Next Generation Taxonomy: Ciliophora and their bacterial symbionts as a proof of concept

Project Information

NGTax

Grant agreement ID: 872767

DOI

10.3030/872767

Project closed

EC signature date 27 November 2019

Start date 1 June 2020

End date 31 March 2026

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 1 274 200,00

EU contribution

€ 984 400,00

Coordinated by

UNIVERSITA DI PISA
Italy

Periodic Reporting for period 1 - NGTax (Next Generation Taxonomy: Ciliophora and their bacterial symbionts as a proof of concept)

Reporting period: 2020-06-01 to 2024-01-31

Summary of the context and overall objectives of the project

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 requires the further and amplified integration of the most advanced genomics and bioinformatics techniques, taking into account also the holobiont concept. NGTax project establishes an international and inter-sectoral network of organisations across the EU, Africa, China and USA working on a joint research programme in the field of the Next Generation Taxonomy of ciliates and their symbionts, constituting a holobiontic unit. The proposed approach is strongly multidisciplinary, involving the expertise of participants on different disciplines including classical morphological analyses, ultrastructure, molecular tools, genomics and bioinformatics.
NGTax will pursue six central objectives: i) validate the NGTax approach on many holobiont systems from different ciliate groups in order to create a new standard for species description to be widely used by the scientific community; ii) contribute rejuvenating taxonomic discipline to ensure traditional expertise is not lost but complemented with sequencing technologies; iii) consolidate and disseminate the NGTax approach to perform the characterization of eukaryotic organisms; iv) train staff members in NGTax, in order to outline novel scientific positions, boost their careers and import/export useful, both traditional and new 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 and developing new interaction with developing countries.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The NGTax project allowed the sampling in different areas of the word, in different environments realizing more than 285 ciliate cultures. This enabled the network to realize multidisciplinary characterizations of ciliates and their symbionts (whenever present) following the NGTax best standards. Several in-depth description of ciliates and their symbionts have been already performed and published and early stage researchers have been trained in the Next Generation Taxonomy workflow. Indeed, the NGTax workflow was applied to different holobiont systems and many different ciliate species, obtaining good results. We demonstrated its suitability within the Phylum Ciliophora, obtaining complete datasets for at least thirteen (13) different ciliate genus (e.g. Euplotes, Thuricola, Lacrymaria, Phialina, Chaenea, Kentrophoros, Tracheloraphis, Leiotrocha, Trichodinopsis, Paramecium, Frontonia, Pseudokeronopsis, Copemetopus) and at least five (5) symbionts (“Ca. Gromoviella”, Verrucomicrobiota spp., Pseudomonadota, “Ca. Kentron”, “Ca. Bandiella”, etc.).
The bioinformatics analyses are presently ongoing although the Whole Genome Amplification technique was already applied on more than 100 ciliate specimens and genome sequencing was carried out on several products. From those sequencings more than 50 ciliates’ mitochondrial genomes and 9 symbiont genomes were already analysed, assembled, and annotated.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Thanks to the work carried so far the network demonstrate that it is possible to apply the NGTax workflow to holobiontic ciliates and described several species using innovative molecular and bioinformatic tools, associated with more traditional morphological analyses. This represents a step forward in the way to describe living beings and constitutes an effective method to rejuvenate taxonomic disciplines. Further data about transcriptomic will further implement our analyses and will potentially shed light on the kinfìd of interactions occurring between ciliates and their symbionts.
Moreover, the work carried out so far contribute towards European policy objectives and strategies and is expect to have a beneficial impacts the SMEs involved in the network. Although the interaction with companies was difficult due to several pandemic restrictions, in this first part of the project University members always kept good contacts with the companies’ coordinators, laying down good premises to work further and fruitfully in the second part of the project.
Following such premises we foreseen multiple beneficial effects for the companies of the network, such as new customers and customer services for Genewiz, scientific publication and useful data about biological process and organisms (i.e. ciliates) connected with the good functionality of the waste water treatment plant (Cuoiodepur) or the restored ecosystems (Palustrine).

Logo of the NGTax project