Forage 2021: Microbiomes: Cities in the soil

Imagine a community. Every citizen in the community has a job. Some work in manufacturing. Some work in repair. Some haul off the garbage. Some prepare food. Some…well, we’re not sure what some of them do. They all have a function, but they all have needs that must be met. And they all have the same goal–to survive.  

Now, imagine that community being too small to see, and being in every square inch of soil, touching every plant in the world. 

That’s a plant microbiome. 

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In the last 10 years, plant microbiomes have caught the attention of scientists who study agronomy, horticulture and energy.  

As the world looks toward renewable energy, there is increasing focus on improving the efficiency of plants–specifically, those that can be used for biofuels. While that big, sexy topic is attracting attention and grant dollars, that research and its findings is being applied and expanded on in studies that will benefit agriculture in general.  

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Peggy Lemaux is a Cooperative Extension specialist with the University of California, Berkeley. She grew up on a small farm in Ohio, but when it was time to choose a career, she thought she’d find something easier than agriculture. So she became a microbiologist in medical research. After becoming disillusioned with medical research, she decided to apply her medical research background to plants. 

Microbiomes in the human body pioneered the research into understanding microbiomes, which are complex communities of microscopic organisms that interact with nearly every living thing. Some are beneficial, some are detrimental, but all exist solely for their own survival, Lemaux said. 

Lemaux’s research has been primarily on the effects of drought on sorghum and its microbiome, and understanding what makes sorghum more drought-tolerant. The Department of Energy funded a $12.3 million grant for the research Lemaux and her colleagues did on the subject. Sorghum is an important plant for biofuel use, and is more drought-tolerant, but also more flooding-tolerant than corn. It also has forage value, so a lot of industries have an interest in optimizing the efficiency of sorghum production, Lemaux said. 

While one would think that identifying the organisms in the microbiome would be the first step in learning their functions and requirements, Lemaux said their research primarily works backward from a genetic standpoint, by identifying individual genetic sequences and then figuring out the function, and identifying the bacteria that perform that function. “You can’t isolate each bacteria and figure out what it is,” she said. “But you can take this whole mash of genomes and put them back together. By figuring out what genomes are there you can figure out what bacteria are there.” 

A lot of research on these types of subjects is performed in a growth chamber, greenhouse or other controlled environments. Lemaux, though, wanted to know how real conditions affect the plant and its microbiome. So her research was performed in fields in California, where her team repeated the same experiments for three years in a row, taking samples of roots, leaves, soil and rhizosphere, a tiny layer between the root and the soil, every week for 17 weeks. “Every year is a little bit different. What we learned one year is fine, but if we do it for two to three years are we going to get the same answer? Not for everything. A lot of the microbe reactions and plant reactions are the same from year to year. We’re putting together three years of expression levels of genes that are in the plant roots. So we can know what kinds of things does the plant think it has to make or do? How is it protecting itself? A lot of those things, by looking at three years of data, are the same. That’s reassuring to those of us who do research.” 

During the study they discovered that the microbiome reacts faster than anyone anticipated to changes in water conditions. For example, when the plants were droughted for eight to nine weeks, the diversity of microbe types in the rhizosphere dropped from maybe 100 different bacterial species down to maybe 10, Lemaux said. Once water was added back to the plants, within 24 hours the number of species in the rhizosphere spiked back up to 100. The microbial community in the soil stays the same, drought or not; it’s just the rhizosphere community that changes dramatically. 

Lemaux pointed out that the soil they were studying isn’t “natural.” It’s been used for Extension agronomy studies for decades, so it was essentially converted to cropland. “Even so, it’s very diverse in terms of its microorganisms,” she said. “We hadn’t gotten rid of the microbes in the soil. That’s good.” 

Volker Brozel is a professor at South Dakota State University and is studying microbiomes in the context of “natural” soil compared to cultivated soil. One of SDSU’s study sites is the Sioux Prairie in eastern South Dakota, which has been owned by The Nature Conservancy since the 1960s, Brozel said. “It gives a comparison to what it looked like before people came with plows.” Brozel studies primarily the nitrogen cycle. “The prairie takes care of itself. Which, obviously, it did for many thousands of years. We do know there’s a lot of microbial activity involved in the root environment and inside the plant. When one gets to cultivated cropland there’s a whole different story, as a lot of the natural microbiota has been lost due to monoculture.”  

Brozel points out that most of the major breakthroughs in farming in the last few decades have been above-ground, plant-focused or on the physical properties of soil, as with no-till farming. “People have increasingly wondered what’s happening below ground. We don’t see it, but it’s very much part of the plant. Every plant has a root system.” 

The question they’re asking now is how to make the plant system more efficient at the underground level. “There are a lot of lifeforms and a lot going on there–fungi, protozoa, bacteria, insects,” Brozel says. “I think the important thing to realize for a producer is it’s not as simple as good guys and bad guys. Every organism in there is in the game of surviving, from their perspective. A plant wants water, phosphorus, nitrogen. A bacterium wants food. Sometimes it benefits the plant, sometimes it’s to the detriment of the plant.”  

Brozel points out, though, that the focus needs to be on the community, not on finding a “magic” bacterium that will make everything better. “There is something to that, but the soil is very diverse. It’s not that simple because you’re introducing it to a complex world. My lab asks how does that world work in its totality. Before we fix the engine, can we understand how it works and tweak it?” 

A natural grassland, Brozel says, is very capable of supplying itself with enough nitrogen through fixation. In a plant monoculture, like most farmground, some of that ability is lost. “If we can find out how that works we understand better the pieces to put back into monoculture. These nitrogen fixers can boost plants if you can boost their happiness. Fixing nitrogen takes a huge investment from the bacteria. It’s a very energy-intense reaction. Bacteria don’t do this because they feel like they want to do a good deed for the plant. They have to get something in return. Understanding how that interplay works is important for us.” 

Sen Subramanian is a professor in agronomy, horticulture and plant science at SDSU. His research focuses on how microbiomes affect nodule development in soybeans, and, in partnership with Kansas State University, how microbes affect chilling tolerance in sorghum. Sorghum would be a desirable crop on the Great Plains, as it doesn’t require as much water or fertilizer as corn, can tolerate flooding more than corn and can be used in both energy and agriculture applications. However, because it’s sensitive to early-stage chilling, meaning it needs a higher soil temperature than other crops, it often can’t use winter moisture for germination, and it sometimes freezes before it’s harvested. For fields that aren’t suitable for corn, or other cultivation, sorghum could be a valuable crop if scientists can solve that one small problem.   

The research is still relatively new, but several companies are in the early stages of offering farmers microbial options for improving growth and pest resistance. They identify a few species of bacteria that have a beneficial function and add them through seed coat or specific application. One company, called BioConsortia, is developing, or has developed, biologics to address nematodes, insects and fungus, plus nitrogen fixation and biostiumlants, which they say consistently improves the yield of various fruit and vegetable crops by 15 percent, according to their website.  

Brozel and Lemaux both pointed out that microbiomes are specific to ecoregions, so the microbes that would be beneficial to cucumbers in California wouldn’t be much help to millet in Montana. “They have to be tailored to soil structure and a range of factors, like temperature and rainfall,” Brozel said. “What would work in eastern South Dakota wouldn’t necessarily work in western South Dakota.”  

The scientists all hope their research will add another piece to the puzzle of what goes on underground that affects how plants perform and survive. “One can apply concepts to closely-related crops,” Subramanian said. “A benefit of doing this detailed analysis is you can identify what microbe, but also what quality in that microbe is performing a function. You can find another microbe that already exists in another environment that provides the same benefit.”

Like the communities in the world, microbiomes all have unique aspects, and they don’t all have the same needs or functions. Billings doesn’t need gondoliers and Venice doesn’t usually need snowplow drivers. The key, scientists are discovering, is figuring out who is doing which job, and who to hire and who to fire to get the important jobs done.