CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

Pawłowski, Jan; Audic, Stéphane; Adl, Sina M.; Bass, David; Belbahri, Lassaâd; Berney, Cédric; Bowser, Samuel S.; Čepička, Ivan; Decelle, Johan; Dunthorn, Micah; Fiore-Donno, Anna Maria; Gile, Gillian H.; Holzmann, Maria; Jahn, Regine; Jirků, Miloslav; Keeling, Patrick J.; Kostka, Martin; Kudryavtsev, Alexander; Lara, Enrique; Lukeš, Julius; Mann, David G.; Mitchell, Edward A. D.; Nitsche, Frank; Romeralo, María; Saunders, Gary W.; Simpson, Alastair G. B.; Smirnov, Alexey V.; Spouge, John L.; Stern, Rowena; Stoeck, Thorsten; Zimmermann, Jonas; Schindel, David E.; Vargas, Colomban de

doi:10.1371/journal.pbio.1001419

Cited by 506 publications

(503 citation statements)

References 55 publications

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“…The case of the Nebela collaris complex therefore illustrates well the current under-estimation of protist diversity. The fact that so many new species can be found in well-studied ecosystems within relatively large and conspicuous groups of protists is in line with the idea that protists dominate eukaryotic taxonomic diversity (Pawlowski et al, 2012).…”

Section: Diversity Of the N Collaris Complexsupporting

confidence: 61%

Eight species in the Nebela collaris complex: Nebela gimlii (Arcellinida, Hyalospheniidae), a new species described from a Swiss raised bog

Kosakyan

Pillonel

Mitchell

et al. 2015

European Journal of Protistology

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We describe here a new species of sphagnicolous testate amoeba found abundantly in the forested part of the Le Cachot peatland (Jura Mountains, Neuchâtel, Switzerland) based on microscopical observations (LM, SEM). The new species, called Nebela gimlii was placed in a phylogenetic tree based on mitochondrial cytochrome oxidase sequences (COI), and branched robustly within the N. collaris complex next to the morphologically similar N. guttata and N. tincta. It is however genetically clearly distinct from these two species, and differs morphologically from them by its smaller size and stouter shape of the shell. This new species completes the phylogeny of the Nebela collaris species complex, with now eight species described, mostly from peatlands and acidic forest litter, and further demonstrates the existence of an unknown diversity within testate amoebae. Improving the taxonomy of testate amoebae in peatlands and clarifying the ecology of newly discovered species should make these organisms even more valuable as bioindicators and for palaeoecological reconstruction.

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Section: Diversity Of the N Collaris Complexsupporting

confidence: 61%

Eight species in the Nebela collaris complex: Nebela gimlii (Arcellinida, Hyalospheniidae), a new species described from a Swiss raised bog

Kosakyan

Pillonel

Mitchell

et al. 2015

European Journal of Protistology

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609

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“…We do not know whether the less familiar and less readily observable protists-microbial eukaryotes that are not animals, plants or fungi 10 -inhabiting these same ecosystems exhibit similar diversity patterns. To evaluate if macroorganismic diversity patterns are reflected at the microbial scale with protists, we conducted an environmental DNA metabarcoding study by sampling soils in 279 locations in a variety of lowland Neotropical forest types in La Selva Biological Station, Costa Rica, Barro Colorado Island, Panama and Tiputini Biodiversity Station, Ecuador.…”

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confidence: 99%

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

et al. 2017

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High animal and plant richness in tropical rainforest communities has long intrigued naturalists. It is unknown if similar hyperdiversity patterns are reflected at the microbial scale with unicellular eukaryotes (protists). Here we show, using environmental metabarcoding of soil samples and a phylogeny-aware cleaning step, that protist communities in Neotropical rainforests are hyperdiverse and dominated by the parasitic Apicomplexa, which infect arthropods and other animals. These host-specific parasites potentially contribute to the high animal diversity in the forests by reducing population growth in a density-dependent manner. By contrast, too few operational taxonomic units (OTUs) of Oomycota were found to broadly drive high tropical tree diversity in a host-specific manner under the Janzen-Connell model. Extremely high OTU diversity and high heterogeneity between samples within the same forests suggest that protists, not arthropods, are the most diverse eukaryotes in tropical rainforests. Our data show that protists play a large role in tropical terrestrial ecosystems long viewed as being dominated by macroorganisms.S ince the works of early naturalists such as von Humboldt and Bonpland 1 , we have known that animal and plant communities in tropical rainforests are exceedingly species rich. For example, one hectare can contain more than 400 tree species 2 and one tree can harbour more than 40 ant species 3 . This hyperdiversity of trees has been partially explained by the Janzen-Connell model 4,5 , which hypothesizes that host-specific predators and parasites reduce plant population growth in a density-dependent manner 6,7 . Sampling up in the tree canopies and below on the ground has further led to the view that arthropods are the most diverse eukaryotes in tropical rainforests 8,9 .The focus on eukaryotic macroorganisms in these studies is primarily because they are familiar and readily observable to us. We do not know whether the less familiar and less readily observable protists-microbial eukaryotes that are not animals, plants or fungi 10 -inhabiting these same ecosystems exhibit similar diversity patterns. To evaluate if macroorganismic diversity patterns are reflected at the microbial scale with protists, we conducted an environmental DNA metabarcoding study by sampling soils in 279 locations in a variety of lowland Neotropical forest types in La Selva Biological Station, Costa Rica, Barro Colorado Island, Panama and Tiputini Biodiversity Station, Ecuador. This metabarcoding approach has the power to uncover known and new taxa on a massive scale 11 . By amplifying DNA extracted from the soils with broadly targeted primers for the V4 region of 18S rRNA and sequencing it using the Illumina MiSeq platform, we were able to detect most eukaryotic lineages, and assess the diversity and relative dominance of free-living and parasitic lineages.

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“…Environmental DNA surveys are revealing a huge unknown diversity of microbial eukaryotes both globally and within individual samples (Epstein and Lopez-Garcia 2008;Lopez-Garcia et al 2001;Pawlowski et al 2012). This high diversity in turn suggests the existence of extremely complex, but mostly undocumented ecological interactions.…”

Section: Introductionmentioning

confidence: 99%

“…Assessment of environmental micro-eukaryotic diversity is almost exclusively done by sequencing partial or entire ribosomal genes (Pawlowski et al 2012). Besides biases in DNA extraction, PCR and possibly cloning, copy numbers of ribosomal genes in eukaryotes are known to vary over more than four ranges of magnitude, from one in the picoplanctonic Nannochloropsis salina to 12,000 in the large dinoflagellate Akashiwo sanguinea (Zhu et al 2005).…”

Section: Introductionmentioning

confidence: 99%

“…Thus, in many cases the community structure or biomass evaluation inferred from rDNA studies are not always reliable (Crosby and Criddle 2003;Morgan et al 2010;Weber and Pawlowski 2013;Von Wintzingerode et al 1997). Selecting the optimal barcoding marker is not trivial either; ribosomal genes (SSU and LSU rRNA) are most useful for coarse taxon discrimination, while ITS has been shown to present intra-genomic variation in some groups and is therefore not suited as a barcoding gene for all eukaryotic groups (Pawlowski et al 2012).…”

Section: Introductionmentioning

confidence: 99%

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Environmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa; Arcellinida; Hyalospheniidae)

Kosakyan

Mulot

Mitchell

et al. 2015

European Journal of Protistology

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Environmental DNA surveys are used for screening eukaryotic diversity. However, it is unclear how quantitative this approach is and to what extent results from environmental DNA studies can be used for ecological studies requiring quantitative data. Mitochondrial cytochrome oxidase (COI) is used for species-level taxonomic studies of testate amoebae and should allow assessing the community composition from environmental samples, thus bypassing biases due to morphological identification. We tested this using a COI clone library approach and focusing on the Nebela collaris complex. Comparisons with direct microscopy counts showed that the COI clone library diversity data matched the morphologically identified taxa, and that community composition estimates using the two approaches were similar. However, this correlation was improved when microscopy counts were corrected for biovolume. Higher correlation with biovolume-corrected community data suggests that COI clone library data matches the ratio of mitochondria and that within closely-related taxa the density of mitochondria per unit biovolume is approximately constant. Further developments of this metabarcoding approach including quantifying the mitochondrial density among closely-related taxa, experiments on other taxonomic groups and using high throughput sequencing should make if possible to quantitatively estimate community composition of different groups, which would be invaluable for microbial food webs studies.

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CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

Abstract: A group of protist experts proposes a two-step DNA barcoding approach, comprising a universal eukaryotic pre-barcode followed by group-specific barcodes, to unveil the hidden biodiversity of microbial eukaryotes.

Cited by 506 publications

References 55 publications

Eight species in the Nebela collaris complex: Nebela gimlii (Arcellinida, Hyalospheniidae), a new species described from a Swiss raised bog

Eight species in the Nebela collaris complex: Nebela gimlii (Arcellinida, Hyalospheniidae), a new species described from a Swiss raised bog

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

Environmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa; Arcellinida; Hyalospheniidae)

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