We worked with regional bat associations to find suitable sampling sites and volunteers. We were lucky to have a large team of very dedicated individuals across France, who collected bat droppings for the project at the same time each month in summer, during two years. Their incredible effort has laid a solid foundation for the project.
In the lab, we first had to develop the protocol to recover the focal taxonomic groups as we needed to start from large volumes (many droppings pooled to represent the colony) and to extract viruses, many of which have RNA genomes which are fragile and degrade quickly, in addition to the DNA of the bats, insects, plants and fungi – all from the same starting material. Although protocols exist for each of these aspects, a single optimised protocol addressing all aspects wasn’t available. Within the first year of the project, we successfully optimised a combined viral enrichment metagenomics protocol with a multi-taxon metabarcoding approach.
The majority of the diversity recovered was insect taxa (5,547 OTUs), which was expected as the two bats used are insectivorous. Significant regional variation in the diet was revealed (e.g. Brittany versus the Mediterranean), and orders of soft-bodied insects were found to predominate at some sites, though these orders were not previously reported as being an important part of the diet. Likewise, substantial temporal variation was also evident. A high diversity of fungal and plant taxa were recovered (4,660 and ~1000 OTUs, respectively). More than half of the viruses recovered were those of insects, with the next largest proportion being ‘unknown’ viruses. This is a common occurrence in viral metagenomics due to the massive diversity of this group. Nevertheless, plant and fungal viruses were also detected. The project aims and progress were presented on a dedicated website, and at three international conferences in 2020 and 2021.
Together, the EcoScan team is working on analysing the temporal variation in diversity, and associations between taxa. We will also examine how climate and land-use impacts on diversity and ecological interactions. Although the number of sites used in EcoScan is low, our proof-of-concept study has nevertheless demonstrated the great potential for non-invasive biodiversity monitoring with bats as landscape samplers.