The Essential Book of Fermentation (5 page)

2. Nitrogen-fixing bacteria
colonize certain plants’ roots. They take molecules of nitrogen from the air (N
₂
) and split them apart by rearranging their electrons, like taking apart a Chinese wire puzzle. These freestanding atoms of nitrogen are then reassembled by the bacteria with oxygen atoms to form soluble nitrates, which plants absorb to make new living tissue. The end result is the same as with nitrifying bacteria but by a different process.

3. Denitrifying bacteria
are usually anaerobic, meaning they operate without the presence of air. They convert the nitrogen in dead plant tissue to nitrogen gas molecules (N
₂
) that are given off into the air. Remember that the air we breathe is four-fifths nitrogen, some of which is recycled back into plant nutrients by the nitrogen-fixing bacteria. Instead of aerobic decomposition, anaerobes cause putrefaction—the reason putrid piles of wet plants smell.

4. Actinobacteria
are aerobic microbes that are central to the process of decomposing dead plants’ nitrogen-rich amino acids into ammonium salts, which are further converted to ammonia. Their activity turns dead plant tissue into sweet-smelling humus, which is a critical component of healthy soil.

5. Fungi
are also important in decomposing organic matter into nitrates that living plants can use as food. A succession of fungal species colonizes organic matter during its decomposition, beginning with those that decompose sugars and starches, succeeded by those that are able to break down the tough materials of cellulose and lignin, releasing the nitrogen from their proteins.

The Phosphorus Scavengers

A bacillus is a rod-shaped bacterium (left). A coccus is round (right).

A special type of fungus called mycorrhizal fungi has a symbiotic relationship with its host plants. It lives in the soil and colonizes the roots of plants. Their plant hosts exude sweet syrup through their roots that the fungus uses for food. In return, the fungus sends long, threadlike strings called hyphae far into the surrounding soil to gather phosphorus and transport it back to the plant roots, where it’s absorbed. Phosphorus, a macronutrient essential for plant health, is often in short supply in many soils, so you can see the valuable service mycorrhizal fungi play in the natural ecosystem. If the plants are harvested and removed, then the phosphorus will eventually be depleted in that soil and must be added back as fertilizer. If the plants are growing wild, the phosphorus will be recycled back into the soil through decomposition.

The Carbon Managers

Then there is the genus
Lactobacillus,
which includes the microbes at the heart of the fermentations that do so much for our health. They turn sugars into lactic acid, an acid that links carbon with hydrogen and oxygen to form the molecules of adenosine triphosphate (ATP) in our bodies that provide us with energy as it is broken down into its constituent pieces. We have only about eighty-five grams (about three ounces) of ATP in our bodies at any one time, and when exercising we’d soon use it all up, but the body is a marvelous piece of work and has several systems for resynthesizing ATP from its breakdown products. One of those systems depends on lactic acid, and lactobacilli move the carbon from sugars to lactic acid in our intestines, so you can see their importance. This genus is composed of at least 120 species, with possibly more as yet undiscovered.

The lactobacilli operate under a variety of conditions. When working under the brine in our fermentations, they are anaerobes that don’t need air to function. Yet they also work in the presence of air, where they play a major role in the decomposition of plant organic matter. They are rod-shaped eukaryotes; that is, they have nuclei inside their cell walls that contain their genetic material. On the human body, they are found primarily in the digestive tract and in the vagina. Lucky that they live there, too, for the vagina is the birth canal, and baby’s trip out into the world seeds its little gut with these benign, essential bacteria. But lactobacilli presence in the vagina is good for women, too. They maintain balance in the vaginal ecosystem, and they protect the lining of the vagina by producing a thick layer of cells that are a barrier to pathogens—including
Candida albicans
, the pesky yeast that causes yeast infections. They maintain the vagina’s pH at an acidic 4.5. And they generate H
₂
O
₂
—hydrogen peroxide—which carries that extra oxygen atom to a pathogen or parasite, where the oxygen combines with and kills the offender. They protect against various kinds of pathogens. They are symbiotic with their human hosts in both these places, living off the human body and in turn giving the human beneficial substances like lactic acid and performing a wide range of health-promoting activities.

Of course, nobody’s perfect, and that includes the lactobacilli. A high count of lactobacilli in the mouth has been a standard test for dental caries for many years. It seems that they promote the progression of tooth decay by turning sugar into lactic acid—normally a good thing, but when it happens in the plaque clinging to your teeth, the lactic acid tends to dissolve the minerals in the teeth, leading to cavities. So brush your teeth, and don’t forget to floss. But forget the antibacterial mouthwashes, which have the same effect on the healthy bacteria in the mouth as fungicides do on soil microorganisms. A potent strain of
Streptococcus salivarius
, found in the mouths of healthy humans, is called BLIS K12, and it fights pathogens that cause bad breath, among other maladies. Antibacterial mouthwashes wreak wholesale havoc on bacterial ecologies in the mouth and kill off
S. salivarius
and beneficial lactobacilli.

Besides lowering pH and inhibiting pathogens, the lactobacilli can reduce inflammation and fight cancer. A 2009 study by researchers at Beth Israel Deaconess Medical Center and UCLA showed that some strains of these bacteria help the body fight off cancer and prevent tumor formation. Animal studies have shown inhibition of liver, colon, bladder, and mammary tumors when lactobacilli were added to the animals’ diet.

For the chemists among us (and you know who you are), here’s the reaction where glucose is reduced to lactic acid in a process called homofermentation (because only one compound is produced):

C
₆
H
₁₂
O
₆
2 CH
₃
CHOHCOOH

Some strains of lactobacilli produce what’s called a heterofermentation, because more than one compound is produced. Here’s a formula for the reduction of glucose into one molecule of lactic acid, one molecule of ethanol, and one molecule of carbon dioxide:

C
₆
H
₁₂
O
₆
CH
₃
CHOHCOOH + C
₂
H
₅
OH + CO
₂

In both cases, the lactobacilli turn the sugar molecule into either one or two molecules of lactic acid. And as we just found out, lactic acid is part of one of the ways the body resynthesizes ATP to power our systems.

The primary mechanism of ATP production is a reduction of glucose in the blood into pyruvate, a process called glycolysis that is facilitated by lactic acid, which acts like an enzyme. One of the results of glycolysis is the release of hydrogen ions (protons). It’s not the lactic acid that causes the pain in muscles when they are worked really hard, but rather the buildup of protons in the cells, causing the pH of the cells to drop and turn acidic.

ATP production in the cells happens by an electron transport chain. Just picture a molecule of glucose coming apart into pyruvate molecules, and energy jumping from electron to electron, producing ATP’s precursors, and finally, with the help of lactic acid, producing ATP itself. To power the body’s cells in their many functions—working muscles, active digestive system, firing of nerve cells—the cells disassemble ATP back into its precursors, and the lactic acid is there to reassemble it for further energy. In effect, in the anaerobic conditions inside the cell, glucose is effectively undergoing lactic acid fermentation.

If we turn now to the organic garden or farm, we find that plants, too, use ATP to energize their systems. During the production of ATP in plant cells, hydrogen atoms (each is a proton and an electron) are stripped of their electrons, leaving positively charged protons—and in effect, the synthesis of ATP in root hairs creates proton pumps that send protons into the soil solution, as groundwater is called. Proton pumps are simply membranes that enclose the cell’s nucleus and mitochondrion and form the whole cell’s walls. They collect protons and store them to be used as an energy source in a wide range of cell functions in both plants and animals. Plants seeking nutrients release stored protons through the cell walls of root hairs into the groundwater. These protons find their way to humus particles in the soil. Humus is what’s left after the decomposition of once living tissue is completed. Humus is marvelous stuff, and soils handled organically are full of it. Its surfaces are negatively charged and hold positively charged ions of plant nutrients to themselves: ammonium, calcium, magnesium, and potassium, among others, which prevents these plant foods from being washed away by rain or irrigation.

As the protons from the plant root hairs reach the humus particles, they kick the plant nutrients loose from the humus and replace them at the humus surface attachment sites. The plant nutrients then float back to the plant roots and feed the plants. This function is called the Cation Exchange Capacity of a soil, and the more humus, the more energetic the soil’s Cation Exchange Capacity. This is one reason organic soils have it all over soils fertilized with chemicals. The latter are soluble and wash away, where they can cause environmental damage due to flooding groundwater with overloads of soluble nutrients.

Why do I bring this up in a book on fermentation and human nutrition? Because we also have proton pumps in our gastrointestinal system, especially in our stomachs. In our stomachs, these positively charged protons find negatively charged ions of chlorine (Cl-), derived mostly from NaCl (salt), and link up to form HCl—hydrochloric acid, which is our gastric juice and a strong acid that is one of the first stages of digesting the food we swallow. So proton pumps have similar functions in plants and in us—they aid in our ability to feed ourselves.

Fermented foods can help balance the production of hydrochloric acid. Too little—sometimes a consequence of advancing age—reduces the stomach’s ability to give food a bath in strong acid that begins to reduce the food to its nutritional constituents. Fermented foods can increase the acidity of the stomach’s gastric juices because of the lactic acid they contain. But they act as a buffer if the stomach overproduces this very strong acid (pH 2.0). Kefir has a pH of about 4.0, and sauerkraut about 3.0. As the fermented foods pass through the stomach, they can help protect the intestinal lining from the hydrochloric acid in the gastric juice.