staff

Loïc Pillet

Postdoctoral fellow in Molecular Systematics & Environmental Genomics

  • T: +41 22 379 30 73
  • office 4078b (Sciences III)
  • High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems. Sci Rep 2015 ;5():13932. srep13932. 10.1038/srep13932. PMC4564730.

    abstract

    Environmental diversity surveys are crucial for the bioassessment of anthropogenic impacts on marine ecosystems. Traditional benthic monitoring relying on morphotaxonomic inventories of macrofaunal communities is expensive, time-consuming and expertise-demanding. High-throughput sequencing of environmental DNA barcodes (metabarcoding) offers an alternative to describe biological communities. However, whether the metabarcoding approach meets the quality standards of benthic monitoring remains to be tested. Here, we compared morphological and eDNA/RNA-based inventories of metazoans from samples collected at 10 stations around a fish farm in Scotland, including near-cage and distant zones. For each of 5 replicate samples per station, we sequenced the V4 region of the 18S rRNA gene using the Illumina technology. After filtering, we obtained 841,766 metazoan sequences clustered in 163 Operational Taxonomic Units (OTUs). We assigned the OTUs by combining local BLAST searches with phylogenetic analyses. We calculated two commonly used indices: the Infaunal Trophic Index and the AZTI Marine Biotic Index. We found that the molecular data faithfully reflect the morphology-based indices and provides an equivalent assessment of the impact associated with fish farms activities. We advocate that future benthic monitoring should integrate metabarcoding as a rapid and accurate tool for the evaluation of the quality of marine benthic ecosystems.

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  • Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data. Environ. Sci. Technol. 2015 Jul;49(13):7597-605. 10.1021/es506158m.

    abstract

    Diatoms are widely used as bioindicators for the assessment of water quality in rivers and streams. Classically, the diatom biotic indices are based on the relative abundance of morphologically identified species weighted by their autoecological value. Obtaining such indices is time-consuming, costly, and requires excellent taxonomic expertise, which is not always available. Here we tested the possibility to overcome these limitations using a next-generation sequencing (NGS) approach to identify and quantify diatoms found in environmental DNA and RNA samples. We analyzed 27 river sites in the Geneva area (Switzerland), in order to compare the values of the Swiss Diatom Index (DI-CH) computed either by microscopic quantification of diatom species or directly from NGS data. Despite gaps in the reference database and variations in relative abundance of analyzed species, the diatom index shows a significant correlation between morphological and molecular data indicating similar biological quality status for the majority of sites. This proof-of-concept study demonstrates the potential of the NGS approach for identification and quantification of diatoms in environmental samples, opening new avenues toward the routine application of genetic tools for bioassessment and biomonitoring of aquatic ecosystems.

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  • PROTELPHIDIUM NIVEUM () AND THE TAXONOMY OF “LOWER” ELPHIDIIDS The Journal of Foraminiferal Research 45 (3), 250-263; 10.2113/gsjfr.45.3.250

    abstract

    A small planispiral rotaliid, Nonion? niveum, was described by Lafrenz from the Eemian (upper Pleistocene) of the Baltic Sea. Since then, the species has several times been attributed to other genera (Haynesina, Protelphidium), resulting in taxonomic confusion. Recently, a morphologically identical foraminifer has been found in the White Sea, which is the first documented occurrence of the species from this area. In-depth investigation of its test morphology revealed that the species has features common to modern Haynesina representatives and particularly to the extinct Paleogene species Protelphidium hofkeri. This was especially evident in the architecture of the umbilical area. With the help of a comparative morphological study of several other elphidiids, the species in question was attributed to the genus Protelphidium, as its only living member and with the necessary emendation of the diagnosis. We believe that the redescription of Protelphidium niveum helps to clarify the taxonomy of the basal “lower” elphidiids by coupling the revision of morphological features with molecular data.

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  • The genome of the foraminiferan Reticulomyxa filosa. Curr. Biol. 2014 Jan;24(1):11-8. S0960-9822(13)01446-2. 10.1016/j.cub.2013.11.027.

    abstract

    Rhizaria are a major branch of eukaryote evolution with an extensive microfossil record, but only scarce molecular data are available. The rhizarian species Reticulomyxa filosa, belonging to the Foraminifera, is free-living in freshwater environments. In culture, it thrives only as a plasmodium with thousands of haploid nuclei in one cell. The R. filosa genome is the first foraminiferal genome to be deciphered.

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  • Deep relationships of Rhizaria revealed by phylogenomics: a farewell to Haeckel's Radiolaria. Mol. Phylogenet. Evol. 2013 Apr;67(1):53-9. S1055-7903(12)00489-7. 10.1016/j.ympev.2012.12.011.

    abstract

    Rhizaria is one of the six supergroups of eukaryotes, which comprise the majority of amoeboid and skeleton-building protists living in freshwater and marine ecosystems. There is an overall lack of molecular data for the group and therefore the deep phylogeny of rhizarians is unresolved. Molecular data are particularly scarce for the clade of Retaria, which include two prominent groups of microfossils: foraminiferans and radiolarians. To fill this gap, we have produced and sequenced EST libraries for 14 rhizarian species including seven foraminiferans, Gromia and six taxa belonging to traditional Haeckel's Radiolaria: Acantharea, Polycystinea, and Phaeodarea. A matrix was constructed for phylogenetic analysis based on 109 genes and a total of 56 species, of which 22 are rhizarians. Our analyses provide the first multigene evidence for branching of Phaeodarea within Cercozoa, confirming the polyphyly of Haeckel's Radiolaria. It confirms the monophyly of Retaria, a clade grouping Foraminifera with other lineages of Radiolaria. However, contrary to what could be expected from morphological observations, Foraminifera do not form a sister group to radiolarians, but branch within them as sister to either Acantharea or Polycystinea depending on the multigene data set. While the monophyly of Foraminifera and Acantharea is well supported, that of Polycystinea, represented in our data by Spumellaria and Collodaria is questionable. In view of our study, Haeckel's Radiolaria appears as both, a polyphyletic and paraphyletic assemblage of independent groups that should be considered as separate lineages in protist classification.

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  • Transcriptome analysis of foraminiferan Elphidium margaritaceum questions the role of gene transfer in kleptoplastidy. Mol. Biol. Evol. 2013 Jan;30(1):66-9. mss226. 10.1093/molbev/mss226.

    abstract

    Foraminifera from the genus Elphidium are heterotrophic protists that graze on diatoms and sequester chloroplasts from their algal preys, while digesting the rest of the diatom cell. During that process, known as kleptoplastidy, the acquired plastids remain active inside the foraminiferan cell for several months. As most of the genes required to sustain the activity of the chloroplasts are encoded in the diatom nucleus, it is unknown how the host cell can maintain the photosynthetic activity without this information. It has been proposed that maintenance of kleptoplastids could be explained by horizontal gene transfer (HGT). To test this hypothesis we obtained 17,125 EST sequences of Elphidium margaritaceum, and we screened this data set for diatom nuclear-encoded proteins having a function in photosynthetic activity or plastid maintenance. Our analyses show no evidence for the presence of such transcriptionally active genes and suggest that HGT hypothesis alone cannot explain the chloroplast's longevity in Elphidium.

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  • Intra-genomic ribosomal RNA polymorphism and morphological variation in Elphidium macellum suggests inter-specific hybridization in foraminifera. PLoS ONE 2012 ;7(2):e32373. 10.1371/journal.pone.0032373. PONE-D-11-21607. PMC3290570.

    abstract

    Elphidium macellum is a benthic foraminifer commonly found in the Patagonian fjords. To test whether its highly variable morphotypes are ecophenotypes or different genotypes, we analysed 70 sequences of the SSU rRNA gene from 25 specimens. Unexpectedly, we identified 11 distinct ribotypes, with up to 5 ribotypes co-occurring within the same specimen. The ribotypes differ by varying blocks of sequence located at the end of stem-loop motifs in the three expansion segments specific to foraminifera. These changes, distinct from typical SNPs and indels, directly affect the structure of the expansion segments. Their mosaic distribution suggests that ribotypes originated by recombination of two or more clusters of ribosomal genes. We propose that this expansion segment polymorphism (ESP) could originate from hybridization of morphologically different populations of Patagonian Elphidium. We speculate that the complex geological history of Patagonia enhanced divergence of coastal foraminiferal species and contributed to increasing genetic and morphological variation.

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  • Molecular identification of sequestered diatom chloroplasts and kleptoplastidy in foraminifera. Protist 2011 Jul;162(3):394-404. S1434-4610(10)00079-9. 10.1016/j.protis.2010.10.001.

    abstract

    Kleptoplastidy is the ability of heterotrophic organisms to preserve chloroplasts of algal preys they eat and partially digest. As the sequestered chloroplasts stay functional for months, the "host" becomes photosynthetically active. Although remaining a marginal process, kleptoplastidy was observed in different protist lineages, including foraminifera. Previous studies showed at least eight species of the foraminiferal genera Haynesina and Elphidium grazing on diatoms and husbanding their chloroplasts. In order to characterize more precisely the origin of kleptochloroplasts in these genera, we obtained 1027 chloroplastic 16S rDNA sequences from 13 specimens of two Haynesina and five Elphidium species. We identified the foraminiferal kleptochloroplasts using a reference phylogeny made of 87 chloroplastic sequences of known species of diatoms and brown algae. All the analyzed specimens were performing kleptoplastidy and according to our phylogenetic analyses they seem to retain exclusively chloroplasts of diatom origin. There is no apparent specificity for the type of diatom from which chloroplasts originated, however some foraminiferal species seem to accept a wider range of diatoms than others. Possibly the diversity of kleptochloroplasts depends on the type of diatoms the foraminiferans feed on.

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Generally interested in evolutionnary processes, I'm working on benthic Foraminifera from the genus Elphidium. As these cosmopolitan organisms are found in almost all shallow waters around the world, they represent a very good tool to study the biodivesity in relationship with the ecological factors. The genus Elphidium is particularly interesting because it inclues many morphological descibed species, even if the systematic of this group based on morphology is not completly clear yet. In order to get a different point of view to this problematic, I'm using genetic tools and morphometry to try to compare the newly obtained phylogenies with the ones based on morphology. Linking all these aspects, genetics, ecology and morphology, I'm trying to explain the concept of species within Foraminifera.