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Periodic Report Summary 1 - GEOMETAGENOMICS (A second metagenomics generation to better understand plant virus ecology and evolution)

GEOMETAGENOMICS: A second metagenomics generation to better understand plant virus ecology and evolution

Overall objective
Our over-arching hypothesis is that the emergence of socially/economically relevant viral diseases is in many cases linked with ecological disturbances caused by human intrusions into natural ecosystems. Specifically, we propose that the displacement of natural plant species by intensive agriculture is an important subset of these intrusions12;13 that represent fundamental disturbances in the diversity, demographics and evolutionary dynamics of viral communities inhabiting natural ecosystems. We here propose to test this hypothesis by acquiring fine-scale “geo-referenced-metagenomic” data on contemporary viruses present within preserved areas, and within contexts of fynbos-edging agro-ecosystems (Objective1) and on “ancient” viruses present within fynbos plant specimens stored in French and South African herbaria (Objective2). Objective3 is to revive infectious geminiviruses recovered from herbarium specimens and the fynbos ecosystem and use these together with inferred ancestral viruses to retrace the emergence and spread over the past 100 years of African geminivirus species.

Description of the work performed since the beginning of the project and description of the main results achieved so far

Objective1: Exploring contemporary plant viral dynamics within a defined spatiotemporal framework. During the outgoing phase of this project, we have completed the experimental tasks (sampling and molecular analysis) and improved the computational analysis of the geo-metagenomics (i.e. spatially informed metagenomics approach) dataset. Using this innovative metagenomics-based approach, we have discovered 94 apparently novel plant-associated virus species within just a small fraction (~40 Km2) of the Earth’s vegetated area, encompassing farmland and natural environments. Our findings emphasize how little is currently known about the diversity of plant-associated viruses and provide insight into the impacts that agriculture has had on their distribution and prevalence. Notably, we have found (i) that virus prevalence increases within cultivated areas; (ii) that members of some phytovirus and plant-associated mycovirus families display distinctive spatial distributions at the agro-ecosystem scale; and (iii) that these distributions are often associated with land use history.

Objective2: Using preserved herbarium specimens to analyse past viral diversity. Methodological studies have been carried out in 2016. We have tested several RNA extraction methods and estimated the minimum weight of leaf material needed for obtaining a reliable detection of RNA viruses. We are therefore now ready to start the inventory of RNA plant viruses contained within herbarium plant specimen. Besides performing these methodological assays, I have collected >800 herbarium specimen from the Bolus Herbarium of the University of Cape Town between March and June 2016. We will process these herbarium samples in 2017. I have also started in 2016 building a consortium of virorogists, botanists, and bioinformaticians from Europe, USA and South Africa. Curators have been contacted and have agreed on participating to this consortium: University of Montpellier, National Museum of Natural History and the University of la Réunion (France), University of Mauritius (Mauritius), the Bolus herbarium, University of Cape Town (South Africa), Michigan State University (USA), Arizona State University (USA).

Objective3: Using the geminivirus model to study virus adaptation and emergence. Since September 2015, in collaboration with Darren Martin (University of Cape Town), Gordon Harkins (University of the Western Cape) and Philippe Lemey (Katholieke Universiteit Leuven), we are coupling computational inferences with ancestral virus synthesis and phenotypic characterization to investigate the evolution of Maize streak virus (MSV) pathogenicity through time and space. All experimental tasks have been fully achieved in 2015/2016: (i) production of infectious clones of MSV genomes, (ii) reconstruction of six ancestral viral genomes, (iii) synthesis of infectious clones of these six ancestral viral genomes and (iv) production of data on disease symptoms and virus replicative fitness for infectious clones in three different maize host genotypes. We are now starting the computational tasks that will capitalize on a phylogenetic diffusion model developed by the South African teams that has gained considerable traction for phylogeographic inference, but readily adapts to describe a wide range of quantifiable phenotypic traits while jointly inferring phylogenetic relationships.

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Life Sciences
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