Advanced search
1 file | 64.09 MB Add to list

Identifying drivers of microbial dynamics in aquaculture : from single-cell technology to metagenomics

Jasmine Heyse (UGent)
(2022)
Author
Promoter
(UGent) , (UGent) and (UGent)
Organization
Abstract
The growing world population necessitates a reliable supply of high-quality protein, which is increasingly provided through aquatic animal products. The frequent outbreaks of diseases and the economic losses associated with these outbreaks is one of the main restraints for a further sustainable expansion of the aquaculture sector. To meet the increasing demand, aquaculture systems must become more efficient through sustainable, long-term biosecurity management strategies that reduce the occurrence of diseases. In light of these diseases, bacterial pathogens are of major concern. Over the years, it has become clear that bacteria do not only play a role in the emergence of diseases, but that they are of great importance for many functional aspects in the aquaculture ecosystem, in which they are involved in cycling of nutrients, degradation of organic matter etc.Therefore, a holistic approach where not only the potential pathogens, but the entire microbial community is monitored and manipulated, is needed to effectively manage aquaculture ecosystems. To develop and perform this management in practice we need, on the one hand, to understand which microbiomes lead to optimal performance and how we can steer microbiomes towards that state, and on the other hand, to be able to monitor the microbial communities during the cultivation. It is widely accepted that rearing water has a strong influence on the host microbiomes, and, hence, plays an essential role in the emergence of diseases. Therefore, proper management of the rearing water microbiome is considered crucial for obtaining productive systems. The research presented in this dissertation has aimed to acquire insights into the microbial community ecology of rearing water bacterial communities and their community members, and in the process, to contribute to the development of tools that can be used for investigating and monitoring these rearing water microbiomes. In Chapter 2, we have acquired new insights in the dynamics, assembly and sources of rearing water communities of a Litopenaeus vannamei larviculture farm. We tracked the bacterial densities of the rearing water microbiomes of 5 replicate cultivation tanks through a high-resolution sampling campaign and show that bacterial densities increased with 2 log-units over an 18 day cultivation. When studying the dynamics of the community composition of these microbiomes, we determined two community shifts that could be related to the dynamics of the algae in the water. Hence, our study illustrates that even when algae are added in low abundance to be used as a feed product, they can have a steering role on the bacterial community. We found that stochastic processes dominated the community assembly in the water over time, which could be linked to the high observed heterogeneity between the replicate tanks. Through a better understanding of the community assembly processes that are prevailing in an ecosystem, we should be able to make informed decisions about optimal monitoring schemes and management practices, such as dosing of probiotics. Hence, further investigations regarding how widespread this dominance of stochastic community assembly is across farm layout and in relation to different farm management practices, will be a crucial step to improve management practices. During the sampling campaign, we additionally investigated the microbial communities present in the live (algae and Artemia) and dry feed products, and the exchange water. For each of these peripheral microbiomes we found a high batch-to-batch variability, both in terms of bacterial abundance and community composition. Additionally, for the live feeds, we found a high within-batch variability in bacterial densities. The most striking dynamics were those of the Artemia storage basins where in each batch, bacterial growth was observed over 24 hours, leading up to a 10-fold difference in bacterial densities for samples originating from the same batch. We have quantified the contributions of these peripheral microbiomes to the rearing water and found that ± 10 % of the rearing water operational taxonomic units (OTUs) were introduced through these sources. Together, these OTUs were responsible for 37 % of the rearing water community over the entire cultivation. These results illustrate the importance of peripheral microbiomes. Given this large contribution, careful preparation and storage of these inputs will be paramount to maintain stable, healthy systems. Determining the composition of microbial communities is an essential step in both microbiome management and research. In Chapter 3, we have developed a new pipeline that allows to predict the presence and abundance of taxa in environmental communities based on flow cytometric measurements. Using cell-sorting, we validated that the model correctly associates taxa to regions in the cytometric fingerprint, where they are detected using 16S rRNA gene amplicon sequencing, illustrating the reliability of the constructed models. This pipeline expands the existing flow cytometric toolbox for the assessment of community status in a fast, cheap and high-throughput manner. While some further validation of the developed models is recommended, this pipeline holds great potential to be integrated in routine monitoring schemes and early warning systems for the aquaculture sector. Rearing water microbiomes contain a large diversity of bacterial taxa. In Chapter 4, we investigated the in situ life strategies of 67 taxa present in the rearing water. We found evidence for niche separation between r- and K-strategists in the communities, with r-strategists typically encoding for more and more diverse transporters and metabolic pathways and having a higher fitness for exploitation of spatially structured nutrient hotspots. This niche separation provides an explanation for the coexistence of r- and K-strategists in the rearing water. Additionally, we found that the in situ growth activity of r-strategists could be linked better with the cultivation performance as compared to the distribution of relative abundances of r- and K-strategists in the rearing water. Although we could not provide a mechanistic understanding of this relationship between the growth activity of r-strategists and host health based on our study, these findings open a future for further research into the in situ functionalities of r- and K-strategists, and their potential role in mediating the host performance. In conclusion, during this dissertation several insights in the ecology of bacterial communities in rearing water of aquaculture ecosystems were obtained. These insights contribute to the knowledge base that is needed to develop effective management strategies to reduce the occurrence of diseases. Our findings include insights with direct practical implications (e.g. optimization of live feed preparation and storage protocols), as well as insights that can be translated into management strategies after further research (e.g. the implications of stochastic changes in community composition for determining optimal protocols for administering probiotics or optimizing monitoring schemes; management strategies to direct the growth activities of r-strategists). In parallel, a new method was developed that allows to predict the presence and abundance of bacterial taxa via flow cytometric fingerprinting. This method contributes to the toolbox of available pipelines for assessing the status of a microbial community in a fast, cheap manner.

Downloads

  • (...).pdf
    • full text (Published version)
    • |
    • UGent only (changes to open access on 2027-01-18)
    • |
    • PDF
    • |
    • 64.09 MB

Citation

Please use this url to cite or link to this publication:

MLA
Heyse, Jasmine. Identifying Drivers of Microbial Dynamics in Aquaculture : From Single-Cell Technology to Metagenomics. Ghent University. Faculty of Bioscience Engineering, 2022.
APA
Heyse, J. (2022). Identifying drivers of microbial dynamics in aquaculture : from single-cell technology to metagenomics. Ghent University. Faculty of Bioscience Engineering, Ghent, Belgium.
Chicago author-date
Heyse, Jasmine. 2022. “Identifying Drivers of Microbial Dynamics in Aquaculture : From Single-Cell Technology to Metagenomics.” Ghent, Belgium: Ghent University. Faculty of Bioscience Engineering.
Chicago author-date (all authors)
Heyse, Jasmine. 2022. “Identifying Drivers of Microbial Dynamics in Aquaculture : From Single-Cell Technology to Metagenomics.” Ghent, Belgium: Ghent University. Faculty of Bioscience Engineering.
Vancouver
1.
Heyse J. Identifying drivers of microbial dynamics in aquaculture : from single-cell technology to metagenomics. [Ghent, Belgium]: Ghent University. Faculty of Bioscience Engineering; 2022.
IEEE
[1]
J. Heyse, “Identifying drivers of microbial dynamics in aquaculture : from single-cell technology to metagenomics,” Ghent University. Faculty of Bioscience Engineering, Ghent, Belgium, 2022.
@phdthesis{8734215,
  abstract     = {{The growing world population necessitates a reliable supply of high-quality protein, which is increasingly provided through aquatic animal products. The frequent outbreaks of diseases and the economic losses associated with these outbreaks is one of the main restraints for a further sustainable expansion of the aquaculture sector. To meet the increasing demand, aquaculture systems must become more efficient through sustainable, long-term biosecurity management strategies that reduce the occurrence of diseases. In light of these diseases, bacterial pathogens are of major concern. Over the years, it has become clear that bacteria do not only play a role in the emergence of diseases, but that they are of great importance for many functional aspects in the aquaculture ecosystem, in which they are involved in cycling of nutrients, degradation of organic matter etc.Therefore, a holistic approach where not only the potential pathogens, but the entire microbial community is monitored and manipulated, is needed to effectively manage aquaculture ecosystems. To develop and perform this management in practice we need, on the one hand, to understand which microbiomes lead to optimal performance and how we can steer microbiomes towards that state, and on the other hand, to be able to monitor the microbial communities during the cultivation. It is widely accepted that rearing water has a strong influence on the host microbiomes, and, hence, plays an essential role in the emergence of diseases. Therefore, proper management of the rearing water microbiome is considered crucial for obtaining productive systems. The research presented in this dissertation has aimed to acquire insights into the microbial community ecology of rearing water bacterial communities and their community members, and in the process, to contribute to the development of tools that can be used for investigating and monitoring these rearing water microbiomes.

In Chapter 2, we have acquired new insights in the dynamics, assembly and sources of rearing water communities of a Litopenaeus vannamei larviculture farm. We tracked the bacterial densities of the rearing water microbiomes of 5 replicate cultivation tanks through a high-resolution sampling campaign and show that bacterial densities increased with 2 log-units over an 18 day cultivation. When studying the dynamics of the community composition of these microbiomes, we determined two community shifts that could be related to the dynamics of the algae in the water. Hence, our study illustrates that even when algae are added in low abundance to be used as a feed product, they can have a steering role on the bacterial community. We found that stochastic processes dominated the community assembly in the water over time, which could be linked to the high observed heterogeneity between the replicate tanks. Through a better understanding of the community assembly processes that are prevailing in an ecosystem, we should be able to make informed decisions about optimal monitoring schemes and management practices, such as dosing of probiotics. Hence, further investigations regarding how widespread this dominance of stochastic community assembly is across farm layout and in relation to different farm management practices, will be a crucial step to improve management practices. 

During the sampling campaign, we additionally investigated the microbial communities present in the live (algae and Artemia) and dry feed products, and the exchange water. For each of these peripheral microbiomes we found a high batch-to-batch variability, both in terms of bacterial abundance and community composition. Additionally, for the live feeds, we found a high within-batch variability in bacterial densities. The most striking dynamics were those of the Artemia storage basins where in each batch, bacterial growth was observed over 24 hours, leading up to a 10-fold difference in bacterial densities for samples originating from the same batch. We have quantified the contributions of these peripheral microbiomes to the rearing water and found that ± 10 % of the rearing water operational taxonomic units (OTUs) were introduced through these sources. Together, these OTUs were responsible for 37 % of the rearing water community over the entire cultivation. These results illustrate the importance of peripheral microbiomes. Given this large contribution, careful preparation and storage of these inputs will be paramount to maintain stable, healthy systems.

Determining the composition of microbial communities is an essential step in both microbiome management and research. In Chapter 3, we have developed a new pipeline that allows to predict the presence and abundance of taxa in environmental communities based on flow cytometric measurements. Using cell-sorting, we validated that the model correctly associates taxa to regions in the cytometric fingerprint, where they are detected using 16S rRNA gene amplicon sequencing, illustrating the reliability of the constructed models. This pipeline expands the existing flow cytometric toolbox for the assessment of community status in a fast, cheap and high-throughput manner. While some further validation of the developed models is recommended, this pipeline holds great potential to be integrated in routine monitoring schemes and early warning systems for the aquaculture sector.

Rearing water microbiomes contain a large diversity of bacterial taxa. In Chapter 4, we investigated the in situ life strategies of 67 taxa present in the rearing water. We found evidence for niche separation between r- and K-strategists in the communities, with r-strategists typically encoding for more and more diverse transporters and metabolic pathways and having a higher fitness for exploitation of spatially structured nutrient hotspots. This niche separation provides an explanation for the coexistence of r- and K-strategists in the rearing water. Additionally, we found that the in situ growth activity of r-strategists could be linked better with the cultivation performance as compared to the distribution of relative abundances of r- and K-strategists in the rearing water. Although we could not provide a mechanistic understanding of this relationship between the growth activity of r-strategists and host health based on our study, these findings open a future for further research into the in situ functionalities of r- and K-strategists, and their potential role in mediating the host performance.

In conclusion, during this dissertation several insights in the ecology of bacterial communities in rearing water of aquaculture ecosystems were obtained. These insights contribute to the knowledge base that is needed to develop effective management strategies to reduce the occurrence of diseases. Our findings include insights with direct practical implications (e.g. optimization of live feed preparation and storage protocols), as well as insights that can be translated into management strategies after further research (e.g. the implications of stochastic changes in community composition for determining optimal protocols for administering probiotics or optimizing monitoring schemes; management strategies to direct the growth activities of r-strategists). In parallel, a new method was developed that allows to predict the presence and abundance of bacterial taxa via flow cytometric fingerprinting. This method contributes to the toolbox of available pipelines for assessing the status of a microbial community in a fast, cheap manner.}},
  author       = {{Heyse, Jasmine}},
  isbn         = {{9789463574709}},
  language     = {{eng}},
  pages        = {{XVI, 194}},
  publisher    = {{Ghent University. Faculty of Bioscience Engineering}},
  school       = {{Ghent University}},
  title        = {{Identifying drivers of microbial dynamics in aquaculture : from single-cell technology to metagenomics}},
  year         = {{2022}},
}