<i>Dactylomonas</i> gen. nov., a Novel Lineage of Heterolobosean Flagellates with Unique Ultrastructure, Closely Related to the Amoeba <i>Selenaion koniopes</i> Park, De Jonckheere &amp; Simpson, 2012

Hanousková, Pavla; Táborský, Petr; Čepička, Ivan

doi:10.1111/jeu.12637

Cited by 14 publications

(11 citation statements)

References 63 publications

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“…The 18S rRNA gene sequences from the seven unstudied Percolomonas strains were closest by BLASTN search to Percolomonas cosmopolitus strain WS (AF 519443), but with a low identity of 74% to 83%. As in previous studies [14–16, 19, 31, 32], Heterolobosea formed a strong monophyletic group in phylogenetic trees of 18S rRNA gene sequences (Fig 3). The seven new Percolomonas strains and two previously identified sequences branched with the pseudociliate taxon Stephanopogonidae with strong support (100% ML; PP 1; Fig 3) forming the clade Percolatea.…”

Section: Resultssupporting

confidence: 81%

Ecological and evolutionary patterns in the enigmatic protist genus Percolomonas (Heterolobosea; Discoba) from diverse habitats

Tikhonenkov

Jhin

Eglit

et al. 2019

Preprint

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21The heterotrophic flagellate Percolomonas cosmopolitus (Heterolobosea) is often observed 22 in saline habitats worldwide that range from coastal waters to saturated brines. However, only two 23 cultures assigned to this morphospecies have been examined using molecular methods, and their 24 18S rRNA gene sequences are extremely different. Further the salinity tolerances of individual 25 strains are unknown. Thus, our knowledge on the autecology and diversity in this morphospecies is 26 deficient. Here, we report 18S rRNA gene data on seven strains similar to P. cosmopolitus from 27 seven geographically remote locations (New Zealand, Kenya, Korea, Poland, Russia, Spain, and the 28 USA) with sample salinities ranging from 4‰ to 280‰, and compare morphology and salinity 29 tolerance of the nine available strains. Percolomonas cosmopolitus-like strains show few-to-no 30 consistent morphological differences, and form six clades separated by often extremely large 18S 31 rDNA divergences (up to 42.4%). Some strains grew best at salinities from 75 to 125‰ and 32 represent halophiles. All but one of these belonged to two geographically heterogeneous clusters 33 that formed a robust monophyletic group in phylogenetic trees; this likely represents an ecologically 34 specialized subclade of halophiles. Our results suggest that P. cosmopolitus is a cluster of several 35 cryptic species (at least), which are unlikely to be distinguished by geography. Interestingly, the 9 36 Percolomonas strains formed a clade in 18S rDNA phylogenies, unlike most previous analyses 37 based on two sequences. 38 39 40 3 41 Introduction 42 The modern classification of eukaryotic microbes is usually based on molecular sequence 43 information combined with morphological characters obtained using diverse imaging techniques, 44 often including electron microscopy. Many taxonomists have a fundamental question whether small 45 morphological differences among the observed organisms represent multiple species or one variable 46 species [1-3]. Conversely, in protistology, many species (and genera) that were originally proposed 47 based on light microscopy alone have proved to encompass considerable genetic diversity. Also, 48 many morphospecies of protists are cosmopolitan and/or are found across a very wide range of 49 habitats, raising the possibility of recognizing species that are divided more by geography or 50 ecology than morphology [4]. Bickford et al. [1] regarded 'cryptic species' as cases where two or 51more species are distinguished that were previously assigned to a single morphologically defined 52 species (i.e. morphospecies). The concept of cryptic (usually genetically different) species has been 53 examined in a diverse range of protists, e.g. [4, 5, 6]. This concept is widely accepted due to an 54 inconsistency between morphospecies and their DNA sequencing data. Obviously, the estimated 55 number of protist species will vary tremendously depending on the species concept employed [7, 8]. 56The species Percolomonas cosmopolitus (former...

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Section: Resultssupporting

confidence: 81%

Ecological and evolutionary patterns in the enigmatic protist genus Percolomonas (Heterolobosea; Discoba) from diverse habitats

Tikhonenkov

Jhin

Eglit

et al. 2019

Preprint

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“…The latter group is ecologically and morphologically extremely diverse and contains the vast majority of described species; however, its internal phylogeny is still almost exclusively based on SSU rRNA data. Because the traditional classification of Heterolobosea does not correspond with its internal phylogeny as it is currently understood, our database adopted provisional terminology as presented by Pánek et al ( 36 ) and Hanousková et al ( 37 ). In short, we recognize eight main clades of Tetramitia: Selenaionida (syn.…”

Section: Resultsmentioning

confidence: 99%

OUP accepted manuscript

et al. 2020

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The small subunit ribosomal RNA (SSU rRNA) gene is a widely used molecular marker to study the diversity of life. Sequencing of SSU rRNA gene amplicons has become a standard approach for the investigation of the ecology and diversity of microbes. However, a well-curated database is necessary for correct classification of these data. While available for many groups of Bacteria and Archaea, such reference databases are absent for most eukaryotes. The primary goal of the EukRef project (eukref.org) is to close this gap and generate well-curated reference databases for major groups of eukaryotes, especially protists. Here we present a set of EukRef-curated databases for the excavate protists—a large assemblage that includes numerous taxa with divergent SSU rRNA gene sequences, which are prone to misclassification. We identified 6121 sequences, 625 of which were obtained from cultures, 3053 from cell isolations or enrichments and 2419 from environmental samples. We have corrected the classification for the majority of these curated sequences. The resulting publicly available databases will provide phylogenetically based standards for the improved identification of excavates in ecological and microbiome studies, as well as resources to classify new discoveries in excavate diversity.

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“…Furthermore, Heterolobosea was revealed to be the second most abundant group www.nature.com/scientificreports www.nature.com/scientificreports/ (38.6% of total read counts) in the supergroup 'Excavata' using the V9 region, but this group was not detected using the V4 region. Heterolobosea, including amoeba, amoeboflagellate, and flagellate forms, represents one of rare taxa in environmental surveys 17,30,35 , but were commonly isolated from freshwater, marine, soil, and extreme environments [36][37][38][39][40][41][42][43][44][45][46] . Pawlowski et al 17 reported that Heterolobosea comprises <1% of total reads using NGS technology with only the V9 region.…”

Section: Scientific Reports |mentioning

confidence: 99%

Comparative analyses of the V4 and V9 regions of 18S rDNA for the extant eukaryotic community using the Illumina platform

Choi

Park

2020

Sci Rep

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Illumina sequencing is a representative tool for understanding the massive diversity of microbial eukaryotes in natural ecosystems. Here, we investigated the eukaryotic community in a pond (salinity of 2-4) on Dokdo (island) in the East Sea, Korea, using Illumina sequencing with primer sets for the V4 and V9 regions of 18S rDNA from 2016 to 2018 for the first time. Totally, 1,413 operational taxonomic units (OTUs) and 915 OTUs were detected using the V9 and V4 primer sets, respectively. Taxonomic analyses of these OTUs revealed that although the V4 primer set failed to describe the extant diversity for some major sub-division groups, the V9 primer set represented their diversity. Moreover, the rare taxa with <1% of total reads were exclusively detected using V9 primer set. Hence, the diversity of the eukaryotic community can vary depending on the choice of primers. The Illumina sequencing data of the V9 region of 18S rDNA may be advantageous for estimating the richness of the eukaryotic community including a rare biosphere, whereas the simultaneous application of two biomarkers may be suitable for understanding the molecular phylogenetic relationships. We strongly recommend both biomarkers be used to assess the diversity and phylogenetic relationship within the eukaryotic community in natural samples.The advent of next-generation sequencing (NGS) led to a substantial change in the previous knowledge about the microbial diversity in natural ecosystems 1,2 . NGS targeting the 18S rDNA is usually used to evaluate the diversity within all domains of life and provides large quantities of sequencing data for individual investigators. The 454 platform is hardly used anymore and a lot of other platforms are currently used far more widely. The Illumina platforms are representative tools for the investigation of the microbial community although this method can read a relatively short fragment of sequence (200 bp-500 bp) due to the technical limitations 3,4 . Illumina platform is a cost-effective tool per base (priced ~100 times lower than the 454 platform) and can now read longer sequences (200 bp-300 bp) than the initial platform 5,6 . Furthermore, the error rate of the Illumina platform is lower than that of the 454 platform 7 . However, considering the revolutionary application of the Illumina platform, our knowledge about the diversity and phylogenetic relationship of eukaryotes remains poor in field surveys such as those for brackish water 8 .Several studies on the diversity of eukaryotes noted that the V1-V2, V3, V4, and V9 regions of 18S rDNA have been used for better understanding the massive diversity of microbial community 9-11 . The V4 (expected amplicon size, 270 bp-387 bp) and V9 (expected amplicon size, 96 bp-134 bp) regions are considered to be the popular for metabarcoding 12,13 . Based on an in silico analysis, the V9 region of 18S rDNA offers the advantage to reveal the extant diversity of eukaryotes, whereas the V4 region of 18S rDNA is commonly used for studying the phylogenetic relationship of eukaryot...

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Dactylomonas gen. nov., a Novel Lineage of Heterolobosean Flagellates with Unique Ultrastructure, Closely Related to the Amoeba Selenaion koniopes Park, De Jonckheere & Simpson, 2012

Cited by 14 publications

References 63 publications

Ecological and evolutionary patterns in the enigmatic protist genus Percolomonas (Heterolobosea; Discoba) from diverse habitats

Ecological and evolutionary patterns in the enigmatic protist genus Percolomonas (Heterolobosea; Discoba) from diverse habitats

OUP accepted manuscript

Comparative analyses of the V4 and V9 regions of 18S rDNA for the extant eukaryotic community using the Illumina platform

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