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.
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.
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.
Organisations
- Liverpool John Moores University (Lead Research Organisation)
- Natural History Museum (Collaboration)
- South African Institute for Aquatic Biodiversity (Collaboration)
- University of Rome Tor Vergata (Collaboration)
- University of Otago (Collaboration)
- Horniman Museum and Gardens (Collaboration, Project Partner)
- National Marine Park of Zakynthos (NMPZ) (Collaboration)
- Ocean Tracking Network (Collaboration, Project Partner)
- University of Bologna (Collaboration)
- Oregon State University (Project Partner)
- Natural England (Project Partner)
Publications
Jeunen G
(2023)
Characterizing Antarctic fish assemblages using eDNA obtained from marine sponge bycatch specimens
in Reviews in Fish Biology and Fisheries
Albonetti L
(2023)
DNA metabarcoding of trawling bycatch reveals diversity and distribution patterns of sharks and rays in the central Tyrrhenian Sea
in ICES Journal of Marine Science
Cai W
(2022)
Environmental DNA persistence and fish detection in captive sponges
in Molecular Ecology Resources
Mariani S
(2021)
Estuarine molecular bycatch as a landscape-wide biomonitoring tool
in Biological Conservation
Maiello G
(2022)
Little samplers, big fleet: eDNA metabarcoding from commercial trawlers enhances ocean monitoring
in Fisheries Research
Maiello G
(2023)
Net gain: Low-cost, trawl-associated eDNA samplers upscale ecological assessment of marine demersal communities
in Environmental DNA
Harper L
(2023)
Optimized DNA isolation from marine sponges for natural sampler DNA metabarcoding
in Environmental DNA
D'Alessandro S
(2021)
Sifting environmental DNA metabarcoding data sets for rapid reconstruction of marine food webs
in Fish and Fisheries
Cicala D
(2024)
Spatial analysis of demersal food webs through integration of eDNA metabarcoding with fishing activities
in Frontiers in Marine Science
Neave EF
(2023)
Trapped DNA fragments in marine sponge specimens unveil North Atlantic deep-sea fish diversity.
in Proceedings. Biological sciences
Jeunen G
(2023)
Unveiling the hidden diversity of marine eukaryotes in the Ross Sea: A comparative analysis of seawater and sponge eDNA surveys
in Environmental DNA
Description | We have examined the various factors that affect DNA recovery from marine sponge tissues and developed best-practice protocols for the use of these organisms as sources of environmental DNA (published). We have shown, in controlled conditions, how different sponges preserve eDNA in their tissues: some mirror the eDNA decay observed in conventional water samples, some appear to trap the eDNA for longer stretches of time, and some others show poor DNA recovery, due to causes that are still under investigation (published). We have shown that artificial 'biomimetic' tools can also be used as eDNA accumulators, and these have been successfully employed to assess trawl fisheries (published). We have produced a remarkable reconstruction of deep-sea fish assemblages across the North Atlantic, based on DNA extracted from sponge tissues archived in the Natural History Museum (published). This line of research also showed that sponges are effective at characterising deep-sea invertebrate communities as well (in revision). We have shown how sponges that naturally settle on human-made structure can be harvested to recover the open sea assemblage surrounding said structure, in effect becoming low-cost serendipitous biomonitoring tools (in review). We have shown how other "natural samplers" - namely jellyfish and sea anemones - can also function as eDNA troves in marine ecosystems (in revision). |
Exploitation Route | We hope that sea sponges can become more widely employed as natural eDNA sentinels in many habitats and regions. We hope that sponge-inspired biomimetic tools can be employed in a wide range of marine biomonitoring scenarios. |
Sectors | Aerospace Defence and Marine Agriculture Food and Drink Education Environment Leisure Activities including Sports Recreation and Tourism Culture Heritage Museums and Collections |
URL | https://assets.researchsquare.com/files/rs-3710632/v1/3bfe8cfe-ae66-4a30-be28-cf5d23cb0f98.pdf?c=1704831031 |
Description | The interest from Natural England led to a report on a novel biomonitoring approach, assisted through the "metaprobe" device (illustrated in previous sections). The same approach continues to receive interest across the world (well beyond our capacity to engage with every organisation), so we have created a CC-BY-NC-ND page for the free sharing of the device and protocols. |
First Year Of Impact | 2022 |
Sector | Aerospace, Defence and Marine,Agriculture, Food and Drink,Education,Environment,Leisure Activities, including Sports, Recreation and Tourism,Culture, Heritage, Museums and Collections |
Impact Types | Cultural Societal Policy & public services |
Description | Published Natural England Report |
Geographic Reach | National |
Policy Influence Type | Influenced training of practitioners or researchers |
URL | https://publications.naturalengland.org.uk/publication/6249569948794880 |
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 | Testing eDNA metabarcoding as a technique for monitoring subtidal sediment condition - marine Natural Capital and Ecosystem Assessment Programme |
Amount | £19,457 (GBP) |
Funding ID | NEPW_010823_TDNAM |
Organisation | Natural England |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 11/2023 |
End | 03/2024 |
Title | The Metaprobe |
Description | This is a bio-inspired, low-cost, low-impact, 3D-printed device that can make eDNA sampling swift, simple, and globally upscaled. It has been successfully operationalised from both trawler boats and SCUBA divers. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | The tool is currently being used by researchers and practitioners in the UK (Natural England), Italy, Germany (statutory coastal monitoring authorities), USA, Chile, and South Africa. |
URL | https://github.com/GiuliaMaiello/Metaprobe-2.0 |
Title | Data and code for: Trapped DNA fragments in marine sponge specimens unveil north Atlantic deep-sea fish diversity |
Description | Sponges pump water to filter feed and for diffusive oxygen uptake. In doing so, trace DNA fragments from a multitude of organisms living around them are trapped in their tissues. Here we show that the environmental DNA retrieved from archived marine sponge specimens can reconstruct the fish communities at the place of sampling and discriminate North Atlantic assemblages according to biogeographic region (from Western Greenland to Svalbard), depth habitat (80-1600 m), and even the level of protection in place. Given the cost associated with ocean biodiversity surveys, we argue that targeted and opportunistic sponge samples - as well as the specimens already stored in museums and other research collections - represent an invaluable trove of biodiversity information that can significantly extend the reach of ocean monitoring. |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | Yes |
URL | https://datadryad.org/stash/dataset/doi:10.5061/dryad.rbnzs7hhp |
Title | Environmental DNA persistence and fish detection in captive sponges |
Description | This is the data for the study Environmental DNA persistence and fish detection in captive sponges, including raw sequencing data and all documents for bioinformatics and statistical analysis. |
Type Of Material | Database/Collection of data |
Year Produced | 2022 |
Provided To Others? | Yes |
Impact | experimental evidence of variability in eDNA detection efficiency and eDNA persistence in sponge tissues |
URL | https://zenodo.org/record/6603365 |
Title | Optimized DNA isolation from marine sponges for natural sampler DNA metabarcoding |
Description | Full dataset and code to reproduce the results. |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | exhaustive protocols for obtaining good quality environmental DNA from sponge tissues |
URL | https://zenodo.org/record/7264066#.ZAnlTuzP2lM |
Description | Co-supervision of doctoral students |
Organisation | University of Bologna |
Country | Italy |
Sector | Academic/University |
PI Contribution | I am an official co-supervisor of two PhD students registered at the University of Bologna. They will both visit my lab to process some of their samples. |
Collaborator Contribution | Sampling, provision of reagents, full-time labour of early-career researchers. |
Impact | data are yet to be generated. Outputs have not been produced yet. |
Start Year | 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 | They 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 |
Description | DNA-Divers Participatory & Citizen Science Initiative |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | We first engaged with the recreational scuba-diving community to pair their activities with concomitant eDNA sampling, using a low-tech user-friendly protocol. This expanded to a series of locations and events that were part of Natural England's monitoring programmes and the multiannual SEASEARCH network. We also attracted interest from overseas (Norway, South Africa, USA), which led to further samples being gathered by divers in those countries. |
Year(s) Of Engagement Activity | 2022,2023 |
URL | https://dnadivers.wixsite.com/join/about |