Our planet is undergoing a dramatic phase of biodiversity loss, which threatens to destabilise ecosystems and the services upon which we rely. In order to document the extent and the rate of such changes, and be prepared to avert and/or manage them, we must accurately and extensively assess and monitor biodiversity patterns across space and time. Yet, reliable species inventories are challenging, expensive, time-consuming to obtain, and difficult to standardise across taxa. This is particularly true for the oceans, the largest and least accessible habitats on Earth.
The use of DNA sequences for distinguishing and cataloguing species has progressively improved our ability to characterise ecosystems, manage resources and improve policy. Then in the last decade, the field was transformed by the advent of high through-put parallel DNA sequencing technologies, which made it technically possible and inexpensive to reveal taxonomic compositions of complex biological mixtures extracted from water, sediments, faeces, food products and more. The retrieval of "environmental DNA" (eDNA) from cellular material naturally shed by animals in their habitat has become a popular ecological tool, especially in aquatic science. Indeed, DNA can be 'captured' and screened in the same way for whales and bacteria, and the findings can have important applications in conservation biology, fisheries and aquaculture, environmental management and epidemiology.
However, the collection of water from the environment under study is far from straightforward. First of all, most water-collecting methods are limited in their capacity to reliably represent the vastness of the ocean. Furthermore, the target eDNA from aqueous samples is typically very diluted, which requires filtration, a time-consuming process, vulnerable to cross-contamination, and heavily reliant on plastic. To circumvent some of these issues, several research teams across the world are now investing in high-tech solutions, such as various forms of automated underwater vehicles, including "DNAdetecting robots". However, these systems are very expensive to run, difficult to deploy in many habitats where biodiversity information is urgently required, and mostly reliant on single-species detection kits.
Our team recently demonstrated that sponges (phylum Porifera - the world's most efficient water-filterers) concentrate particles in their tissues, from which trace DNA of the surrounding biota can be retrieved and screened. Since sponges are also present in every marine habitat - and are amenable to non-lethal sampling - this offers the exciting prospect of harnessing Nature's own recording devices as biological observers, and hence by-pass some of the most cumbersome steps along the eDNA workflow, through highly reduced costs and minimal environmental impact. This project will thoroughly investigate the mechanisms that will enable to transform this attractive prospect into an operational tool for exploring and monitoring biodiversity across the world's oceans. We will:
quantify the degradation time of the DNA trapped in sponge tissues;
compare species detection ability of sponges with that of water samples in both captive and wild settings;
evaluate sponge "natural sampler DNA" (nsDNA) performance in both benthic and pelagic habitats, and considering a variety of sponge morphologies;
explore the usefulness of sponge nsDNA to identify biodiversity patterns inside and outside protected areas;
evaluate the potential of the nsDNA approach as opportunistic and 'citizen science' tools for recording biodiversity.
The project will deliver an affordable, low-tech bio-monitoring tool (alternative or complementary to high-tech automated equipment), alongside a thorough understanding of the scenarios under which 'natural environmental DNA samplers' can offer the greatest contribution to marine biodiversity assessment.