Drivers that structure coastal marine microbiome with emphasis on pathogens – an integrated approach

Holder: Assoc. Prof. Dr Valentina Turk

PARNTER: prof. dr. Maja Ravnikar

Code: J1-9157

Duration: 1.7.2018 - 30.06.2021

The authors acknowledge the project J1-8156 was financially supported by the Slovenian Research Agency.

Proposal abstract – summary

Outbreaks of diseases in marine organisms are increasing worldwide, causing many viruses, pathogenic bacteria, and toxic species of cyanobacteria and phytoplankton. Despite considerable advances in recent years, knowledge on the importance of pathogenic bacteria in marine organisms is lacking or incomplete. It is necessary to understand the impacts of disease in marine environment due to their fundamental impact on community composition, the dynamics of biogeochemical processes, marine food webs changes and the health of marine ecosystems. Witin the proposed research project we will assess the presence/occurance, abundance, activity and diversity of pathogenic and other potentially harmful microbes in coastal marine environment (the Gulf of Trieste, N Adriatic). First, coastal marine microbiomes of potential hot spots will be assessed and based on this, an extensive list and database of potentially pathogenic and harmful microbial species will be made. Specific bacterial pathogens of interest will be selected, upon screening of the 16S rRNA amplicons dataset and of the sequence database based on the culture collection of microbes, and this will serve as baseline to design specific molecular assays (qPCR, ddPCR, LAMP) for their further detection and quantification during in situ survey. We will develop and test quick, reliable and cost-efficient methods for tracing and quantification of selected pathogenic and harmful microorganisms in the coastal water. At last, the spreading pattern of potentially pathogenic/harmful microorganisms will be predicted by developing oceanographic model and the relationship between microbial community and a set of environmental factors will be assessed using appropriate statistical models. In addition, will be performed a set of enrichment laboratory experiments to investigate adaptation of pathogenic microbes to high salinity and their potential impact on the ambient marine microbial community structure and function.

One of the main outcomes of the project will be the first extensive and reliable database/inventory of the marine microbiomes. At the same time, culture collection of selected strain, represents potential source of microbes for blue biotechnology sector, will be created, archived and made available to innovative research sector, blue economy agents and promoters. The second main outcome of the project are new tools and methods for fast, reliable and precise detection and quantification of pathogenic strains, which could be potentially used/applied in the regular monitoring and to be developed into commercial service/products. Overall, our integrated interdisciplinary approach will provide important inputs for the development of more accurate statistical and oceanographic ecosystem models t can be further applied as warning systems in the coastal environments and as such can contribute to the safeguard of human health and wellbeing.

The project is multidisciplinary oriented, combining knowledge and up-to-date techniques available in marine microbial ecology, metagenomics, bioinformatics, molecular biology, marine chemistry, statistic, biophysics and physical oceanography. The applicant will collaborate with scientists that are experts in different fields. The preliminary scientific experiences and available resources support project feasibility.

This project is of great relevance for broader scientific community because is tackling different areas of research – ecology of marine microbes, effect of natural and/or anthropogenic pressures on marine environment, ecosystem and oceanographic modelling. The scientific results will be published in high-quality international peer-reviewed journals and presented at national and international conferences. We will open a specific website - page for the project, which will be used to disseminated project’s achievements. All genomic results will be deposited at publically available databanks and all publications will be made open access.