Can Abundance of Protists Be Inferred from Sequence Data: A Case Study of Foraminifera

Weber, Alexandra Anh‐Thu; Pawłowski, Jan

doi:10.1371/journal.pone.0056739

Cited by 123 publications

(90 citation statements)

References 41 publications

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“…In most cases, the same species were found in microscopic and molecular data sets, but the relative abundances of sequences and morphotypes were not in agreement, so each approach revealed a different community structure. Other studies prepared mock communities, and the results obtained were similar: all individual taxa were detected, but the relative proportion of sequence types was different from cell mixes (19,20). Overall, the popularization of HTS now allows a high-resolution exploration of protist richness present in natural samples; yet, when it comes to evenness, the picture obtained is still limited.…”

mentioning

confidence: 67%

Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

Giner

Forn

Romac

et al. 2016

Appl Environ Microbiol

112

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High-throughput sequencing (HTS) is revolutionizing environmental surveys of microbial diversity in the three domains of life by providing detailed information on which taxa are present in microbial assemblages. However, it is still unclear how the relative abundance of specific taxa gathered by HTS correlates with cell abundances. Here, we quantified the relative cell abundance of 6 picoeukaryotic taxa in 13 planktonic samples from 6 European coastal sites using epifluorescence microscopy on tyramide signal amplification-fluorescence in situ hybridization preparations. These relative abundance values were then compared with HTS data obtained in three separate molecular surveys: 454 sequencing of the V4 region of the 18S ribosomal DNA (rDNA) using DNA and RNA extracts (DNA-V4 and cDNA-V4) and Illumina sequencing of the V9 region (cDNA-V9). The microscopic and molecular signals were generally correlated, indicating that a relative increase in specific 18S rDNA was the result of a large proportion of cells in the given taxa. Despite these positive correlations, the slopes often deviated from 1, precluding a direct translation of sequences to cells. Our data highlighted clear differences depending on the nucleic acid template or the 18S rDNA region targeted. Thus, the molecular signal obtained using cDNA templates was always closer to relative cell abundances, while the V4 and V9 regions gave better results depending on the taxa. Our data support the quantitative use of HTS data but warn about considering it as a direct proxy of cell abundances. IMPORTANCEDirect studies on marine picoeukaryotes by epifluorescence microscopy are problematic due to the lack of morphological features and due to the limited number and poor resolution of specific phylogenetic probes used in fluorescence in situ hybridization (FISH) routines. As a consequence, there is an increasing use of molecular methods, including high-throughput sequencing (HTS), to study marine microbial diversity. HTS can provide a detailed picture of the taxa present in a community and can reveal diversity not evident using other methods, but it is still unclear what the meaning of the sequence abundance in a given taxon is. Our aim is to investigate the correspondence between the relative HTS signal and relative cell abundances in selected picoeukaryotic taxa. Environmental sequencing provides reasonable estimates of the relative abundance of specific taxa. Better results are obtained when using RNA extracts as the templates, while the region of 18S ribosomal DNA had different influences depending on the taxa assayed. Protists are key components of marine ecosystems, being major players in the global respiration and production budgets (1, 2) and playing central roles in marine food webs (3). Despite their importance and ubiquity, it was only during the past decade that environmental studies, based on molecular (i.e., culture-independent) techniques, revealed an unsuspected protist diversity in a large variety of marine ecosystems (4-13). These studies we...

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mentioning

confidence: 67%

Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

Giner

Forn

Romac

et al. 2016

Appl Environ Microbiol

112

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“…The analysis based on relative abundances yields a pattern with highly consistent results for comparisons between climatic zones and more scatter when comparing samples within a region or within one climatic zone. This is likely due to the fact that the eDNA data only cover a part of the morphological diversity of the foraminifera combined with differential distortion of the original abundance signal due to variation in gene copy number (Weber and Pawlowski, 2013) and primer bias (Bradley et al, 2016).…”

Section: Resultsmentioning

confidence: 99%

Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

et al. 2017

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Abstract. Deep-sea sediments constitute a unique archive of ocean change, fueled by a permanent rain of mineral and organic remains from the surface ocean. Until now, paleoecological analyses of this archive have been mostly based on information from taxa leaving fossils. In theory, environmental DNA (eDNA) in the sediment has the potential to provide information on non-fossilized taxa, allowing more comprehensive interpretations of the fossil record. Yet, the process controlling the transport and deposition of eDNA onto the sediment and the extent to which it preserves the features of past oceanic biota remains unknown. Planktonic foraminifera are the ideal taxa to allow an assessment of the eDNA signal modification during deposition because their fossils are well preserved in the sediment and their morphological taxonomy is documented by DNA barcodes. Specifically, we re-analyze foraminiferal-specific metabarcodes from 31 deep-sea sediment samples, which were shown to contain a small fraction of sequences from planktonic foraminifera. We confirm that the largest portion of the metabarcode originates from benthic bottom-dwelling foraminifera, representing the in situ community, but a small portion (< 10 %) of the metabarcodes can be unambiguously assigned to planktonic taxa. These organisms live exclusively in the surface ocean and the recovered barcodes thus represent an allochthonous component deposited with the rain of organic remains from the surface ocean. We take advantage of the planktonic foraminifera portion of the metabarcodes to establish to what extent the structure of the surface ocean biota is preserved in sedimentary eDNA. We show that planktonic foraminifera DNA is preserved in a range of marine sediment types, the composition of the recovered eDNA metabarcode is replicable and that both the similarity structure and the diversity pattern are preserved. Our results suggest that sedimentary eDNA could preserve the ecological structure of the entire pelagic community, including nonfossilized taxa, thus opening new avenues for paleoceanographic and paleoecological studies.

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“…2007; Lejzerowicz et al, 2010;Bates et al, 2013); however, they still fail to amplify the SSU rRNA genes of a wide range of protists and provide a highly skewed picture of protist communities (Epstein and López-García, 2008;Weber and Pawlowski, 2013;Stoeck et al, 2014). This is exemplified by the negative selection of amoebozoan sequences in PCRprimer-based approaches (Berney et al, 2004;Amaral-Zettler et al, 2009), explaining the virtual absence of nearly the entire supergroup in high throughput sequencing surveys (Baldwin et al, 2013;Bates et al, 2013), whereas the high rRNA gene copy numbers in ciliates (Gong et al, 2013) generally lead to their over-proportional representation.…”

Section: Census Of Soil Protists S Geisen Et Almentioning

confidence: 99%

Metatranscriptomic census of active protists in soils

et al. 2015

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The high numbers and diversity of protists in soil systems have long been presumed, but their true diversity and community composition have remained largely concealed. Traditional cultivation-based methods miss a majority of taxa, whereas molecular barcoding approaches employing PCR introduce significant biases in reported community composition of soil protists. Here, we applied a metatranscriptomic approach to assess the protist community in 12 mineral and organic soil samples from different vegetation types and climatic zones using small subunit ribosomal RNA transcripts as marker. We detected a broad diversity of soil protists spanning across all known eukaryotic supergroups and revealed a strikingly different community composition than shown before. Protist communities differed strongly between sites, with Rhizaria and Amoebozoa dominating in forest and grassland soils, while Alveolata were most abundant in peat soils. The Amoebozoa were comprised of Tubulinea, followed with decreasing abundance by Discosea, Variosea and Mycetozoa. Transcripts of Oomycetes, Apicomplexa and Ichthyosporea suggest soil as reservoir of parasitic protist taxa. Further, Foraminifera and Choanoflagellida were ubiquitously detected, showing that these typically marine and freshwater protists are autochthonous members of the soil microbiota. To the best of our knowledge, this metatranscriptomic study provides the most comprehensive picture of active protist communities in soils to date, which is essential to target the ecological roles of protists in the complex soil system.

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Can Abundance of Protists Be Inferred from Sequence Data: A Case Study of Foraminifera

Cited by 123 publications

References 41 publications

Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

Metatranscriptomic census of active protists in soils

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