability within Myxomycetes is best served by strict application of ICN. Either treating myxomycetes as falling under ICZN or considering them an ambiregnal group would cause serious nomenclatural instability, mainly owing to the incompatibility of the two Codes as to the date of the starting point of nomenclature and to the appearance of numerous homonyms.

Current and future perspectives on the systematics, taxonomy and nomenclature of testate amoebae

Testate amoebae are a polyphyletic assemblage of at least three major, unrelated taxonomic groups of unicellular amoeboid eukaryotes exhibiting a test. The focus on testate amoebae in scientific research has greatly increased in the past 20 years: from an average of about 5 papers a year in the mid-1990s to the current rate of more than 50 papers published yearly. The application range of these organisms is rapidly expanding as well: from the traditional fields of environmental monitoring and paleoecology, to forensic sciences and ecotoxicology studies. These developments are nevertheless strongly dependent on reliable taxonomy and nomenclature. However, scientometric data reveal that despite an ever-increasing necessity for the use of names (the product of taxonomy), the corresponding effort has not been achieved for improving testate amoebae systematics. As a consequence, inaccurate taxonomy yields to misinterpretations in the diversity of the organisms and to potentially incorrect conclusions. These and related problems are discussed in this study, highlighting the outcome of poor taxonomic expertise in accurate classification and phylogeny of testate amoebae, and the consequences derived from it. Additionally, this study is aimed to discuss the current status of testate amoebae classification, and to present all nomenclature and taxonomic changes in higher and lower taxonomic levels of testate amoebae, as a result of recent molecular reconstructions. Finally, we conclude with a list of the needs and suggestions toward a unified and modernized taxonomy of testate amoebae.

The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks

SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources.

Sphenoderiidae (fam. nov.), a new clade of euglyphid testate amoebae characterized by small, round scales surrounding the aperture

Euglyphid testate amoebae are a highly conspicuous group of Cercozoa whose systematics is based mainly on the shape and ultrastructure of the shell. However, only a couple of species have been studied with molecular methods. As a consequence, there are still some genera whose classification remains uncertain. Amongst those are Sphenoderia and Trachelocorythion, two genera with diverging ecological requirements that share a collar composed of small scales around the aperture. We demonstrate here with a molecular and morphological approach that they are closely related, and propose a new family, Sphenoderiidae fam. nov. to group these species. Some species share almost similar morphology in spite of being genetically distantly related (Sphenoderia minuta and S. pseudominuta sp. nov.), underlining the importance of combining ultrastructural and morphological data when describing new species of protists. In addition, we describe here Sphenoderia valdiviana sp. nov., a new species isolated from Southern Chile temperate rainforests.

Amphitremida (poche, 1913) is a new major, ubiquitous labyrinthulomycete clade

Micro-eukaryotic diversity is poorly documented at all taxonomic levels and the phylogenetic affiliation of many taxa – including many well-known and common organisms - remains unknown. Among these incertae sedis taxa are Archerella flavum (Loeblich and Tappan, 1961) and Amphitrema wrightianum (Archer, 1869) (Amphitremidae), two filose testate amoebae commonly found in Sphagnum peatlands. To clarify their phylogenetic position, we amplified and sequenced the SSU rRNA gene obtained from four independent DNA extractions of A. flavum and three independent DNA extractions of A. wrightianum. Our molecular data demonstrate that genera Archerella and Amphitrema form a fully supported deep-branching clade within the Labyrinthulomycetes (Stramenopiles), together with Diplophrys sp. (ATCC50360) and several environmental clones obtained from a wide range of environments. This newly described clade we named Amphitremida is diverse genetically, ecologically and physiologically. Our phylogenetic analysis suggests that osmotrophic species evolved most likely from phagotrophic ancestors and that the bothrosome, an organelle that produces cytoplasmic networks used for attachment to the substratum and to absorb nutrients from the environments, appeared lately in labyrithulomycete evolution.