EXPLORA: Harvesting extreme waters for tomorrow’s bioeconomy

Here, ITENE’s Rosa Doménech and Ana Mencher explain the project’s progress and look ahead to a promising future for the world’s most inaccessible microbes.

The idea that the most punishing corners of our planet could help decarbonise industry and improve human health sounds like science fiction until you meet the organisms that live there. In the acidic waters of Spain’s Río Tinto and in the sun-irradiated surface layers of the Antarctic Ocean, microbial life has evolved survival strategies with potential benefits for sectors as diverse as cosmetics, pharmaceuticals and environmental technologies.

Now EXPLORA, a four-year European research project that started in 2024 and is coordinated by ITENE in Spain, is building the scientific, technological and regulatory foundations to explore those possibilities further, responsibly harvesting antimicrobial and antioxidant compounds, as well as specific enzymes that can help degrade plastics more efficiently.

“Extreme aquatic environments host microorganisms that have evolved to thrive under harsh conditions,” says Rosa Doménech of ITENE. “These are known as extremophiles and they often produce unique compounds with potential applications in health, cosmetics, industrial technologies and chemical processes. EXPLORA is developing and testing innovative and sustainable sampling strategies, combined with ethical and legal compliance protocols, to enable responsible bioprospecting in some of the planet’s most inaccessible and sensitive environments.”

This is no smash-and-grab treasure hunt for exotic ingredients. It’s a methodical effort to understand and unlock microbial biodiversity in ways that support a sustainable bioeconomy, without damaging the fragile ecosystems that make these organisms valuable in the first place.

Why extremes matter

Extremophiles are nature’s prototyping lab. Bombarded by ultraviolet radiation, starved of light, or bathed in acidity and dissolved metals, microbes in these environments deploy biochemical tricks to survive: antioxidants to counter radiation stress; broad-spectrum antimicrobials to compete in sparse communities; and enzymes that stay active at low pH or near-freezing temperatures. These traits map neatly to industrial needs, from drugs and cosmetic ingredients to plastic-degrading enzymes suitable for industrial processes.

The challenge is two-fold. First, the organisms are often scarce and unevenly distributed, so simply collecting “more water” is unlikely to capture the most valuable microbes. “The aim isn’t to collect more,” says Ana Mencher. “It’s to collect better.”

Second, the natural stress conditions that trigger useful metabolites often disappear in the lab, making cultivation and scale-up challenging.

From the outset, the team framed EXPLORA’s work around three strands that mirror Europe’s push for a sustainable bioeconomy. The discovery strand seeks bioactive compounds with cross-sector relevance – antioxidants, antimicrobials, cosmetic ingredients and robust enzymes. The method strand focuses on environmentally responsible sampling approaches that other researchers can reproduce. And the translation strand validates industrial potential by moving beyond discovery to practical assessment – what can be made, how it performs and how it can be produced at scale.

“These objectives align with the EU’s broader goals of promoting a sustainable bioeconomy, enhancing environmental resilience and fostering innovation in biotechnology,” Mencher says. “We want to unlock novel biological resources for multiple sectors while maintaining the ethical and legal standards required for sampling in these environments.”

Methodology

EXPLORA’s workflow begins in the field and ends in the fermenter, with compliance embedded throughout. Targeted sampling uses small autonomous platforms purpose-built for two very different use cases. In Antarctica, is designed for waters exposed to strong sunlight and environmental stressors, where microbial communities are highly active and adapted to extreme conditions. These areas are a key focus due to the unique biological activity they host. In Río Tinto, by contrast, the platform targets zones with steep environmental gradients, where factors such as acidity and mineral content, vary and create distinctive microbial communities. The diversity and resilience of microbes in these challenging environments guide the development of devices capable of capturing representative samples efficiently and responsibly. “High-sensitivity sensors map these gradients in real time and guide pumps and collectors to the just-right zones where microbial communities turn over,” explains Doménech.

The platforms themselves are engineered from sustainable biomaterials to minimise environmental impact if damaged or lost, as Mencher adds. “The vessel provides autonomy, and sensor system is central to ensuring precise sampling where biological and chemical activity intersect.”

Back in the lab, microbial isolation and omics meet as metagenomics identifies organisms and their biosynthetic potential, metabolomics flags interesting chemistry; and bioinformatics ranks candidates for deeper study. EXPLORA is on exploring and characterising microorganisms that show the most promise in terms of the metabolites they produce, as well as those with genetic features of potential interest. “We aim to provide a clear picture of the most promising candidates for future research and applications.” Mencher says.

Compliance

In Spain, sampling sits under the Nagoya Protocol on access and benefit-sharing, with permits issued by the IE University (Spain) to ensure legal compliance; in Antarctica it falls under the Antarctic Treaty System. Permits, geolocation, traceability and benefit-sharing are built in from the start, with project partner the Ukrainian National Antarctic Scientific Centre (NASC) enabling polar access. Doménech stresses that EXPLORA wants to do more than tick boxes: “We’re helping make the workflow visible and reproducible, so responsible bioprospecting becomes the norm.”

EXPLORA is also shaping its outputs to live on long after the project comes to an end. These include its hardware such as autonomous, targeted sampling devices equipped with advanced sensing capabilities, designed to operate efficiently in diverse and challenging environments, and built from sustainable, bio-based materials. Another is its biological results: a curated microbial library of strains that are well-characterised, sequenced and annotated for their biosynthetic potential. “By sequencing the genome, you can infer the molecules a strain can potentially produce,” Mencher explains.

On the chemistry side, the team expects to bring forward validated candidates, from antioxidant and antimicrobial molecules to  to robust degrading enzymes that could be scaled up efficiently for industrial recycling processes. The data layer binds all this together with standard protocols, metadata and prioritisation logic so that other teams can reproduce methods and compare results. Finally, a compliance layer offers practical templates and guidance for permits, traceability and benefit-sharing, aimed at speeding responsible uptake.

Those using these results within the project consortium will span biotech SMEs and corporates, pharma, cosmetics and environmental-tech companies, as well as academic labs and policymakers. Commercial routes will vary, from licensing and royalties to process patents, depending on the result and the partner. “We’re developing the exploitation plan now,” Doménech says. “Each stakeholder has distinct priorities, and our goal is to find a balanced approach that accommodates them all.”

Eleven months in, EXPLORA has completed initial field campaigns in Antarctica and Río Tinto and is now deep into sequencing and analysis. Early microbial discoveries show promising bioactive potential, and the engineering team has matured device and sensor concepts for both environments. Less visible, but equally important, is the shared workflow the consortium has now agreed, from sampling to functional screening, which will help when results are translated and when standard methodologies are offered to the wider community.

Challenges

Microbial cells in these waters are scarce, and their behaviour is tied to stress conditions that evaporate the moment you remove them from their niche environment. Transport must preserve viability and, ideally, the physiological triggers that drive metabolite production. “Maintaining the stress that makes them interesting has been a technical challenge,” Mencher says. “We need enough biomass for industrial applications, but we also need the biology to behave.”

Economics are never far away either. In the ENZYCLE project ((BBI JU/H2020, Grant 887913), coordinated by ITENE, researchers worked with an enzyme capable of breaking down PET in around 16 hours under neutral pH conditions. Building on that experience, EXPLORA now aims to identify enzymes that can degrade PET efficiently under industrial conditions. “We want enzymes that function in conditions compatible with industrial processes,” Doménech says. “That would improve technical performance and reduce costs because we avoid pH adjustment.”

Logistics and regulatory requirements add another layer of complexity. Remote polar operations and sensitive river sites require careful planning and environmental safeguards, and Nagoya permitting involves thorough procedures that can take several months. EXPLORA has built time and expertise into its plan to address these requirements. A key part of the projects’s approach is the development of pathways to transfer relevant genes and pathways into industrial hosts. As Mencher puts it: “We’re not just cataloguing biodiversity. We’re learning which genes and pathways matter, and how to produce those molecules in the right host, at the right cost.”

Beneficiaries

The downstream benefits align closely with Europe’s priorities for a greener economy. Industry stands to gain access to sustainable ingredients and improved processes: skincare actives with high water-binding and antioxidant properties (reducing reliance on staples such as hyaluronic acid); antimicrobials that meet safety expectations; and enzymes that make plastic recycling less energy- and reagent-intensive.

The research community gains a living resource, curated strains, genomes, protocols, and the data frameworks to accelerate discovery and reduce duplication. The environment gains from targeted, lower-impact sampling; from devices designed to minimise harm; and from technological pathways, such as acid-stable depolymerases, that improve circularity.

And society sees cleaner processes, natural-origin products that consumers increasingly prefer, and new value chains anchored in European science and manufacturing. “Consumers are more interested in molecules from natural resources,” Doménech says. “So there is a market pull, and that aligns with EXPLORA’s objectives.”

Policy and regulation

In Spain, the Nagoya Protocol governs access to and export of genetic resources, with geolocation and purpose specified from the outset – research only, or with commercial intent. In Antarctica, access is mediated by the Treaty System, with partners such as NASC securing permits. But the project also wants to inform regulation. “We want to contribute harmonised approaches and recommendations,” Mencher says, “so others can follow clear steps and future bioprospecting is responsible by default.”

“That means publishing standard methods, describing device specifications with sustainability in mind, and offering practical templates for benefit-sharing across public and private stakeholders,” Doménech adds. “Clear guidelines are essential to ensure responsible and consistent practices.”

Looking ahead

By the end of the project, the team expects to leave behind transferable methods, a well-curated microbial library, validated candidates on the molecule and enzyme side, and a set of compliance and data assets that let others move quickly and safely. The near-term vision is a toolbox that works, devices that collect precisely and gently; omics pipelines that prioritise well; and engineered hosts that produce target molecules at pilot-relevant yields.

Beyond 2028, EXPLORA is designed to act as a benchmark for ethical bioprospecting in extreme and sensitive environments. The goal is that researchers, companies, and regulators will have clear guidance and frameworks available: protocols for sampling and assessment, decision tools for evaluating candidates, and templates to ensure fair and traceable benefit-sharing.  Mencher is pragmatic about the path from first sequence to factory floor: “Collect better, not more. Engineer where it makes sense. And build a resource that can support future work.”

“The increasing focus on sustainable solutions and low-impact industrial processes highlights the relevance of this research. This reflects the European Commission’s recognition of both the promise and urgency in exploring extreme aquatic environments,” says Doménech. “As climate change reshapes ecosystems and supply chains, and as industry looks for robust, low-impact solutions, the logic of extremophiles becomes ever clearer: biology already knows how to do hard things. Our job is to learn respectfully, design carefully and scale responsibly.”

EXPLORA’s promise isn’t just in what it finds, but in how it shows others to find it. As Doménech sums up: “We are different stakeholders across the value chain, but we share the same destination. Responsible science that industry can use.”