Microbiome Health Assessment In Greenhouses – Part 1

The Great Unknown: Microbes in Greenhouses

With crop losses of billions of dollars annually, microbial diseases pose a large threat for the hydroponics sector. As most farmers know, the recirculation water in a hydroponics installation is one of the main sources responsible for the introduction and spread (so-called “vector”) of phytopathogens. Hydroponics systems therefore require almost constant water management to control microbial disease pressures on the crops. To be able to manage these systems KYTOS helps farmers and other stakeholders:

  • Identify the water sources where there is a low microbial health situations
  • Connect the health deviations with climate and other operational factors
  • Assess the risk for a disease outbreak
  • Take action via the right treatments

Unfortunately, information regarding the microbiome health within hydroponics greenhouses is incredibly scarce. This makes it difficult for farmers, but also solution providers to know what’s really happening in their greenhouse(s). KYTOS partnered with Tomato Masters to finally shed a first light on the microbial health status within tomato greenhouses. We are proud to share our results with the world.

Our Sampling Approach for Three Greenhouses

Each greenhouse is unique and we thus had to optimize our sampling scheme for each one of them. The first two sampled greenhouses consisted of four tap sections (“kraanvakken“) with individual irrigation systems. The samples were taken from the main tap of the greenhouse (“hoofdkraan“) and from the distribution line at each of the four tap sections (“druppelleiding“). The third greenhouse had a different tap section layout and there we sampled the 204 individual drains (“goten“) that are used to collect drainwater from the plant substrate.

Sampling with our KytoVials is so easy and quick, the team was able to collect over 220 biosecure samples in < 1 hour!

Schematic illustration of the layout of the sampled greenhouses at Tomato Masters. A) Layout of the greenhouses at which the main tap and distribution line in each of the tap sections was sampled. B) Layout of the greenhouse where individual drains were sampled.

Findings

Tap Sections House Different Microbiomes

Our supervised learning toolbox KytoFlow was able to pick up some important observations (Figure 1). The average bacterial load in the main tap and irrigation water of the tap sections were almost identical with only a maximum difference of 3x between the tap sections.

Our recently developed algorithm for the detection of common water molds such as oomycetes spores (e.g. Pythium, Phytophthora) revealed that the lowest load was observed at the main tap while larger differences in oomycete load were found across the tap sections (up to 100x).

In simple terms: the microbial water quality strongly deteriorated over the tap sections specifically due to the accumulation of water mold spores. Tap sections 3 and 4 were found to be of higher risk for greenhouse #1, and sections 2 and 3 for greenhouse #2.

Fun fact: A big advantage of our Oomycetes algorithm is that it is able to identify the zoospores, which are the motile phenotypes of these water molds, and pose the highest risk for disease migration.

Figure 1. Bacterial load and oomycetes risk indicators measured in the main tap and individual tap sections of the two first greenhouses.

Drain Microbiomes Differ Across Tap Sections

Greenhouses are known to have hotspots for microbe-related problems as well as differences in crop performances between production rows. The drains in a greenhouse carry the microbiome from the input water to the plant and substrate microbiomes. The microbiome can thus change considerably due to differences in plant exudates, climate, or farm management. For Tomato Masters, we completely screened the microbial water quality of all production rows (Figure 2).

Bacterial and Water Mold Pressures Can Differ Strongly Between Drains

  • 10 % of all drains could be classified as hotspots (based on IQR of 1.5).
  • Every tap section has hotspots for water molds and bacterial growth.
  • Tap sections #1 (orange) and #2 (red) were the cleanest for water molds, but there were many drains with over 1000-fold higher spore loads.
  • Tap sections #2 (blue) and #4 (teal) had elevated spore loads for nearly all drains.

Diversity and Microbiome Types are Dependent on Tap Section

  • The microbial diversity, which is a proxy for a healthy and resilient microbiome, showed a wavy pattern throughout the greenhouse.
  • Drains with the highest diversity were located at the beginning and end of the tap sections.
  • We identified four different types of microbiome in the drains. Tap sections 3 and 4 were strongly enriched in other microbiome types than the clean drains (1 and 2). More than 50 % of all drains had a type 3 or type 4 microbiome.
Figure 2. Bacterial load, oomycetes risk indicator, diversity and microbiome types measured in 204 individual, consecutive gutters of a greenhouse. Each label color corresponds to a tap section in the greenhouse. The black lines are smoothed lowess fits and highlight the trends in the data.

Take Home

  • Microbial hotspots exist in greenhouses and they can be found both within individual tap sections, as well as concentrated within specific tap sections.
  • There are gradual gradients in microbiome characteristics found across the drains, suggesting climate and design related impacts (ongoing work – part 2).
  • Both incoming and irrigation water can be highly variable in quality despite originating from the same input water.
  • Different drains house different microbiome types, bacterial load and diversity and oomycetes load. Targeted and precise management of these hotpots will be the key.

We hope these data have showcased that the routine analysis of microbiomes is crucial and and that it is the key to improved microbiome management. We believe that farmers can now use these data feeds to create more stable microbial water quality conditions for the benefit of their crops via the targeted use of biostimulants, disinfectants, and other products.

Stay tuned for the launch of our horticulture services which will include the following benefits:

  • Weekly analysis and next business day reporting
  • Logistics arranged for you
  • Flexible sampling schemes
  • Fixed monthly cost

So What’s Next?

In part 2 of this work we’ll discuss more in-depth technical results on how we can relate these microbiome health characteristics to farm KPIs such as row-based production numbers and climate measurements.

About Tomato Masters

Tomato Masters is an innovative Flemish family business that is specialized in the hydroponic farming of tomatoes. The company owns 21 hectares of horticulture, spread across over four greenhouses. Sustainability is one of the key company values and therefore there is a strong effort to use water as efficiently as possible.

Curious about the microbiome health status of your greenhouses?

KYTOS – I&V Bio collaboration makes microbiome management accessible

A Need for Rapid Logistics and Local Microbiome Analysis

Aquaculture has an enormous potential to ensure food security in a sustainable way. Animal health and water quality are therefore crucial aspects. Frequent and unpredictable disease outbreaks are detrimental to farm yields. By better controlling the microbiome based on robust and detailed data, the industry can take the necessary next step towards sustainable and reproducible farming.

KYTOS and I&V Bio are now joining forces to bring rapid sample logistics (I&V Bio) and local microbiome analysis (KYTOS) to the six most important shrimp producing countries (Thailand, Indonesia, India, Vietnam, Ecuador and Bangladesh). The partnership will install local and independent KYTOS labs to serve aquaculture farms and hatcheries with cutting-edge high throughput microbiome management tools.

The partnership combines I&V Bio’s long-standing expertise in serving aquaculture clients every single day of the year with KYTOS’s novel microbial fingerprinting technology that brings a holistic view on the aquaculture microbiome health. Vietnam has been selected as the first country where a central sample collection point, equipped with KYTOS’s automated microbiome analysis platform will be established. The other countries will follow swiftly. 

Today, KYTOS technology can already characterize most of the microbial life (fungi, bacteria and algae) in the water, sediment and shrimp of a pond. Functional indicators, devised using machine learning, connect these data to farm actions such as biofloc formation, water maturation, and microalgae blooms. This ever-expanding list of indicators will help aquaculture farmers to shift the focus from mitigating diseases to an altogether improved management of the microbiome in their systems.

Enabling Precision Farming in Aquaculture

In the fields of water and animal treatments, KYTOS can now open the microbial black box in aquaculture systems by using so-called “microbial fingerprints”. This assessment provides farmers with microbial health insights that empowers them to take targeted actions to optimize animal health and production yields.

“The need for improved health management and disease prevention is as critical today as ever. Effective biosecurity will always be key to boost the commercial viability and environmental responsibility of the shrimp farming industry.“

Frank Indigne, CEO of I&V Bio

KYTOS uses big data and artificial intelligence to reduce aquaculture’s unpredictability by creating practical tools that help all stakeholders make informed management decisions to improve their farm performance. 

Shrimp aquaculture has largely been deprived of the benefits of new microbiome technologies and knowledge. At KYTOS, we’re on a mission to change that status quo. This partnership is an important step to bring our microbial fingerprinting platform to the farmers across the world. By working closely with all stakeholders in the industry we will create a unique opportunity to manage the microbiome together, for the benefit of the industry.

Ruben Props, CEO of KYTOS

About I&V Bio

I&V Bio specializes in the daily and fresh delivery of its live feeds and solutions to the aquaculture industry. 8 years ago, the founders Frank Indigne and Luk Van Nieuwenhove started working on a revolutionary solution that has taken the Artemia-hatching burden away from shrimp hatcheries by creating Artemia hatching facilities. These facilities combine know-how, experience and new technologies to produce Artemia nauplii in a professional and industrial way. Currently, the I&V Bio Group has established Nauplii Centers in 6 countries: Thailand, India (3), Indonesia, Vietnam,  Ecuador and  Bangladesh. 

All the I&V Bio Artemia Centers use a patented technology that allows them to offer pure undamaged Artemia nauplii (Instar1) free of the shell and other impurities, and free of Vibrio. The Artemia nauplii are disinfected, brought into suspended animation and de-watered until a consistent unique live-paste is achieved. The Artemia nauplii are ready to use and can be scooped from the tray directly into the shrimp tank. I&V Bio’s key to success is our guarantee to supply our customers with daily fresh, clean and  disinfected vibrio-free products.

https://www.iandv-bio.com/

About KYTOS

KYTOS is a microbiome technology company developing microbiome management solutions at the frontier of technological innovation. We have our origins in the Center for Microbial Ecology and Technology (CMET) at Ghent University, from which we build on decades of world-leading expertise in the management of microbial communities. We transform our partners into expert microbiome health stewards by empowering them with a unique blend of data science, technology, and microbial ecology insights.  

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!