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Marine Biodiversity as Sustainable Resource of Disease-Suppressive Microbes and Bioprotectants for Aquaculture and Crop Diseases

Periodic Reporting for period 1 - MARBLES (Marine Biodiversity as Sustainable Resource of Disease-Suppressive Microbes and Bioprotectants for Aquaculture and Crop Diseases)

Reporting period: 2021-05-01 to 2022-10-31

MARBLES addresses the urgent need for new treatment methods for aquaculture and crop diseases by exploring and exploiting the microbiomes of natural marine ecosystems. MARBLES will identify and exploit both novel bioactive compounds and microbial consortia that act as bioprotectants against aquaculture and crop diseases, by exploiting the microbiomes of natural marine ecosystems. Bioprotection will be validated following aquaculture and greenhouse trials, taking cognisance of relevant biosafety requirements. Production of prototype small molecule and microbial consortia formulations will be optimized and will be available for subsequent sustainable commercial exploitation post-project.
The overall aim of MARBLES is to harness the unexplored potential of marine microorganisms as producers of novel antimicrobial agents and as bioprotectants in aqua- and agriculture, using an integrative, ecology-based strategy for bioprospecting.
The Specific Objectives of MARBLES are:
a) To discover microbes and microbial consortia to be used as bioprotectants in aquaculture and agriculture.
b) To develop small-molecule and microbial consortia formulations for sustainable commercial exploitation post-project.
c) To discover microbial small-molecule compounds with antifungal or antimicrobial activity.
d) To discover product candidates with potential human health applications, for commercialization post-project.
e) To discover elicitors that enhance expression of silent biosynthetic gene clusters for use in improved screening regimes for novel bioactive molecules from microbes.
f) To provide environmentally friendly alternatives to the prophylactic use of antibiotics in aquaculture and thus reduce the threat of AMR.
g) To provide environmentally friendly alternatives to the continued use of synthetic agrochemicals in agriculture.
h) To build upon existing buy-in with policy makers to provide science-based advice for important ongoing policy discussion related to bio-based biotechnology.
i) To communicate the findings of MARBLES to a diverse range of stakeholders and engage the public in advances in marine biotechnology and understanding the importance of biodiversity.
Bacterial isolates have been obtained from Atlantic Salmon (Salmo salar) skin from three different geographical locations in Ireland and Norway. Metagenomic DNA from these Salmon skin samples and 16S rRNA amplicons have been generated and are being analysed. Metagenomic DNA has been extracted from three shallow water sponge species (Tethya citrina, Cliona celata and Raspailia ramosa) and from three deep-sea sponge species (Stelletta normani, Poecillastra compressa and Inflatella pellicula). Shotgun metagenome sequencing is being performed on these targeted sponge samples. Microbial communities from the marine sponges Geodia barretti, Antho dichotoma, Phakellia ventilabrum and Mycale lingua that were harvested from the Trondheim fjord (Norway). Salicornia europea plants were sampled from Terschelling island (The Netherlands) as a source of microorganisms from halophilic and marine environments and 16S rRNA metagenomic analysis is being carried out
Identification of the most promising ecosystems for natural product discovery in sponges will be performed by linking global sponge biodiversity patterns to both overall microbial diversity and biosynthetic gene cluster (BGC) diversity in Petrosiidae in a variety of marine environments. The first samples have been taken from sponges collected in Curacao. DNA barcoding studies on these sponges has been performed together with selected sponge samples from previous field campaigns.
Panels of pathogens have been selected to test microbiomes, microbial strains and bioactive compounds.
Bioactive strains have been identified, their genomes sequenced and the natural product BGCs identified using antiSMASH. BGCs that could potentially be involved in the antagonism have been identified. A platform to screen simultaneously the chemical diversity in an extract together with its bioactivity is been used to pinpoint to possible novel bioactive compounds. This information together with the environmental knowledge is used to identify elicitors that could activate cryptic BGCs.To further help with the strains and extracts, prioritization MS and (meta)genomes data is being linked by means of a newly developed software. BGC information is also used to start the work on regulation and modification of strains to produce possible new bioactive compounds as well as modified analogues.
Microbial libraries of bioactive strains have been generated and they are being tested against several fish and human pathogens. Extracts have been made and they are also being tested through a High Throughput Screening platform.
The MARBLES consortium has held several meetings online and the Kick-off and the annual meeting in person in Wageningen, The Netherlands (17-18 October 2022).
MARBLES has also joined the AIMS cluster together with 4 other projects funded under the same FNR-11-2020 call. Public engagement and outreach has started with the participation of MARBLES during the Micro Day of Leiden European city of science.
All the MARBLES news, results and updates have been widely communicated through the MARBLES website, social media and e-newsletters.
MARBLES makes use of existing as well as novel technologies to isolate, identify and deliver novel biocontrol agents for agriculture and aquaculture. MARBLES project aims to provide sustainable products such as microbiomes, microbial strains and pure compounds identified from the marine environments. As an example of a typical approach, MARBLES is identifying the most promising ecosystems for natural product discovery in sponges by linking global sponge biodiversity patterns to both overall microbial diversity and biosynthetic gene cluster (BGC) diversity. One of MARBLES strategies is to mimic the natural host-microbiome system, together with studying the evolution of the microbial diversity, at multiple cultivation conditions.
MARBLES is developing novel techniques and software that links (meta)genome data with LC-MS/MS data to prioritize natural products, based on bioactivity, chemical novelty and diversity. Another state-of-the-art technique being used is a screening platform that uses molecular networking, nanofractionation, MS/MS coupled with bioactivity assay to assess possible candidates that could lead to novel molecules with bioactivity, even in the tiniest of samples.
MARBLES is strongly committed to comply with European regulations and to keep a sustainable and environmental use of the marine resources as well as the possible future products. MARBLES has started public-private cooperation by inviting members to the first meeting with the panel of industry experts. International policy impacts have started and a workshop was organized by MARBLES partners at the UN BBNJ IGC5 negotiations and we have met with the Advisory Panel of Policy and Legal Experts (APPLE).
The MARBLES Team during their annual meeting in Wageningen, The Netherlands