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Want Good Soil? Feed the Microbes

Farmers in the U.S. also use burning to deal with wheat stubble as in this Kansas field.

In June of 2014, Grist reporter Nathanael Johnson reported on a battle between two men in New South Wales Australia. Clive Kirkby and John Kirkegaard were having it out over the proper handling of crop residues after harvest. Kirkby was trying to get farmers to stop torching wheat stubble. Rather than letting fire release all that carbon into the atmosphere, he told them that they could increase soil organic matter and build healthier, carbon-rich soils by leaving the stubble in the field. John Kirkegaard, an agronomist, told Kirkby he was wrong. The practice of burning and cultivating was what was growing the best crops.

As most folks will tell you nowadays, cultivating, or plowing, disrupts soil microbes and releases even more carbon into the air. That’s why no-till is becoming increasingly popular. But the practice that Kirkby was promoting didn’t seem to be making a difference either. After six years of leaving stubble in the field, Kirkegaard’s data showed that soil organic matter and the carbon it holds wasn’t increasing, and in some cases, it was even decreasing.

Farmers have been encouraged to leave stubble in the field for the same reason that management-intensive grazing proponents leave plenty of forage behind in pasture: It’s food for the soil. Put more precisely, it’s fuel for a complex, not entirely understood food web of fungi, insects, and microbes eating the residue and each other and transforming plant remains into stable, carbon-rich soil.

But why wasn’t it working as Kirkby expected? Though he was near retirement, the mystery captured Kirkby and he headed back to school. He earned a PhD and, working with Kirkegaard, gathered the evidence that would solve this problem for farmers and ranchers.

It’s the Nutrients!

Electron micrograph of soil microbes. Photo credit: Alice Dohnalkova of PNNL

We talk a lot about microbes “eating” which paints a picture of chewing up bites. But consider the cow and her rumen for a minute. After she’s chewed and swallowed, her rumen microbes take over, and the chemical reactions they produce turns grass into sustenance for the cow’s body. The microbes are more successful when they’ve got the right mix of nutrients. For example, a little extra protein from a supplement makes it possible for a cow to survive on poor quality grass. The nitrogen in the protein supplement helps the rumen microbes turn what would otherwise have been unusable into good quality nutrition.

It’s the same for the soil microbes. Like all creatures on earth they need carbon, nitrogen, phosphorus, sulfur, oxygen and hydrogen to live. By leaving stubble on the ground, farmers gave them access to plenty of carbon. They can get oxygen and hydrogen from the air. But without nitrogen, sulfur and phosphorous, they can’t perform the chemical process to turn the stubble into soil carbon.

When he provided these nutrients, Kirkby and Kierkegaard found that everything changed. The soil microbes could finally consume the plant residue. You can see the difference in the two pans of sandy soil below. On the left is the untreated soil. The light specks are bits of wheat straw. On the right is what happens when nutrients are added. There are microbes in both pans of soil, but only the ones on the right had the right stuff to get their jobs done.

Photo courtesy of CSIRO Plant Industry/CSIRO Agriculture (CA Kirkby, JA Kirkegaard, AE Richardson

As Kirkby told Johnson in his interview, “With the right balance of nutrients, you get a population explosion. And that’s what you want. The carbon is in the soil’s organic matter, and that’s essentially dead bug bits. And live bugs. Humus!”

What This Means for You

The healthier your microbes, the better your soil, the more forage you produce, the more animals you can feed, the better your bottom line. That’s what’s in it for you. While we’ve known for decades that there’s a golden ratio of carbon, phosphorous, sulfur and nitrogen that create humus, Kirkby and Kirkegaard have taken it the next step to show us that the microbiome depends on these nutrients to function and create the humus.

Kirkby and Kirkegaard note that farmers typically fertilize just enough to get optimum plant growth. Their discovery that feeding the microbiome creates healthier soils means that farmers should consider fertilizing in ways that meet the needs of the microbes as well.

What Can You Do With This?

This photo from TomKat Ranch shows what 1/4″ of compost looks like in pasture. Research has shown that this treatment can increase carbon sequestering for up to 30 years.

Organic matter is microbes, and if you want more you need to give them what they need. You can fertilize with these ingredients. But that can be expensive. Here are two alternatives: One is to manage your livestock so that they spread their nitrogen rich manure and urine around the pastures, giving those microbes that added boost they need.

Another option is compost. Farms that apply compost have more soil organic matter and store more carbon in the soil. In fact, research in California has found that applying a half inch of compost doubled forage production, increased soil water holding capacity and increased net ecosystem carbon storage by 25-70%. Check out this two-part series for more about how you can use compost to improve soil health and carbon sequestration, while growing more forage for your livestock. It’s a win-win!


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Kathy Voth
Kathy Voth
I am the founder, editor and publisher of On Pasture, now retired. My career spanned 40 years of finding creative solutions to problems, and sharing ideas with people that encouraged them to work together and try new things. From figuring out how to teach livestock to eat weeds, to teaching range management to high schoolers, outdoor ed graduation camping trips with fifty 6th graders at a time, building firebreaks with a 130-goat herd, developing the signs and interpretation for the Storm King Fourteen Memorial trail, receiving the Conservation Service Award for my work building the 150-mile mountain bike trail from Grand Junction, Colorado to Moab, Utah...well, the list is long so I'll stop with, I've had a great time and I'm very grateful.


  1. David –

    I can’t point you to a specific study, but I’d refer you to a few books that have extensive references. Marschner’s Mineral Nutrition of Higher Plants, Healthy Crops: A New Agricultural Revolution by Chaboussou, Mineral Nutrition and Plant Disease by Datnoff, Elmer, Huber, and of course, Sir Albert Howard’s An Agricultural Testament. Since you are in Australia you should check out Graeme Sait and his company, Nutritech Solutions – they have a lot of info on their website. You can also read some good information from another Australian at It seems like you are on the right track and you are blessed to be in an area with great climate and rainfall(for the time being).

  2. Hi Don,

    Can you point me at some science/well-run trials to backup these statements? Or perhaps the site hosts could comment?

    “Better plant nutrition through organic methods leads to better photosynthetic capacity which means more sugars exuded through the roots to feed the microbiology”

    “Aggressive soil biology produces enzymes and acids that make even more nutrients available to the plant”

    “a foliar application of trace elements can improve your photosynthetic rate, increasing the quality of your crop and the amount of exudates that feed your soil biology, while being more cost effective than applying compost.”



  3. Don’t clip your grass short, unless it is dead/dormant, otherwise you slow or stop photosythesis, which is what is feeding the soil biology. Learn about “tall grazing” and see how that applies to mowing/clipping grasses.

  4. What happens with soil carbon when you mow/slash pasture as against graze it? We have some land in Sth Gippsland which we’re developing as an agroforestry site. We exclude stock for some years after planting as they will eat young trees. We manage the pasture – ungrazed grass can grow to 1.5m in spring – in these fields by slashing it. The area averages rainfall over 1000mm/annum and has a mild climate by northern hemisphere standards although it can reach over 35C in summer. So the soil microbes will generally have reasonably comfy climate conditions to do their thang.

    I’ve been assuming that this will build up soil carbon but would be interested if anyone has any comments, pointers to related research etc.

    We should get some soil tests but because the grass growth is so strong I’ve not worried about it to date. And I could look into cheap onfarm carbon tests if such a thing exists. My first degree was in chemistry so I’m not afraid to wield a testtube.



    • I think the trick to getting the quickest results without livestock or soil amendments while clipping is to manage for earthworms. The ground should be continuously covered with litter in various stages of decomposition and a generous stubble height after clipping to provide shade. It will be a balancing act to be able to let the grass grow to sufficient maturity before clipping so that it doesn’t decompose too quickly and clipping it often enough to provide the earthworms with a fairly constant source of green clippings.

  5. It might be appropriate to mention how those wheat fields were farmed(conventionally, organically, biodynamically). Many pesticides, fungicides, herbicides used to grow wheat conventionally are also detrimental to soil biology and it isn’t surprising that wheat stubble wouldn’t break down. Better plant nutrition through organic methods leads to better photosynthetic capacity which means more sugars exuded through the roots to feed the microbiology. Aggressive soil biology produces enzymes and acids that make even more nutrients available to the plant, which creates even more photosynthetic capacity, etc. It’s imperative to feed your soil biology and photosynthesis trumps compost. A lot of times a foliar application of trace elements can improve your photosynthetic rate, increasing the quality of your crop and the amount of exudates that feed your soil biology, while being more cost effective than applying compost. Either way – feed your soil biology and you’ll increase water holding capacity, have healthier crops, and sequester carbon in your soil.

  6. Burning wheat stubble or grass residue is not 100% combusted, a small fraction remains as a biochar which has been addressed previous. This is an extremely stable form of carbon and becomes a home for soil microbes.

    There is also evidence from ISU and elsewhere that patch burned pasture is preferred by grazing livestock, (Ryan Harr) in his trials they were able to establish a semi-rotational impact by have a three year burning regimen.

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