A Revised Taxonomy of Diplonemids Including the Eupelagonemidae n. fam. and a Type Species, <i>Eupelagonema oceanica</i> n. gen. &amp; sp.

Okamoto, Nobuhiko; Gawryluk, Ryan M.R.; Campo, Javier del; Strassert, Jürgen F. H.; Lukeš, Julius; Richards, Thomas A.; Worden, Alexandra Z.; Santoro, Alyson E.; Keeling, Patrick J.

doi:10.1111/jeu.12679

Cited by 19 publications

(20 citation statements)

References 39 publications

(83 reference statements)

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“…They are a clade of heterotrophic flagellates overwhelmingly known from marine habitats. This previously homogenous group has now been sub-divided into four well-supported clades: Diplonemidae ( 14 , 42 ), Hemistasiidae ( 14 , 42 , 43 ), Eupelagonemidae ( 44 , 45 ) and the DSPD II clade ( 44 ). Their branching order cannot be reliably resolved on the basis of the SSU rRNA gene and the current taxon sampling.…”

Section: Resultsmentioning

confidence: 99%

“…The largest fraction of recovered sequences belonged to hyperdiverse Eupelagonemidae (453 sequences, 86%). Of these, all but one, belonging to the uncultured type species Eupelagonema oceanica ( 45 ), lack any formal taxonomic description. An overwhelming majority of the Diplonemea sequences was environmental, with most obtained from marine plankton, some from a hydrothermal plume or oxygen-depleted sea water, while only six were benthic (Figures 1 B and D).…”

Section: Resultsmentioning

confidence: 99%

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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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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

OUP accepted manuscript

et al. 2020

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“…In contrast, the Eupelagonemidae occurs mostly in the mesopelagic zone (Lara et al ., 2009; Okamoto et al ., 2019) and represents up to 97% of diplonemids in the plankton (Flegontova et al ., 2016). So far, they are known only from environmental 18S rRNA sequences and low‐coverage single‐cell genomes accompanied by light microscopy images (Gawryluk et al ., 2016; Okamoto et al ., 2019). Only six out of 100 of the most abundant diplonemid operational taxonomic units (OTUs) were found predominantly in the mesoplankton size fraction (180–2000 μm), suggesting that a symbiotic or parasitic lifestyle with mesoplankton is not widespread among eupelagonemids (Flegontova et al ., 2016).…”

Section: Introductionmentioning

confidence: 99%

Environmental determinants of the distribution of planktonic diplonemids and kinetoplastids in the oceans

Flegontova

Flegontov

Londoño

et al. 2020

Environmental Microbiology

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We analysed a widely used barcode, the V9 region of the 18S rRNA gene, to study the effect of environmental conditions on the distribution of two related heterotrophic protistan lineages in marine plankton, kinetoplastids and diplonemids. We relied on a major published dataset (Tara Oceans) where samples from the mesopelagic zone were available from just 32 of 123 locations, and both groups are most abundant in this zone. To close sampling gaps and obtain more information from the deeper ocean, we collected 57 new samples targeting especially the mesopelagic zone. We sampled in three geographic regions: the Arctic, two depth transects in the Adriatic Sea, and the anoxic Cariaco Basin. In agreement with previous studies, both protist groups are most abundant and diverse in the mesopelagic zone. In addition to that, we found that their abundance, richness, and community structure also depend on geography, oxygen concentration, salinity, temperature, and other environmental variables reflecting the abundance of algae and nutrients. Both groups studied here demonstrated similar patterns, although some differences were also observed. Kinetoplastids and diplonemids prefer tropical regions and nutrient-rich conditions and avoid high oxygen concentration, high salinity, and high density of algae.

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“…The under-studied and puzzling Hemimastix similarly turned out to be a new, high-ranking phylogenetic lineage of eukaryotes (Lax et al 2018). Predatory protists with Colponemid-like morphology and behavior are also very intriguing and evolutionarily important, as they are falling in severaldifferent parts of the tree, and contribute to the understanding of the origin of photosynthesis, parasitism, and evolution of mitochondrial genome (Gawryluk et al 2019;Janouškovec et al 2013Janouškovec et al , 2017Tikhonenkov et al 2020).…”

Section: Discussionmentioning

confidence: 99%

Heterotrophic flagellates and centrohelid heliozoans from marine waters of Curacao, the Netherlands Antilles

Prokina

Keeling

Tikhonenkov³

2020

Preprint

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Recent progress in understanding the early evolution of eukaryotes was tied to morphological identification of flagellates and heliozoans in the natural samples, isolation of their cultures and genomic and ultrastructural investigations. These protists are the smallest and least studied microbial eukaryotes but play an important role in functioning of microbial food webs. Using light and electron microscopy, we have studied the diversity of heterotrophic flagellates and centrohelid heliozoans from marine waters of Curacao (The Netherlands Antilles), and provide micrographs and morphological descriptions of observed species. Among 86 flagellates and 3 centrohelids encountered in this survey, five heterotrophic flagellates and one сentrohelid heliozoan were not identified even to the genus. Some flagellate protists have a unique morphology, and may represent undescribed lineages of eukaryotes of high taxonomic rank. The vast majority (89%) of identified flagellates are characterized by wide geographical distribution and had been reported previously from all hemispheres and various climatic regions. More than half of the species were previously observed not only from marine, but also from freshwater habitats. The parameters of the species accumulation curve indicate that our species list obtained for the Curacao study sites is far from complete, and each new sample should yield new species.

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A Revised Taxonomy of Diplonemids Including the Eupelagonemidae n. fam. and a Type Species, Eupelagonema oceanica n. gen. & sp.

Cited by 19 publications

References 39 publications

OUP accepted manuscript

OUP accepted manuscript

Environmental determinants of the distribution of planktonic diplonemids and kinetoplastids in the oceans

Heterotrophic flagellates and centrohelid heliozoans from marine waters of Curacao, the Netherlands Antilles

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