The Functions and Value of Soil Bacteria

The Functions and Value of Soil Bacteria

The Functions and Value of Soil Bacteria

by Karl F. Kellerman, excerpted from USDA Yearbook of Agriculture, 1909


After reaching maturity and dying, plants decay and become again an indistinguishable portion of the soil in which they grew. Only recently the science of bacteriology has shown how remarkable is this transmutation of the dead plants back to soil; in fact, bacteriology, and more especially soil bacteriology, has changed our conception of a soil. It is no longer thought of as merely an inert mixture of substances forming the earth’s crust, but rather as a mixture of substances supporting various definite groups of soil bacteria, and usually supporting other forms of plant life.

Bacteria themselves are plants. They form the simplest group of the fungi, or plants that are lacking in chlorophyll. They are exceedingly minute; the largest forms may reach a diameter of 0.008 mm (0.003152 inch), though the majority are not more than 0.005 mm (.0000197 inch) in diameter, and it is believed that some bacteria exist which are too small to be seen even with the aid of the most powerful microscope. In spite of their small size, however, they are concerned with every phase of our daily life and by their incredible numbers and ceaseless activity overcome their apparent insignificance. Bacteria cause diseases, make milk sour, spoil jars of preserved fruit, form ptomaine poisons in meat, and in many ways are a most troublesome scourge. In spite of all the evil that some species of this group of plants cause, however, other species, and even some of the troublesome species under different conditions, are so beneficial that, biologically speaking, bacteria must be considered the most important factor in the great drama of life upon the earth.


The bacteria of the soil are chiefly of the beneficial types. They occur in almost infinite numbers, a fertile soil having from one-half a million to ten million to the gram (from 15,000,000 to 300,000,000 to the ounce). Their functions and value are variable, both because the kinds of bacteria differ in soils and because any given species may vary physiologically with certain limits according to environmental conditions. The moisture, the temperature, the degree of pulverization, the rock formation or the geological history of the soil, the aeration, the drainage, etc., are all factors which partly determine the action of soil bacteria; and perhaps more important than any of those with which it is closely associated, or, more broadly speaking, the effect of the associative or competitive action of the various groups of micro-organisms which act and react upon each other.

If the conditions are favorable, it is the province of some of these groups of micro-organisms to decompose dead plant and animal matter into simpler compounds, to reconstruct various inert materials, and in this way to form new soil constantly and maintain it in a state of high fertility. If, on the other hand, conditions of food supply and environment are unfavorable, certain groups of bacteria may destroy the potential fertility of a soil in ways that will be explained later. It should be remembered that soil fertility has a relative rather than a definite meaning, for a soil may be fertile with respect to one crop and infertile with respect to another; cowpeas might grow luxuriantly where cotton would barely exist, and oats do well where corn was a failure.


It is known that different species of bacteria are responsible for certain changes in sulphur compounds, phosphorus compounds, carbon compounds, etc., yet those groups which transform the nitrogen compounds have been more thoroughly investigated. They illustrate very satisfactorily how intimate is the connection between successful agricultural practice and the maintaining of a proper environment for the desirable bacteria, as well as indicating some of the conditions under which bacterial activity may be a serious menace to the productivity of a soil. It is generally recognized that a field capable of producing a good yield of any of the usual crops, such as corn, wheat, potatoes, or cotton, must contain a supply of nitrogen which can be dissolved in the soil water. To be in its most available form, that is, in a form best adapted for the crop to assimilate, this nitrogen must be oxidized to nitrate.

Assuming that sufficient nitrates and other foods for a corn crop were present to allow the corn plants to mature and thus form starch, oil, plant proteins, etc., the changes of the nitrogen compounds that are due to soil bacteria might proceed as follows: The stalks may be left on the field and thus add a small quantity of nitrogen in the form of protein or plant albumin, a substance that other corn plants could not assimilate as such. The ears of the corn may be fed and some of the nitrogen of the seed may go to building up beef or horse flesh; if the animal dies and the carcass be pulverized and spread over the field the nitrogen of this fertilizer would be in the form of an animal protein, such as constitutes a large part of blood or muscle. Here, again, the nitrogen would not be in a condition available to a corn crop. Of course, all the nitrogen of the corn which was fed was not used in building up the animal’s flesh and blood, but even the nitrogen excreted by the body processes and returned to the field as fresh manure is not in available form.

These complex nitrogen compounds which have been carried back and spread over the field or were left there (the cornstalks, the dead animal fertilizer, and the fresh or unrolled manure) are made useful by the ammonifiers which grow and multiply in them and are one of the largest groups of bacteria which cause decay. As the name of this group indicates, the function of these bacteria is to split up the complex nitrogenous compounds and to form ammonia. A second group of bacteria changes the ammonia into nitrite, a substance which if present in large quantities is poisonous to most plants. As soon as nitrite begins to accumulate, however, a third group of bacteria oxidizes it to nitrate; this combination of nitrogen is most suitable for plant food, being for plants practically what meat is for man. Some plants, notably the cereals, are said to be able to assimilate nitrogen in the form of ammonia. Greenhouse experiments, however, indicate that even if this be true better results are obtained after the ammonia is in turn acted upon by nitrifying bacteria and changed to nitrate.

The nitrogen changes, however, are not confined to the series just reviewed. There are contrary groups of bacteria which, under slightly different conditions, are capable of doing the exact opposite of the three groups just mentioned. With organic food and nitrate accumulated in abundance one group reduces the nitrate to nitrite, a second reduces the nitrite to ammonia, and a third group may reduce the ammonia to free nitrogen gas. This loss of gaseous nitrogen, or denitrification, is very injurious, for, as may readily be seen, it actually decreases the potential productiveness of the soil. There are other changes, however, which for want of better terms are also classed with denitrification. Many kinds of bacteria, especially those which act upon nitrate compounds in forming the protein compounds of their own cells, as they increase in number may utilize much of the nitrogen of the substances upon which they feed. It is evident, therefore, that a change of nitrate into organic or protein nitrogen may take place without the aid of either higher plants or animals, and in this more or less insoluble form nitrogen that otherwise might be carried away by rains and drainage water is preserved to become available to growing crops at some future time.

The Functions and Value of Soil Bacteria

Fig. 2 — Diagram showing the nitrogen changes produced in the soil by the action of bacteria. The arrows indicate the course of the changes which various groups of bacteria may produce in the nitrogen compounds of the soil. A, Action of ammonifying bacteria which change organic nitrogen to ammonia; B, action of nitrifying bacteria which change ammonia to nitrite; C, action of nitrifying bacteria which change nitirite to nitrate; D, assimilation of nitrate by green plants; E, action of denitrifying bacteria which change nitrate to nitrite; F, action of denitrifying bacteria which change nitrite to ammonia; G, action of denitrifying bacteria which change ammonia to nitrogen gas; H, action of bacteria which change nitrogen gas into proteid nitrogen; I, action of bacteria which in symbiosis with leguminous plants change nitrogen gas into proteid nitrogen; K. action of bacteria which in sytmbiosis with certain nonleguminous plants change nitrogen gas into proteid nitrogen.

The reciprocating or complementary action of the various groups of bacteria which transform nitrogen compounds is more easily expressed by a diagram. In Figure 2 the ammonifying bacteria, as indicated by the line A, are represented as changing the organic nitrogen, formed by the growth of plants and animals, into ammonia. This transformation often takes place so rapidly that much of the ammonia is given off as a gas, a fact that anyone who has been near a manure heap during the warm spring days will remember. The ammonia that is retained in the soil now becomes part of the food of the nitrate bacteria, indicated in the diagram by the line B. If the supply of air in the soil is sufficient to furnish the nitrite bacteria with an adequate supply of oxygen, which is an essential in all these processes of nitrification, they will gradually oxidize the ammonia to nitrite. A large number of species of bacteria are able when in the soil to bring about this change, but many of them lose this power shortly after they are isolated and grown as pure cultures in a laboratory. As previously stated, an accumulation of nitrite would be injurious to crops, but in the processes of nature the phenomena are so adjusted that the selfish struggle of each individual for food conduces to the welfare of all. If the soil is in good condition, long before sufficient nitrite is formed to injure the crop the nitrate bacteria, indicated by the line C, are at their feast transforming nitrite into nitrate, or, in other words, preparing the nitrogenous food for the crop. The assimilation of nitrate by crops is indicated by the line D. If now to this soil which is rich in nitrate there is added a large quantity of organic matter, for instance, by applying dried blood or by turning under a heavy green manure or by a heavy top-dressing of manure, and especially if the soil becomes too compact or becomes water-logged, so as to exclude air, undesirable bacteria which feed partly on nitrate and nitrite and partly on organic matter will develop rapidly. These bacteria reduce the nitrate to nitrite and the nitrite to ammonia, as indicated by the lines E and F. Complete denitrification, or the breaking up of ammonia and the giving off of free nitrogen as that gas which forms four-fifths of the air, will take place as indicated by the line G, the quantity given off depending to a considerable degree upon the paucity of the air supply and the abundance of nitrate and the abundance and kind of organic matter. It is interesting to note that there is a wide difference in the range as well as in the rapidity of the reducing power of different species of the denitrifying group. For instance, some species of bacteria can only change nitrate to nitrite, while others cannot act upon nitrate at all but can change nitrite to ammonia; on the other hand, certain species can change nitrate to nitrite, nitrite to ammonia, and ammonia into free nitrogen gas.

The Functions and Value of Soil Bacteria

Fig. 3 — Diagram showing the percentages of nitrate nitrogen, nitrite nitrogen, and ammonia nitrogen produced by bacteria in a 35-day denitrification and nitrification test. Soil supersaturated with a 0.2 percent solution of nitrate in an infusion made by heating 10 grams of young alfalfa plants in 100 grams of water. Unbroken line represents nitrate nitrogen; broken line, ammonia nitrogen; dotted line, nitrite nitrogen.

The following records of recent experiments upon the action of the various groups of bacteria in garden soil when supersaturated with solutions of nitrates and organic matter illustrate the relative speed and the sequence of these processes. The relative quantities of nitrate, nitrite, and ammonia during the course of the investigation are shown as curves in Figure 3. The soil was supersaturated with an infusion of alfalfa plants made by heating 10 grams of young alfalfa plants in 100 grams of water to which was added 0.2 percent of nitrate. With the dilution due to moisture normally in the soil, together with a slight absorption by the soil particles, the nitrate in solution was reduced to 0.17 percent at the beginning of the experiment; at this time neither ammonia nor nitrite was present. Two days later the denitrifying bacteria had reduced the nitrate to 0.01 percent and had formed considerable quantities of nitrite and some ammonia. By the fifth day these bacteria had left only a trace of nitrate, had reduced the nitrite to 0.01 percent, and had increased the ammonia. For the next five days no change was apparent, though it should be noted that some of the nitrogen was given off as free nitrogen gas and some was changed into protein nitrogen. At the end of the fifteen-day period the activity of the denitrifying bacteria had subsided and the nitrifying bacteria were building up nitrite and decreasing the ammonia, and five days later this action had progressed until the nitrite had reached 0.05 percent, while the ammonia had fallen to 0.01 percent. At the twenty-five day period the nitrate-forming group of the nitrifying bacteria had produced an appreciable quantity of nitrate and had left only traces of nitrite. From this time until the close of the experiment at the thirty-five day period the ammonia and nitrite were kept very small in quantity, and the nitrate was slowly but steadily produced. The groups of nitrifying bacteria were evidently well adjusted during these twenty-five days, for almost as fast as the ammonifiers produced ammonia the formers of nitrite changed the ammonia to nitrite, and similarly as the nitrite was produced the formers of nitrate changed it to nitrate. During the course of this experiment none of the nitrogen was given off as a gas.


Aside from certain symbiotic relationships with bacteria, crops can not assimilate nitrogen gas. It might seem, therefore, as if all of the nitrogen of the earth might eventually be transformed into the gaseous state, thus starving out all crops.

Recurring to the discussion of Figure 2, it is evident that with proper farm management no such danger is imminent, for the free nitrogen of the atmosphere can be fixed or combined with other substances to form organic compounds. There are three groups of processes, indicated by the lines H, I, and K, by which the soil bacteria perform this function, which is perhaps one of the most remarkable, if not the most valuable, of all the reactions of the soil flora.

(H) The direct fixation of nitrogen by bacteria alone is the first process. There are several species of bacteria that are known to have this power. Among them may be mentioned Clostridium pasteurianum, Bacillus alcaligenes, Bacillus tumescens, Pseudomonas radicicola, Granulabacter, and several species of Azotobacter. The latter genus of bacteria occurs in practically all soils, and by its relative abundance seems to indicate what may be termed the natural soils which are rather readily exhausted of their nitrogen the bacteria of the genus Azotobacter occur only in the few top inches, perhaps from the first to the tenth. In the deep and almost exhaustless soils of some parts of the West, on the other hand, these bacteria are found in active condition even down in the fifth foot.

(I) The second process is the fixation of nitrogen by the root-nodule organisms in association with the various legumes. This has been described in former publications and is probably the manner in which the major part of the nitrogen of the air is transformed into plant food. The great economic importance of these desirable bacteria may be seen from the fact that for many years investigators have worked at the problem of disseminating them in soils where they do not naturally occur. Pure cultures for inoculating soils to grow alfalfa, clovers, vetches, and other legumes are not distributed by several American and foreign experiment stations, including the United States Department of Agriculture.

(K) The fixation of nitrogen by bacteria in symbiosis with plants other than legumes is the third process. It is impossible to determine at the present time whether this is a scientific curiosity or a fact of practical value. Bacterial nodules occur upon at least one species of Alnus (alder), upon Ceanothus americanus L. (red root, New Jersey tea), Ceanothus velutinus (New Jersey tea), Eleagnus argentea Pursh. (silver berry), Lepargyraea argentea (Nutt.) Greene (buffalo berry or rabbit berry), Podocarpus macrophylla Don, and several genera of the cycads, though it must be admitted that the nodules of the latter group of plants are quite different in some ways from the nodules of legumes.


In this brief review of the course of a few of the essential changes which are brought about in soils by definite groups of bacteria it is impossible to discuss the intimate relationship, as yet but partly understood, between the constitution or action of the microscopic flora of the soil and the methods of cultivation, crop rotation, fertilization, etc. Years of research will be necessary before the details are known of the interaction upon each other and upon the soil of the various kinds of bacteria, though from analogy we have good reason for believing that they are grouped and that each type has its particular functions, each seeking and devouring its own kind of food and endlessly forming food for other organisms. Their struggle for existence is undoubtedly similar to that of other and larger organisms, and without their endless struggle and activity plant and animal life would rapidly pass from the earth.

By proper methods of tillage, crop rotation, or green manuring, and even by the application of fertilizers, the interaction between prevailing soil conditions and biological phenomena may be modified so as to promote the activity of desirable micro-organisms and retard the development of the undesirable ones. And as we recognize that bacterial growth is an important factor in the transformation of various materials into available plant food, we appreciate the importance of further investigation for securing more exact and more complete data bearing upon the interdependence of agricultural products and the micro-organisms of the soil. With the application of bacteriology to farm practice, as with the application of the data secured by the plant breeder, the chemist, or the meteorologist, it is for the farmer himself to say whether the net results of farm labor shall be on the side of profit or of loss. The methods he employs in his work are indications of this grasp of the scope and importance of these various investigations, for progress in farming, as in anything else, is in reality progress in methods brought about, perhaps slowly, perhaps suddenly, by a more and more rational comprehension of why we do the things we do.