With a predicted global population of 9 billion by 2050, there is a need for increased, sustainable food production. Additionally, climate change will have an effect on soil and crop health, due to changes in weather patterns and disease distribution.
Dr Philippe Rolshausen at the University of California in Riverside specialises in tree crops, viticulture and plant pathology. In today’s podcast, he explains the role plant microbiomes , and how increased understanding of small changes in plant environments is helping to improve crop health.
Read some of their latest work here: https://doi.org/10.1093/femsec/fiaa053
Image source: Alberto Gardin / Shutterstock.com
Transcript:[00:08] Will Mountford: Hello, I’m Will, welcome to Research Pod. There are two important numbers to think about as you listen to today’s podcast. The first is that the most expensive bottle of wine ever sold is a bottle of 1947 French Cheval Black that sold at auction for $304,375. The second number is that in 2014, the UN Food and Agricultural Organization warned that global soils were degrading so quickly that they had in effect only 60 harvests left due to desertification.
Both of those numbers are somewhat out of proportion and not necessarily reflect the true values of what’s happening on planet Earth at the moment. But soil health and crop health are absolutely important to our survival on this planet and essential to the work of Philippe Rolshausen from the University of California Cooperative Extension. Today we’re talking about the years long planning and the microscopic innovations that future harvests may yet need to survive. Philip, thank you so much for joining us today. Just by way of introduction, could you tell me and the folks listening at home a bit about yourself, where you’ve come from and where you are now?[01:23] Philippe Rolshausen: Hello, I’m Philippe Rolshausen. I am a French native, was born in France, and I got a bachelor degree in plant science at the University of Tours. Later on, I obtained my master’s at the University of Bordeaux in viticulture and moved to the United States where I got my PhD in plant pathology at the University of California in Davis. And in 2012, I was hired at the University of California in Riverside. And I currently hold the position as a Cooperative Extension Specialist at UCR. [01:59] Will Mountford: What does an average day for a Cooperative Extension Specialist look like? [02:03] Philippe Rolshausen: So we are publicly engaged scholars who ensure that the university research is applied to help California community to solve problems. So we are part of what’s called the University of California Agriculture and Natural Resources, also called UCANR. That is a statewide network of researcher and educators dedicated to the welfare of agricultural, natural, and human resources. [02:30] Philippe Rolshausen: So my responsibilities focus on tree crops mostly, with an emphasis on subtropical agriculture. So I work commonly with citrus, grapes, avocado, coffee, mango, and I conduct applied research to extend the scientific knowledge and coordinate public outreach activities. So in a nutshell, that’s what I do. [02:54] Will Mountford: It’s been, I suppose, a mounting question over the last couple of decades. And with every new IPCC report, there seems to be more and more emphasis on we need to ensure planetary health to ensure public health, environment and human sustainability are very intricately linked. And I suppose in your own words, if I could ask you to explain to anyone listening to this, why crop health matters, if not to their life and to the well-being of the human species. [03:23] Philippe Rolshausen: Well, from a grower standpoint, crop health equals revenue and profit. And for the state of California, it equals to jobs it’s a huge agricultural state. So that’s why it matters. I think at the global scale, we’re going to have to feed 9 billion people in 2050. So improving crop health is of huge importance, obviously. So, we are facing with several challenges. One of them is the shrinking ag-land. So we have to produce more per surface basis. That’s the number one. So crop health is obviously very important in that regard. And also, growers have to face more and more environmental challenges. So climate change is obviously the main one with extreme weather patterns and invasive pest and disease that will impact crop productivity. So if we can optimize crop health, that will help with those challenges that are coming up. [04:28] Will Mountford: Well, to bring things to the more kind of immediate realm of your work. There is a biome to lots of things, not just in ecology, out in the world that you might have deserts and forests, any organism might have its own biome. There’s different kind of levels of involvement, even down to the microbiome thing about the bacteria inside of us. To kind of set the scale of the plant biome alongside human scales, because obviously, humans and plants have coexisted for so long, those microbiome or those macrobiome scales, how they interact and what kind of levels of involvement there are at each stage, [05:08] Philippe Rolshausen: I think you can look at plants and humans as an assemblage of living organisms. So virus, bacteria, fungi, we are all living in a community as one organism, so to speak. And so the microbiome is the collection of all those organisms. And for both the human and plants, the microbiomes have similar functions. So in both cases, they help us absorb food. So for humans, specifically, they help us absorb carbon, vitamins, and so on and so forth. And there’s been a lot of research on the human gut microbiome. For agriculture, it’s a little different, but I think we’re far behind human research, although it has been expanding really quickly in the past 10 years, I would say. And now we look at the roots of the plants similar to the guts of the human. [06:06] Philippe Rolshausen: Someone made the statement that actually plants, we have the gut on the outside, because the root of the plants are always called the rhizosphere, is the place where you have a large microbial activity and the microbiome helps plants absorb nutrients. And so that’s a similar function to the gut in that regard. The other function that the microbiome help with is against diseases and help us help plant and human cope with diseases and stress. So those are parallel that you can make between plants and humans with regards to the microbiome. So you have to look at plants, plants are not moving, right? Unlike humans, they can’t adapt by moving to a different environment. They are growing in one space and they have to adapt. So if you look at the continental scales, the major limiting factor to plants are daylight and temperature. [07:06] Philippe Rolshausen: And those are obviously major driver to what crop you can grow. So for instance, you are not going to be able to grow a citrus plant in cold areas because citrus is very sensitive to frost. Whereas the citrus plants like grapes are flourishing in temperate climates. And so, and they do need cold weather to do better. If you try to grow a wine grape in a tropical environment, you will end up with poor wine quality. So that’s at the continental scale, that’s a major limiting factor. Like now you go down to a regional scale, plants are more dependent on topography, the soil climate or mesoclimates. And so factors that are limiting more like what variety you can grow. [07:57] Philippe Rolshausen: So let’s say if you take grape as an example, Pinot Noir for instance, is a variety that does well or better in cooler climates. Whereas some other variety like Cabernet Sauvignon needs much hotter weather, longer day, longer season to develop all its characteristics. Now at the field level, which as you narrow down the scale, plants are more dependent on microenvironment. So, for instance, the slope of a vineyard or an orchard can create poor air movement. And so, during frost, like plants can be more susceptible to frost pockets where you have poor air movements, for instance. Or if a crop is planted on a hard pen, you have poor drainage. And so your plants doesn’t perform as well because the water doesn’t drain well. Or another example, if you plant crops next to trees, trees cause shading to the plants. And so, the photosynthesis is not optimized. And so, the plants doesn’t perform as well. [09:05] Philippe Rolshausen: So those are some microclimates that affect the plants as a whole, but also it affects the communities associated with the plants, the microbiome that’s living with the plants. So the microbes that are associated with the plant helps the plant cope with those different environmental challenges that it’s facing. And what plants do is that they send signal through the root system in the environment, in the rhizosphere to recruit microbes and they trade carbon in the form of sugar with microbes in exchange of services such as acquiring nutrients from the soil or increasing the root surface to absorb more water or fight off pathogen by producing antimicrobial compounds. So this is one mechanism on how plant can adapt to local environmental changes. [10:06] Will Mountford: The global scale of the wine industry, it feels almost in opposition to those microclimate changes that can come to bear and that when you talk about the slope of a particular vineyard having an effect on the wind speed or the ice pockets that might form and what that can do to any one vineyard or any one vintage of the scale of the amount of wine produced in the world per year. Tiny details, very involved at the small scale and very productive at the large scale. And if you could just tell me more about that. [10:37] Philippe Rolshausen: Well, first of all, it depends when we talk about grapes, you have to separate table grapes from raisins from wine production, which are very different crops and with very different goals. Obviously for table raisin grapes, their goal is to produce high quality crops and lots of it. Whereas wine grapes, it’s a fine balance because when you produce a lot, you kind of dilute quality. So I think wine grape growers, their goal should be aiming for quality of the grapes. And so it is a fine balance between vegetative growth and reproductive growth. And so microbes helps plants achieve quality because they help the plants assimilate some of those nutrients that are in the soil or they help the plants fight some of those pathogens that naturally occurring. [11:32] Will Mountford: And how can we connect that microbial and that genetic changes and protection to the wellbeing of the wine, the crops, the terroir, I’m still not saying that right, I apologise, the terroir, how does that tiny, tiny change affect what ends up in the bottle that people enjoy? [11:52] Philippe Rolshausen: So we talked that the regional scales, our plants are limited by topography, the soil characteristic and the climates. In viticulture, those geographical and environmental boundary shape what’s called appellations. So it is the place, appellations is the place of origin of a wine where wine is produced. So in some countries, the appellation also imposes the type of variety that can grow, the yield you can have, and also the alcohol content. So, if you compare France and the United States, the appellation rules will be very different. So terroir in French is the, originates from the word terre, which means land or soil. But the meaning of the word is more ecosystem. So terroir and appellations are comparable terms in the sense that they both refer to the identity of a wine region. Although in my opinion, terroir embodies the identity of a vineyard, that includes not only the characteristic of the soil, but also the climate, the variety, and also the viticultural practices. [13:01] Philippe Rolshausen: So for instance, if we talk about organic versus conventional farming, it will change the characteristic of the wine and also the natural strains that are used for fermentation. For instance, there’s these commercial strains that sometimes winemakers use for fermentation. So those characteristics will influence the characteristic of the wine. And what winemakers try to do is to really encapsulate those unique traits into the bottle. Will Mountford: Another important part of the brewing process is of course the yeast that is a microbe of its own right, and it’s one that we have tamed and engineered and selected. What makes a good yeast versus a bad yeast versus an infectious yeast? [13:47] Philippe Rolshausen: Well, there’s a lot of debate about this. I think there’s a different school and different philosophies. There is the commercial yeast and there is the wild yeast. So some growers or winemakers like to use the natural yeast that are occurring in the vineyard or in the region and use that for their fermentation process because they think it adds depth and complexity to the wine. Whereas when you use a commercial yeast, it negates the effects or the benefits of those natural strains. So when you use a commercial strain of Saccharomyces cerevisiae, then you go away from the notion of terroir in that sense because you’re making some wine that has characteristic that your neighbor can make or that someone in a different wine region can make. So in that regard, it’s going against the notion of terroir. It is challenging if you’re a wine growers and you try to use some of those wild strains because you’re taking a big risk, right? [14:50] Philippe Rolshausen: You can, first of all, face what they call fermentation stock where the fermentation doesn’t take place. The yeast takes the sugar that the plant makes and accumulates in the berries and transform it into ethanol, which is the alcohol part. But if during the stock fermentation, that process doesn’t take place, the yeast is actually not able to take that sugar and ferment it all the way. So you basically take a huge economic risk by doing that. Whereas if you use a more commercial strain, you know that you’re taking less risk and you can complete your fermentation all the way. So those are the challenges that one may face. I mean, often it is a business decision, right? And I think when you’re a small wine grape grower, it’s more challenging and more rewarding to actually use the wild strain. Whereas when you make large scale production, you often don’t want to take those risks and you tend to go with a more commercial strain. And some, you know, are perfectly fine and do a great job. I think it’s just a personal preference from the winemaker standpoint. [15:59] Will Mountford: I suppose another factor of agricultural instability is the risk of disease, is the risk of some pathogen making it to the crop and that contributing to food instability in the future. What kind of role does that play either in vineyards specifically or any kind of facet of your research that’s looking to secure that stability, security of the fruit, or just preserving the taste of something that is so volatile? [16:22] Philippe Rolshausen: When you are a grape grower and a vineyard manager, you want to farm your vineyard for 25 years or more. And some of those best wines are made with older grapes. So that’s something you try to achieve. I mean, it is an economic decision, it’s a business decision at the beginning, how long are you going to farm your plants? So if you have a disease that comes early on at the establishment of the vineyard and reduce the longevity of your vineyard to, let’s say 10 or 15 years of production, then you have a problem. You have an economic problem because you have to pull your vineyard out to replant. So those are not something you want to do. And also for the winemaker standpoint, you don’t want to have grapes that are rotten that go into fermentation because you can have off flavors in the wine later on. So obviously that’s not something you want to achieve. [17:20] Philippe Rolshausen: So there is huge decisions that are on the shoulder of the vineyard manager to make sure that the grapes that’s being produced is of high quality. So management of diseases are through either conventional agrochemicals or organic agrochemicals. Conventional agrochemicals use synthetically produced ingredients, whereas organic agrochemicals use natural sources. So those include, for instance, a substance derived from plants, insects, microbes. So you talk about, for instance, pheromones from a microbe to disrupt the mating of the pest, minerals such as copper or sulfur or microorganisms. Many organic pesticides or agrochemicals are less toxic to their synthetic counterparts, but that doesn’t mean that they are safe to the environment or to humans. [18:19] Philippe Rolshausen: So there’s often a misconception about that organic pesticides are safer than synthetic agrochemicals. The efficacy of organic pesticides is commonly lower than a synthetic pesticide. And one must often spray organic pesticides more frequently to achieve similar disease control. So in an environment that is conducive to disease, such as you can imagine warm temperature or rain, it can be very challenging for crop to grow crops organically. And you can be actually very unfriendly to the environment in that sense, because you have to, there’s a lot of chemical input in the environment to manage disease. So, I’ll give you an example. For instance, boulder mixture, which is a copper based chemical. This is the first pesticide used on grapes and probably one of the first pesticide used on any other crops. It’s been used for 130 years now and commonly used to control fungal and bacterial diseases. [19:25] Philippe Rolshausen: It’s been accumulating in soil of the France and now all over the world for decades now. And we see signs of phytotoxicity, but there’s also copper resistance bacteria and fungi are developing. It’s accumulating in soil and it’s has a negative effect on the microbial diversity, but it also affecting food quality parameters. So for instance, it affects the fermentation process. It accumulates in the berries and affect the fermentation process and mediate oxidation reaction that also decrease the intensity of some of the wine aromas. So to produce enough food and to feed the global population in an eco-friendly manner, we need to adopt integrated farming practices where pesticides, so both organic and synthetic agrochemicals are reduced and deployed only when necessary. [20:31] Philippe Rolshausen: Here I’m not preaching to stop using synthetic agrochemical just because I think it’s unrealistic given the number of invasive pest and disease outbreaks linked to climate change. So we do, growers do need those chemicals, but we do need to reduce the amount that we are using. And we need to foster sustainable farming practices because it is instrumental to our long-term success. So what are sustainable farming practices that relies on ecosystem management using practices that promote and enhance the agro-system health and maintain and increase the long-term soil fertility. Microbial activity correlates to soil fertility, so ensuring the biodiversity of the soil and the plant is key to success. And so reducing chemical input that limit microbial activity is really here instrumental to our success. [21:30] Philippe Rolshausen: So what growers can do to limit organic and synthetic agrochemical is to use a biopesticide or bioinoculants. And this is a way to really engage with sustainable farming. Introducing bio fertilizers to promote nutrient acquisition in place, instead of adding nutrients in cell for instance. So you will use a microbe that will help the plant fix nitrogen or solubilize phosphorus will have better function than really adding nitrogen or phosphorus to your soil. You can also introduce biological control agent into a system to combat a pest or a disease instead of using synthetic or organic pesticides. [22:29] Philippe Rolshausen: I think you need to look at disease as disequilibrium with microbes and when everything is in harmony, you have what’s called homeostasis, which is the microbes and the hosts living in harmony together. But when you have an imbalance in that microbial equilibrium, it’s called a dysbiosis, then it leads to a state of stress. This is where you can have disease. So I think a lot of people start to understand that the plant interaction with the microbes or the human interaction with the microbe is very important. And understanding that interaction is key to alleviate some of that stress and manage some of those disease. And that you don’t always have to use synthetic chemicals to kill a pathogen. And perhaps you can remediate the stress or disease by making sure the microbes are in equilibrium. And so there’s a lot of the market of pesticides for instance, or bio products has exploded in the past 10 years because of those reasons. Because of the science behind the microbiome and how that translates into economic opportunity and market opportunities, the development of technologies that could be marketed and commercialized to production. [23:50] Will Mountford: There’s a concern amongst some quarters that it is not scalable to address the size of food security that is needed for the future or sustainable in and of itself that eventually there will be an end to the natural resistances, the natural immunities that some pathogens might bring about. Any thoughts on where this could lead? [24:10] Philippe Rolshausen: If you look at the compound annual growth rate for agricultural biological products, it’s growing at a faster pace than conventional chemicals. So it is already happening, but there will be some challenges into developing more bio products and putting those bio products on the market because first of all, you need to optimize the efficacy of those products. And we don’t always understand how those biological works and a lot of those bio products that are available, commercially available have not been optimized or have not been developed for a specific crop. And so until we understand how those microbes function and benefit the plant, then we will not be able to achieve higher yield and better disease management. One of the other issue is also our technicals, like storage, for instance, how do you store those organisms on shelves so they don’t die? And also, I think a lot of it comes from the consumer standpoint and changing consumer behavior is going to be key. [25:19] Philippe Rolshausen: We want to buy food or food products that are of high quality. We do not want to buy a grape that has little rot stain on it on the berry, or you know we want to buy the perfect product. And so until we change that behavior, this is going to be really hard to achieve by using bio products only because unlike with conventional chemicals that sometimes you could have 100% disease control, you’re not going to be able to achieve this. And we’re going to have to understand that maybe the perfect product does not always exist. And we’re going to have to accept eating products that are not perfectly, cosmetically perfect, but that are as good quality as a product that has used conventional chemical or perhaps even better because it doesn’t have any residual chemistry in the skin or in the flesh. [26:16] Philippe Rolshausen: So I think a lot of it comes from consumer education, but I believe that consumers start to understand that and there’s been a strong change in consumer behavior towards more chemical free or better quality products for food and food products. I think the idea of farming with no conventional chemical is not sustainable because we do need conventional chemicals to control some of those diseases. I think what has to change is the philosophy of how food is being produced and doing it in a more sustainable way. So using less of the conventional chemicals that are being used and more of the bio products will definitely help in this regard. We’ve made a lot of progress formulating some of those pesticides since the Green Revolution. And so we’ve been wasting less and less chemicals by improving the formulation and the delivery of chemicals. [27:21] Philippe Rolshausen: But we’re not nearly close to what we can do, and I think the developing technology today, like nanotechnologies, for instance. Nanotechnology is the science conducted at the nanoscale. Scientists and engineers are finding a wide variety of ways to make materials at the nanoscale and they take advantage of their enhanced property. So for instance, they have higher chemical reactivity. And so we can use those properties in agriculture. And so for instance, targeted delivery of pesticides using less active ingredients, which improves the efficacy and decreases the chemical leaching in the environment. This technology will help manage diseases that I’m working on specifically, the targeted diseases of the vascular system of plants, because it is difficult to deliver active ingredient inside. [28:30] Will Mountford: I suppose that’s the almost returning to nature style of doing organic farming, but the future approaches or any new technological approaches thinking about, you know, omics, insights and screening and kind of bringing the very cutting edge of biological application to vineyards, is that something that could maybe be a different avenue to explore? [28:49] Philippe Rolshausen: Yeah, so the omics technology really helps identify what product we should grow or what microbes we should go after. And this is some of what my research does. It’s like we’re trying to identify key microbes that are beneficial to grapes or citrus and by using omics technology. So we talked about the microbiome and how it’s helping plants absorb nutrients and cope with stress. So my lab is using omics technology to profile the microbes associated with tree crops specifically. Omics technology aims at the collective characterization and quantification of pools of biological molecules that translate into the structure, function and dynamics of an organism or organisms. So when I talk about pool of biological molecules, it can be genomes, RNA, proteins or metabolites. [29:51] Philippe Rolshausen: I’m looking specifically at the genetic materials of microbes and that are recovered from different environmental sample. And I measure the community composition and diversity on the different conditions. So what we are interested in is the microbes that are associated with roots because we talk about the importance of the roots with the nutrition and the stress adaptation. And also the microbes that are living inside the plant tissue or organs. So plant sap, for instance, stems, flower, fruit. We want to know where those organisms are coming from, what are their role and how can we utilize the good microbes that are found associated with the plant and support plant health and productivity. [30:41] Will Mountford: Are there any more specifics you can tell us about either the technology or the delivery? [30:47] Philippe Rolshausen: So I want to give like two examples about my research that kind of encapsulate what we’ve talked about today. The first one is a disease of grapevines called Pierce’s disease. It’s a bacterial disease that affect the vascular system of the plant, the xylem specifically. So the xylem is, you can look at the xylem of plant, which is the stem, as the freeway that conducts water, nutrients and signals across the plant. And so when vines are affected by this disease, the signal is obstructed, the xylem is obstructed. So there’s poor translocation of water, poor translocation of nutrients and signals across the plant. And so the plant struggles, lose vigor and eventually dies. And so that disease is a vector by an insect that feeds on the plant and transmit the disease and the bacteria, the pathogens multiplies and kills the plant. [31:53] Philippe Rolshausen: There are no current product that targets the pathogen itself. The only way you can manage the disease is by spraying, is controlling the insect vectors. So you have to use insecticides to manage the disease. So my research has focused on try to target, to identify biological control agents that target the pathogen itself. So what we’ve done using Omics technology is look at grapevines with a range of disease symptoms across California that express Pierce’s disease. And we collected tissue samples from those grapevines and look at microbial community that resides inside the vascular system of the plant. And what we found was that there were two bacteria specifically that correlated negatively with the pathogen. So the more abundant those bacteria were, the less abundant was the pathogen. [32:54] Philippe Rolshausen: And so we isolated those two organisms of interest and reintroduced them in a system in a greenhouse. And so when grapevine were affected with the disease, were inoculated with those biological control agents. They tend to do better and perform better. We alleviated disease symptoms and sometimes even cure the plants from the disease. And so now that we have our proof of concept, we are testing those strains on their field trials and we hope we can license those technology to companies so they can be developed into commercial product. That’s the first example. The second example that I want to talk about is on citrus, on the disease called Citrus Huanglongbing, it’s very different. [33:52] Philippe Rolshausen: It’s, Citrus Huanglongbing is very similar to Pierce’s disease that we talked about earlier. It is vector by an insect as well. And the insect vector comes and feed on the plant and transmit a bacterium as well, a pathogenic bacterium. Here the bacteria feeds on the phloem. So the pathogen is limited in a different compartment of the plant. It’s still the stem but the phloem. [34:22] Will Mountford: In my head, I’m picturing, you know, GCSE biology diagram of xylem going one way and phloem going the other. There’s a little bit of a memory in there somewhere. [34:30] Philippe Rolshausen: That’s right. So I’m trying to for people to understand. I don’t know if I need to go into that much details. So the bacteria resides in the phloem of the plant. And very much like Pierce’s Disease, the plant chokes because it cannot translocate sugar from the leaves into the root system and into the fruits. You can really make the analogy between that disease Huanglongbing and actually AIDS to humans because basically the plants become weaker and weaker and then there are other pathogens that comes in and kill the plant. So we did the same thing as we did with Pierce’s Disease. We collected root samples across orchards that express different range of symptoms on citrus Huanglongbing and try to look at the microbial communities that were associated with those roots. And what we found is that healthy plants, we found stronger association between healthy plants and fungus that’s called the mycorrhizae. [35:30] Philippe Rolshausen: And what mycorrhizae do is actually helps plants absorb nutrients, phosphorus especially nitrogen and also water and help the plant cope with stress as we discussed before. So what we’re trying to do here is develop practices that really foster that symbiosis between the citrus and the mycorrhizae, because if we are able to do that, then we are more likely to extend the longevity of the orchard or the citrus trees by creating the association between the mycorrhizae and the citrus tree. We extend the lifespan of a tree, and for a grower, it means more profit and more income. So if we can understand how plants interact with microbes or how humans interact with microbes, then that will definitely help us cope with those stress and help us achieve higher food production and crop production, crop quality. I think that’s my take home message. So if you can eat sustainably, eat local and eat healthy.