KYTOS toolbox Expanded with Oomycetes Detection Algorithm

Chicory: a Unique Crop Cultivation

Chicory (“witloof“) is a traditional Belgian vegetable, which, unlike most other vegetables, has to be grown twice. The chicory is sown in regular soil to allow the development of roots. The roots are then harvested from the field and planted in trays, stacked vertically in large, dark storehouses. Recirculating water circuits across the trays distribute nutrient solutions to the crops, making them highly susceptible to diseases.

Oomycetes Plague the Horticulture Industry

Oomycetes are a group of fungus-like microorganisms that include a wide range of pathogens. They are among the most problematic groups of disease-causing organisms in both agri- and aquaculture. Some of the most damaging diseases include potato late blight (“aardappelziekte“), downy mildew (“valse meeldauw“), and root rot (“wortelrot“).

Chicory or “Witloof” cultivation is traditionally farmed in vertically stacked hydroponic systems.

New KYTOS offering Helps to Take Immediate Action Against Oomycetes

With crop losses of billions of dollars annually, these diseases pose a large threat for global food security. The genera Pythium and Phytophthora affect a wide range of crops and are difficult to treat and get rid of. During their life cycle, oomycetes produce spores which can spread the disease quickly. This spread is amplified in hydroponic installations though intensive water recirculation.

We are happy to announce:

  • A novel Oomycetes detection algorithm has been added to our growing KYTOS toolbox.
  • KYTOS services can now empower horticulture companies even more to take targeted and timely management strategy for their water system.
  • Routine microbiome health surveillance is key to assessing root rot risks for each batch.

KYTOS Partners up with Innovators

Primalof, an innovative Flemish company, is specialized in the hydroponic cultivation of chicory. Primalof is working with Praktijkpunt Landbouw Vlaams-Brabant to optimize their water reuse, in order to further improve on the environmental friendliness of their production processes. To help assess their water treatment and guarantee microbial water quality, our microbiome health service was used, which included our latest KYTOS algorithm for the detection and risk assessment of oomycetes spores.

We are looking at applying ultrafiltration to make this water reuse safer. A quick and accurate analysis of the water quality is essential for our trial.

Yannah Cornelis, Researcher at Praktijkpunt Landbouw

Novel Oomycetes insights revealed by KYTOS algorithms

We put our latest KYTOS algorithm for the detection and quantification of oomycetes spores to the test. As usual, we found some very exciting things:

  • The abundance of zoospores was quantified and the water treatment efficacy could be tracked for each batch.
  • Water preparation is key. Oomycetes spores are seeded primarily at the start of the cultivation.
  • Treatments took 5 – 7 days to take significant effect.
  • Our precise zoospore quantification demonstrated that oomycetes remained highly abundant for several days.
KYTOS Oomycetes risk indicator measured during the 23 day cultivation of Chicory / Witloof.

Are you also seeking to:

  • Minimize disease risk
  • Improve water quality
  • Foster more stable production conditions
  • Promote and control microbial health

Contact us now!

Introducing WorldFish interns, Jonabel and Ngan

KYTOS is partnering with WorldFish to conduct microbiome research in carp polyculture and tilapia farming systems. Together, we want to bring KYTOS technology closer to farmers. As a precursor for further investment in this project, two interns will be reviewing the current state of knowledge. Ms. Bui Ngoc Minh Ngan will be focusing on the microbiomes of carp polyculture systems, while Ms. Johnabel Huavas will be doing the same for tilapia farming systems. Both interns are funded by WorldFish under the project, Aquaculture: Increasing income, diversifying diets and empowering women in Bangladesh and Nigeria.

Meet Jonabel and Ngan! Check out the press release here.

Jonabel Huavas

Can you tell us something more about your background?

I earned my Master’s degree in Aquaculture Major in Health Management from Ghent University in 2021 through the VLIR-UOS scholarship. I have a Bachelor’s degree in Biology Major in Microbiology from the University of the Philippines Los Baños. My interests revolve around applied microbiology, molecular biology, alternative feeds and aquaculture nutrition, microbial management, and fish physiology.

Why did the WorldFish internship appeal to you?

When I first read about the internship post, one word stood out: microbiome. During my studies, I’ve learned and became fascinated about the huge impact and application of microorganisms.  Working for WorldFish is also a great opportunity for me to learn from and work alongside aquaculture experts. The worldwide network and connection established by WorldFish is also an opportunity for me to meet and know different tilapia farmers and researchers across the world.

What are you looking to learn from the internship?

I wanted to learn about the current status of tilapia aquaculture in the perspective of microbial community management. During my graduate studies in the midst of pandemic, I was not able to do fieldwork and internship in commercial farms or other research centers. Doing this comprehensive study and networking with different stakeholders of the tilapia industry will help me learn about the current situation when it comes to microbiome management. I am also interested to learn about Kytos technology and how it can further improve aquaculture practices.

Jonabel Huavas, who will be reviewing the current state of knowledge of microbiomes in tilapia systems.

Any particular achievement you want to reach?

Being in the scientific research field, writing is inevitable. First achievement that I want to reach through this internship is to become a better writer and storyteller. Next goal in mind is to provide a tangible output that will help level up current tilapia farming systems into data-driven, microbiome-based management.

Farmers have been waiting for decades on microbiome management technologies, where do you see yourself have the biggest impact?

I see myself having the biggest impact in establishing the baseline—the current perception and appreciation towards microbiome-based management. My contribution lies into looking for the gaps between the farmers’ present understanding towards microbiome and assisting with the preparation of potential research project that will incorporate Kytos technology for best tilapia farming practices.

Bui Ngoc Minh Ngan, who will be reviewing the current state of knowledge of microbiomes in carp polyculture systems.

Bui Ngoc Minh Ngan

Can you tell us something more about your background?

I am a Master Graduate in Aquaculture at Ghent University. My research interests are in understanding the interaction of aquaculture species with their environment in order to produce healthy animals. I specialize in fish physiology, microbial community management, the host-microbiome, and microbe-microbe interactions. My objective is to work in an enriching atmosphere that promotes lifelong learning and professional growth.

Why did the WorldFish internship appeal to you?

As a graduate student in aquaculture, I want to work in a professional environment to put my acquired knowledge into practice and increase my network. WorldFish is the ideal workplace for me to start my professional career. I want to contribute and to learn how they create, advance, and translate scientific research on aquatic food systems into scalable solutions to ensure sustainability in aquaculture.

What are you looking to learn from the internship?

I am looking for opportunities to stimulate international network, extend existing knowledge, gain new insights, and learn new techniques. An internship at WorldFish would be a promising position that offers a good chance for my personal growth and contribution to the team.

Any particular achievement you want to reach?

I want to use my abilities and expertise to provide dependable and successful outcomes in the field of the microbiome in carp polyculture systems. Moreover, by working in WorldFish, I want to correct my shortcomings and upgrade my abilities to advance my career.

Farmers have been waiting for decades on microbiome management technologies, where do you see yourself have the biggest impact?

With the internship at WorldFish, my research about microbiomes in carp polyculture systems can be transformed into a series of research and practical techniques. It can help in the creation of prediction models for the microbial communities of commercial fish species to avoid invasive pathogens and improve fish health.

Ruben’s guest lecture at the 2021 German Cytometry Conference

Computational analysis of microbial flow cytometry data

DGfZ | Microbiology Session | Friday, October, 1st, 2021, 11:00am – 12:30pm

Flow cytometry (FCM) is an important technology for the study of microbial communities. It grants the ability to rapidly generate phenotypic single-cell data that are both quantitative, multivariate and of high temporal resolution. Microbial FCM data have a number of different characteristics and challenges compared to immunophenotyping FCM data. Most prokaryotic cells are much smaller in size and volume than human or mammalian cells, and although most cells are small, the size range within which microbial cells lie is larger than for mammalian cells, covering a range between 0.2 and 500µm. Microbial communities also comprise high levels of phenotypic and phylogenetic complexity (e.g. 1000s of taxa). In this talk, I will provide an overview of common pitfalls of traditional FCM computational techniques on these microbial data, and describe how we can move towards a tailored and reproducible approach for microbial ecology studies. Finally, I will list a number of open challenges to the field and offer further motivation for the use of standardized flow cytometry in microbial ecology research.

Effective microbial management key to farming efficiency

A great collaboration with INVE aquaculture, Benchmark’s Advanced Nutrition group, and Jasmine Heyse (PhD candidate at CMET) resulted in novel insights into the way microbial communities assemble, and are influenced by artemia-, algae-, and dry feed-associated microbiomes, in shrimp hatchery systems.

In this study, we found that the microbial community assembly in the hatchery rearing water over time was dominated by stochastic effects. This demonstrates that random fluctuations in growth and death of bacterial species cause microbiomes in identical shrimp tanks to become more dissimilar over time. Two major shifts in microbial community structure that were tightly coupled to the abundance of Chaetoceros algae were observed. Using a newly developed source tracking algorithm we could quantify that 37% of all bacteria in the hatchery rearing water were introduced either by the live or dry feeds, or during water exchanges. The contribution of the microbiome from the algae was the largest, followed by that of the Artemia, the exchange water and the dry feeds.

These findings have significantly improved our fundamental knowledge on the assembly processes and dynamics of rearing water microbiomes and illustrate the crucial role of the peripheral microbiomes in maintaining health-promoting rearing water microbiomes.

Press release Link to the publication

A novel, rapid method for identifying bacterial threats in aquaculture

Nico, professor at CMET – Center for Microbial Ecology and Technology and our KYTOS thought leader, provided some context on our journey from academia to spin-off in an interview with the fishsite.

His main take-away: “In the very near future we will be able to translate these complex microbial fingerprints into specific management advice that empowers farmers with actionable microbial management

Check out the full article!

Microbiome insights: few and far between

Ruben and Jasmine Heyse, PhD candidate at Ghent University discuss the limitations and knowledge gaps in microbial ecology in shrimp aquaculture in the 2019 issue of HatcheryFeed (volume 7, issue 4). They argue that the establishment of effective and sustainable microbial management strategies would be greatly accelerated by increasing our knowledge regarding the microbial ecology of these systems. A concerted effort among both industrial stakeholders, who have access to diverse aquaculture platforms, and academic partners, who have access to the know-how of next-generation technologies, is paramount to revolutionize the fundamental basis on which aquaculture microbiome management must be based.

Full column available here!