The role of Microbes in Aquaculture: understanding the functional role of oyster microbiomes in response to changing climates and diseases

Project Information

MicroAqua

Grant agreement ID: 101105991

DOI

10.3030/101105991

Project closed

EC signature date 19 April 2023

Start date 1 September 2023

End date 30 November 2025

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 223 424,67

Coordinated by

UNIVERSITY COLLEGE CORK - NATIONAL UNIVERSITY OF IRELAND, CORK
Ireland

Periodic Reporting for period 1 - MicroAqua (The role of Microbes in Aquaculture: understanding the functional role of oyster microbiomes in response to changing climates and diseases)

Reporting period: 2023-09-01 to 2025-11-30

Summary of the context and overall objectives of the project

Owing to the ecological and economic importance of bivalves, understanding their functional role in habitats, and their susceptibility to climate change and diseases is of great importance. In Europe, aquaculture produces 1.3 million tonnes of seafood, with molluscan aquaculture production of oysters, clams and mussels contributing ~47%. Bivalve production has a low environmental footprint and plays a substantial role in economic decoupling by achieving economic growth while preserving a healthy environment by recycling nutrients (removal of nitrogen and carbon), stabilising sediments, and enhancing biodiversity. In addition to the production of bivalves for human consumption, bivalve stock production is vital for the restoration of lost native oyster habitats.
Environmental stressors and emerging pathogens represent serious limitations to the sustainable production of bivalves and their role in ecological functioning of ecosystems. A changing climate and marine environment challenges bivalve physiology leading to increased susceptibility to infection and the diversion energy from reproduction and growth. These challenges limit sustainable biomass production as well as the socioeconomic and ecological benefits that bivalve culture provides to near shore coastal communities.
While significant research has been conducted on the larger scale regarding production and the ecological role of oysters, as well as whole organism responses to changing climates and pathogens, little research has been conducted on the role of oyster-associated microbes in relation to oyster health. Improvements in understanding host-microbe interactions and the roles of microbes in host
functioning have increased the recognition of microbial associations in ecology. Research in humans and other higher organisms has shown that these small scale communities play important roles in disease resistance and individual performance (longevity and reproductive ability/fecundity). Therefore, in the case of oysters, the functional role of microbiomes in resistance to climate change and disease susceptibility may be a crucial factor for production and continued persistence that has not been explored in-depth.
The overarching aim of the MicroAqua project is to address critical knowledge gaps in our understanding of how oyster microbiomes contribute to oyster functioning, health, and resistance to pathogens under climate change. Through the implementation of multidisciplinary work packages, this project will (1) gain insights into spatio-temporal and tissue specific microbiota of oysters, (2) assess how various climate change scenarios impact oyster microbiomes and oyster health, (3) investigate the impact of emerging pathogens on oyster microbiomes and health, and (4) assess the potential of marine bivalve-derived bacteria as probiotics to reduce mortality in oysters.
This project intended to use a combination of next-generation sequencing technologies to provide a greater understanding of the functional role of oyster microbiomes, and the potential importance of host-microbe interactions for these important aquaculture species.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The MicroAqua project combined ecological experiments with molecular microbiology to investigate the importance of host-microbe interactions within oysters. At the start of the fellowship, the Research Fellow undertook substantial training in molecular microbiology, microbial culturing, and bioinformatics to allow the undertaking of the research independently. Such training was vital, and enabled the Fellow to apply these newly acquired microbiome analysis tools to investigate the effects of environmental change on these marine organisms.
The first application of the gained molecular biology techniques allowed the characterisation of tissue-specific microbiomes in the European flat oyster (Ostrea edulis). Results showed that microbial communities within oysters differ significantly between tissues such as the gut and gills. Further, microbial communities differed across sampling locations and seasons, indicating that both environmental conditions further influence oyster microbiomes. It was also observed that oyster microbiomes also contain a number of antibiotic resistance genes, however further work is required to understand the sources of such genes. Following the initial baseline characterisation of oyster microbiomes, a series of laboratory experiments were conducted to investigate how future climates and bacterial pathogens affect the oyster microbiome, and the overall health of oysters.
Experimental results indicated that environmental stress alone did not consistently cause mortality in oysters, although future warming conditions produced subtle shifts in microbial community composition. Pathogen exposure, however, resulted in increased mortality in some cases, and was associated with significant disruption of the oyster gut microbiome. Morbid oysters were observed to have an increased abundance of pathogenic bacteria including Vibrio species. Shotgun metagenomic sequencing was also conducted during one of the climate change experiments, which will reveal additional insights into the functional role of oyster microbiomes, however further work is required to fully analyse the data.
In parallel with experiments investigating potential impacts on oyster microbiomes, a biobank of bacteria were isolated from marine bivalves. These isolates were screened for antimicrobial activity against aquaculture and human pathogens, resulting in a collection of approximately 40 bacterial isolates exhibiting antimicrobial activity. One strain exhibited particularly strong inhibitory activity against important aquaculture pathogens. Whole-genome sequencing of this bacterium revealed genes encoding antimicrobial compounds, including a potentially novel bacteriocin. These findings highlight the potential for microbiome-based approaches to improving disease resistance in aquaculture.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The results from MicroAqua demonstrate that oyster-associated microbiomes play an important role in host health, disease susceptibility, and responses to environmental stress. These findings contribute to a growing recognition that host organisms and their microbial communities function as integrated biological systems. With oyster microbiomes being highly structured and tissue-specific, results show that microbial communities within oysters are actively associated with the host rather than simply reflecting surrounding seawater, thereby increasing our understanding of bivalve ecology and the potential role of the microbiome in oysters. Experimental results further indicate that disease outcomes in oysters are closely associated with microbiome disruption, rather than the presence of pathogens alone. Oysters experiencing mortality following pathogen exposure exhibited highly altered gut microbiomes dominated by pathogenic bacteria, suggesting that maintaining microbiome stability may be an important factor in preventing disease outbreaks in aquaculture systems. The project also revealed species-specific responses to environmental stress and pathogen exposure with European flat oysters and Pacific oysters showing contrasting mortality patterns under environmental change and pathogen exposure levels. These differences suggest that microbiome dynamics may contribute to variation in species resilience to climate change. Lastly, the identification of antimicrobial-producing bacteria from marine bivalves further demonstrates the potential role of host-associated microbiota in preventing severe outcomes from infections, and highlights the potential for microbiome-based disease management strategies in aquaculture. Such approaches could help reduce reliance on antibiotics and support more sustainable shellfish production systems. Overall, MicroAqua advances the field by integrating microbiome science with marine ecology and aquaculture research, highlighting the importance of host–microbe interactions for understanding organismal resilience under environmental change.