Guano-based monitoring of ecosystems – a novel approach to capture ecological processes underlying ecosystem health

The overall goal of the project is to develop a novel method of ecosystem monitoring with the help of bats.


Biodiversity underpins fundamental ecosystem processes and provides invaluable services. Current approaches of biodiversity monitoring may be limited to individual taxonomic groups and typically measure the end-state, but not the underlying processes. Drastic biodiversity loss and climate change have made the development of rapid, high-throughput multi-trophic ecosystem monitoring protocols a pressing need. These methods have the potential to complement existing biodiversity monitoring methods, giving us a better understanding of ecosystem health and a affording us better chance of acting in time to preserve our fragile environment.


Plants are the primary producers responsible for oxygen production and carbohydrate synthesis and form the base of almost all global ecosystems. They are known to accumulate viral loads in response to climate-related stress. Plants, and their viruses, are eaten by phytophagous insects (with their own viral load), which are in turn eaten by a top consumer such as a bat.


We will take advantage of this natural aggregation through trophic levels by collecting bat guano which contains a snap-shot sample of the environment. We are targeting two species of bat which use distinct foraging styles: Rhinolophus hipposideros (lesser horseshoe bat) which forages in closed/cluttered environments and Eptesticus serotinus (serotine bat) which forages in open habitats. Bats are the ideal aggregator taxon as they effectively sample the environment for us, and deposit a large amount of this material in fixed locations (at their summer roosts which they they are faithful to every year).

At CBGP we will then use the latest in high-throughput sequencing protocols in metabarcoding and viral metagenomics to retrieve the identity of insect, plant, fungi and bats and their viromes. Temporal sampling across climatic zones and habitats will ensure that complex and seasonal ecosystem processes are captured. We will explore taxon diversity and associations, and how these change over time and in response to environmental conditions.

This will increase our knowledge on biodiverse but understudied groups, shed light on ecosystem processes and how they respond to climate change, and provide proof of concept results for ‘aggregation’ as a means to rapidly survey ecosystem health on a global scale.


This collaborative project involves researchers and many dedicated volunteers who are undertaking the sampling which is conducted each month across three regions in France (Atlantic, Continental, Mediterranean zones). See the ‘People‘ tab for more details.


ECOSCAN is a 2 year project funded by the European Union under the Marie Skłodowska-Curie actions (MSCA) program