Plant-Bacteria Cooperation: Producing Nitrogen Fertilizer

May 8th, 2012

Last November I bought a pound of fava beans at Claudio’s in the Italian Market for less than $2.00, soaked them overnight and planted them everywhere in my plot as a winter cover crop. Now it is May, and my plot is a blossoming sea of fava beans beginning to set pod.

Fresh fava are always a treat, but what I really wanted was an over-wintering green manure. Fava is one of the few beans that prefer cold weather and can overwinter in our area. Because they are legumes, they form mutually beneficial relationships with special bacteria in the soil which can take nitrogen from the atmosphere and supply the plant (and your garden) with its own supply of fertilizer. What could be better?

Every living cell on earth requires nitrogen. It is an essential component of protein-based amino acids and DNA. But although more than three-quarters of the atmosphere is composed of nitrogen, it is chemically non-reactive and unavailable except to special bacteria which can break the tough triple-bonds of free nitrogen and covert it to ammonium which plants use to create the first layer in the food chain that supports all life.

These bacteria usually team with plants to perform this feat. The finely-tuned communication between plant and bacteria begins when the plant exudes flavonoids from its roots to attract symbiotic rhizobial bacteria living freely in the soil. The attracted bacteria respond by producing an enzyme called “nod factor” which causes root hairs on the bean to curl up and develop into little round nodules which provides a home and food for the bacteria. The bacteria quickly colonize these nodes and begin transforming nitrogen from the air into ammonium, the form of nitrogen fertilizer that the plant can use.

The small round objects on the roots are nodules where the bacteria do their work

Fritz Haber

While bacteria have been doing this for billions of years, humans only learned how to fix nitrogen a little over 100 years ago. The immediate motivation was the impending threat of WWI and the need for raw materials to manufacture TNT and other explosive weapons. In 1909 Germany, Fritz Haber patented the process which is still the only economically viable way to produce synthetic nitrogen fertilizers. Haber’s process requires large amounts of energy, temperatures of about 930 degrees Fahrenheit, and pressures of several hundred atmospheres.

Constructing a nitrogen fertilizer plant costs hundreds of millions of dollars, yet nitrogen-fixing bacteria manage to do it under normal temperature using only the energy their plant host gets from the sun.

The enzyme the bacteria use to convert atmospheric nitrogen to ammonia works best in the absence of oxygen, so the plant has devised a helpful strategy for keeping oxygen out of the way of the bacteria. Root cells produce a red protein similar to the hemoglobin in our own blood. The red protein that legumes produce is called leghemoglobin. It colors the inside of root nodules actively fixing nitrogen to a pinkish or reddish color and protects the bacteria from unwanted oxygen.

Cut-away view: An active nitrogen-fixing nodule is red or pink inside

The downside of this relationship is that supporting the bacteria’s substantial energy requirements during nitrogen fixation is very expensive for the plant [costing up to 20% of all the carbohydrates it produces], so during pod-fill the plant will cut off food supply to the bacteria and the nodules will lose their red color and may even be discarded. Similarly, when high amounts of ammonium are already present in the soil, the genes controlling nodulation and nitrogen synthesis are turned off and the plant simply uses what is already there rather than having bacteria manufacture it anew.

So how do you get the nitrogen from the plant into your soil? Just cut the plant off at soil level and leave the roots in the ground (unless, of course, you would like to pull up a few to admire the nodules). Their massive root system and nitrogen-rich nodules penetrate the soil deeply and will break down over time to enrich your soil to a depth of 1 or 2 feet. You could compost the tops (they make fabulous compost material) but I prefer to simply chop them up and scatter them on top of the soil where they dry out and become a rich mulch in a couple of weeks.

If you are only interested in green manure and don’t care about beans, cut the plants just before they start setting pod to get the maximum amount of nitrogen for your soil.

NOTE: All photos are of plants I actually grew in my plot during the winter of 2011-12. Photos were taken in May 2012.

- Barbara

Why Don’t Organic Gardeners Use Chemical Fertilizers?

April 26th, 2012

Have you ever wondered why organic gardeners don’t use chemical fertilizers? Everybody knows why pesticides are harmful to people and the environment, but what’s wrong with a little Miracle-Gro or other non-organic fertilizer once in a while?

Last weekend an empty 25lb bag of Miracle-Gro turned up in the garden trash, so this is a great time to review why chemical fertilizers are harmful. There are two major reasons: first, inorganic ferti- lizers are composed of soluble chemical salts, and since plants can only use a small percentage of what is applied, the rest leaches into groundwater & causes pollution of lakes, streams, rivers, people’s well-water, and other bodies of water.

The second (and to me, the more immediate concern) is that the salts in chemical fertilizers actually kill the beneficial bacteria and fungi that are the hallmark of rich, fertile soil. Have you even seen a gardener killing slugs by sprinkling them with table salt? Same thing happens when beneficial microorganisms are hit with the salts in chemical fertilizers.

Soil is a complex interrelated web of life which supports the planet’s food chain and the global recycling of nutrients. The microscopic community of creatures in the soil breaks down dead plant and animal matter and makes it once again available to growing plants. Fungi and bacteria not only break down these nutrients but are also able to immobilize them in their bodies until they are consumed by other microorganisms in the soil. This slow release insures that plants get just the amount they need at just the right time. Nitrogen which is not needed immediately is bound up in the soil for later use and does not leach into the groundwater.

Actinomycetes give the earthy fragrance to soil as they break down cellulose and chitin. They can also fix nitrogen and produce antibiotics to kill soil pathogens.

The fungi and bacteria in healthy soils have ancient, complex and mutually beneficial relationships with plants. For example, all legumes (beans, peas, clover, vetch, fava) are host to bacteria that convert nitrogen from the atmosphere into the ammonia and nitrates that plants need. Mycorrhyzal fungi, in contrast, form associations with plant roots and, in exchange for sugars that the root exudes, transport water and nutrients (especially phosphorus) back to the plant, thus extending the reach of the roots much further than they could normally go and making them less susceptible to drought and nutrient deficiencies. Microorganisms also have a lot to do with maintaining good soil structure, which promotes infiltration and drainage of water, soil aeration, vigorous root growth and most important, the ability of the soil to retain water and nutrients so they are available when plants need them.

But once the microscopic inhabitants of the soil food web have been killed, the soil loses its ability to function as the base of the food chain. The only way to keep producing crops is to apply ever increasing quantities of chemical fertilizers to the dead soil that no longer supports the natural processes of decay and growth. To reverse this situation requires us to stop using chemical fertilizers and re-innoculate the soil with beneficial organisms. The good news is that this is relatively easy — just a little of Grant’s superb compost will get the good guys working again for you and your plants.

If you feel your plants need a boost of nitrogen, why not sprinkle a little alfalfa meal or organic blood meal on your soil instead? Or perhaps a bit of organic bone meal to rev up your phosphorus? Micro-organisms in the soil will break these down into slow-release forms and retain them in the soil until they are needed. Best of all, these organic fertilizers will never damage the microbes that support your soil.

__________ is a superb resource for viewing videos of microorganisms in action. This one shows beneficial organisms in compost:

If you would like to read more about the fascinating micro-organisms which support the soil food web, see The Soil Biology Primer from the Soil and Water Conservation Society or Soil Microbology: A Primer from the University of Vermont.

Here’s a fun rant by Mike McGrath of “You Bet Your Garden” called Forget Chemicals–Make Compost!

Want to dig a little deeper into soil biology? Two excellent books on the subject are: Tales from the Underground: A Natural History of Subterranean Life and Life in the Soil: A Guide for Naturalists and Gardeners.

– Barbara


July 21st, 2011

Mycorhyzal fungi extending the reach of plant roots

We all know great garden soil when we see it – rich, crumbly, with a characteristic deep earthy fragrance that is especially wonderful after rain. In addition to plants, great soil is host to a dynamic interrelated community of bacteria, fungi, earthworms and various other small organisms that recycle nutrients, produce antibiotics against certain diseases, and contribute to the well being of plants in general. But it is Mycorrhizal fungi which give that special fragrance of good earth. If this sounds surprising, remember that truffles & chanterelles are the fruits of especially prized mycorrhizal varieties and both smell wonderful.

But Mycorrhyzal fungi [pronounced mike-o-RISE-el] do a lot more than just smell good. These fungi form symbiotic (mutually beneficial) relationships with plant roots, extending them to much greater distances than the roots themselves could go and therefore increasing the plant’s reach tremendously. In exchange for sugars exuded by roots, the fungus frees nutrients in the soil and transports them and water back to the plant. The fungal mycellium is especially good at tapping phosphorus and nitrogen in the soil, needed by both plant and fungus. Thus plants grown with mycorrhizae are more resistant to drought and nutritional deficiencies than plants without them.

Fungi are also important in building soil structure because they bind soil together and make microhabitats for bacteria and other organisms as well as enhance the soil’s ability to hold moisture. There are approximately eight miles of mycelium threading through each cubic inch of soil so you could even say that fungi are responsible for the crumble factor in good soils. Knowing that the soil is alive with these structures makes me reluctant to dig or step too much on my beds.

I start most of my plants from seed. I like to make sure that my seedlings have plenty of fungal symbionts to help them get started, so I add commercial mycorrhizal powder to my seed starting soil. I’ve discussed this with Grant, who says the jury is still out on how effective this is, so if you hesitate to import your microbes, just put a little fresh compost in the bottom of the hole when you set out your plants. Although we are not sure exactly what is in the compost, there are sure to be friendly local mycorrhizae and bacteria in the mix.

–Barb McKenzie

NOTE: Paul Stametz, who owns Fungi Perfecti in Washington State (where I get my mycorrhiza powder) spoke about fungi at a recent TED conference. Paul collects fungi in the old growth forests of the Pacific Northwest, and the beneficial uses which he has discovered, e.g., bioremediation, natural pesticides, or medical uses, amaze and delight me.

For a fascinating read on the complicated web of life that exists underground, see David Wolfe’s Tales from the Underground, especially Chapter 5 which discusses mychorrhizal fungi and their symbiotic relationships with plants.

Urban Garden Soils

July 11th, 2011

Urban garden soils can best be described as “anything soil”. Since our garden started out as a paved-over schoolyard, much of its soil had to be carried in from elsewhere or built up over time by mulching and compost.

Henry Berk School, circa 1906, where our garden now stands

Libby, founder of the SWQV garden, says in the early days a pickaxe was the garden tool of choice, and Irene can tell stories about gardeners using carpet remnants to stabilize soil above the base of broken masonry that constitutes the garden floor. Then there is the infamous purple carpet that even a few years ago was still being excavated from certain plots. Every once in a while a sinkhole opens up so we can actually look down and see what’s under there.

Have you ever noticed more raised beds towards the back of the garden? That’s because concrete slabs and masonry debris are closer to the surface there, while plots near the fence have deeper soil and fewer raised beds. And although some plots have marvelous soil developed over many years by patient gardeners, others have dead soil lacking sufficient organic matter. Even if you start out with very good soil, organic matter needs to be continually re-supplied to maintain soil quality.

So what do gardeners use to build soil? Almost anything organic: municipal compost and herbivore zoo manure from the Phila Recycling Center in Fairmont Park, last year’s decaying hay mulch, recycled Starbucks coffee grounds, compost from the garden compost heap, compost from the Water Dept’s Biosolids Recycling Center by the airport, bales of garden center peat, cover crops grown off-season and incorporated into the soil or used as mulch, cut-up legumes and other spent crops, kitchen vegetable peelings, PHS topsoil, licorice root top dressing, mushroom soil, autumn leaves — you name it. As a result, the soil in each plot reflects the practices of the gardeners cultivating it — and it’s usually pretty good, a compliment to those who tend it.

But since the components could have come from anywhere, Libby once suggested I add greensand to insure necessary trace elements. And because the garden is built over a bed of building debris, our soils tend to be alkaline (high pH) from lime leached from the underlying cement and mortar. Hydrangeas are excellent indicators of pH because they tolerate a wide range of pH and flower pink in alkaline soils and blue in acid soils. The hydrangeas in our garden are all shockingly pink.


High pH locks up nutrients so they are no longer soluble and therefore no longer available to plants. What appears to be a nutrient deficiency is often a pH problem in disguise. Chlorosis (when leaves turn yellow except for narrow green areas next to veins) is caused by a deficiency of magnesium (yellowing of older leaves) or iron (yellowing of young leaves), either of which prevents the plant from making enough chlorophyll. Several years ago a peony growing over a concrete slab only a foot below soil level in my plot developed a horrendous case of chlorosis. Fortunately the problem was localized to a few square feet.

Blossom-end rot

Tomatoes growing next to the afflicted peony got blossom-end rot, a calcium deficiency sometimes also caused by high pH. Calcium is needed to form pectin which bonds cell walls, and without sufficient calcium the tomato could not make enough healthy skin to cover its blossom end. A few handfuls of garden sulfur fixed both problems by lowering the pH toward neutral, thus making nutrients that were already in the soil available to my plants.

A quick soil test will confirm whether the problem is pH or not. Soil testing kits and analysis services are available from the Agricultural Analytical Laboratory at Penn State University: click here for brochure

An interesting research paper from the State University of New York (SUNY) discusses some of the problems associated with highly disturbed soils characteristic of urban environments.

–Barb McKenzie


July 7th, 2011

2009 was the bicentennial of Charles Darwin’s birth as well as the 150th anniversary of the publication On the Origin of Species. Special talks, articles, and exhibitions were everywhere, and to mark the occasion I decided to look into some of his writings.

During his lifetime Darwin was almost better known for his work on earthworms and their role in the creation of topsoil (which he referred to as “vegetable mould”) than he was for the theory of evolution.

And Darwin’s observations on worm populations in garden soil and their earth-moving capabilities are stunning. Although numbers vary depending on soil, climate and season, I wanted to translate some of his numbers, given in acres and tons, into equivalents for a 20’ x 15’ SWQV garden plot.

His 53,767 estimated worms/acre in English gardens translates to 370.3 worms/SWQV plot. Another of his estimates suggests English earthworms may move at least 7.56 tons of soil per acre annually (and up to 16.1 tons), the low number of which translates to an equivalent 117 pounds annually for a SWQV plot. Amazing!

Moving that much earth and depositing it as castings on the surface provides a rich source of plant nutrients, aerates the soil and allows for better absorption of rainwater. Good enough reason to never spade or plow or otherwise disturb these quiet soil builders (there are other reasons not to dig, but more on that later).


Darwin developed a discernable fondness for these “shy creatures”. He writes: As I was led to keep in my study during many months worms in pots 
filled with earth, I became interested in them, and wished to learn 
how far they acted consciously, and how much mental power they 
displayed. I was the more desirous to learn something on this 
head, as few observations of this kind have been made, as far as I 
know, on animals so low in the scale of organization and so poorly 
provided with sense organs, as are earth-worms.

Darwin concluded that earthworms do display intelligence because of the way they use leaves to plug the entrances of their burrows, but even more interesting to me was his investigation of their sense of taste and food preferences.

By offering a smorgasbord of selections, Darwin observed that onions, cabbage, horseradish and celery were “attacked with relish” and that earthworms preferred carrots “above all others, even celery.” But “leaves of an Artemisia and of the culinary sage, thyme and mint, mingled with the above leaves, were quite neglected excepting those of the mint, which were occasionally and very slightly nibbled. These latter four kinds of leaves do not differ in texture in a manner which could make them disagreeable to worms; they all have a strong taste, but so have the four first mentioned kinds of leaves; and the wide difference in the result must be attributed to a preference by the worms for one taste over another.”

So I always save my vegetable peels (as well as egg shells, coffee grounds and tea leaves) and tuck them under the hay in my plot in hopes that the earthworms will enjoy the feast and that I will get even more than my allotted 370.3 worms per plot.

–Barb McKenzie

Link to Darwin’s On the Formation of Vegetable Mould

This Year’s Great Hay Experiment

July 4th, 2011

Let me confess: I am a lazy gardener. I don’t like to weed. I don’t like to dig. And I especially don’t like to water. So last winter when I was searching Amazon in anticipation of the growing season ahead, I was particularly attracted to the writings of Ruth Stout: “Gardening without Work: for the Aging, the Busy, and the Indolent.” Or how about “How to Have a Green Thumb without an Aching Back”? Or simply “The Ruth Stout No-Work Gardening Book”. Stout was a pioneering advocate of mulching who wrote for Organic Farming & Gardening in the 1950′s and was a passionate proponent of no-work gardening. I was instantly attracted to her method.

Mulching. But how much? I had always done some mulching, but Stout advises “a lot more than you think” — in fact, 8 to 10 inches. Eight to ten INCHES! For my plot that translated to eight bales of hay. But I was committed, even at the risk of becoming a minor laughing-stock of my fellow gardeners.

Most of the spring my plot looked like a lumpy haystack or a rundown feedlot. But the most amazing thing happened since. My twenty-three tomato plants are deliriously happy, the zucchini is quietly plotting to take over the world, I have more cucumbers than I can give away. And if I put my hand under the 8 inches, the soil is cool and moist, even on the hottest days. So Ruth is right. It takes more than you think…

To view a charming interview with Ruth Stout when she was in her 90′s and hear her explain her mulching method, CLICK HERE.

–Barb McKenzie

Rebuilding the Compost Bins

April 22nd, 2011

Grant & Ted redesigned and rebuilt the compost bins in March 2011 and as a result the garden now boasts a first-rate composting system. For more on the construction process, click here to see Thom’s photo documentation.

Don’t Tread on the Microbes

September 28th, 2010

Welcome to the first ever installment of the Southwark-Queen Village Community Garden’s Compost Blog. Is there anything even remotely interesting to say about decomposing vegetable matter? I can assure you that there will be more to each post than, “Turned piles today” or, “Temperature reached 140° F”. In each posting, I plan to, yes, give an update on the status of the piles at our garden, but also explain some things about compost and the composting process and to link to others in the world who are doing interesting things with compost. What? Compost sculpture? The new Southwark Compost Diet? Hmmm…I doubt it.

So first, about compost: What is it?
Compost: “Organic residues, or a mixture of organic residues and soil, that have been piled, moistened, and allowed to undergo biological decomposition. Mineral fertilizers are sometimes added. Often called artificial manure or synthetic manure if produced primarily from plant residues.” (2008. Brady N.C & R.R. Weil. The Nature and Properties of Soils.)
Man, I really think that this definition is about as opaque as they come. I’ll find a better one for next time. This one happened to be close at hand. No wonder soils class was so difficult. Many people conflate compost with soil. It’s dark and crumbly and dirty and it smells earthy, it must be soil, right? Nope. Soil is composed of sand silt and clay that have eroded from rock in order to form the medium in which plants and fungi grow and animals (including insects and smaller creatures) live. Added to soil, compost provides a community of microbial creatures that help plants to grow, that fight disease and improve the water holding capacity of the soil or other media in which plants are growing.

In my experience as a gardener, I have noticed great differences between plants grown with and those grown without, compost. An experiment you could try in your own garden to see for yourself is to apply compost to one plant and none to another plant of the same kind. Depending on the quality of the compost (not all compost is created equal) I’ll bet you will see one robust, healthy looking plant and another that is spindly and looks thirsty all the time. Try it and let me know, ok? (Probably best done in the spring or summer). We grew some great garlic this past season in a plot that was amended with a 3” layer of compost.

I promise more about what compost is and the process of making it for next time, say in 2 weeks. Meantime, a brief note on this past month’s turning of the 4 bin composting system we use at SWQV: with an extraordinarily large pile of fresh stuff in the first pile, I saw a challenge in getting it all to fit into pile #2. So, I decided that since I saw a picture, during a presentation by Will Allen about Growing Power Inc. in Milwaukee [ ] of a kid jumping up and down on one of the pallet composters used there, that it would be a great idea to try it. That was Sunday. On Wednesday, I got discouraged when the temperature of the pile #2 struggled to make it past 90° F. Since March, with each turning, pile #2 has been reaching 140° F for at least a week, sometimes two. On Thursday, the temperature had risen to 130° F. I had visions of the temperature reaching 150° F even. Today when I took the temperature, it was back down to 80 – 90° F. Lesson: don’t tread on the microbes. Remedy: pull pile apart, pile it up again (without jumping on it) and add moisture to one layer at a time.
Hasta la next time!