Project description

The BioMarKs project united 10 research institutes and 60 experts in protist taxonomy and marine biology, molecular ecology and bioinformatics, to assess the biocomplexity along the European coast line of the least explored compartment of our Biosphere: the unicellular eukaryotes or protists.

Our strategy was to sample entire protistan communities, from the smallest to the largest cells, across 3 organismal size fractions and 3 depths, and using 3 types of data: genetic, morphological, and contextual. All together we built up a homogenous collection of >3,000 genetic and morphological samples obtained during 10 cruises from the Arctic ocean to the Black Sea, through Norway, France, Spain, and Italy.

With the help of Genoscope, we pioneered the use of Next Generation Sequencing (NGS) technologies to explore eukaryotic organisms in these samples and obtained >220 million clean environmental metabarcodes from both marine water columns and sediments, stored in what is today the largest community resource available on EU marine coastal unicellular eukaryotic biodiversity. We developed novel comprehensive databases of taxonomically curated reference DNA barcodes, as well as bioinformatics and statistical tools to analyze the BioMarKs database.

This unveiled a wealth of novel protistan lineages, including novel groups of primitive marine fungi and parasites, ciliates, foraminifers, haptophytes, which typically express their biodiversity primarily in marine sediments. Discoveries of the BioMarKers are published in a series of 50 papers, with an estimated 25 additional coming in 2014-2015. All together, the material and methods assembled in BioMarKs provide a complete toolbox for modern, cheap, and accurate biomonitoring of marine eukaryotic biodiversity.

BioMarKs is a ERA net program funded by BiodivERsA’s national partners.
BiodivERsA is a project funded under the Framework Programme of the European Commission.

Marine protists represent the least explored biodiversity compartment on Earth, despite being one of the most reactive and influential in terms of global ecology and climate change. Protists contains all ‘simple’ eukaryotic organisms beyond the derived lineages that developed complex multi-cellularity - macroalgae, fungi, plants, and animals. All together, less than 200,000 species of protists have been described and classified into 7 super-groups and >100 morphological lineages often older than plants or animals. The BioMarKs project united 10 research institutes and 60 experts in protist taxonomy and marine biology, molecular ecology and bioinformatics, to assess the biological and economical complexity of protistan communities along the European coast line.

The BioMarKers first developed effective protocols to sample genetic, morphological, and contextual data from size-fractionated protistan communities from marine water bodies and sediments. The international team organized 10 cruises from the Arctic ocean to the Black Sea, through Norway, France, Spain, and Italy, constructing at the end a collection of >3,000 genetic and morphological samples embedded in series of contextual data. With the help of Genoscope, the BioMarKers then pioneered the use of Next Generation Sequencing (NGS) technologies to generate massive datasets of DNA sequences (barcodes) representing the entire eukaryotic diversity in any given sample. Interestingly the NGS technologies available at the beginning of the project were not able to unveil the entire protistan diversity in any of the BioMarKs sample. The shift to Illumina sequencing allowed covering most of the diversity, permitting exploration of the world of rare species and unveiling a wealth of novel diversity at all taxonomic levels, from new toxic species, to novel lineages of parasites, to new ancestral groups of marine fungi. The BioMarKers developed also novel bioinformatics and statistical approaches to assemble the massive environmental protistan DNA barcodes diversity into coherent units, and to assign putative taxonomy to the genetic units and study their ecological distribution and community structuring.

All together, BioMarKs generated >220 million clean environmental DNA/RNA barcodes from EU marine protists, together with a suite of sampling, molecular ecology, NGS sequencing, bioinformatics, and ecological statistics protocols. The material and methods assembled in BioMarKs led to the publication of 50 scientific papers, with an estimated 25 additional coming in 2014-2015; they provide also a complete toolbox for modern, cheap, and accurate biomonitoring of marine eukaryotic biodiversity. BioMarKs data and ideas were finally assembled into a website which represents today the largest community resource on EU marine unicellular eukaryotic biodiversity, providing a reference platform for current and future projects dealing with this important biodiversity compartment.