EcoFarming Daily: Compost & The Promise of Microbes

March 23, 2018

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.

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