Perspectives from Ten Years of Protist Studies by High‐Throughput Metabarcoding

Santoferrara, Luciana F.; Burki, Fabien; Filker, Sabine; Logares, Ramiro; Dunthorn, Micah; McManus, George B.

doi:10.1111/jeu.12813

Cited by 87 publications

(73 citation statements)

References 130 publications

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“…Environmental high-throughput sequencing (HTS) studies of protists have now been performed for over a decade (Santoferrara et al 2020). During that time, a large diversity of dinophyte DNA sequences has also been uncovered.…”

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confidence: 99%

The windblown: possible explanations for dinophyte DNA in forest soils

Gottschling¹,

Czech

Mahé

et al. 2020

Preprint

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Dinophytes are widely distributed in marine- and fresh-waters, but have yet to be conclusively documented in terrestrial environments. Here we evaluated the presence of these protists from an environmental DNA metabarcoding dataset of Neotropical rainforest soils. Using a phylogenetic placement approach with a reference alignment and tree, we showed that the numerous sequencing reads that were assigned to the dinophytes did not associate with taxonomy, environmental preference, nutritional mode, or dormancy. All the dinophytes in the soils are most likely windblown dispersal units of aquatic species, and are not biologically active residents of terrestrial environments.

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confidence: 99%

The windblown: possible explanations for dinophyte DNA in forest soils

Gottschling¹,

Czech

Mahé

et al. 2020

Preprint

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“…Clearly, more investigations employing laboratory observations and visualisation (e.g., the development of fluorescent in situ hybridisation probes) are needed to confirm the nature of the interaction between foraminifera and the Group I Syndiniales (Santoferrara et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

Single-cell metabarcoding reveals biotic interactions of the Arctic calcifierNeogloboquadrina pachydermawith the eukaryotic pelagic community

Greco

Morard

Kučera

2020

Preprint

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Isotopic and trace-element signals in the calcite shells of the planktonic foraminifera Neogloboquadrina pachyderma represent key proxies to reconstruct past climatic conditions in northern high latitudes. A correct interpretation of these chemical signals requires knowledge of the habitat and trophic interactions of the species. Direct observations on the biological interactions of N. pachyderma in polar environments are lacking and to date no consensus exists on the trophic behaviour of this species. Here we use single-cell metabarcoding to characterise the interactions of 39 specimens of N. pachyderma from two sites in the Baffin Bay with the local eukaryotic pelagic community. Our results show that the eukaryotic interactome of the foraminifera is dominated by diatoms, accounting for > 50% of the reads in 17 of the samples, but other groups such as Crustacea and Syndiniales are also present. The high abundance Syndiniales suggests that these parasites could infect N. pachyderma and may play an important role in its population dynamics. Moreover, the strong but taxonomically non-specific association with algae, existing irrespective of depth and occurring in specimens collected far below the photic zone indicates that opportunistically grazed diatom-fuelled marine aggregates likely represent the main interaction substrate of N. pachyderma.

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“…Different timescales can be investigated on between-and within-OTU levels: phylogenetic trees of the representative amplicon sequences (between-OTU level) visualize comparatively older processes (e.g., past effective dispersal and speciation events), whereas the internal network structure of Swarm OTUs (within-OTU level) may display more recent divergences on subspecies level. Albeit we are pretty sure to have ascertained genetic differentiations that evolved on different time scales, the distinction between intra-and interspecific sequence deviations remains blurry (Santoferrara et al, 2020).…”

Section: Considerations For Innovative Pattern Inference On Between-amentioning

confidence: 99%

Genetic Diversity in Marine Planktonic Ciliates (Alveolata, Ciliophora) Suggests Distinct Geographical Patterns – Data From Chinese and European Coastal Waters

et al. 2021

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Unraveling geographic distribution patterns of planktonic protists is a central goal in marine microbial ecology. Using a novel combination of recently developed phylogenetic and network analyses on a V4 18S rDNA metabarcoding dataset, we here analyzed the genetic diversity of marine planktonic ciliate communities in Chinese and European coastal waters. Thereby, our approach provided an unprecedented perspective on geographic patterns inferred from ciliate genetic diversity and accomplished a very fine resolution down to single nucleotides within operational taxonomic units (OTUs). While most OTUs (87%) exclusively contained sequences of either Chinese or European origin, those OTUs detected in both regions comprised the vast majority of reads (84%). Phylogenetic analyses of OTUs belonging to the same taxon revealed genetically distinct clades that were geographically restricted to either Chinese or European coastal waters. The detection of signature nucleotides emphasized this genetic distinction of Chinese and European clades. Second-level clustering of OTUs and reference sequences in two selected taxa (the oligotrichid Spirotontonia and the tintinnid Tintinnidium) revealed the presence of several potentially new species or ones lacking genetic reference data. Geographic patterns were also discovered by network analyses within 700 widespread and abundant OTUs; in 77 of these OTUs, European and Chinese sequences formed significantly assortative groups. These assortative groupings indicated a higher genetic similarity among sequences from the same region than between sequences from different regions. Our results demonstrate that detailed analyses of metabarcoding data down to single nucleotide differences expand our perception of geographical distribution patterns and provide insights into historic and ongoing effective dispersal in protists. The congruent discovery of geographic patterns at different levels of resolution (between and within OTUs) suggests that cosmopolitan distribution in marine planktonic ciliates is less common than previously postulated.

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Perspectives from Ten Years of Protist Studies by High‐Throughput Metabarcoding

Cited by 87 publications

References 130 publications

The windblown: possible explanations for dinophyte DNA in forest soils

The windblown: possible explanations for dinophyte DNA in forest soils

Single-cell metabarcoding reveals biotic interactions of the Arctic calcifierNeogloboquadrina pachydermawith the eukaryotic pelagic community

Genetic Diversity in Marine Planktonic Ciliates (Alveolata, Ciliophora) Suggests Distinct Geographical Patterns – Data From Chinese and European Coastal Waters

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