Periodic Reporting for period 1 - COMBO (Innovative cultivation methods for marine biodiscovery)
Reporting period: 2024-01-01 to 2025-06-30
Despite their well-recognized potential, marine bioactive molecules are still difficult to source due to a lack of controlled culturing and processing infrastructures, and their chemical synthesis is hampered by their chemical complexity. The main sources of the high-value biomolecules are corals, sponges, algae, involving industrial end-users in the medical and pharmaceutical, food, and cosmetic sectors. Therefore, new approaches are urgently needed in marine biotechnology as microbial engineering has not fully met the expectations for producing the marine bioactives identified in invertebrates and seaweeds. Omics technologies have transformed the way the complexity of the marine holobiont can be viewed and today the integration of omics data such as genomics and metabolomics can increase our understanding of the functioning and processes of living organisms including their metabolic pathways. COMBO will allow the transfer of knowledge from terrestrial to marine biotechnology through the engineering of marine metabolic pathways using Omics approaches. The rationale behind COMBO lies in the power of synthetic consortia of host cells and microbial cells based on the concept of holobiont and auxotrophy. COMBO will therefore expand the potential offered by underused marine sponges and seaweeds known to produce bioactives such as terpenoids and alkaloids for the cosmetic and pharmaceutical markets
The objectives of COMBO are:
- O1 To identify and characterise hosts and associated microbiota for targeted groups of seaweeds (Dictyota and Laurencia) and sponges (Crambeidae and Haplosclerida) using integrative taxonomy - WP2 and WP4.
- O2 To develop innovative cell cultivation methods for seaweed and sponge species at cell, aquaria, and mesocosm scales and optimization of the conditions WP3
- O3 To study the co-metabolism based on auxotrophy and the identification of the secretome in WP3, WP4, and WP5.
- O4: O1, 2 and 3 will allow the elucidation the metabolic pathways of seaweed terpenoids and sponge alkaloids targeted using –omics approaches – WP2 WP3 and WP4
- O5 Develop and propose new chassis cells for marine active compounds from seaweeds and sponges. – WP5
- O6 To develop green downstream processes for the isolation of the four families of seaweed and sponge targeted active compounds using cultivation systems in WP3 and WP5 - WP6 WP7.
- O7 Screen the targeted families of metabolites for anti-inflammatory, antitumoral antimicrobial and antiaging applications – WP6.
The objectives of COMBO are:
- O1 To identify and characterise hosts and associated microbiota for targeted groups of seaweeds (Dictyota and Laurencia) and sponges (Crambeidae and Haplosclerida) using integrative taxonomy - WP2 and WP4.
- O2 To develop innovative cell cultivation methods for seaweed and sponge species at cell, aquaria, and mesocosm scales and optimization of the conditions WP3
- O3 To study the co-metabolism based on auxotrophy and the identification of the secretome in WP3, WP4, and WP5.
- O4: O1, 2 and 3 will allow the elucidation the metabolic pathways of seaweed terpenoids and sponge alkaloids targeted using –omics approaches – WP2 WP3 and WP4
- O5 Develop and propose new chassis cells for marine active compounds from seaweeds and sponges. – WP5
- O6 To develop green downstream processes for the isolation of the four families of seaweed and sponge targeted active compounds using cultivation systems in WP3 and WP5 - WP6 WP7.
- O7 Screen the targeted families of metabolites for anti-inflammatory, antitumoral antimicrobial and antiaging applications – WP6.
O0 During the first part of the project we were delighted to be funded to include another partner NKUA (Fay Ioannou and Vassilios Roussis) from the widening country Greece through a HOP ON project.
The COMBO website and a corresponding webdatabase have been created and linked to the COMBO MS teams group to track all the samples and progress in the project
Eight scientific articles and reviews related to COMBO have already been published and they are available open access through the website.
O1. More than 350 samples of sponges and seaweeds have been collected during this first half of the project which is above the target aimed. Importantly, bioprospecting expeditions to South Africa afforded new species of sponges that are being currently described . More than 50% of the macroorganisms collected have been identified using morphology and molecular data. The microbiota associated with three of the four targeted groups have been cultured and more than 200 microbes have been grown and sequenced for their identification. Another approach using metagenomics provided a more exhaustive view of the associated microbiota for three species belonging to three distinct targeted groups.
O2. Cells of the model sponge Geodia barretti have been successfully cultured and for seaweeds Dictyota dichotoma from Ireland has been maintained and grown in aquarium. A first trial changing light and temperature conditions was performed and led to the identification of the best conditions for the production of the targeted compounds by Dictyota.
O4. The metagenomes and metatranscriptomes have been obtained for one sponge of the genus Haliclona and one seaweed of the genus Dictyota. The search for biosynthetic gene clusters has started in both genomes and transcriptomes.
O5 Two marine yeasts and bacteria have been studied and selected as best chassis cells for future heterologous expression of genes.
O6 The optimisation of the purification processes has been developed for the four targeted families of natural products at lab scale. It will be adjusted for the upscaling of the process following sustainability rules.
O7 More than 350 fractions prepared from COMBO samples have been tested for antibacterial, cytotoxicity and antifungal activities. At least 100 fractions have shown strong activities for one of the three activities tested. One of the targeted seaweed species collected in South Africa led to 7 pure compounds that showed very promising bioactivity.
The COMBO website and a corresponding webdatabase have been created and linked to the COMBO MS teams group to track all the samples and progress in the project
Eight scientific articles and reviews related to COMBO have already been published and they are available open access through the website.
O1. More than 350 samples of sponges and seaweeds have been collected during this first half of the project which is above the target aimed. Importantly, bioprospecting expeditions to South Africa afforded new species of sponges that are being currently described . More than 50% of the macroorganisms collected have been identified using morphology and molecular data. The microbiota associated with three of the four targeted groups have been cultured and more than 200 microbes have been grown and sequenced for their identification. Another approach using metagenomics provided a more exhaustive view of the associated microbiota for three species belonging to three distinct targeted groups.
O2. Cells of the model sponge Geodia barretti have been successfully cultured and for seaweeds Dictyota dichotoma from Ireland has been maintained and grown in aquarium. A first trial changing light and temperature conditions was performed and led to the identification of the best conditions for the production of the targeted compounds by Dictyota.
O4. The metagenomes and metatranscriptomes have been obtained for one sponge of the genus Haliclona and one seaweed of the genus Dictyota. The search for biosynthetic gene clusters has started in both genomes and transcriptomes.
O5 Two marine yeasts and bacteria have been studied and selected as best chassis cells for future heterologous expression of genes.
O6 The optimisation of the purification processes has been developed for the four targeted families of natural products at lab scale. It will be adjusted for the upscaling of the process following sustainability rules.
O7 More than 350 fractions prepared from COMBO samples have been tested for antibacterial, cytotoxicity and antifungal activities. At least 100 fractions have shown strong activities for one of the three activities tested. One of the targeted seaweed species collected in South Africa led to 7 pure compounds that showed very promising bioactivity.
More than 300 samples have been collected in Ireland and South Africa including some targeted groups. At least 20 new species of seaweeds and sponges collected in South Africa are being described following an integrative approach. The inclusion of the new partner NKUA will increase the potential for discovery of bioactive metabolites from Greek seaweeds. Two metagenomes have provided for the first time for one targeted seaweed and one targeted sponge.
The cell culture of the model sponge Geodia barretti has been set up and the chemical composition of the cell culture is ongoing. The cell cultures of seaweeds have proven to be more challenging than expected but the culture of Dictyota in a semi enclosed system has been successful and allowed for the identification of the ideal conditions of light and temperature for the production of the targeted diterpenoids. This will correspond to an increase of TRL for the seaweed in land aquaculture. The first coculture of yeasts with a targeted seaweed was performed for the first time and led to promising results in terms of yeast growth. The companies involved in COMBO will be able to perform the demonstration of the method.
The biological screening of more than 350 fractions present in the COMBO repository have highlighted at least 100 fractions of interest for antimicrobial, antitumoral or antiinflammation bioactivities and the work is ongoing to purify and identify the structures of the bioactive metabolites . Two new halogenated acetogenins have been identified from a species of Laurencia collected in South Africa and two new bioactive guanidine alkaloids have been identified in a sponge collected in Papua New Guinea present in the biorepository at Galway. Diterpenoids from Dictyota have shown promising cytotoxicity on tumoral cell lines and would therefore correspond to the first hit in COMBO. A peptide identified in an Irish sponge has shown potent antiinflammatory activity and corresponds to a second hit.
Companies have been contact from the cosmetic and pharmaceutical fields to investigate the potential of applications of seaweed and sponge biomolecules respectively as planned.
The cell culture of the model sponge Geodia barretti has been set up and the chemical composition of the cell culture is ongoing. The cell cultures of seaweeds have proven to be more challenging than expected but the culture of Dictyota in a semi enclosed system has been successful and allowed for the identification of the ideal conditions of light and temperature for the production of the targeted diterpenoids. This will correspond to an increase of TRL for the seaweed in land aquaculture. The first coculture of yeasts with a targeted seaweed was performed for the first time and led to promising results in terms of yeast growth. The companies involved in COMBO will be able to perform the demonstration of the method.
The biological screening of more than 350 fractions present in the COMBO repository have highlighted at least 100 fractions of interest for antimicrobial, antitumoral or antiinflammation bioactivities and the work is ongoing to purify and identify the structures of the bioactive metabolites . Two new halogenated acetogenins have been identified from a species of Laurencia collected in South Africa and two new bioactive guanidine alkaloids have been identified in a sponge collected in Papua New Guinea present in the biorepository at Galway. Diterpenoids from Dictyota have shown promising cytotoxicity on tumoral cell lines and would therefore correspond to the first hit in COMBO. A peptide identified in an Irish sponge has shown potent antiinflammatory activity and corresponds to a second hit.
Companies have been contact from the cosmetic and pharmaceutical fields to investigate the potential of applications of seaweed and sponge biomolecules respectively as planned.