Beneath the surface: a new view on marine microbiome sampling

Microscopic societies

When the ancient Greek storyteller Aesop first wrote the words "United we stand, divided we fall," he was onto something profound. This proverb, typically associated with human cooperation, holds true in the natural world as well. In nature, organisms frequently form vital associations, including with microorganisms. Take humans, for example; we are not just solitary beings comprised of our own cells. Our bodies harbour a thriving ecosystem of microorganisms. The fascinating concept of the microbiome isn't limited to land; it extends to the watery realms of our planet, including the oceans.

Marine microbiomes comprise a community of microorganisms and viruses dwelling in oceans and seas. These ecosystems also encompass interconnected environments such as the seafloor, marine animals, and plants. Marine microbiomes account for 90% of the total living marine biomass, showcasing their significant impact on underwater ecosystems. 

Marine microbiomes

Marine microbiomes constitute a community of microorganisms and viruses inhabiting oceans and seas. These ecosystems span interconnected environments such as the seafloor, marine animals, and plants, contributing to 90% of the total living marine biomass. Despite their significance, we have not explored marine microorganisms as much as their land counterparts in the quest for bioactive compounds – molecules with substantial biological effects sought after for pharmaceutical, medical, or industrial purposes.

Historically, investigations into marine sources focused on invertebrates like corals or jellyfish and their associated microbiomes have raised ethical, economic, and environmental concerns. Collecting them and extracting their bioactive compounds may harm or disrupt their natural habitats lying solely on them for large-scale production might not be economically viable; the limited availability of certain invertebrate species poses scalability challenges for research purposes.

In response to these concerns, researchers are exploring alternative sources for bioactive compounds that are both ethical and environmentally responsible. This entails investigating microorganisms, algae, or other marine organisms to offer a sustainable and economically viable alternative. By diversifying the sources of bioactive compounds, researchers aim to address ethical issues, reduce environmental impact, and create more sustainable practices in marine biotechnology.

Uncharted territories: eutrophicated environments

In ecosystems experiencing eutrophication, excessive nutrients foster increased microbial activity, starving other forms of life of oxygen. But these eutrophicated environments, often considered 'waste' areas, harbour significant potential for valuable bioactive compounds. Although extensive research has been conducted on soil and marine invertebrate microbiomes, environments affected by eutrophication have received limited exploration until now. Shifting focus to eutrophicated environments opens both new avenues for sustainable bioprospecting and addresses ethical, economic, and environmental concerns associated with traditional sources.

The MetaFluidics European project delved into the possibilities within the eutrophicated Mar Menor lagoon—a shallow saltwater lake in Spain marred by human-induced pollution. The repercussions of this pollution manifested as a concerning state of eutrophication, triggering the overgrowth of algae and various microorganisms. The research unveiled a trove of novel natural products, including potent antimicrobials capable of inhibiting or eradicating the growth of bacteria, viruses, and fungi. This groundbreaking discovery addresses the environmental challenges posed by eutrophication and opens avenues for harnessing valuable resources from ecosystems previously perceived as degraded.

Life in the extremes

Microbial communities can thrive in extreme environments because they develop molecular strategies to resist their harsh physical and chemical surroundings. Despite previous studies exploring extreme environments from an ecological standpoint, research addressing the functional diversity and operational mechanisms of these resilient microbial communities is scarce.

One example of such resilient communities is found in biofilms—structured microbial communities existing as surface-attached clusters or suspended aggregates—that can inhabit locations experiencing both low and high tides. “Biofilms are exposed to desiccation, radiation, and many other extreme conditions. When they are underwater, they are protected against radiation but when the tide is low, they get exposed to radiation and they start to dry out” explains Eduardo Gonzalez-Pastor, a researcher at Centro de Astrobiología (CAB), CSIC-INTA. 

In the pursuit of a more comprehensive understanding of these unique ecosystems, the EU project Bluetools is investigating biomolecules in various marine environments, particularly those that have been underexplored, such as extreme environments. Simon Charnock, CEO at Prozomix Limited who works on the project, says that both academic institutions and companies are working together to find ways to scale up enzyme production.

Focusing on biofilms, the project aims to unravel the molecular mechanisms behind their adaptations. Understanding how extreme microorganisms adapt to these environments holds not only biotechnological applications but also implications for agriculture. “Due to climate change, plants are more sensitive to changes, for example, solar radiation” explains Gonzalez-Pastor. This is why introducing genes related to radiation or desiccation resistance found in these marine communities could enhance plant performance.

In exploring the microscopic societies within marine environments, we uncover hidden potential for sustainable bioprospecting. From the depths of eutrophicated environments to the resilience of extreme ecosystems, researchers are forging new paths in marine biotechnology. Projects like MetaFluidics and Bluetools signify a shift towards ethical and environmentally responsible practices, diversifying our sources of bioactive compounds. As we venture into these uncharted territories, we not only address environmental concerns but also open doors to innovative solutions with broad implications for fields like medicine and agriculture. The microscopic societies in the oceans may hold the key to a more sustainable and interconnected future, subtly weaving nature, and humanity together.