Nurturing the soil’s microbiome

A short story of manure, microbes, medicinals--and a woodpecker

Italy was not the first place where humans domesticated grains. By all accounts, this happened in China or India about ten thousand years ago with millet and spelt. This was followed closely by barley cultivated in the fertile floodplains of the land we now call Iraq. But Italy, blessed with wide, flat valleys in its north and central regions, farmed grains intensively to feed its growing population and support its expansionist ambitions during the Roman period. There were divinities of the Roman pantheon devoted to farming, fertility, and grain--some, like Ceres, were echoes of the Greek gods (Demeter in this case, the goddess of cereals and the seasonal harvest). But others were added by the Romans themselves to hold sway over all the details of farming life. One such divinity was Picus, who ensured the fertility of the fields and was credited with teaching humans how to use cow manure to promote abundant harvests.

While it is likely that humans added animal manures to their fields from the very beginning, it is interesting to note that a god explicitly associated with these matters first appeared during a time when urbanization and military expansion were central concerns. To support a growing population of non-farmers, agriculture needed to increase yields and manure was essential. Sure, people had been taking their cattle up to the hilltops and mountain fields for thousands of years, and those fields had benefitted from the rich manure left behind as the cows grazed. But by fertilizing wheat fields and irrigating them using concrete aqueducts many miles long, Roman farmers and engineers took agriculture to an intensive level, reporting yields well over a thousand pounds per acre1. While this might not seem like a lot today, Italy was outpacing almost everywhere else in the Mediterranean basin two thousand years ago. 

Presiding over it all was Picus. His origins are somewhat mysterious: some say he was one of the kings in Latium, the fertile region in central Italy where Rome was founded. Some ascribe to him a divine origin: son of Saturn, perhaps; or maybe son of Sterculius himself, the god of, well--excrement. In any event, Picus knew the value of the rich fertilizer that animals produce, and the legends say that his fields were the most glorious, golden waves of grain. It was all thanks to manure.

Manure in field

While we usually think of organic soil amendments like manure as sources of bio-available nutrients plants need to grow and develop, we rarely talk about manure's microbial content and its importance to fertility. First off: not all composted animal poop is the same. Cow manure, for example, reliably increases phosphorus content in the soil, while horse manure does not 2. And cow manure builds microbial diversity and activity in the soil much more than pig poop does3. These are questions of degree, and cow manure seems like one of the best options. But all manure increases the total bacterial biomass in the soil and enhances its microbial diversity, too.

There are other methods for supporting the riot of microbes you'll find in living, thriving soil. One is adding "green manure": a cover-crop, such as oats, or clover, or buckwheat (and many more), that gets turned or layered into the soil, where it starts to degrade. Just as with wood chips, or with old dead tree roots, fungal mycelium begins to invade and decompose this fresh organic material 4. This is a good thing, as fungi are a part of soil's healthy microbial complement and manure does less to enhance this side of the spectrum. This means that composted manure and a cover crop make a great two-step treatment for quickly juicing up the soil's microbiome.

In practice, I like planting oats on new, raw topsoil even if it's rocky and has poor fertility. You can sow oats and add just a little well-aged manure on top to cover the grain, helping to keep it moist while it sprouts. After about two months, the unripe, "milky" seed heads will be close to harvest, and you can collect these if you'd like. Then, a healthy application of manure goes right on top, followed by another round of oat seeds. These will sprout but won't survive the winter (at least here in the Northeast). In the spring, you will have a layer of oatstraw mulch, a layer of composted manure, a layer of decomposing green manure, and the topsoil below will already be rich in microbes. While some might till this all under, I prefer to leave it. You can repeat the whole process again if you have time--round two of oats will be much more vigorous--or just dig holes for your transplants and put them right in. This low-till method preserves the straw mulch, which helps control erosion, and is kind to earthworms.

When manure is used in a low-till setting, the added microbial biomass seems to improve the soil's carbon- and nitrogen-capturing abilities5. That is to say, the soil ecology seems able to draw more CO2 and nitrogen from the air and inject it into its metabolic cycles, keeping it out of the atmosphere. This happens especially in the first few inches of the soil, where manuring dramatically increases microbial diversity and quantity especially when compared to synthetic fertilization6. In the end, a field with a rich microbiome produces healthier, higher-yielding plants7.

Another way to support soil ecology is to add medicinal plants to your garden here and there, or to your field in long "buffer zones" between crops. While clearly beneficial for pollinators, herbs go further: building the microbiome and helping with detoxification are two examples. One class of bacteria, the Rhizobium genus involved in nitrogen fixation, requires a signal from members of the Fabaceae (peas and beans, but also red clover and alfalfa). This isoflavone signal is secreted by the plants' roots, and it draws bacteria in, where they find a safe place to live and multiply8. But unhybridized, wild medicinal plants (many would be known as weeds) help build the soil's microbiome just by growing9. And many herbs are excellent bioremediation agents, helping to clear pollutants and heavy metals from the soil10.  This fact remind us not to collect from former industrial sites or wastelands where the herbs might have taken up harmful pollutants.

Animal manure, green cover crops, and medicinal plants: by enhancing the quality, diversity, and quantity of your soil's microbial life, these allies help nurture and protect everything that grows in it. And we humans are lucky to live and work around such soil! A microbe such as Bacillus coagulans, found both in manure and in healthy soil, seems to be an important part of our own intestinal microbiome, too. This makes sense: we've been eating roots from living soils for a long time, long enough to develop a healthy relationship with soil bacteria. Another microorganism, Mycobacterium vaccae, is also part of a healthy human microbiome ("vaccae" means "of the cow" in Latin, since this microbe was first discovered in cow dung). Researchers are finding that M. vaccae can interface with and modulate our serotonin systems and may be part of what we need to support a healthy mood11 and immune system12. Soil bacteria colonize our skin readily, increasing the diversity and resilience of our skin's microbiome13. So, a living soil ecology isn't just good for the plants, it's good for the people who live close by, too. Microbes and fungi--our friends, by and large--are essential players here. And poop catalyzes an explosion in microbes and fungi.

The legends like that of Picus, animal poop, and fertile fields always have a bittersweet twist to them. We cannot deny that soil management techniques (like manuring) have supported urbanization and population growth, while also helping to maintain the health of our gardens and fields. At this point, we are dependent on the gifts of Picus as much as we've ever been--even more so today, as we discover the drawbacks of synthetic fertilization. But there are still echoes of our old, pre-agricultural life entangled in these mythological threads. One day Picus left his golden fields for a long walk in the forest. Little did he know that, at the same time, the herbalist-goddess Circe was wandering the same woods wild-harvesting herbs for her apothecary. She spied Picus in a clearing and, after watching him for a while, decided he would become her lover. Here accounts differ: some say Picus rejected Circe's advances, claiming to be engaged to another. Others say the two spent that day in the forest together, and that Picus's child Faunus, the woodland satyr, was born of their union. But whatever happened, the outcome was the same: as Picus returned home, he found his footfalls were lighter and lighter, and he started moving more and more swiftly. His arms lengthened and began to sprout feathers. As he looked down to his body in mid-flight, he discovered that Circe had transmuted him into a woodpecker.


Picus remained in this form, an immortal bird rapping at the edge of the farm field, reminding us to feed and nurture our soils to keep our children well-fed and nourished. But I can't help thinking that a part of him always looks back to the forest, and Circe, and the wild plants that grow there, and his son, Faunus the wild satyr. The forest floor, with is moldering humus, has a thriving microbiome, and long ago was the source of all our needs. Today we may live in a different world--but the land that feeds us still needs that microbial richness, and Picus helps us remember how to achieve it. In so doing, we build health all around: the dirt becomes alive, the plants thrive, pollinators dance across the fields, and human stays strong too.

  1. Ligt, Luuk de; Northwood, S. J. (2008-01-01). People, Land, and Politics: Demographic Developments and the Transformation of Roman Italy 300 BC-AD 14.
  2. Parham, J. A., et al. "Long-term cattle manure application in soil. II. Effect on soil microbial populations and community structure." Biology and Fertility of Soils 38.4 (2003): 209-215.
  3. Das, Suvendu, et al. "Composted cattle manure increases microbial activity and soil fertility more than composted swine manure in a submerged rice paddy." Frontiers in microbiology8 (2017): 1702.
  4. Elfstrand, Sara, Katarina Hedlund, and Anna Mårtensson. "Soil enzyme activities, microbial community composition and function after 47 years of continuous green manuring." Applied Soil Ecology 35.3 (2007): 610-621.
  5. Banger, K., et al. "Impact of long-term additions of chemical fertilizers and farm yard manure on carbon and nitrogen sequestration under rice-cowpea cropping system in semi-arid tropics." Plant and soil 318.1-2 (2009): 27-35.
  6. Peacock, A. ggrD, et al. "Soil microbial community responses to dairy manure or ammonium nitrate applications." Soil Biology and Biochemistry 33.7-8 (2001): 1011-1019.
  7. Hepperly, Paul, et al. "Compost, manure and synthetic fertilizer influences crop yields, soil properties, nitrate leaching and crop nutrient content." Compost Science & Utilization 17.2 (2009): 117-126.
  8. Subramanian, Senthil, Gary Stacey, and Oliver Yu. "Distinct, crucial roles of flavonoids during legume nodulation." Trends in plant science 12.7 (2007): 282-285.
  9. Köberl, Martina, et al. "The microbiome of medicinal plants: diversity and importance for plant growth, quality, and health." The plant microbiome and its importance for plant and human health (2015): 45.
  10. Chen, Shu-Hwa, and Michael D. Aitken. "Salicylate stimulates the degradation of high-molecular weight polycyclic aromatic hydrocarbons by Pseudomonas saccharophila P15." Environmental science & technology 33.3 (1999): 435-439.
    Singer, Andrew C., David E. Crowley, and Ian P. Thompson. "Secondary plant metabolites in phytoremediation and biotransformation." TRENDS in Biotechnology 21.3 (2003): 123-130.
  1. Lowry, Christopher A., et al. "Identification of an immune-responsive mesolimbocortical serotonergic system: potential role in regulation of emotional behavior." Neuroscience 146.2 (2007): 756-772.
  2. Smith, David G., et al. "Identification and characterization of a novel anti-inflammatory lipid isolated from Mycobacterium vaccae, a soil-derived bacterium with immunoregulatory and stress resilience properties." Psychopharmacology (2019): 1-18.
  3. Grönroos, Mira, et al. "Short‐term direct contact with soil and plant materials leads to an immediate increase in diversity of skin microbiota." MicrobiologyOpen 8.3 (2019): e00645.
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