Soil bacteria, bacilli

(from things my father, Steve Mesaros, taught me and Holden Leaves, Winter 2011-2012)

I was eight or nine years old when I first “helped” my father spread compost over our vegetable garden in Independence.  He scooped up a small handful of soil and said, “Do you know there are thousands of good bacteria in this soil?”

I was alarmed.  Thousands?  Good bacteria?  I’d learned only about the bad germs I needed to protect myself from.  Was my father telling me the first lie he’d ever told me?  Or worse, was he teasing me in the way some annoying adults teased children, thinking they were relating to them?

After we finished in the garden and cleaned up, he handed me an article about soil in his latest issue of Organic Gardening and gently suggested I should quit calling it “dirt.”  My faith in my father was restored, and my respect for soil was increased.

Since my first exposure to the subject, I learned that a teaspoon of productive soil contains between 100,000,000 and 1,000,000,000 bacteria.  So it doesn’t surprise me that a ton of microscopic organisms may be active in each acre of productive soil.

Most of the organisms are decomposers that consume substances released by plant root systems and fresh plant litter, thus converting energy in soil organic matter into forms useful to the other organisms in the soil food web.

Soybean root nodule with nitrogen-fixing bacteria

Some bacteria form partnerships with plants, such as the nitrogen-fixing bacteria that live in nodules on the roots of plants in the legume family, such as peas, beans and clover.  These bacteria “fix” nitrogen from the air that can be used by the host plant and by any plants that grow in the soil after the host plant dies.

And other bacteria may be pathogens, causing disease.

The question that has always bothered me is, with up to one billion microbes in a teaspoon of soil, how do you know what’s doing what?

Laurel Kluber, PhD, a postdoctoral scholar at Case Western Reserve University (CWRU) and a visiting scientist at Holden’s Research Department, explains, “We sequence their DNA.

“Thanks to DNA sequencing, scientists have found a large diversity of microorganisms in soil, and these communities can vary greatly depending on the environment they were sampled from.”

For example, soils frozen under arctic ice, soils that have absorbed years of runoff from acid mines and soils collected from Yellowstone all contain highly diverse microorganisms.

Had their DNAs not been sequenced, scientists never would have known what species were present and what beneficial processes they were initiating.  “Soil microbial communities are the foundation of a healthy ecosystem, and these techniques allow us to not only determine who is in the soil, but also what they are doing,” Kluber concluded.

Sarah Kyker, PhD, also a postdoctoral scholar from CWRU and a visiting scientist at Holden, compared earlier efforts to study soil microbes with today’s DNA sequencing.  Previously, researches spread the soil in a petri dish with nutrients and observed what grew.

Once DNA processing was used in the lab, scientists discovered that 98% of soil microorganisms wouldn’t grow in petri dishes.  “This is the main reason why DNA sequencing has become so popular for studying microorganisms in soil,” Kyker said.

I do believe that my father bought the first and all subsequent issues of Organic Gardening.  It was he who taught me to plant nitrogen-fixing clover in between my corn plants, which quickly deplete soil of nitrogen.  And who taught me to plant soybeans and winter rye as “green manures.”  And who was almost as excited as I was when one Mother’s Day, my present was my very own Troy-Bilt Tiller.

Fathers are the gifts that keep on giving.  I’m fortunate to be the beneficiary of so many of those gifts so generously bestowed.

For more information about soil microbes, go to


Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )


Connecting to %s