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Management practices that promote beneficial soil and plant microbiomes

Management practices to support soil microbial communities.

June 19, 2019  By Presented by Bobbi Helgason, University of Saskatchewan, at the Soil Management and Sustainability Summit, Feb. 26, 2019, Saskatoon.

No-till encourages mycorrhizal fungi. Photo by Bruce Barker.

Healthy soils are alive. Up to one quarter of the Earth’s species live in soil if you include plants and their roots, mammals, small and large invertebrates, and my area of research focus, which is microorganisms. In terms of soil microbes, in one teaspoon of soil there are more microbes than there are human beings on the Earth, and in that same teaspoon of soil there are tens of thousands of different kinds of microbes.

The microbial biomass in a typical arable soil is 0.0025 grams per gram of soil. It doesn’t seem like very much, but if you scale it up, it’s equivalent to about a hundred sheep per hectare or 40 sheep per acre in terms of actual living biomass. Different than sheep, soil microorganisms have a remarkable genetic diversity, and that means that they can perform a remarkable diversity of functions.

What are some of the practices that we can use to support soil microbial communities?

Some of these beneficial practices are continuous cropping, reduced physical disturbance, balanced nutrient management, organic amendment application, diverse crop rotation, cover cropping and use of inoculants. All of them have the commonality that they build soil organic matter.


Think of the size of the microbial community in soil like a biological engine that’s driving numerous important processes. The bigger the engine, the more capacity you have to drive those processes when and where the time comes that they’re needed.

The importance of microbial diversity in soil can be a little trickier to understand. We have this definition that we call “functional redundancy.” What that means is, at any one time in the soil, a diverse community will have more than one population capable of performing a critical function under different conditions. Let’s take nitrogen mineralization as an example. We need nitrogen mineralization to be occurring early in the spring when the soil is cold. We need it to be occurring during growing season when soil conditions are warm and perhaps drier. We need nitrogen mineralization occurring in the fall when there are no living plants there. It’s the functional redundancy aspect of microbial diversity that ensures that there’s a population there that can perform that function of nitrogen mineralization under all of those different conditions. When the conditions prevent one species or population from performing the function you need, there is another that can take over.

So it’s kind of like insurance. You have critical soil functions that are performed by soil microorganisms and a highly diverse community gives you the insurance that that process will occur under a variety of environmental conditions that may or may not be under your control.

Why do healthy microbial communities matter?

Healthy soil microbiomes nurture healthy plant microbiomes. The microbiome is just the totality of all microorganisms that inhabit a particular environment. Every single time we plant a crop, we’re planting it into a soil that is full of microbial life. If we’ve got a healthy soil, we’re optimizing the opportunity for that plant to capitalize on that microbial life. If we’re planting our crop into an unhealthy soil, we have an immediate disadvantage.

The answer to many of our problems is soil organic matter in one way or another. That’s because soil organic matter improves soil physical properties. It’ll improve the infiltration of water. Soil organic matter provides food, water, shelter, and aeration for microorganisms. When we think about carbon in soil and soil organic matter, the idea of building soil carbon is actually pretty simple – carbon in minus carbon out equals storage. So if we want to increase soil organic carbon levels, we can either increase the amount of incoming carbon, for example by increasing plant carbon inputs, or we can decrease the amount of carbon leaving the systems by decreasing the amount of loss, unwanted loss due to microbial activity.

What are soil biota and those soil microbes doing?

They provide ecosystem services. They’re controlling plant growth. They produce hormones. They directly associate with plants in symbioses. They also suppress pests and disease, so a healthy microbial community will be more competitive against pathogens that might try to take over. Other ecosystem services include the maintenance of soil structure and hydrology, gas exchange and carbon storage, as well as soil detoxification or the breakdown of unwanted contaminants in soil.

Continuous cropping encourages soil microbial communities

The first example of how soil microbial communities are facilitating all of these different ecosystem services is a simple experiment that’s been running for a really long time that shows how putting in more carbon into the soil increases microbial abundance. The Rotation ABC historical experiment in Lethbridge, Alta., began in 1910 when the research station was established and the native prairie was broken. At that time, researchers wanted to understand what the effect of fallow/wheat/wheat versus continuous wheat would be on soil productivity.

This is a comparison of a long-term continuous wheat experiment, “long-term” being a hundred years. In the 1960s when the use of nitrogen fertilizer became common, these plots were divided and they started applying nitrogen at a rate of 45 kilograms per hectare. About five years later, they split the plots again and applied phosphorus. So we have wheat grown continuously for a hundred years and a wheat-wheat-fallow rotation with no fertilizer whatsoever. Even under a really drastic N and P imbalance, there is still higher microbial carbon where there is a crop every year (in continuous wheat). And the same holds true for all of the other fertilizer treatments. The bottom line here is if you feed the bugs, you will support their abundance. Even in the absence of balanced fertility, more carbon input is very likely to build more microbial biomass. However, this is not what I would call a healthy soil.

One of the tools that I use a lot in my research program is the Carbon-13 (13C) stable isotope tracer. We can tell which organisms generally or sometimes very specifically have utilized carbon. And then we can also tell what’s left behind in the soil as well as the proportion of our tracer that’s lost during respiration. We use it in order to follow carbon that we’ve added to see which microorganisms use it, what’s left behind, and how much is lost.

As part of a trial looking at how fungal nitrogen cycling affected nitrous oxide emissions, I looked at how reduced physical disturbance, in this case no-till seeding, affected the microbial biomass. We looked at four different long-term research trials of about 25 years at Swift Current and Scott, Sask., and Ellerslie and Breton, Alta. – representing four different climates and soil types.

The first thing that we saw was that indeed no-till increases the amount of microbial biomass in the soil, particularly right in the zero- to five-centimetre range where the crop residues are left, but also deeper in the soil profile. Conversion to no-till decreases the amount of carbon out of the soil, thereby increasing the amount of storage and in this case, also the amount of microbial biomass.

I looked at community composition and the ratio of fungi to bacteria. In all four of these systems, although microbial biomass increased under no-till, there was no difference in the ratio of fungi to bacteria whatsoever. That was a real surprise, because it was very commonly accepted that decreased physical disturbance would promote fungal dominance within a soil system.

One thing that we did see was that no-till promoted mycorrhizal fungi. Mycorrhiza is an obligate symbiont. It uses carbon from the plant and then it in return provides nutrients and water back to that plant. So in the absence of a host, its fungal hyphal network is really kind of stranded in the soil. When you till mycorrhizal networks, it sort of kicks those Arbuscular mycorrhizal fungi (AMF) in the teeth.

Crop rotation diversity improves microbial diversity

More recently we had a Carbon-13 tracer study set up at 10 different sites across the country. One site is in Lethbridge, Alta., and another in Ottawa. We compared these two sites because one was a semiarid prairie system versus a more humid, wetter system in the east; the rules that govern microbial communities in wetter and drier soils aren’t always the same. We grew out barley in a chamber with 13C labelled gas, so now we have barley residues with 13C tracer in them. That enables us to follow it as it gets incorporated into the soil, used by microorganisms, and lost as CO2 in the end. We either incorporated those residues in the top 10 centimetres or we left them on the surface to mimic no-till.

An important thing about this study is that we added the residues with the tracer in 2007. Every year since, we’ve gone back and added barley residues without the tracer. That allows us to follow those carbon molecules that we added in 2007 through to today and beyond without starving the system for carbon in the meantime.

For the microbial work, we looked at six months, 12 months, and 24 months after residue addition. If you compare incorporated to surface-applied at Ottawa, there actually isn’t that much difference – approximately 25 per cent of that residue remains after two years in the more humid climate. But if you compare no-till to tilled in the prairie conditions, a lot more residue 13C remains two years later under no-till when it’s drier.


In Lethbridge, less residue remains when incorporated, whereas in Ottawa, incorporation makes less of an impact on the decomposition of residue. Source: Helgason et al. 2014, Soil Biology and Biochemistry.

We looked at the microbial community composition in this experiment. For the Ottawa site, there seemed to be a bit of a community difference when we surface-applied or incorporated the residues but no differences in community in the depth of residue incorporation.

Conversely, in the Lethbridge soils, microbial communities were strongly differentiated by both depth and whether or not we incorporated the residues. This tells us different microorganisms were actively chomping on that 13C residue whether we incorporated it or surface-applied it.

The next question then becomes what does this mean for the actual composition of the soil organic matter? This leads to the observation that often in no-till, more soil carbon doesn’t necessarily mean that we have increased nitrogen mineralization capacity because perhaps the quantity of soil organic matter might be higher but not as high quality, for example.

Another beneficial practice for promoting health soil microbiomes is the use of diverse crop rotations. Two long-term studies, one in Swift Current, Sask., and the second in Harrow, Ont. looked at crop rotation diversity. At Harrow, continuous corn was compared to a corn-soybean-wheat rotation. At Swift Current, continuous wheat was compared to wheat-canola-wheat-pea rotation. Dr. Jennifer Town, who’s a postdoctoral researcher that works with me, is conducting this work. We looked at various aspects of microbial abundance, microbial community structure, and most importantly microbial community function in these systems.

You would expect that with higher above-ground diversity you might see higher below-ground diversity. Surprisingly we found that there was no difference in bacterial diversity in the soil whatsoever as a result of improving the rotation diversity.

However, we did see that there was a difference in the community structure and function. In the diverse corn rotation in southern Ontario we saw more mineralizable carbon. At another sampling time point we saw more amino sugars, which is a readily available carbon source that comes from the microbial biomass itself once it dies; as well as beta-glucosidase activity, and that’s another carbon-cycling enzyme. So definitely we saw accelerated carbon cycling in the diverse rotation compared to the continuous corn.

I mentioned that mineralizable carbon seems to be positively associated with crop rotation diversity. That’s a good thing, we think. One of the reasons for this is that we also measured the lignin content in soils. Lignin is a structural component of plant tissue. But, it has a really high C-to-N ratio and it’s not that palatable to microbes, so it takes longer to break down. In both the wheat and corn systems, we’re seeing really quite a significant accumulation of lignin, and all different types of lignin derivatives. So not only have we changed how the system is functioning but actually this is a very clear indicator that we’ve changed the composition and the quality of the soil organic matter, and that likely has to do with that yield boost that we saw in the diverse rotation.

Balanced nutrient management favours microbes

The last example of beneficial practices that I’m going to talk about is balanced nutrient management. It is a long-term cropping system at AAFC Scott, and compares long-term organic versus conventional management. It’s not a good-news story for the organic system, but I want to make it clear that I certainly do not want to pick on organic management with this example.

The defining criteria of the organic system is that there are no synthetic inputs and there’s a high amount of tillage in order to combat weeds. The reduced input conventional system uses very judicious use of fertilizers and pesticides and no-till. In both systems, we have diversified crop rotations with either an annual grains-based-rotation or a second rotation that has three years of perennial alfalfa in it.

Throughout the course of the 18-year study – three full six-year rotations – yields in the organic system were declining. There was a phosphorus problem – Scott soils inherently are quite low in phosphorus – and the researchers also knew that they weren’t getting enough nitrogen into the system.

After 18 years, soil tests showed nearly 3.5 per cent total carbon in the annual grains conventional system, compared to 2.75 per cent in the organic system. Available nutrients were also drastically different. If you look at the available phosphorus column, you can see that that conventional annual treatment is far, far higher than all of the other three treatments. It also had more available nitrogen.

Soil properties after 20 years of organic and conventional management.

We also wanted to understand how microbial communities were functioning in these soils. Postdoc Melissa Arcand, who is now professor in the soil science department at the University of Saskatchewan, did this work. The high-fertility conventional annual rotation had the highest microbial biomass, not surprisingly, and that microbial biomass was significantly reduced in the other three soils, and lowest in the organic annual soil. This was also reflected in soil microbial function. We saw reduced turnover of phosphorus, nitrogen, and carbon – reduced microbial biomass and impaired microbial function.

We looked at microbial community structure of those organisms that were actively munching on added 13C barley residues, and we tracked them through time over about a hundred days as the residue decomposed. By the end of our experiment the conventional annual system had the most abundant and robust microbial community and highest fertility while the community composition really didn’t change that much over the course of the hundred days.

The take-home message from this particular experiment is that, because in the organic system we weren’t using any organic amendments – there was no manure application – managing crop residues is a critical aspect of restoring fertility. We have to get more nitrogen and phosphorus into the system certainly, but even if we can manage to do that, it’s going to take a long time to get our soil carbon back in check by the time we get yields up and residue returns coming back into the system.

We need to remember that carbon just isn’t carbon. It carries the energy that fuels all of these microbial processes. I think of carbon as this molecule that carries energy around our ecosystem. That’s why building soil carbon can be so impactful if you have an imbalance in your soil. By improving practices, as example no-till or diverse crop rotations or using perennials in rotation, we can improve soil organic carbon content, but it takes a long time.

It is important to remember that storing carbon in the soil in and of itself doesn’t realize its capacity to function in the ecosystem. It actually has to be utilized to be doing its job. Yes, we want to store more carbon in the soil, but we also want to improve the use of that carbon by biota in the soil, including plants, through the actions of a healthy soil microbial community.

More from the 2019 Soil Summit

Watch Bobbi Helgason talk about long-term soil health and several practices that promote sustainability and improve soil health in her Speaker Spotlight video. To see other presentations and speaker spotlight videos, visit our archives for the 2019 Soil Management and Sustainability Summit.


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