Compost & The Promise of Microbes

Scientist David C. Johnson Explores Microbial Communities, Carbon Sequestration and Compost

David C. Johnson’s experimental findings and openness to new insights have turned him into a champion of microbial diversity as the key to regenerating soil carbon — and thus to boosting agricultural productivity and removing excess atmospheric CO₂. His research, begun only a decade ago, affirms the promise of microbes for healing the planet. It has attracted interest from around the world.

Johnson didn’t come to science until later in life. At age 51 he left a rewarding career as a builder, specializing in custom homes for artists, to complete his undergraduate degree. He planned to use his education “to do something different for the other half of [his] life,” though what he didn’t know. He said a path opened up and opportunities kept coming his way. After completing his undergraduate degree, Johnson kept going, earning his Masters in 2004 and Ph.D. in 2011, both in Molecular Microbiology. With his first advanced degree in hand, he got a job at New Mexico State University, where he was going to school and currently has an appointment in the College of Engineering.

He credits a fellowship program that placed undergraduate students in different labs with sparking his fascination with the composition of microbial communities as a graduate student. Johnson, who once farmed as a homesteader in Alaska, says he was once “an NPK junkie” but considers himself to be “13-years reformed.”

Charged with finding a way to process manure from factory dairy farms that would be beneficial to cropland, he and his wife — and behind the scenes collaborator — Hui-Chun Su designed a bioreactor for producing fungal-rich compost. Previous researchers on the project had only been able to make highly saline composts that proved harmful to plants. Johnson went on to demonstrate the remarkable power of his compost to dramatically boost crop growth and carbon sequestration in soil, which correlates with its high fungal to bacterial ratio. Currently, he is experimenting with this compost as a seed inoculant and working to expand the scope of this critical research through collaborations with other interested researchers.

Interviewed by Tracy Frisch

Microbes in Action

ACRES U.S.A. At what point did you fall in love with microbes?

DAVID C. JOHNSON. I guess when I started seeing results. Through a fellowship I had at New Mexico State University, I was put in a lab with Dr. Geoff Smith who was looking at biodegradation of toluene in a lake in Mexico. All the oil from the cars was washing down into the lake. We have a pond here that all the roads drain into. I got a sample of that soil and put it in the bioreactors. The toluene completely degraded overnight. That kind of set my path. Every lab situation has taught me something about what I’m looking at today. What I learned about the structure of clays and their ability to catalyze reactions was part of this as well. You always wonder why are you doing this. I stopped asking that question. Now I think let’s see what happens.

ACRES U.S.A. How did you get on the research path you’ve been pursuing?

JOHNSON. For my Ph.D., I was looking at microbial community structures for hydrogen production. It’s bio-hydrogen, where you can make hydrogen using hydrogen-producing microbes with certain substrates. At the same time, I was working on a project with USDA to figure out what to do with dairy manure.

ACRES U.S.A. I haven’t been to New Mexico for a number of years, but I remember seeing what looked to be very large CAFOs (concentrated animal feeding operations).

JOHNSON. Many dairy CAFOs moved to our area from California to get away from the regulations there on the disposal of their manure and effluent. Some of these CAFOs are still here, but a lot of them have gone further east, to the other side of the state, and to states like Texas. One of the problems with the dairy manure was it was very saline. Researchers had been working on the project for about a decade before I got assigned it. They experimented with making compost with the manure but had concluded that compost was bad for soils.

ACRES U.S.A. How were they making the compost?

JOHNSON. They were using a windrow composting process. I started with windrows, too. But then my wife changed the way of doing it. She stepped in and said, “You’re coming home with too many dirty clothes, turning these piles. We’re going to figure out a better way.” So we developed a no-turn static composting process that also kept the pile aerated, which was essential for allowing the fungal community to begin to dominate in the piles.

ACRES U.S.A. She sounds like a good collaborator. What’s her background?

JOHNSON. She has a talent for recognizing the obvious, which is quite commonly missed and she is very creative.

ACRES U.S.A. Why wasn’t the windrow method successful for composting this manure?

JOHNSON. With windrows, most of the time it’s anaerobic. Then every time you turn it, you’re disturbing the fungal community’s households. Basically you’re throwing everything out in the street and having them start over. At the beginning, you’d turn it up to twice a day. Later you taper off to turning once a day, and then usually to about twice a week and on down, as the process continues. But every time you turn the pile, you disturb it. We found out that with the windrow process, the salinity stays the same or increases. The compost would have from 30 to 44 millisiemens conductivity. But plants can’t take anything over, say, 10, and they really like it at under 3 millisiemens.

ACRES U.S.A. I imagine you already have a salinity issue in a dry state like New Mexico.

JOHNSON. Yes, and the more fertilizer they put on, the more severe the salinity is becoming. The fertilizers seep down into the water table, and now they’re pumping those salts back up when they irrigate their fields with groundwater. That’s pretty detrimental to our soils.

ACRES U.S.A. Of course, that’s one of the causes behind the downfall of the great irrigation civilizations.

JOHNSON. You’re correct there. But add the fertilizers and you compound the problem. We originally had the ability here to leach [the salt out of] these fields because we have a shallow water table with a significant amount of water. But now that they’ve pumped out the aquifers, they’re down in the phreatic zone. The result is they’re just putting out more salty water right on top of salty soil.

ACRES U.S.A. Are there parts of New Mexico where ag land has already been abandoned due to its salinity?

JOHNSON. Not yet, not like Arizona, but we’re really close and the farmers are really concerned. The one redeeming thing is the Rio Grande, which goes through Las Cruces. That water is pretty low in salinity so farmers are still able to leach out the salts. But the Rio Grande’s flow rate depends on Colorado having a good snowpack and the last decade has been pretty dry.

ACRES U.S.A. Last year I did a story with a farmer who does static pile composting for his vegetable farm. To aerate it he uses PVC sewer pipe and a little squirrel cage fan that he only has to run intermittently for a week. He makes his compost very fast. Would that be too quick for fungi to take hold?

JOHNSON. That’s more a mulch than compost. From what I’m seeing in the research, my compost is not even mature at six months. The compost I put out is like clay. It oozes between your fingers when you squeeze it. The analysis of its community structure shows at least a four times increase in the biodiversity of the microbes. More importantly, I see that fungal community really thrives.

ACRES U.S.A. Do you do this analysis yourself or do you send it out to a laboratory?

JOHNSON. The equipment is about $1.5 million, a bit out of my budget, so I send it out to a lab.

ACRES U.S.A. How are the fungal bacterial ratios determined? Is it based on the chemical composition?

JOHNSON. I use two processes. The cheaper, less expensive process is called 16S or 18S analysis. The 16S does bacteria; the 18S does fungi. The tests are about $40 to $50. In some cases it gives me the bacteria or fungi down to the species level.

ACRES U.S.A. Is this DNA-based?

JOHNSON. Yeah, it’s genomics. The technology was developed in 2004 or 2005. I also run metagenomics on it. This basically breaks apart all of the DNA and sequences and reassembles it and then assigns it to an organism that matches the closest. Those tests run from $400 to $800.

ACRES U.S.A. It’s amazing that they could do that.

JOHNSON. We have information overload now.

 ACRES U.S.A. What should we know about the Johnson Su Bioreactor you and your wife designed?

JOHNSON. It’s a relatively simple, inexpensive bioreactor made of readily available materials. It is simple to put together and fill and requires no turning or maintenance once built and filled. You don’t need any electricity. We designed it so it can be applied anywhere from the Third World to an industrial setting. Material costs are approximately $40/reactor and can be used multiple times. The bioreactor is made of remesh, used in concrete construction; landscape cloth (the woven cloth, 5 oz. or greater); a pallet; and 4-inch perforated plastic pipes, though they are only used for one day. After that first day, fungal hyphae will have stabilized the pile so much that you can pull the pipes out. The six cores will stay open and allow air to flow up from under the pallet, which is slightly elevated. The most important thing is allowing it to go long enough — for a year. The instructions are available in video and PDF form.

ACRES U.S.A. Do you need to use a certain ratio of nitrogen-rich materials and carbonaceous materials?

JOHNSON. I really didn’t follow that. I started out trying to adhere to a ratio, but my big problem was figuring out how to get airflow into the dairy manure because it was too dense. We put the tubes in the center because we found out that anything over 1 foot away from ambient air would start to go anaerobic. To get the dairy manure to compost, we had to add other materials. You could mix hay with the manure and you’d be fine. But then I used one-third dairy manure, one-third yard trash and one-third wood chips. Now I’m using all leaves. Of course, leaves have a carbon to nitrogen ratio of 50 or 60:1, but they compost just fine. I’ve actually composted straight wood chips just to see. They make a really nice, rich black compost, but it’s not practical time-wise.

ACRES U.S.A. How much material would you need to fill one of your bioreactors?

JOHNSON. It’s 5 feet tall. For wet leaves, it takes three pickup truckloads to fill a bioreactor. That’s 1,700 pounds. I pack them down. You get about a third of that height in finished compost.

ACRES U.S.A. I have some old round bales of grassy hay. Could I use hay alone or would I want to put other materials in?

JOHNSON. I would run it through a chipper shredder, so you could get more in. Otherwise, it would be really tough to pack. It would be good to throw in some manure and whatever other waste you have. Nature doesn’t discriminate, as long as there’s a carbon bond in it.

ACRES U.S.A. What’s the goal for moisture?

JOHNSON. It’s so dry here that I put all the materials through a water bath. It can be 113 degrees with 10 percent humidity, and in a day we’ll lose an inch of water on a pool or in a field.

ACRES U.S.A. What form is the CAFO manure in?

JOHNSON. They just pile it up. The cows are locked up, standing outside.

ACRES U.S.A. The initial charge of the project was to figure out a composting solution for the CAFO dairy manure that’s good for the soil. Did you succeed?

JOHNSON. If the project had gone further, we’d have been able to develop an industrial plant that could parallel process it. Two of the biggest problems with composting operation are odors and leaching. This process has neither of these problems. You can stand right next to one of the bioreactors and you wouldn’t be able to tell what it’s doing. We’ve been to composting operations all over the United States. When we went to one in Disney World, we had to run upwind. The ammonia was so powerful that we couldn’t breathe. In an anaerobic process, ammonia and all your volatile fatty acids — the ones that really smell — are released. They’re the issue that’s most likely to shut down most composting operations. The second issue is leaching. Most often, the compost is on a pad on the ground, and it’s watered. If you get a heavy rain, effluent leaches out of the piles and flows into rivers or the aquifer. The way the pile in the bioreactor is made, it will absorb almost any amount of rain it gets. It’s up off the ground, it’s aerobic and more porous, so it holds much more water before there’s any leachate.

ACRES U.S.A. What happens to the ammonia when you’re using high-nitrogen feed stock in the bioreactor?

JOHNSON. If it’s aerobic, the right microbes will be breaking it down and putting it into their cell structure.

ACRES U.S.A. I didn’t realize that. You’ve said that compost shouldn’t be considered a nutrient source. What do you consider compost to be?

JOHNSON. That goes to the root of the problem. For so long, in agriculture, we’ve thought that we have to amend the soil in order for anything to grow. That’s a dangerous mindset. Nobody fertilizes the rain forest! Nature does this handily without any nutrients. Rain forests are the most productive ecosystems on the planet, and they do this with biology. When I do the analysis, I find a lot of free-living, nitrogen-fixing bacteria in these soils, and in this compost as well, since I don’t abide by that recommended carbon to nitrogen ratio in making compost. If nature has a need for nitrogen there are a lot of organisms that can supply it.

ACRES U.S.A. That is revolutionary. I hear you suggesting that all the dogma we’ve learned about compost may be incorrect.

JOHNSON. How we look at soil today is counterproductive. It’s a living system, not a sponge that you put nutrients into so that plants grow. We need to ask the question, what biology do I need, not what fertilizers do I add. Besides free-living, nitrogen-fixing bacteria, I’m also finding phosphorus-solubilizing bacteria. We probably have a 40-year supply of phosphorus from fertilizer in agricultural soils but it’s inaccessible by plants without the right microbes to make it available. I also see microbes that secrete plant growth-promoting hormones. This system is beautifully and exquisitely dynamic in nature. If we can restore it back on our farmlands and rangelands, there’s a lot of potential.

ACRES U.S.A. You stress the desirability of a high fungal to bacterial ratio. Tell me what the implications are for growing plants.

JOHNSON. I currently see such a ratio as a coarse measure of soil fertility and soil health. Practically everything we’ve done in agriculture is detrimental to fungal communities. Now from what I’m seeing, using the metagenome, I think that bringing the fungi back is an indicator of good soil health.

ACRES U.S.A. Let’s make a list of what’s detrimental to fungal communities.

JOHNSON. There’s the plowing we do and the application of herbicides. One study figured out that applying glyphosate at 1/100th the recommended rate kills half the Aspergillus nidulans fungi. At 1/50th of the rate, it kills all of them. We need to reconsider things like that. When we leave a soil in a bare fallow, it’s probably the worst thing we could do to a soil. Soil depends on energy flow to function, just like we do. If the energy flow isn’t there, they won’t have a dynamic microbial community.

ACRES U.S.A. When you talk about energy flow, I’m assuming you’re referring to plants photosynthesizing using solar energy and carbon dioxide from the atmosphere to make energy for themselves and soil microbes.

JOHNSON. Basically the majority of our energy supply on this planet is what has happened that way. With that carbon flow the plants put a significant amount of root exudates into the soil to feed these soil microbial communities. I did a greenhouse experiment to try to tease out what percentage of the carbon flow went into the soil, and I found that in a bacterial-dominant, low-carbon soil, 96 percent of the carbon captured by the plant went into the soil.

ACRES U.S.A. To try to heal the soil because the soil was in a desperate condition?

JOHNSON. Yeah. If a plant is going to put that much of those valuable resources into the soil instead of growing itself, there’s a reason. In my experiment, in a healthy soil 46 percent of that carbon flow went into the soil to feed the microbes.

ACRES U.S.A. What happens in soils that are heavily contaminated with pesticide residues?

JOHNSON. We don’t have a good handle on that. It’s a dynamic system. We only have to look at our own microbiome and consider how significant an impact it has on our health. The microbes in our digestive system are turning on and off genes in our body that affect our appetites, our cravings and our immune system. If a person’s microbial community has been decimated by antibiotics they can get Clostridium difficile, IBS, IBD and Crohn’s disease. Doctors may give them more antibiotics to try to fix it and even cut out sections of the intestines to help them survive. Now they’ve found that a simple fecal transplant can cure most of these patients, some within 24 hours. They’re just getting the right biology back into the system.

ACRES U.S.A. Are you saying there’s an analogy with plants?

JOHNSON. That’s what I’m observing — soil is just like us. I suspected it, but it took putting in about seven years of research.

ACRES U.S.A. I like how you’ve referred to humans and plants as superorganisms that depend on many times more microorganisms to thrive. Is symbiosis then far greater than what we learned in school?

JOHNSON. Most assuredly. We are outnumbered 10 to 1, cell to cell. And we only have 30,000 genes to their 8 million. If there wasn’t a beneficial relationship for both sides, we would be just a tasty morsel to that many microbes.

ACRES U.S.A. Going back to your bioreactor, after you made that first good compost, what was your next step?

JOHNSON. In order to prove to USDA that it was a good product, I compared it to eight other composts available in the area. I did a standard inorganic chemical analysis and I threw in measurements of fungal and bacterial biomass. I had taken Elaine Ingham’s class and was curious how significant those results would be. For my growth test, I grew chili pepper plants in each of the different composts. In one of my tests I watered my bioreactor compost daily in the greenhouse for five months to see what would leach out, and how well the plants would grow in this medium. That material was better than all the others, including my raw bioreactor compost. Overall the two materials from my bioreactor supported twice as much plant growth as the next best compost. When I looked at the levels of nitrogen, phosphorus and potassium in the different composts, the correlations with plant growth were less than .05. (Some of the commercial composts had been amended with inorganic nitrogen.) The correlation with organic matter was poor as well, but the fungal to bacterial ratio gave a correlation of about .88. That’s pretty good odds, if you’re in Las Vegas!

ACRES U.S.A. That seems quite amazing.

JOHNSON. This was serendipity for me. I didn’t expect it, but it got me started looking at the fungal-to-bacterial ratio and the biological dynamics. I set up several experiments to look at what happens if I use this compost as a soil inoculant. I had already used my compost in the bio-hydrogen reactors with some interesting results and that reinforced this new path. That’s what I got my Ph.D. on. The microbial community that developed from the compost for bio-hydrogen broke every rule of hydrogen production. The rules are: hydrogen production happens at a pH of 5; at low headspace pressures, so in the reactors we keep the headspace pressure as low as possible; at mesophilic temperatures, which is around body temperature and low headspace hydrogen partial pressure. But the microbial community that came out of my bioreactor compost produced hydrogen down to a pH of 3. That’s a very significant amount lower than the pH that they say it happens at. The hydrogen bioreactors achieved high enough pressures to blow up, around 45 psi. The microbes produced hydrogen at room temperature and also at 100 percent hydrogen partial pressure in the headspace, and at headspace pressure of 45 psi. None of these conditions are supposed to allow microbes to produce any hydrogen. That was the clue telling me to look at the microbes. Going back to the growth test with the chili peppers, I had noticed that seeds wouldn’t germinate in some of the composts. When I transplanted seeds from my bioreactor compost into other composts, I found that eventually boosted their productivity, suggesting it could be an inoculum. All these little observations got me thinking. The first time I used my bioreactor compost in the field I put on a dusting of 400 pounds per acre. I only used it once. From that point on, it’s how you manage the soil. I say it’s 2 percent inoculant and 98 percent management. The biology needs oxygen, water and food and to be taken care of, just like any other organism. My wife says it’s the fifth animal on the farm that you need to consider to keep it alive.

ACRES U.S.A. Talk about the longer-term tests you’re doing.

Microbes in the Field

JOHNSON. In the seven-year test — which is going on eight years now — I was looking at a mechanism to pay farmers to put carbon into the soil. I’d grow a cover crop, green chop it and disc it back into the soil. Then I’d immediately replant and grow another crop. Everything went back into the soil. I used no fertilizers or amendments besides that initial compost application. From the first year until now, I’ve had a five times increase in net primary productivity in my winter cover crops. At one year there was about 50 grams of dry biomass per square meter of production on the control versus 250 grams on the treated. Then, from that soil to what I have now, production jumped 250 to almost 1,200 grams. By improving the biology in the soil I observed a quintupling of its ability to grow a crop.

ACRES U.S.A. It would be interesting to continue to compare the inoculant treatment to a control that has also been planted in the cover crops for a number of years.

JOHNSON. That’s the second test, which ran for four years. For this test, I wanted a soil that didn’t have legacy issues — no herbicides — so I picked a sandy desert soil that doesn’t grow much without the microbes. For four years I grew a cover crop, cut it, hauled it off and planted another crop. One plot was inoculated and one wasn’t. I wanted to know the best-case scenario so I irrigated the plots. I noticed there was always a defined line between the control and the treated. I planted them right next to each other to see if there was any drift or movement. I saw none.

ACRES U.S.A. You mean you found that the microbial life didn’t move over and colonize another area?

JOHNSON. As a microbiologist, we think everything is everywhere. When I did the composting here, I did an analysis of where the microbes were from. There were some that were first discovered in the Arctic and in the Antarctic. There were pelagic or ocean-going bacteria and also intestinal bacteria. All of them were in Las Cruces, New Mexico, which is a little strange. For this experiment I thought we’d do a treated plot and an untreated plot, and we’d see no difference. If the microbes are there, they just need to be fed. But there was a difference. The final annual productivity on the untreated plot was about 2,200 grams of dry biomass per square meter. That’s as much as the most productive terrestrial ecosystems on the planet, like old-growth forests. But the treated plot produced 3,200 grams, another 1,000 grams above that.

ACRES U.S.A. In other words, you found the desert soil was quite productive when it had a cover crop?

JOHNSON. With a cover crop and the right biology. Both are integral.

ACRES U.S.A. Right, because you have plants feeding the soil microorganisms.

JOHNSON. But with the microbial inoculant, it was half again more productive. Our first season with the winter cover on the treated was about 800 grams. The second season was over 1,600 grams. The third winter crop season was almost 2,200 grams. There’s some overlooked ability in these soils.

ACRES U.S.A. What’s your climate like?

JOHNSON. It’s pretty temperate. We have a long growing season. It can get down to -16°F in the winter. We usually have about a half-inch of rain every month in the winter. We plant the cover crop in the fall, and it doesn’t grow over a couple inches tall. Then in mid-February, growth just takes off. There’s no winterkill. We’ve seen these plants freeze, the leaves become like potato chips and you can go out and crush them. Yet by 10 a.m. when it starts to thaw, they’re busy photosynthesizing. That winter cover crop is ready for harvest at the end of April. In those 10 weeks, it grew 2,200 grams of dry biomass per square meter.

ACRES U.S.A. Are other researchers and farmers doing trials of similar systems of making compost in other settings?

JOHNSON. In other countries, they are. I just got an email from Pakistan today. We presented in Australia. Last week people in New Zealand contacted us.

ACRES U.S.A. Are there active trials where people have made bioreactors, used the finished compost and are now reporting results?

JOHNSON. They’re in the process. It takes a year to make this compost.

ACRES U.S.A. What are your current thoughts on different application methods?

JOHNSON. I’ve done applications of up to 400 pounds per acre. I’m looking at much lesser amounts. I’ve been making a slurry out of the compost and coating seed before planting. I see a difference in the growth dynamics compared to a control. In Australia, they are doing something similar. Their application rate for a very similar fungal to bacterial compost product is 1 kg per hectare. From what I’ve heard and read, they’re having pretty good success. They make an extract by vigorously stirring their compost, either with air or mechanically in water, to make a homogenous solution. They use about a kg of compost per 70 liters water, or a pound per 15 gallons. Then they inject it when they plant. In an area that normally produces about 1.6 tons of wheat on an early spring grain crop, they’ve reached up to 3 tons. This is the work of Ian and Diane Haggerty in dryland Western Australia. Their neighbors have gone broke trying to grow crops conventionally in that area. The Australian government is invested in improving their soils because they know that’s their future. Farmers could get started right away by using cover crops. There’s no reason to wait just because you don’t have the right compost. But once you do, at least in that desert soil, there’s a definite difference between inoculated and not inoculated.

ACRES U.S.A. If you use this sort of compost to inoculate seed or you apply it under dry conditions, would the bacteria and fungi go dormant and then be revived in the soil?

JOHNSON. I think what you’re putting out there is a lot of spores and cysts. When you let the compost go this long, without the recommended carbon-to-nitrogen ratio of feedstocks, you get lot of free-living, nitrogen-fixing bacteria in the pile. And when the whole system senses that it’s running out of usable resources, the fungi will form spores and bacteria will encyst. There still would be living organisms, like the worms processing it, and the compost would continue to mature.

ACRES U.S.A. Is your compost similar in composition to what ancient farmers were producing?

JOHNSON. Judging by the description in Farmers of Forty Centuries, the Chinese did it for 4,000 years. My wife, who is from Taiwan, was growing up during the shift to using synthetic fertilizers. She said they noticed that they had a lot more rice, but lost their protein source. All the fish and cockles and frogs that lived in the paddies died. Applying fertilizer completely decimated the whole system. The Amazonian Indians seem to have done something similar with Terra Preta del Indio. They used Terra Preta for 2,000 to 5,000 years.

ACRES U.S.A. I understand that if you use raw biochar, rather than allowing microorganisms to colonize it, it can pull nutrients out of the soil so plants grow poorly.

JOHNSON. Yeah, it becomes detrimental, as does biochar over 15 tons per acre.

ACRES U.S.A. Are you able to focus on your compost-related research, or are you involved with other topics?

JOHNSON. This has been part-time research. Since things grow slowly, I’ve had time to do other research here at the university. Mostly I’m working on technologies for purifying water, with reverse osmosis and electro-dialysis reversal methodologies.

ACRES U.S.A. What are your next steps?

JOHNSON. We want to scale up the bioreactor and do trials in different locales. There are a lot of people interested all over — in Australia, New Zealand, India, Africa, Canada, Mexico and Europe, and hopefully we’re going to get into China. A month ago, we were in Finland talking about their possibly using it to restore the Baltic Sea by reducing or eliminating all of the fertilizers and herbicides flowing into that water body.

ACRES U.S.A. You could find those types of scenarios practically everywhere around the world.

JOHNSON. Yeah. And there are some people using similar practices that are seeing dramatic results.

ACRES U.S.A. Can you give some examples of where people are using similar practices, with or without inoculation?

JOHNSON. Roland Bunch has been doing this in Africa and South America for 30-odd years. He is seeing that cover crops can bring these soils back. And it’s bringing that biology back that makes it work. But mostly, people consider compost as an amendment that has to be applied in large amounts. What they’re not realizing is that if they allow compost to mature, they can use it as a microbial inoculant. That’s now starting to come to light. Now that I have an improved soil, I’ve gotten an idea of what the biology’s supposed to look like. That’s going be what I’ll be comparing to, but I had to have that first.

ACRES U.S.A. That’s great because there are many questions about how to select good measures of soil health. Some of the measures being used may not be very appropriate.

JOHNSON. I agree.

Soil Carbon

ACRES U.S.A. Often there seems to be a lack of understanding of how to increase soil carbon. People are still thinking it comes from crop residues or adding something to the soil, rather than from the action of microbes in the soil. While I don’t know the science in much detail, I recognize it’s really about a paradigm shift, which hasn’t fully caught on yet.

JOHNSON. Nobody knows the science yet. I’m trying to learn.

ACRES U.S.A. Could some persistent carbonaceous molecules in compost be the mechanism for increasing soil carbon?

JOHNSON. From what I have seen, I don’t believe that is the mechanism.

ACRES U.S.A. Yet there are people still dwelling on questions like, what kinds of carbon compounds are present in a particular compost.

JOHNSON. They are asking that. One paper I recently read pretty much characterized any carbon entity in the soil as being fair game to a microbe. They’ve found sugars that are 10,000 years old, though sugars are supposed to degrade really fast. They’ve found aromatic ringed carbon structures that are supposed to be more resistant to microbial breakdown, but they degrade in a month.

ACRES U.S.A. Well, microbes inhabit every kind of environment on the planet, including those considered extremely inhospitable, but they have figured out how to use whatever substrate is available as an energy source.

JOHNSON. Yeah. We have to look at this a little differently. It’s not that we want to put carbon in the soil and lock it up. It’s a living system, and carbon is the lifeblood of this system. We have to allow it to flow. With our modern farming techniques we’ve cut back the efficiency of the system for capturing carbon. Remember, I said I had a five times increase in productivity. I’ve seen that in the greenhouse and in my field experiments. I’ve talked to Richard Teague and he has seen it in grazing management.

ACRES U.S.A. Tell us who Richard Teague is.

JOHNSON. Richard Teague is the rangeland ecologist at Texas A&M AgriLife Center in Vernon. He has been looking at how we can change grazing management on the planet. Along with Johan Zietsman in Africa, Terry McCosker in Australia, and others, he sees that we need to mimic how the bison grazed the Great Plains. It was a complete system that functioned properly. The animals would take about 30 to 40 percent of the grass and move on because predators were behind them. They deposited their manure. Dung beetles rolled it up into little balls and put it into the ground. That was the perfect environment for it to compost in place. It started to build soil carbon up and that’s what I’m trying to mimic. We have to slow the velocity of the carbon moving through the system. So little carbon is left in the soil, and there is going to be a certain amount of respiration always taking place in soils just to keep it alive. We have to create a system that’s capturing more carbon than it’s respiring. Reinvigorating the microbial community structures seems to also increase carbon-use-efficiency of the soil microbes as well.

ACRES U.S.A. Your research finds that the amount of carbon in a soil that’s respired off as carbon dioxide varies. It’s not a fixed percentage of soil carbon, or even a fixed amount. What factors influence the magnitude of soil carbon loss through respiration?

JOHNSON. From what I’ve seen in my research, it depends on the microbial community structure. I did both a greenhouse study and a one-year field study that looked at respiration in different soils with different levels of carbon and different biology. In the low-carbon, bacterial-dominant soil, over 50 percent of the original soil carbon was respired. Yet as you moved to a soil that was more fungal dominant and had more carbon, only 11 percent of the original carbon in the soil was respired. Increasing the rate at which we capture carbon while decreasing the rate at which that carbon is respired is how we will begin to reduce atmospheric CO₂. Now this contradicts what most scientists are saying — that when we increase soil carbon we’ll increase respiration.

ACRES U.S.A. That sounds like linear thinking.

JOHNSON: Very, and nature has never been linear. In the greenhouse, I had soils with an 18 times increase in soil carbon, compared to the lowest treatment, and a 5 times increase in microbial biomass, and respiration was only four times greater. In a field study conducted for one year, I had soils ranging from less than half a percent up to 7 percent soil carbon. With the fourteen-fold increase in soil carbon there was only a doubling of the respiration.

ACRES U.S.A. What’s the significance of carbon respiration?

JOHNSON. Ninety-seven percent of carbon that’s respired into the atmosphere comes from microbes or plants. Plants and microbes have metabolic processes that are very similar to ours. In order to stay alive, they, like us, respire and release CO₂. In plants for the most part this occurs only at night. Plants just also have the ability to fix carbon during the day and capture CO₂.

ACRES U.S.A. How does the amount of respiration of crop plants compare to the amount of carbon that they capture?

JOHNSON. Plants capture enough CO₂ in their photosynthetic processes to offset 97 percent of CO₂ emissions and they keep it pretty balanced. It is the other 3 percent, our emission of CO₂ from burning fossil fuels, that tip this balance.

ACRES U.S.A. Talk more about that 3 percent of the atmospheric carbon.

JOHNSON. That’s what we, as humans, contribute by burning fossil fuels. When you look at the ratios, the 3 percent we contribute is a relatively small component. We can reduce this one of two ways; make big changes in a small system by reducing our emissions or make small changes in a large system by improving plant productivity and regenerating carbon into soils. We have a choice here, and I believe it will be easier to achieve a reduction in atmospheric CO₂ by regenerating carbon in our soils than by drastically reducing fossil fuel consumption.

ACRES U.S.A. When did we go wrong?

JOHNSON. We started out by adopting the European model of farming, where agriculture extracted nutrients and carbon out of soils and then farmers moved on to areas with undisturbed soils to repeat these soil-degrading practices. Then in the early 20th century came the Haber-Bosch process for manufacturing nitrogen fertilizers. Before 1940, you could produce six units of food energy for one fossil fuel unit. Now it takes 10 units of fossil fuel energy to produce and deliver 1 unit of food energy, even though the solar energy to grow the plant is free. So the last great hope I see is soil, and microbes.

ACRES U.S.A. Under this scenario how much greater could carbon sequestration in the soil be?

JOHNSON. In my transitional soils, those that I’ve just started using a biologically enhanced agricultural management (BEAM) approach, I have observed 10.7 tons carbon per hectare per year over the first 4.5 years of application. That’s a 0.25 percent annual rate of soil carbon increase.

ACRES U.S.A. I’ve been led to believe that soil carbon levels are hard to measure since they fluctuate a lot. If that’s the case, how are you able to say they’ve increased?

JOHNSON. There’s too much noise in soil carbon data to measure annual increases. But at four and a half years, I feel pretty confident in what I’ve observed and the analyses I’ve done. I’ve done multi-core sampling, composites and triplicates of those samples run with a LECO test, which is a combustion test. It’s the gold standard of soil carbon estimation. As you get the carbon back in the soil, you also see that change in growth dynamics, and the increased tonnage of carbon in above ground biomass. But let me give a caveat. If we want to build the carbon up, a certain amount of the cover crop has to go back into the soil. On the desert soil, when I’m harvesting everything off, I see only minimal increases in soil carbon. It’s like any relationship — you’ve got to give something back.

ACRES U.S.A. Do you have a big enough field experiment to divide your treatments in half and in some plots put some of the biomass back and in others, not?

JOHNSON. No, none of mine are big enough. I’ve been doing this research on a shoestring budget. The ag schools have yet to see its value. I funded a lot of this work myself. In the last couple of years the Thornburg Foundation has been very kind and helped me, but the plots are not big enough. This research needs to be replicated here and in other areas under different conditions. But I know it has potential with the right biology. I see what Gabe Brown and other people have done with grazing management and other changes, and how these progressive farmers are turning their farms around.

ACRES U.S.A. Is there research into whether the importance of the high fungal bacterial ratio holds in other places where people are sequestering significant amounts of carbon? I’m wondering if anyone has looked at this ratio on Gabe Brown’s farm.

JOHNSON. Not that I’m aware of. I would definitely like to compare his soil to what I’m seeing here with the biology that I have.

ACRES U.SA. Perhaps you and other researchers will determine that the fungal bacterial ratio, plus ongoing management, are the decisive factors, and then measuring soil carbon might take a back seat. Or maybe carbon is a better and cheaper measurement?

JOHNSON. There are still questions on all of this. I’ve had good luck in the lab and in the greenhouse, where I can control everything, but once you get out into nature that changes. In the greenhouse, I was able to use pretty much the same microbial community all the way through the test, but with different fungal to bacterial ratios. That allowed me quite a bit of latitude to eliminate all the other variables. If I were to get soil from Gabe Brown with a certain fungal bacterial ratio and then try to compare it to the soil I have here, it would be complicated by differences in the structures of the microbial communities.

ACRES U.S.A. Right. There are all kinds of confounding factors.

JOHNSON. This is such a dynamic system, and we think linearly.

ACRES U.S.A. It seems quite urgent to get other people interested in doing allied work.

JOHNSON. Yes, it’s critical, and not just for the soil carbon part. In my estimation, the carbon is just the icing on the cake. There are so many benefits for agriculture, like increasing crop productivity and improving crop water use efficiency. I did a cotton crop this year just to see how it would turn out.

ACRES U.S.A. I saw the incredible photos!

JOHNSON. The cotton grew 6 feet high. Of course, tall cotton doesn’t mean that you’re going to get a crop, but when we harvested it last weekend, there was a little over five bales of cotton per acre without fertilizers, herbicides or insecticides, just biology. The average in our area is about two and a half. This was on the improved soil in my seven-year field trial. As a scientist, you have to be half skeptic and half optimist. I’m always wary and expect failure, but nature has been pleasantly surprising.

ACRES U.S.A. Do you have any opportunities to talk with farmers in New Mexico and elsewhere?

JOHNSON. Yes, Rudy Garcia, the regional NRCS manager, has been pulling me into a lot of his meetings to do presentations, as has Ray Archuleta. In California certain groups like Chico State are really interested. They see that it’s the microbes that are making this work.

ACRES U.S.A. Even on a shoestring you seem to be doing a remarkable job of letting people around the world know about this.

JOHNSON. We have a lot of help. Carbon Underground is helping us. Terry McCosker with Carbon Link in Australia is an intermediary between the ranchers and the carbon market there, which actually has money.

ACRES U.S.A. How do you get this on the ground in a large enough number of places to make the big difference in our atmosphere we need? How do you get farmers to try and implement things?

JOHNSON. You never know what one connection will lead to. That has been proven to me over and over. I get frustrated, but then something seems to come through every time it needs to. Carbon Underground took us to Finland because Finland is interested in this. I’m talking with Patagonia now.

ACRES U.S.A. Is Patagonia still buying organic cotton?

JOHNSON. That’s what I’ll be working on. I’ll be sending them the results on that cotton, so there is potential.

ACRES U.S.A. A recent study led by scientists at Woods Hole Research Center and published in the Proceedings of the National Academy of Sciences found that agriculture had removed 133 billion tons of carbon from the top 2 meters of soil. Could your approach potentially put some of that carbon back?

JOHNSON. I think we can do better. There is a limit to the percent carbon increase you can get in a soil, but there’s no limit to the amount of carbon increases you can get as you build up new soil.

ACRES U.S.A. The USDA promotes the false notion that it takes 500 years to create a half-inch of soil. What’s your evidence that we could increase the amount of soil?

JOHNSON. In the United States, our average loss rate is about 10 tons of soil per hectare per year, but we have demonstrated the ability to rebuild more than 10 tons of carbon per hectare per year on top of that. That’s how nature did it on the Great Plains. How else could they get the 6-foot deep topsoils that we have so destructively mined for the last 75 years or more? That was our carbon bank account and we’ve pretty much withdrawn it all the way down. It’s up to us to build it back up because that’s where the fertility is. It’s by putting that carbon back in there and letting the microbes function optimally that we’ll see an increase in primary productivity.

ACRES U.S.A. Do you have any critics or detractors?

JOHNSON. People do say it’s not going to work, but they don’t come up with a good argument of why it won’t. Nature is doing it every day. My work is about aligning ourselves with nature enough to understand how she does it.

ACRES U.S.A. Do you have any thoughts on why more people haven’t seen this?

JOHNSON. I think it comes from assuming procedures that other people used in the past are the best. My approach has always been different. I wouldn’t have discovered the bio-hydrogen community had I not challenged what other people had done before me. I approached things different. I’ll be the first to admit there was a certain amount of luck in it. We pasteurized the compost at six different temperatures and in triplicates. One out of the 18 went crazy. It produced over 200 ml of hydrogen while the others were producing less than 10. I can’t argue with fate. I nurtured that microbial community for over two and a half years while I was doing research on it and it kept producing. It was trying to tell me then to look at the biology. I ignored it until I got working at the Plant Science Center here at NMSU and started using biology again.

ACRES U.S.A. As a building contractor, did you just do the normal things, or were you taking risks?

JOHNSON. I did specialty and custom homes, a lot of homes for artists. They’re always unique in how they looked at things, and how they wanted things put together. I won an award for the design of one of the homes. My wife Hui-Chun and I did everything. Sometimes we would work for a year and a half with a customer on a set of house plans. We ended up friends with all of our clients.

ACRES U.S.A. How should education change to facilitate greater openness and vision in people?

JOHNSON. Right now, with the reductionist viewpoint in science, we’re missing the dynamic part of this planet. We need to realize that the Earth is a living organism. It’s going to be very complex, and we may never figure this out.

ACRES U.S.A. You mean we might not have the capacity to understand exactly what’s going on?

JOHNSON. I think that’s a distinct possibility.

ACRES U.S.A. Perhaps it doesn’t matter. Without characterizing every microbe in our gut, we probably can know that certain practices are health-promoting and others promote disease or sterility.

JOHNSON. You can see almost every pathogen known to man in these soils. Yet most likely they have a function there. It depends on the environment they’re in. When we destroy the composition of that microbial community, that’s when we start having problems. Like you were saying about soil health or soil fertility, I don’t know that anybody can really define it right now. I don’t know that we ever will, but I believe we’re going the right direction when plants grow better. Supporting that seems like a good goal. And building that soil carbon also takes care of water issues. Seventy percent of the world’s water goes toward agriculture. If we can double the production of a commodity crop with the same amount of water the efficiency of that water use doubles. We see that in rangeland management. Nancy Ranney in New Mexico has been practicing adaptive multi-paddock grazing management. They built dikes to supply stock tanks. For the first couple of years, they filled up, but as they improved their soil and grew better grasses, the tanks stopped filling up. Their aquifer level started coming up. They went from four species of grasses to 44. This is the direction we need to go.

This article first appeared in the April 2018 issue of Acres U.S.A. magazine.