The World Under Our Feet: Biological Soil Health in Vegetable Production

February 29, 2024

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Organic matter plays a critical role in soil health. Cycling of organic matter and plant nutrients is mediated through complex food webs in the soil habitat. These interactions are characterized by an astonishing level of biodiversity that includes soil organisms such as bacteria, fungi, nematodes, arthropods, and earthworms. Learn about how the interactions between these lifeforms influences soil biological health and in turn successful crop production.

The 2024 MI Ag Ideas to Grow With conference was held virtually, February 19-March 1, 2024. This two-week program encompasses many aspects of the agricultural industry and offers a full array of educational sessions for farmers and homeowners interested in food production and other agricultural endeavors. While there is no cost to participate, attendees must register to receive the necessary zoom links. Registrants can attend as many sessions as they would like and are also able to jump around between tracks. RUP and CCA credits will be offered for several of the sessions. More information can be found at:

Video Transcript

Welcome everybody to the MI Ag Ideas to Grow With Session For today, it's going to be focused on biological soil health. I'll approach this topic through a vegetable production perspective, but soil biology, so it really touches all aspects of agriculture because a lot of what determines the health of the soil is what the critters in the soil are up to. Let's just get into it here, All right? So when we talk about soil quality, you know when you see it, right, quality soil, it's dark, it has good structure. When you feel in your hand, it has a rich smell to it. Similarly, a poor quality soil, it's going to be dry, very good structure. When you feel in your hand, it's going to be not as dark of a color. So there's a lot you can tell about soil quality using just your five senses, right? But there are many other specific indicators of soil quality that have been articulated as well, split up into three main categories. There's the physical indicators of soil quality. This is your bulk density measure of compaction, your aggregate stability, your posdy infiltration rates. So how Pm it is to crusting? There are the chemical indicators of the amount of reactive carbon. For instance, electrical conductivity which is a measure of Slit typically, so nitrate levels, so ph and of course your cat on exchange capacity. Then that third category which may often be overlooked is the biological indicators of So quality. You can measure different enzymes in the soil. Earthworms are often used as a direct indicator of So quality, because they're so visible, can measure the respiration rates of the soil. The big one, soil organic matter, which we'll talk about a bit more in a sec. Here the NRCS, the Natural Resource Conservation Service, have articulated these four main principles for optimizing for these three indicators of soil quality. And those are to minimize soil disturbance. Maximizing the number of living roots in the soil to increase organic matter, reduce erosion. Similarly, maximizing your cover, keeping a layer of armor over the soil to again reduce erosion. Maximizing the overall biodiversity of the system. The goal being, again, to optimize for these three categories. We've talked, I mentioned soil organic matter, but what exactly is it and why is it so important? We all know that ecosystems are composed of these different intersecting food webs. The soil habitat is no different. Food web is extremely complex and diverse. All the energy is ultimately coming from the sun. But that organic matter, bacteria for example, which feed protozoeod, which may feed larger forms of soil life like arthropods all the way up the food web. And when you contemplate these interactions in the soil habitat, I think that the quote from the naturalist and conservationist John Muir comes to mind, tug on anything in nature and you'll find it connected to everything else. I think that that quote really captures soil ecology in a nutshell. Soil organic matter, that part of the soil that consists of the tissues of different animals, plants, fungi, other micro organisms, other forms of soil life in various stages of decomposition. Organic matter ultimately feeds all types of soil organisms, and all types of soil life ultimately contribute to soil organic matter when they die and decompose through their waste products, through their activity, so on and so forth. The majority of soil organic matter is in fact carbon. We all know the carbon cycle, right? Just to breeze through it. Here they take CO two and you use it along with the energy from light and water to create photosynthates of sugars which they used to build their plant tissue. That plant tissue is broken down by soil microorganisms to form organic matter and organic matter. So organic matter, it can be classified into different types based on how quickly it breaks down. Right? Humus is a very resistant form of organic matter. That's not to be confused with hum, the chickpea spread, but, um, very resistant to decay. It lasts a long time, so it contributes a lot to soil structure, but there are other more labile forms of soil carbon, solorganic matter, that break down more quickly. By different organisms like bacteria, fungi, earthworms for example. Those organisms will respire and release CO two feeding directly back into the cycle, that's carbon cycle. With soil organic carbon being a key link. Nitrogen cycle is a bit more complicated, not going to really get into it in too much detail here, but basically, nitrogen enters the soil through organic materials like animal manure or plant residues enter through nitrogenous fertilizers as well. Or nitrogen gas in the atmosphere can be converted into plant available forms through the process, through the activity of these nitrogen fixing bacteria that live in a symbiotic relationship with plant roots. Common common one that you're probably familiar with is rhizobia, Which forms that symbiotic relationship with legume plants like green beans or soy beans. Again, turning that two in the atmosphere into a plant available form. Those nitrogen fixing bacteria can also live freely in the soil habitat as well. Nitrogen, it can be lost from the soil through downward leaching, through volatilization. It can be moved off site as runoff and get into the nearby bodies of water cause all kinds of issues. Also, it can be loss through denitrification. Denitrification is the loss of nitrogen back into the atmosphere through the activity of these denitrifying bacteria, which tend to be anaerobic. Denitrification tends to be going on in the more water logged hypoxic parts of your field, or garden carbon and nitrogen to key nutrients when it comes to solorganic matter, when we talk about building soil organic matter, a lot of it boils down to what amendments you're using. Certainly compost animal manure, cover crops, crop residues or organic mulches like straw or wood chips are going to break down, be decomposed by soil organisms contributing to the organic matter levels of the soil. Solarganic matter has many positive functions in terms of soil structure, so organic matter has lots of different cores of different sizes. It has these little nooks and crannies that hold water like a sponge, plant roots, and other organisms are able to access that water in those little pockets. Similarly, the activity of different organisms lead to these biopores. Okay? The tunnels and channels through the soil where makes water infiltrate more easily. It decreases compaction, right? It allows oxygen and other gases to diffuse through the soil much better. That is like highways for different kinds of soil organisms, right? They can travel more freely. Overall, increasing activity. Roots and Mics hype help to bind soil together as well into aggregates. Root exudates and some microbio byproducts also act as organic glues that bind soil particles together as well. All contributing to improve soil structure. To touch on this concept of the rhizosphere real quick, The rhizosphere is just referring to that soil sub habitat that is directly surrounding plant roots. Rhizospheres tend to be quite active, mostly due to because they tend to be rich in organic matter. So deposits are just different types of organic materials that are deposited by roots. Some examples are root edudates, which would include mucilage. Mucilage is it's a root aid. The X is like a lubricant that allows roots to force their way through the soil better. Certain root exudats will enhance nutrient availability in the root zone. Certain allelochemicals might be released, depending on the plant, to inhibit growth and activity of other rhizosphere organisms. You get, you get carbon coming from other sources, say like epidermal cells emanating from the root tissue. All that is going to feed the soil organisms living in association in the root zone. The root zone tends to be quite a biodiverse hot spot as well. We talk a bit about soil biodiversity. One teaspoon of healthy, active soil famously can have over 10,000 different species in it. Most of those are going to be bacterial, but still pretty impressive. Some benefits of enhanced soil biodiversity, accelerated nutrient cycling, you get a diversity of organic inputs that contribute to your organic matter levels. You can get a reduction in pest build ups because there's so many different kinds of soil organisms around, it keeps one pest or pathogen from dominating because of the high biodiversity. This diagram here is taken from James Nardi, University of Illinois. Again, I think that this pyramid really illustrates nicely that the hierarchy between different forms of soil life, for example, protozoa feed nematodes, which may feed mites being spring tails all the way up the pyramid. We'll get into a bit more in depth on those interactions here in a second. Basically, soil life can be split up into three main categories based on size. The microfauna, the Meso fauna, and the megafauna. We'll start by talking about the microfauna. These are the organisms less than 100 micros in size. Okay, the most abundant type of microfauna is the bacteria, of course, tend to be the most abundant in terms of individual number of organisms. Bacteria we know can be either beneficial or pathogenic, or neutral, I suppose they tend to be dominant in more alkaline or neutral ph soils and also soils that are frequently disturbed. Many of our agricultural fields where we grow annual vegetables are going to be bacterially dominant because that regular tillage disrupts fungi, for instance, from creating the microizal structures. And it's generally supportive of bacterial activity. Bacteria tend to be infamous for developing resistance to pesticides and antibiotics because they're able to swap their genetic material out, so readily, certainly not only vertically through reproduction, right? But also horizontally. Through this process of conjugation, bacteria form these structures that allows them to swap genetic material directly with other bacteria in their environment. Through this process of horizontal gene transfer, bacteria can either be beneficial or pathogenic. Of course, some examples of beneficial bacteria are the nitrogen fixing bacteria we mentioned earlier, Actinomycetes, which form these branched growth patterns that help accelerate nutrient cycling. Then plant growth promoting rhizobacteria, GPR, which is just this catch all term for root associated bacteria that benefit the crop or the plant in some way. Some positive functions. Again, just a review, talk about nutrient cycling. They release those sticky molecules, those polys staterides that help to bind soil particles together. They support the higher trophic levels. Lots of different kinds of soil life feed on bacteria. They're the pathogenic kinds, of course, for vegetable production. Some examples of bacterial diseases include black rod of braskas, bacterial wilt, curbates, bacteria spec tomatoes. Some forms of bacteria are going to be human pathogens, which is why produce safety is such an important area. Keep those pathogens off the surface of our pros move on. Another type of microfauna are the fungi. Fungi tend to be the most abundant in terms of overall biomass. If we look at this diagram, we can see the comparison between a human hair to a fungal thread, to a bacterial cell to a virus. That fungal thread is going to be much larger than the bacteria, bacteria. They tend to inhabit the more acidic, undisturbed soils like forest habitats. The basic life cycle of bacteria, fungi, fungi starts off as the spore, the sex cell grows into the micros structures. The hype Mics is they form an extension of the plant roots. They help find nutrients and minerals in exchange for photosynthates from the plant. They symbiotic relationship. Then of course the reproductive structures, the mushroom phase, which takes many different forms. I've talked about the pathogenic fungi for a second here. Various fungal diseases of vegetables include braska, leaf spot alterna, corn smut, or anthracnose. Those are true fungi, but there's another group that closely resembles fungal diseases but are actually protests. These are known as the mycetes or the water molds. Okay, and these include many of our most severe diseases in vegetable production. Downy mildew, whether that's downy, mildew of braskas, onions, lettuces, curbts, tapthter, very damaging disease, tomatoes, peppers, soybeans, asparagus and pythium, which also has a pretty wide host range. Again, these are true fungi, these are in the produce kingdom. These are omits speaking of protsts. Another type of microfauna is the protozoa. The protozoa, these are your amoebas, your ciliates, your flagelts. Protozoa are very important for nutrient cycling and mineralization. Not only because they feed the higher levels in the soil food web, but they literally go about grazing on bacteria all day long. They'll engulf them with their entire bodies and trap them and then digest them that way. And the protozoa, when they consume these bacteria, those bacteria tend to be higher in nitrogen than the amount of nitrogen that the protozoa need. And they'll excrete that excess nitrogen directly back into the soil habitat which is immediately plan available. That's an example of their importance for mineralization. Okay, moving on to the Meso fauna. These are the forms of soil life that are between 100 microns and 2 millimeters. The most abundant form of Messfana are the nematodes. The nematodes are these microscopic roundworms. They have different mouth parts depending on what they feed on. A lot of our plant parasitic nematodes, they have a mouth part known as a stylet, which is basically a very sharp needle like appendage for penetrating plant cells. Some types of nematodes can also be beneficial and pasi insects, some of our pest species and vegetables like thrips, flea beetles, cabbage maggots, There are different entymopathogenic nematodes that prey on them. The first pathogenic nematodes good example would be root nematode, which feeds on the roots of crops like carts causing those galls that really reduce crop quality. Garlic blotto similarly, can cause discoloration in garlic bulbs. Potatoematode feeds on the roots of nightshade crops like tomatoes, potatoes, eggplant tomatoes, that sort of thing. Another type of meso fauna are the tardigrades. Again, these are microscopic animals. They're nicknamed the water bears because they live in water films on the surface of mosses or in the soil. Water tardigrades are pretty famous for being able to withstand harsh environmental conditions. They've been known to survive in Antarctica, or the vacuum of space. One strategy that they have for withstanding the freezing or dry conditions, they form this structure called a ton. Basically, they expel all the water from their body and they shrivel up into the state where they can survive indefinitely until they're rehydrated, quite resilient. This is what a tardigrade looks like under normal microscope. A peculiar creature in the meso fauna category. Another type of mesofuna organism are the rotifers. Like the tardigrades, these need soil water in order to survive. They're filter feeders, more specifically vortex feeders. They have these mouth parts with a very fine cilia on them. They act as like propellers to draw water into their mouth where they filter out the organic debris or the bacteria. Okay, Yeah, like tardigrades, they can form a resistant ton if there's no water present and survive like that. And here you can see in this slip, that propeller action with the rotifer mouth parts. It also important to touch on mites are in the class Keta, close relatives of ticks and spiders. There are over 20,000 different types of soil, different species that have been classified. It's estimated that there's about three times that many still waiting to be discovered. Mites can either be predators, which case they'll feed on fungi, nematodes, smaller mites, or they may be detritivores, breaking down that plant litter. Spring tails are another type of micro arthropod. They are these small translucent arthropods, most of them are detritivores. They shred organic matter into smaller pieces, which important for nutrient cycling because it increases the surface area which allows micro organisms to break down that organic matter. A quick, like earthworms, Colombola or springtails, tend to be a pretty good indicator of soil quality. They really thrive in high organic matter. Moist soils, I've helped with onion harvest before, and muck soils. Muck soils very high in organic matter, up to 80% for some fields, compared to like a mineral soil, which you'd be lucky to get 5% organic matter, but you can just see the soil teeming with those colmbola because again those muck soils are high in organic matter and soil moisture. Fun fact about these bitters is they have this rear appendage called the Furcula, okay? Which they used to spring themselves away if they get cornered by predators, hence the name springtail. Okay. The final category I want to highlight is the macrofauna. These are the organisms between 2 millimeters and 20 millimeters. It's not just columba. We have many other different types of arthropods in the soil as well. Centipedes, millipedes, spiders beetles, pseudoscorpions, pill bugs. The list goes on. Some services they provide, of course, feeding the higher trophic levels, they tend to act as either predators, the tridior, their waste products contribute to soil organic matter in their brewing activity really helps to aerate and mix the soil as well. Another type of macrofauna are the molluscs, your gastropods. Your snails and slugs. Snails have that external, harder shell made out of protein and calcium carbonate. Slugs have an internal softer shell underneath the flesh, their tissue. The way that these gastropods feed is they have this mouth part called the regula is like a saw like tongue that they use to scrape away food particles before they ingest them. Here you can see a close up of that slug regula and note that Abs, sharp texture, similar services as other macrofauna waste products, nutrient cycling, brewing activity, et cetera. Sometimes slugs may be an issue in your vet, in your vegetable plantings. In which case, you might need to take actions to reduce slug feeding. You can alter the environment by drying out the soil, increasing light transmission, reducing ground cover for example. Or you might resort to special practices like copper barriers, diatomaceous earth, or even resorting to a specialized slug bait if you're feeding is severe enough. Finally, earthworms, like the rock stars of soil life because they're so visible, they're generally sometimes used as a direct indicator of biological soil quality. Certainly they have many benefits there. Burrowing creates those biopors which helps increase drainage. Their casting very high in nutrients. Of course, they provide food for even larger organisms. All right, so to synthesize everything that we've talked about in this presentation. Basically the three types of soil quality, physical, chemical, biological. With organic matter being important for all but especially that biological category because it feeds the different types of soil life. In order to build our soil organic matter, there are many established practices. Minimizing disturbance, maximizing living roots and soil cover, and maximizing overall biodiversity, and adding different kinds of organic amendments. Back to this principle of nutrient cycling, organic matter feeds many different types of soil organisms. Even the higher level organisms are going to contribute to that organic matter through their waste products, through the activity when they die and decompose. Basically optimize for soil activity and soil diversity. And your organic matter levels will build over time, contributing to a better soil structure and overall improved crop productivity. I think that's that. I just wanted to remind everyone that MSU programs are open to all regardless of background or identity. Yeah, thank you for your attention. All right. Thank you so much, Chris, for an excellent presentation. Somebody had asked thoughts on dairy doo in bulk. Yeah, certainly. We talked about adding compost and how that's going to improve your organic matter bulk would probably be the most cost effective way to order it if you wanted to do. I would be happy to elaborate on that more. I'm just not quite sure exactly what you're looking for there. But yeah, dairy doo, excellent product compost is going to be very good for your soil biology. Somebody asked. I'm working on my microscopy skills. Are there any visual resources that will help me to distinguish the various types of microbes? Yeah, that's a good question. I can't think of a place where you could find all these different types of like the research that I did for this presentation, I use multiple different sources. There's not like a one handbook that I can think of for identifying the different types of microbes or even mesopuna or macrofauna. Yeah, I guess I'd have to think about that. But there's a lot of information out there, especially in the academic literature, that would even be useful for identification. Our annual applications of cattle manure and issue for vegetable crops. Not necessarily. As long as you keep food safety in mind for crops that are going to be in contact with, potential contact with the manure. I believe it's 120 days from manure application to harvest to let that compost or let all the human pathogens die in the animal manure. And 90 days for crops that aren't going to be in direct contact with with the manure. Yeah. As long as you're smart, from a food safety from a protein safety perspective, cattle manure can be excellent source of nitrogen. In particular opinion on no to for acreage, it's hard to change from grandpas turning soil. I'm not sure what you're asking there for acreage. No till. oh no till. Okay. Yeah, no till can be fantastic. A lot of the principles that we talked about in presentation that the NRCS had articulated, keeping that soil covered, maximizing living roots in the soil using cover crops. And no till is just going to build your soil organic matter faster. It depends on what vegetable you're growing. Certainly some are more conducive to no til than others, like pumpkins do very well in no till. There are some caveats there. But generally it's very advantageous for biological quality. As part of an organic farm that has heavy clay, I'm applying compost every year and don't tell. Will this heavy clay layer eventually develop a good soil structure? Yeah, yeah, certainly organic matter is going to only improve soil structure. It might take a while. Organic matter tends to build slowly. But certainly, yes. Yeah, it'll only help, I guess I'll say that much again. Those wait times for manure contact, 90 days for crops that aren't going to contact the manure and 120 days for the others. Those can be found online quite easily.