From mudflat to photobioreactor:
the BIO-Tide story
How marine ecologists and a microalgae company developed a new way to cultivate the microalgal biofilms that sustain tidal-flat ecosystems
The living film that appears at low tide
A tidal flat may look almost bare when the sea retreats. Look more closely, and parts of its surface are covered by an intense brown film. Under a microscope, that film reveals a dense community of microorganisms dominated by benthic microalgae, particularly diatoms.
During daylight, they move towards the sediment surface and photosynthesise so actively that bubbles of oxygen can form around them. The organic carbon they produce rapidly enters the food web. It passes through bacteria and microscopic animals living among the sediment grains, then onwards to shellfish and other organisms. These biofilms help sustain the rich animal life found on tidal flats, despite their apparently barren surface.
BIO-Tide studied these communities during field campaigns in France and the Netherlands. Researchers traced carbon as it moved through the food web and investigated how microalgae interacted with bacteria, nematodes and other organisms. Laboratory experiments were combined with ecological modelling and remote sensing to examine processes ranging from individual cells to entire tidal flats.
The findings showed that both biofilm production and carbon cycling depended on relationships among organisms almost invisible to the human eye. Different combinations of diatoms and bacteria affected biomass production. Nematodes could stimulate biofilm growth through grazing and movement within the sediment.
At low tide, benthic microalgae form brown biofilms on the sediment surface. Under a microscope, these films reveal diverse communities dominated by diatoms, while intense photosynthesis can produce visible bubbles of oxygen. By combining remote sensing with physical modelling, researchers mapped integrated daily primary production across the Brouage mudflat in March, May and July, with estimated totals of 2.06, 1.42 and 0.80 tonnes of carbon, respectively.
Photos: BIO-Tide. Maps adapted from Méléder et al. (2020)
An unexpected route towards aquaculture
The work also revealed properties that could be useful beyond the mudflat. BIO-Tide initially planned to investigate whether benthic microalgae could support oyster production. Discussions with the aquaculture company Benth’Ostrea led the researchers in a different direction.
The company was interested in sea urchin cultivation. A critical stage occurs when swimming larvae settle onto a surface and transform into juveniles. BIO-Tide experiments found that biofilms formed by the diatom Nitzschia laevis could stimulate this transformation.
Cultivated diatom biofilms could also provide a more controlled alternative to natural biofilms, which may bring unwanted organisms or contamination into aquaculture facilities. Follow-up experiments confirmed the initial results.
Other work within BIO-Tide examined the lipids produced by different benthic diatoms and their possible value for aquaculture and biotechnology. The project had identified organisms with useful ecological and biochemical characteristics. Producing enough of them reliably was another matter.
Small organisms can substantially influence biofilm production. Diatom biovolume production increased with species richness, while the presence of bacteria altered and strengthened this diversity–productivity relationship (A). A natural nematode community also stimulated the accumulation of biofilm biomass over time compared with the control treatment (B).
Adapted from Koedooder et al. (2019) and D’Hondt et al. (2018).
A reactor designed for the wrong way of life
Most photobioreactors keep microalgae suspended and circulating in water. Benthic diatoms live differently: they attach to surfaces and form cohesive biofilms. Systems built around stirring and circulation are therefore often poorly suited to them, making it difficult to produce enough biomass for experiments or explore possible applications.
During BIO-Tide’s extension in 2020, the Nantes team met with SYNOXIS ALGAE, a French company that designs adaptable photobioreactors for research, biotechnology and aquaculture. Together, they agreed a roadmap for adapting one of the company’s systems to cultivate benthic diatoms.
Rather than circulating the algae through water, the proposed reactor would allow them to grow as a film on a vertical porous surface, receiving water and nutrients through the material while remaining exposed to light and air.
A photobioreactor designed around the natural growth form of benthic diatoms. In the porous-substrate photobioreactor, diatoms grow as an attached biofilm on cultivation discs, while culture medium circulates through a separate reservoir. The comparison at right shows how this differs from conventional suspension cultivation and submerged-biofilm systems.
Adapted from Podola et al. (2017) and Arnaldo (2023).
Developing the system together
The roadmap agreed during BIO-Tide was taken forward through doctoral research. The Nantes team and SYNOXIS engineers refined the system as they learned how the diatoms responded to the growth surface, light, nutrient delivery and operating conditions. Its specifications evolved with the research rather than being fixed from the outset.
The collaboration went beyond ordering a piece of laboratory equipment. SYNOXIS contributed engineering expertise, facilities and technical support, while the researchers provided the biological knowledge needed to guide each adjustment.
Tests later showed that the adapted reactor achieved higher biomass and lipid productivity than conventional flask cultures, confirming its potential as a laboratory-scale system for cultivating benthic diatoms.
The Nantes laboratory eventually acquired the reactor and incorporated it into further research and training. The system also allowed researchers to revisit some of BIO-Tide’s original questions under controlled conditions, including how interactions with bacteria influence the development and productivity of diatom biofilms.
Diatom biofilms can support a critical stage in sea urchin cultivation. After 72 hours, biofilms of Nitzschia laevis, natural biofilms, a mixed-diatom treatment combined with GABA, and diatom-colonised oyster shells induced metamorphosis in more than 90% of competent Paracentrotus lividus larvae. Other treatments were considerably less effective.
Adapted from Castilla-Gavilán et al. (2020).
Allowing the research to change
BIO-Tide’s private-sector collaborations did more than provide services or disseminate results. They changed the research itself. Benth’Ostrea redirected part of the work from oysters towards a concrete challenge in sea urchin cultivation. SYNOXIS joined later, once another practical barrier had become clear. Neither contribution was fully prescribed when the project began.
These collaborations could take shape because BIO-Tide had generated the scientific knowledge, stakeholder relationships and flexibility needed to respond as new questions emerged. In both cases, the exchange began with a practical problem rather than a predetermined product.
The collaboration with SYNOXIS resulted in a shared research tool that extended the questions both partners could pursue and created a new way to bring one of the mudflat’s least visible communities into the laboratory.
BIO-Tide combined laboratory cultivation and microscopy with field campaigns, sediment sampling, in situ measurements and controlled experiments. These complementary approaches allowed researchers to examine processes ranging from individual microorganisms and experimental communities to carbon flows across entire tidal-flat ecosystems.
Photos: BIO-Tide.
In brief
- At low tide, dense brown biofilms can appear across the surface of mudflats. Formed largely by microscopic algae, these thin living layers produce organic carbon, support coastal food webs and help stabilise sediment.
- BIO-Tide investigated how the diversity of microalgae, bacteria and minute animals influenced these ecological functions. Its research also revealed potential applications for benthic microalgae, from aquaculture to the production of valuable lipids.
- But cultivating them presented a problem: most photobioreactors are designed for algae suspended and mixed in water, while benthic species naturally grow attached to surfaces. A collaboration initiated through BIO-Tide brought researchers together with SYNOXIS ALGAE to adapt the technology. The reactor developed through the collaboration has since supported doctoral research, scientific publications and further experimentation with microalgal biofilms
Explore more impact stories
This summer, Biodiversa+ looks back at research projects supported through its predecessor, BiodivERsA, exploring how scientific collaboration has contributed to policy, practice and innovation. Each story highlights what changed, how researchers worked with stakeholders, and what future projects can learn from their experience.
