Full Title: “Next Generation Taxonomy: Ciliophora and their bacterial symbionts as a proof of concept”
Grant agreement ID: 872767
Topic(s): MSCA-RISE-2019 - Research and Innovation Staff Exchange
Call for proposal: H2020-MSCA-RISE-2019
Funded under: EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions
Project duration: 1st June 2020 – 31st March 2026
Total cost: € 1 274 200
Coordinator: Univ
ersity of Pisa (Italy)
Web pages: https://cordis.europa.eu/project/id/872767 and https://www.ngtax.org/
Our goal: Restoring taxonomy’s past glory
Having undergone a crisis in recent decades, taxonomy – the science of classifying biological organisms based on shared characteristics – needs to be rejuvenated. The integration of the most advanced genomics and bioinformatics techniques, also taking into account the holobiont concept, has been proposed as a solution. The EU-funded NGTax project aims to expand and explore this approach by creating an international and inter-sectoral network of organisations across the EU, Africa, China and USA. To this end, it works on a joint research programme in next-generation taxonomy of ciliates and their symbionts, constituting a holobiontic unit. Brief description and objectives
Taxonomy - the science of defining and naming groups of biological organisms based on shared characteristics - faced a significant crisis in the last decades and nowadays a rejuvenation of this discipline is required. For this reason, we recently proposed the integration in taxonomy of the most advanced genomics and bioinformatics techniques, taking into account also the holobiont concept (Serra et al., 2020): we named this approach Next Generation Taxonomy. NGTax explores and expands this rationale establishing an international and inter-sectoral network of organisations across the EU, Africa, China and USA. The consortium works on a joint research programme in Next Generation Taxonomy of ciliates and their symbionts, constituting a holobiontic unit. The proposed approach is strongly multidisciplinary including classical morphological analyses, ultrastructure, molecular tools, genomics and bioinformatics. NGTax is pursuing six central objectives:
i) validate the NGTax approach on many holobiont systems from different ciliate Classes;
ii) contribute rejuvenating taxonomic discipline to ensure traditional expertise is not lost but complemented with state of the art sequencing technologies;
iii) consolidate and disseminate the NGTax approach to perform the characterization of eukaryotic organisms to let it become a “new reference standard”;
iv) train staff members in NGTax, in order to outline novel scientific positions, boost their careers and import/export useful know-how across sectors, disciplines and countries;
v) provide advanced training to male and female researches, including researchers from cultural and religious minorities, from developing countries in order to contribute to boost their academic careers and their integration in international collaborative research networks;
vi) support European companies in performing know-how exchange with academic sector, developing new services, and creating new interaction with developing countries. NGTax Consortium
We are 13 members, 10 Academies and 3 Companies from all over the world:
University of Pisa, University of Pavia, Consorzio Cuoio Depur S.P.A. (Italy)
Innsbruck University (Austria)
University of Wuppertal, Max Planck Institute, Genewiz/Azenta (Germany)
Palustrine Design Oy (Finland)
Addis Ababa University (Ethiopia)
Egerton University (Kenya)
Free State University of Bloemfontein (South Africa)
Ocean University of China (People's Republic of China)
Joint Genome Institute of the Berkeley University (California, USA)
The NGTax workflow
The NGTax workflow will start from environmental sampling (water and sediment) in order to find and isolate potentially interesting ciliates or ciliate-symbiont/s systems (=holobiont). The selected organisms will be analyzed to obtain:
TRADITIONAL TAXONOMY / INTEGRATIVE TAXONOMY
• Morphological description of the ciliate via live observations, Feulgen staining, silver impregnation, Protargol staining.
• Detection of bacterial symbiont/s of ciliates: screening through microscopy live observations, fluorescence in situ hybridization (FISH) with universal bacterial/archaeal probes, and diagnostic PCRs.
• Ultrastructural description of the ciliate/holobiont via transmission and scanning electron microscopy.
• Molecular and phylogenetic characterization of the ciliate and its symbiont/s: after DNA extraction, sequencing of commonly used molecular markers for eukaryotes (e.g. 18S rDNA, COI) and prokaryotes (16S rDNA), and tree reconstructions.
• Information on symbiont life-cycle: cross infection experiments, killer tests, symbiont cultivation attempts. INNOVATIVE ASPECTS OF NGTax
• Genomics data: Whole Genome Amplification (WGA) on single ciliate cells or several morphologically identical cells, followed by genome sequencing through Next Generation Sequencing (NGS) techniques.
• Bioinformatics data: assembly and annotation of the mitochondrial genome of i) the ciliate (mitogenome), ii) the genome of symbiont/s, iii) the nuclear genome of the ciliate.
• 16S rDNA metabarcoding: characterization of the microbiome associated to the ciliate.
• Transcriptomic data: description of the host-symbiont interactions via the analysis of up-regulated and down-regulated gene expression in the presence of the symbiont.
