Understanding and harnessing the power of the microalgae microbiome aiming the maximization of marine microalgae productivity

Microalgae are important CO2 sinks and sustainable biomass feedstocks for the bioenergy and bioproducts industries worldwide. These features have attracted great interest in the industrial cultivation and exploitation of several microalgae, including marine microalgae such as Nannochloropsis oceanica CCAP 211/4 and Phaeodactylum tricornutum CCAP 1055/1 that are able to synthesize important and valuable compounds such polyunsaturated fatty acids (PUFAs) and carotenoids (e.g. fucoxanthin), and are used in a wide range of biotechnological applications.

Nevertheless, the industrial production of these microalgae faces several challenges. Under large-scale production facilities such as photobioreactors and raceways, microalgae are i) susceptible to environmental stress conditions (i.e. temperature shifts, shading and irradiation, osmotic stress), ii) mostly cultivated devoid of their natural microbiota, and are posteriorly impacted by non-specific contaminants and microbial pathogens from the environment, which decreases overall microalgae productivity. Moreover, not much is understood about the factors that lead to the synthesis and accumulation of bioactive compounds by N. oceanica and P. tricornutum.

All these factors lead to a decrease in microalgae productivity and negatively impact their production costs. One way to address these challenges may reside on the efficient use of beneficial microalgae-associated bacteria. Recent studies have unveiled the vital role of the microbiome in regulating and potentiating the development of several eukaryotic hosts, including microalgae. In this sense, beneficial symbiotic and mutualistic members of the microbiome can promote microalgae growth and production of bioactive compounds, through a variety of beneficial syntrophic relationships as well as the modulation of microalgae developmental programs. For example, beneficial bacteria can facilitate nutrient acquisition by microalgae (i.e. vitamin B12, ammonia, PO4, organosulfur compounds, iron); produce/catabolize phytohormones (e.g. indoleacetic acid, 1-aminocyclopropane-1-carboxylate) that impact microalgae growth or compete with pathogens and protect microalgae from microbial pathogen attack. Ultimately, the application of selected beneficial microalgae associated bacteria can lead to an increased microalgae growth, stress resistance, and accumulation of bioactive compounds, thus, potentiating microalgae productivity.

Despite the known beneficial properties of some members of the microalgae microbiome, not much is understood about the microbiome assembly of relevant microalgae such as N. oceanica or P. tricornutum under natural or large-scale industrial production facilities, nor the molecular mechanisms involved in beneficial microalgae-bacteria interactions. Moreover, there is a lack of co-inoculation strategies aiming at increasing microalgae productivity in large-scale production facilities. The PHYCOμBIOME project aims to study the microbiome (at both ecologic and functional levels) of the marine microalgae N. oceanica and P. tricornutum when grown in selected natural Portuguese sea and estuarine waters, and, in the ALGATEC industrial facilities in Portugal; to gain new insights into the mechanisms governing algae-bacteria interactions, and, finally, to develop co-inoculation strategies to potentiate microalgae productivity (biomass and valuable compounds) under industrial conditions.

This innovative research plan multidisciplinary and based on the use of several next-generation omics techniques (metagenomics, genomics, transcriptomics, and metabolomics), bioinformatics, applied microbiology, integrated bioprocesses, and advanced mathematical modeling.

Overall, a new sustainable solution for improving microalgae productivity under laboratory and industrial conditions will be achieved. The detailed analysis of the microalgae-bacteria interactions will reveal novel information regarding the molecular and biochemical basis of the beneficial microalgae-bacteria associations. The integration of the data obtained from the analysis will lead to the development of new innovative co-cultivation strategies that are expected to potentiate microalgae productivity (biomass, PUFAs, carotenoids) by ~20%.