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How microbiomes boost plant health

Why maintaining a sterile growing environment is crucial. Or is it?

Often there is chatter about the level of sterility in a CEA facility, where most growers would swear that they are up to 99% sterile. However, Paul Rutten, an indoor farm microbes specialist, is debunking these 'myths'.

"Whether a vertical farm or a greenhouse where people are packed with hazmat suits and all surrounding buzz around it, there is always a community of microbes present. "Instead of asking, are there microbes present, instead you should check; if my plants are growing, there are microbes there. Plants would not be able to grow without microbes and typically we'd find hundreds or thousands of different species of bacteria, fungi and Oomcytes in any system that we study," says the founder and CEO of Concert Bio.

The startup is developing services and tools that growers need when growing indoors, either greenhouse or vertical farm to harness the plant microbiome taking advantage and getting the most out of these microbes.

Paul Rutten

Microbiomes boost plant health
Just like us, plants rely on their microbiome which allows them to live. There has been a lot of research done on understanding these microbiomes. Start taking advantage of these by adding the right microbes into the soil to prevent diseases, improve yield, and the ability of these plants against drought and so on. However, a lot of that work has not yet touched upon soilless agriculture. However, there is a microbiome in these systems. In many ways, we're going about this very differently as we're often trying to eliminate microbes as much as possible indoors," says Paul.

However, as a result of that, the plant expects to have a million microbes around it when it grows, given the many years back in traditional agriculture, suddenly finding itself in an environment that is very microbes-deprived.

Breaking the offering into three parts, the first Concert Bio is offering is the monitoring of microbiomes. "You can't improve what you can't measure. With our services, we help growers understand what's going on with their microbiome, to adopt potential changes if required." This data will then be used to develop microbial products, which is the second service that Concert Bio can provide. Designed for soilless agriculture and the unique needs and challenges that plants face in a system where many things have already been optimized. "Microbes can help boost plants in perfectly controlled systems like CEA."

Through DNA sequencing, all microbes in an indoor environment are analyzed, such as pathogens, beneficials, bacteria, fungi, Oomycetes, and a whole other bunch. "Everything comes out of this analysis providing a lot more information about what's going on in the systems." Then the low-hanging fruit of this, as Paul puts it, is pathogen detection, which means all plant and human pathogens detected, which are not just the usual suspects "as normally you'd not even check for these."

The final and most important part of the DNA sequencing process is understanding the ecosystem and getting a concrete idea of how the community is doing as a whole, "rather than just one individual pathogen and measure its diversity."

However, according to Paul, a side note is that this process will provide a humongous amount of data which might cause an information overload, however, Concert Bio has seen this hurdle and built a dashboard for this process. The dashboard tells growers what the information gathered is telling them. One of the key questions that are often asked is, "How healthy is my microbiome and is it good, or bad?" Indicating the diversity of microbiomes present, the dashboard will present how variety of microbiomes there are in the system. "Diversity in soil plant-microbe interactions has been repeatedly shown to be quite a good indicator of the health of the system."

A high diversity of microbes indicates a more different species in the system, the plants tend to grow better because they have more microbes around them that they can recruit from. When a new pathogen attempts to enter an ecosystem with a large presence of microbes, it will be much harder to survive and attack the plant.

"As we gathered thousands of samples across systems in the UK, Europe, the US, and many other places, we can put these diversity metrics and analysis into context and provide a clear number. Following that we can explain to growers whether that number is relatively high or low compared to what we typically would find in a greenhouse or vertical farm. We are there to help put it into context, to help what's going on," Paul explains.

Same inputs, different outputs?
One advantage of DNA sequencing, Paul points out, is to receive a list of all the microbes species that are present in the system. And often, there is a lot more variation in a facility than you might expect from these systems. As they are all connected to the same water loop, it is often assumed that the community of microbes in the nutrient solution is quite similar given it's very well mixed.

"However, we found that different ponds, even located near each other and on the same water loop, had a different community of microbes. As for vertical farms with different chambers and different water loops, you can have a very different community of microbes in different parts of the farm. This is not even academic, as you can see the impacts of that on the yield of plants, how often they would be struck by disease and the impact of it. That kind of difference is the biggest thing that we can exploit trying to understand what a good and bad microbiome looks like given they all receive the same inputs."

Where can we find the microbes?
As research has shown the Concert Bio team, some cultivars have better growth and some are more prone to disease. To analyze this, the team has been able to figure out what is going on with the microbiomes and use that to understand what 'good and bad' looks like. Another big find is the location of microbiomes in a hydroponic system. Monitoring many locations, Paul shares that they've mainly looked at the substrate, nutrient solution and roots.

Over and over again, the highest diversity of microbes are found in substrate, especially organic ones. Another favorite meeting place of microbes is the nutrient solution as they show to be very different from to soil, as they can be put into parallel with microbes present in a steam, lake, or river. "It's very different to what a plant would expect to find itself when it's growing in soil." The most surprising location would be the roots of the plants, as they tend to be the smallest one out of all data points.

"One of the things we found is the ratio of beneficial or pathogenic microbes, which is the sort of thing that you can look at when you've got DNA sequencing, tends to be a better predictor of the health of the system. Even whether there is going to be disease rather than looking at any individual pathogen or a combination of pathogens together. So if there's a drop in pathogens in your data, that's a very clear sign of a disease outbreak or there is about to be one."

For more information:
Concert Bio
Paul Rutten, Founder and CEO of Concert Bio
[email protected]