SpongeDNA - Bolstering marine biodiversity exploration and monitoring through natural environmental DNA samplers

Lead Research Organisation: Liverpool John Moores University
Department Name: Sch of Biological and Environmental Sci

Abstract

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 "DNA-detecting 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: i) quantify the degradation time of the DNA trapped in sponge tissues; ii) compare species detection ability of sponges with that of water samples in both captive and wild settings; iii) evaluate sponge "natural sampler DNA" (nsDNA) performance in both benthic and pelagic habitats, and considering a variety of sponge morphologies; iv) explore the usefulness of sponge nsDNA to identify biodiversity patterns inside and outside protected areas; v) 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.

Planned Impact

The main beneficiaries will be: 1) Governmental Environmental Agencies, 2) Environmental NGOs, 3) the General Public in the UK and globally, 4) the Private Sector.
1) Governmental Agencies tasked with carrying out biomonitoring of marine habitats and communities are keenly looking into the application of novel molecular tools with a view to strengthening and streamlining their monitoring activities. Given the establishment of the UK DNA Working Group, in which PI Mariani has participated since its inception six years ago, we will maintain regular and fruitful dialogue with the relevant end-user community, which includes, among others, Natural England (project partner in this proposal), the Environment Agency (partner in the NERC Highlight Topic project "SeaDNA") and CEFAS (partner in the NERC-CASE project "StockDNA"). With such a robust stakeholder involvement, we will effectively update the end-user community on project advances and potential applications. Furthermore, with the opportunity to join the NHM's CryoArks Biobank initiative, we will be able to appropriately store tissue samples for the future and contribute to the creation of biodiversity baselines.
2) In recent years, Environmental NGOs have shown remarkable interest in DNA-based evidence to tackle marine conservation challenges, such as the protection of elusive, high-profile marine megafauna, the illegal trade in wildlife, and the design of marine protected areas. Mariani and Riesgo have good working relations with several of these foundations, including the Pew Charitable Trusts (who funded Mariani's first eDNA investigation of tropical shark communities), Oceana, the Bertarelli Foundation and the Wildlife Conservation Society. As the project develops, we will endeavour to disseminate updates on the efficacy of sponge nsDNA as an enhancement of eDNA science. To this end, we will organise and engage in seminars, multi-stakeholder workshops, and special sessions at selected conferences that typically value synergies among academic research, advocacy and policy (e.g. the International Marine Conservation Congress).
3) The role of the general public and civil society in escalating positive change in nature conservation is pivotal. We will ensure that the project findings and applications are clearly disseminated to society at large. The idea of a sea full of 'natural marine sentinels" that regularly record biodiversity data is a fascinating way to get people closer to the threats faced by ocean life and the actions that can be taken to mitigate them. Following the positive experience of previous projects, we will use Twitter to establish and maintain social media presence, which will be used as a platform for communicating all project achievements. Both PIs have an established track record of public engagement, writing articles and blogs (e.g. The Conversation; The Marine Biologist) and engage with radio, TV and science festivals to popularise research. We will also benefit from the unrivalled outreach opportunities afforded by the NHM, with its over six million visitors per year, and its regular, interactive events, such as NatureLive and NHMLates. Finally, we will also engage with Scuba-Diving clubs in the UK, Italy and Spain, to initiate a campaign of specimen collection, storing tissues as part of the CryoArks initiative, and georeferencing samples in an open-access online tool.
4) Several consultancies and private companies now offer DNA-based services for biodiversity monitoring. Our sponge natural sampling approach could be harnessed by private companies, offering a flexible, low-tech, affordable, and consistent method for eDNA sampling. Some companies could even be interested in "farming" certain sponge types for deployment on fixed structure and later harvesting for biomonitoring purposes. Others could be inspired to design artificial devices modelled on the biomechanics of sponges.

Publications

10 25 50
 
Description Natural Samplers for Marine Environmental DNA Monitoring
Amount £70,000 (GBP)
Funding ID Internal LJMU QR funding 
Organisation Liverpool John Moores University 
Sector Academic/University
Country United Kingdom
Start 09/2020 
End 09/2023
 
Description Horniman Aquarium 
Organisation Horniman Museum and Gardens
Country United Kingdom 
Sector Academic/University 
PI Contribution Designing experiment, providing consumables, carrying out experiments in their facilities.
Collaborator Contribution Providing facilities, providing live materials, ensuring health, safety, and ethical compliance.
Impact A full study has been completed (corresponding to "Objective 1" in the original project proposal). The manuscript arising from this work has been submitted to an academic journal in March 2022.
Start Year 2020
 
Description Natural History Museum, London 
Organisation Natural History Museum
Country United Kingdom 
Sector Public 
PI Contribution We metabarcoded sponge samples, analysed data and drafted a manuscript for submission. This initial activity was at the foundation of the whole project proposal.
Collaborator Contribution Procurement of invaluable sponge tissue samples from the Mediterranean and Antarctica. After this initial study, the NHM team engaged with the co-creation of the project proposal for this grant.
Impact A paper was published in 2019 (see relevant section). A grant proposal based on these ideas was submitted to the July 2019 NERC Standard Grant round (NE/T007028/1), then becoming the present project.
Start Year 2018
 
Description Natural Marine Park Zakynthos 
Organisation National Marine Park of Zakynthos (NMPZ)
Country Greece 
Sector Charity/Non Profit 
PI Contribution Piloting a unique comparison among coastal biodiversity surveillance with natural sampler DNA approach at its core.
Collaborator Contribution supporting local sampling and visual census activities
Impact no outputs yet. Initial stage.
Start Year 2021
 
Description Ocean Tracking Network 
Organisation Ocean Tracking Network
Country Canada 
Sector Public 
PI Contribution We provided detailed sampling protocols, materials, and molecular genomics expertise.
Collaborator Contribution They provided person-power, research vessel, storing and filtering facilities; they also arranged shipment of samples.
Impact Some of the samples have already been analysed. Academic outputs arising from this project component are expected during the summer/autumn 2022.
Start Year 2020
 
Description SANBI & SAIAB - "Deep Connections" 
Organisation South African Institute for Aquatic Biodiversity
Country South Africa 
Sector Public 
PI Contribution I have provided advice on eDNA and sponge natural DNA sampling approaches; I am co-supervising their PhD student; I will join sampling activities in the Indian Ocean in May 2022.
Collaborator Contribution The organised the sampling and will lead the investigation, focusing on emblematic marine fishes in South Africa.
Impact no outputs available yet.
Start Year 2021
 
Description University of Otago, New Zealand 
Organisation University of Otago
Country New Zealand 
Sector Academic/University 
PI Contribution We are sharing protocols for sponge DNA extractions, in view of collaborative historical ecology projects.
Collaborator Contribution New Zealand is an ideal setting to investigate the impact of colonisation, industrialisation and exploitation on coastal marine biodiversity, and we hope that preserved sponge specimens may serve as "biodiversity time capsules". We also intend to use this approach to study changes in antarctic ecosystems (with an emphasis on climate)
Impact no outputs yet. We are at an initial stage.
Start Year 2020
 
Description University of Rome 
Organisation University of Rome Tor Vergata
Department Department of Biology
Country Italy 
Sector Academic/University 
PI Contribution We have metabarcoded samples of "trawl slush" from survey vessels, in order to generate total biodiversity data.
Collaborator Contribution carried out sampling from Southern Italian continental shelf and slope.
Impact A manuscript has been submitted to the journal Frontiers in Ecology & the Environment, titled "All is fish that comes to the net: metabarcoding for rapid fisheries catch assessment".
Start Year 2018