PFR²: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution

Abstract

Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the marine carbon cycle, and their exceptional fossil record serves as the basis for biochronostratigraphy and past climate reconstructions. A major worldwide sampling effort over the last two decades has resulted in the establishment of multiple large collections of cryopreserved individual planktonic foraminifera samples. Thousands of 18S rDNA partial sequences have been generated, representing all major known morphological taxa across their worldwide oceanic range. This comprehensive data coverage provides an opportunity to assess patterns of molecular ecology and evolution in a holistic way for an entire group of planktonic protists. We combined all available published and unpublished genetic data to build PFR(2), the Planktonic foraminifera Ribosomal Reference database. The first version of the database includes 3322 reference 18S rDNA sequences belonging to 32 of the 47 known morphospecies of extant planktonic foraminifera, collected from 460 oceanic stations. All sequences have been rigorously taxonomically curated using a six-rank annotation system fully resolved to the morphological species level and linked to a series of metadata. The PFR(2) website, available at http://pfr2.sb-roscoff.fr, allows downloading the entire database or specific sections, as well as the identification of new planktonic foraminiferal sequences. Its novel, fully documented curation process integrates advances in morphological and molecular taxonomy. It allows for an increase in its taxonomic resolution and assures that integrity is maintained by including a complete contingency tracking of annotations and assuring that the annotations remain internally consistent.

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

“…The PFR 2 taxonomic framework derives from single-cell genetic studies where the molecular taxonomy (definition of genetic types) was based on phylogenetic inferences and/or automatic delimitation methods. The delimited cluster of sequences were then compared to ecological and biogeographical data to validate their status as genuine biological species (see Morard et al, 2015, and references herein). Of the 3322 sequences available in PFR 2 , 2418 sequences covered the fragment of the region 37f.…”

“…These sequences represent eDNA exported to the seafloor from the plankton. With the recent development of the Planktonic Foraminifera Ribosomal Ref- erence Database (PFR 2 ; Morard et al, 2015), the environmental sequences belonging to planktonic foraminifera in the eDNA libraries generated by Lecroq et al (2011) can now be, for the first time, thoroughly analyzed and assigned to the morphological and cryptic species levels The extensive knowledge on the distribution and abundance of planktonic foraminiferal shells in surface sediments (Kucera et al, 2005) enabled the eDNA data to be directly compared with data derived from classical taxonomy. We thus assess to what extent the eDNA originating from plankton is representative of the source community, which is an essential prerequisite for interpretation of the eDNA archive in the sediment.…”

Common species link global ecosystems to climate change: dynamical evidence in the planktonic fossil record

“…The taxonomy of planktonic foraminifera is based on test (shell) morphology, and despite the presence of cryptic diversity, the validity of extant morphological taxa is generally supported by ribosomal sequence data [18,19]. Global patterns of morphospecies richness of extant planktonic foraminifera have been linked to various environmental factors, including sea surface temperature, mixed layer depth, productivity, geography and ocean currents [20,21].…”

Methodology for Single-Cell Genetic Analysis of Planktonic Foraminifera for Studies of Protist Diversity and Evolution

“…However, in order to avoid over-interpretation of sequence differences caused by sequencing errors or intra-individual variability, interpretation of HTS studies relies on the existence of a comprehensive sequence database that allows identification of HTS sequences with a high taxonomic resolution (Guillou et al, 2013;Yilmaz et al, 2014). Such a combined sequence and taxon database can only be established when based on sequences obtained by using the single-cell approach, where an accurate taxonomic description of molecular sequences can be obtained (Morard et al, 2015).…”

“…Following a large multi-laboratory effort to merge single-cell sequence data into a comprehensive database (Morard et al, 2015), we realized a need to review the different methodologies developed throughout the era of single-cell molecular analysis of planktonic foraminifera and to provide guidelines for method standardization for future research. To this end, we review all such methods and evaluate them using a dataset on success rates obtained in multiple laboratories over two decades, reflecting a range of methodological parameters.…”