The micro-organisms of the soil

In the preceding chapters it is shown that the soil is normally inhabited by a very mixed population of organisms, varying in size from the smallest bacteria up to nematodes and others just visible to the unaided eye, on to larger animals, and finally earthworms, which can be readily seen and handled. These organisms all live in the soil, and therefore must find in it the conditions necessary for their growth. We have dealt in the first chapter with the supplies of water, air, and heat, without which life is clearly impossible. Equally necessary is the source of energy, for the organism requires energy material as surely as the motor engine requires petrol, and it ceases to function unless an adequate supply is forthcoming.

All the energy comes in the first instance from the sun, if we exclude the unknown but probably small fraction coming from radio-active elements. But this radiant energy is not utilisable by the soil population, excepting surface algæ; it has to be transformed into another kind. So far, chlorophyll is the only known transformer; it fixes the energy of sunlight and stores it up in bodies like hemicellulose, sugar, starch, protein, etc. The transformation is imperfect; even the heaviest yielding crops grown under glass, in conditions made as favourable as our knowledge permits, utilise only about 4 per cent. of the total energy available during their period of growth; in natural conditions not more than 0·4 per cent. is utilised. Such as it is, however, the energy fixed in the plant represents all, indeed more than all, that the soil organisms can obtain.

In the state of Nature, vegetation dies and is left on the soil. Two things may then happen. It may become drawn into the soil by earthworms and other agents; the energy supply is thus distributed in the soil to serve the needs of the varied soil population. This is the normal case, associated with the normal soil population and the normal flora. If, however, the mingling agents are absent, the dead vegetation lies like a mat on the surface of the soil, only partially decomposing, unsuitable for the growth of most seedlings, and effectually preventing most of the vegetation below from pushing a way through: thus there comes to be no vegetation at all, or only a very restricted and special flora. The soil population becomes also specialised. Peats and acid grassland afford examples.

On the neutral grass plots at Rothamsted, the dead vegetation does not accumulate on the surface but is rapidly decomposed or drawn into the soil, leaving the surface of the earth bare and free for the growth of seedlings. On the acid plots dead vegetation remains long on the surface, blotting out all new growth excepting two or three grasses which form underground runners capable of penetrating the mat, and sorrel, the seedling roots of which seem to have the power of boring through a fibrous layer of this sort. It is possible to remove the mat entirely by bacterial action alone, if sufficient lime be added periodically to make the reaction neutral, but failing these repeated additions the mat persists.

We shall confine ourselves to the normal case where earthworms bring the source of energy into the soil.

Directly the energy is available, it begins to be utilised. Two laws govern the change. The first is well-known to biologists: it states that the total energy of the system remains constant and can neither be increased nor diminished except from outside; in other words, that energy can be neither created nor destroyed. The second law is less familiar: it is that energy once transformed to heat by one organism cannot be used again by another. It is not destroyed; it remains intact, but is useless to the organism. One cannot have an indefinite chain of organisms living on each other’s excretory products; there was a certain quantity of energy in the food eaten by the first, and no more than this quantity can be got out whether one organism obtains the whole or whether others share it.

The outside value for the amount of energy fixed in the soil is obtainable by combustion of the soil in a calorimeter, but much of this is not available to the soil organisms. The normal sedimentary soils of England still contain decomposition products of the débris of plants and animals originally deposited with them, but in the long course of ages much of the extractable energy has been utilised. The soil population is thus dependent on recently grown vegetation, and it is therefore largely confined to the layer, usually in this country about 6 inches thick, through which the recently dead vegetation is distributed. Below this level there may be sufficient air, water, temperature, etc., but there is insufficient source of energy for any large population.

Unfortunately there is no ready means for distinguishing between the total and the actually available quantity of energy in the soil. But it is not difficult, by adopting the Rothamsted analytical method, to ascertain the approximate amount of energy that has been transformed in a given period. The Rothamsted plots are periodically analysed and a balance sheet is drawn up showing how much of each constituent has been added to and removed from the soil in the intervening period. For two of the Broadbalk plots the results are shown in Tables XV., XVI.

The dunged plot receives 14 tons farmyard manure per annum, a quantity in excess of what would usually be given; the unmanured plot, on the other hand, has received no manure for many years and is abnormally poor. Normal soils lie somewhere between these limits, but tending rather to the value for the dunged than for the unmanured plot. It will be seen that each acre of the dunged land loses on an average 41,000 calories per day, while each acre of the unmanured land loses on an average 2700 calories per day.

TABLE XV.—MATERIAL BALANCE SHEET: BROADBALK SOIL, ROTHAMSTED.
(Lb. per Acre per Annum.)

TABLE XVI.—ANNUAL ENERGY CHANGES IN SOIL: BROADBALK. APPROXIMATE VALUES ONLY.
Millions of Kilo Calories per Acre per Annum.

These numbers are interesting when we reflect that the human food produced on the dunged land yields only 7000 calories per day, from which it is clear that our agricultural efforts so far provide more energy for the soil population, for which it was not intended, than for ourselves.

The account is not complete; we have omitted all reference to the oxidation of ammonia and of elements other than carbon. Nature seems to be in an unexpectedly economical mood in the soil, and all compounds which can be oxidised with liberation of energy seem to have corresponding organisms capable of utilising them. Even phenol, benzene, hydrogen, and marsh gas can all be oxidised and utilised as energy sources by some of the soil population.

Even with this remarkable power the soil population has insufficient energy to satisfy all its possibilities; our present knowledge indicates that energy supply is, in this country at any rate, the factor limiting the numbers of the population. Increases in the water supply or the temperature of the soil produce no consistent effect on the population, but directly the energy supply is increased the numbers at once rise.

Material Changes.

These transformations of energy involve transformations of matter. The original plant residues may be divided roughly into substances forming the structure of the plant, such as the hemicelluloses, the pentosans, gums, and the contents of the cell—the protoplasm and the storage products, protein; in addition, there are smaller quantities of fats and waxes and other constituents. Some of the easily-decomposable carbohydrates never reach the soil at all, being broken down by intracellular respiration or attack of micro-organisms. But much of the structure material—hemicelluloses, pentosans, etc.—remains.

Once the plant residues pass through the earthworm bodies they become completely disintegrated and lose all signs of structure.

The only visible product so far known is humus, the black sticky substance characteristic of soil and of manure. Two modes of formation have been suggested. Carbohydrates, sugars, pentosans, etc., are known to yield furfuraldehyde or hydroxymethylfurfuraldehyde on decomposition, and it has been shown at Rothamsted that this readily condenses to form a humus-like body, if not humus itself. In the laboratory the reaction is effected in presence of acid, but even amino-acids suffice. All the necessary conditions occur in the soil, and humus formation may proceed in this way.

Some of the structure material—the lignin—contains aromatic ring groupings. Fischer and Schrader have shown that in alkaline conditions these ring substances absorb oxygen and form something very like humus. It is quite possible that humus formation also proceeds in the soil in this way. Whether the two products are chemically identical is not known.

The scheme can be represented thus:—

The disintegration of the cell and the first stages in the decomposition of the structure material are almost certainly brought about by micro-organisms. Whether they complete the process is not known: purely chemical agencies could easily account for part.

The decomposition of protein in the soil has not been studied in any detail. From what is known of the acid hydrolysis and the putrefactive decompositions, however, it is not difficult to draw up a scheme which, at any rate, accords with the facts at present known. It is probable that the protein gives rise to amino-acids, which then break down by one of the known general reactions.

Two types of non-nitrogenous products may be expected: The aliphatic amino-acids give rise to ammonia and fatty acids; these form calcium salts which break down to calcium carbonate. The aromatic amino-acids—tyrosin, phenylalanine, etc.—which would account for about 6 per cent. of the nitrogen of vegetable proteins, would be expected to give ammonia and phenolic substances. Now phenols are poisonous to plants and if no method existed for their removal the accumulation would ultimately render the soil sterile. Matters would be even worse on cultivated soils, since cows’ urine, which enters into the composition of farmyard manure and is the chief constituent of liquid manure, contains, according to Mooser, no less than 0·25 to 0·77 grams of p-cresol per litre,[I] a quantity three to ten times that present in human urine. Fortunately this contingency never arises, for the soil contains a remarkable set of organisms capable of decomposing the phenols and leaving the soil entirely suitable for plant growth. This affords an interesting case of an organism—in this case the plant—growing well in a medium in spite of some adverse condition, not because it is specially adapted to meet this condition, but because some wholly different agent removes it.

Other ring compounds, e.g. pyrrol, arise in smaller quantity in the decomposition of protein, but their fate in the soil is not known.

We may summarise the probable changes of the protein as follows:—

It must be admitted that the evidence is indirect. The rate of oxidation of ammonia by bacteria in the soil is more rapid than the rate of formation, so that ammonia is practically never found in the soil in more than minimal amounts (1 or 2 parts per 1,000,000); indeed, the only evidence of its formation was for a long time the fact that no compound other than ammonia could be oxidised by the nitrifying organism. It has, however, since been shown at Rothamsted that ammonia accumulates in soils in which the nitrifying organism has been killed.

Nothing is known of the mechanism of the oxidation of ammonia beyond the fact that it is biological; the reaction is not easily effected chemically at ordinary temperatures. Possibly the organism assimilates ammonia at one end of a chain of metabolic processes and excretes nitrates at the other. Or, the reaction may be simply a straight oxidation for energy purposes, the ammonia changing to hydroxylamine and then to nitrous and nitric acids.

The nitrate does not remain long in the soil. Some is taken up by the plant and some is washed out from the soil. Part, however, either of the nitrate itself or of one of its precursors is converted into an insoluble form: probably it is changed into protein by the action of micro-organisms; it then goes through the whole process once more.

These are the general outlines; they present no particular chemical difficulties. When we come to details, however, there is much that cannot be understood.

First of all, there is the slow rate at which complex nitrogen compounds disappear from the soil in comparison with the rate of oxidation of the carbon. Thus, in the original plant residues, there is some forty times as much carbon as nitrogen: before they have been long in the soil there is only ten times as much carbon as nitrogen; this seems to be the stable position. What is the reason for this preferential oxidation of the carbon? No explanation can yet be given.

An equally difficult problem arises in connection with the length of time the process will continue. Decomposition of the nitrogen compounds never seems to be complete in the soil; it dribbles on interminably. In the year 1870 Lawes and Gilbert cut off a block of soil from its surroundings and undermined it so that the drainage water could be collected and analysed. The soil has been kept free from vegetation or addition of nitrogen compounds from that time till now; yet it has never failed to yield nitrates, and the annual yield falls off only very slowly (Fig. 24). This same peculiarity is seen in the yield of crops on unmanured land: it decreases, but very gradually; even after eighty years the process is far from complete, and there is no sign that it will ever come to an end.

TABLE XVII.—APPROXIMATE LOSS OF NITROGEN FROM CULTIVATED SOILS: BROADBALK WHEAT FIELD, ROTHAMSTED, FORTY-NINE YEARS (1865-1914.)

A further remarkable fact connected with the decomposition of the nitrogen compounds is that it seems invariably to be accompanied by an evolution of gaseous nitrogen. Apparently there are two cases. Under anaerobic conditions many of the soil organisms have the power of obtaining their necessary oxygen from nitrates, thereby causing a change in the molecule which leads in some cases to liberation of gaseous nitrogen; but the same result seems to be attained in aerobic conditions, especially when carbon is being rapidly oxidised.

It is possible that the reaction is the same, and that in spite of the general aerobic conditions there is locally an anaerobic atmosphere. But it is also possible that some direct oxidation of protein or amino-acids may yield gaseous nitrogen. However it is brought about it affects a considerable proportion of the entire stock of nitrogen, and it becomes more serious as cultivation is intensified. Thus, on the Broadbalk plot receiving farmyard manure the loss is particularly heavy; on the unmanured plot it cannot be detected. The nitrogen balance-sheet is shown in Table XVII.

The oxidation of carbonaceous matter, however, is not invariably accompanied by a net loss of nitrogen; in other circumstances there is a net gain. In natural conditions there seems always to have been some leguminous vegetation growing; the gain may, therefore, be ascribed to the activity of the nodule organism. In pot experiments, however, it has been found possible, by adding sugar to the soil, to obtain gains of nitrogen where there is no leguminous vegetation, and this is attributed to the activity of Azotobacter.

The nitrogen cycle as observed in the soil is as follows:—

There has been but little study of the process of decomposition of the other compounds in plants. Part, if not all, of the sulphur is known to appear as sulphate, and some of the phosphorus as phosphate. It is certain that the plant constituents decompose, for there is no sign of their accumulation in the soil. They may exert transitory effects, but there is nothing to show permanent continuance. The toxic conditions which cause trouble in working with pure cultures of organisms in specific cultures media do not, so far as is known, arise in the soil. All attempts to find bacterio-toxins or plant toxins in normal soils have failed. The product toxic to one organism seems to be a useful nutrient to another, and so the mixed population keeps the soil healthy for all its members.

There is little precise knowledge as to the part played by the different members of the soil population in bringing about these changes.

We know in a general way that earthworms effect the distribution of the plant residues in the soil, and serve to disintegrate them; there is no evidence, however, that they play any indispensable part in the decomposition. Many root and other fragments do not go through this process; observation shows that fungi can force a way in, and they may be followed by nematodes which continue the disintegration. Possibly some of the flagellates help, and certainly the bacteria do. After that nothing is certain. We cannot, with certainty, assign any particular reaction in the decomposition to any specific organism, with the exception of the oxidation of the phenolic substances, the conversion of ammonia to nitrite and nitrate, and the fixation of nitrogen. With these exceptions many organisms seem capable of bringing about the reactions, and indeed some of the reactions may be purely chemical and independent of biological agencies.

The relationships between the soil population and soil fertility are readily stated in general outline, but they are by no means clear cut when one comes to details; fertility is a complex property, and some of its factors are independent of soil micro-organisms.

The general relationship between plants and soil organisms is one of complete mutual interdependence. The growing plant fixes the sun’s energy and converts it into a form utilisable by the soil organisms; without the plant they could not exist. The plant is equally dependent on the soil organisms in at least two directions: their scavenging action removes the dead vegetation which would, if accumulated on the surface of the soil, effectively prevent most plants from growing. Further, the plant is dependent on the soil population for supplies of nitrates. Nothing is known about the relative efficiencies of the various soil organisms as scavengers. Numerous fungi and bacteria are effective producers of ammonia, the precursor of nitrates; it is not known, however, whether flagellates and such higher forms as nematodes act in this way.

This widespread power of producing ammonia makes it impossible in our present knowledge to regard any particular group of organisms as par excellence promoters of fertility. Indeed, it is safest not to attempt to do so. The primary purpose of the activities of a soil organism is to obtain energy and cell material for itself; any benefit to the plant is purely incidental. For cell material it must have nitrogen and phosphorus; here it competes with the plant. If it produces more ammonia than it utilises—in other words, if it is driven to nitrogen compounds for its energy, then the plant benefits. If, on the other hand, it absorbs more ammonia than it produces, as happens when it derives its energy from non-nitrogenous substances, the plant suffers. Thus, addition of peptone to the soil or an increase in bacterial numbers effected without addition of external energy (e.g. by partial sterilisation) leads to increased ammonia supply, and, therefore, to increased fertility. But addition of sugar to the soil causes so great an increase of numbers of bacteria and other organisms that considerable absorption of ammonia and nitrate occurs, and fertility is for a time depressed.

Both actions proceed in soils partially sterilised by organic substances, such as phenol, which are utilised by some of the soil organisms; there is first a great rise in numbers of these particular organisms with a depression of ammonia and nitrate, then a drop to the new level, higher than the old one, and an increased production of ammonia and nitrate resulting from the partial sterilisation effects.

We must then regard the soil population as concerned entirely to maintain itself, and only incidently benefiting the plant, sometimes, indeed, injuring it; always essential, yet always taking its toll, and sometimes a heavy toll, of the plant nutrients it produces.

This effect makes it difficult to deduce simple quantitative relationships between bacterial activity and soil fertility, and the difficulty is increased by the fact that bacteria and plants may both be injured or benefited by the same causes, so that high bacterial numbers in a fertile soil would not necessarily be the cause, but might be simply the result of fertility.

The circumstance that certain soil organisms—bacteria, algæ, and fungi—themselves assimilate ammonia and nitrate may account for the remarkable slowness of nitrate accumulation, to which reference has already been made. The protein formed from the assimilated nitrogen remains in the bodies of the organisms, living or dead, till decomposition sets in. It is not difficult to picture a cycle of events in which much of the nitrate formed is at once reabsorbed by other organisms, and only little is actually thrown off into the soil. Such a process might continue almost interminably so long as any carbonaceous material remained.

Finally, we come to the very interesting problem—is it possible to control the population of the soil?

The problem may seem superfluous in view of the difficulties just mentioned. Some aspects of it, however, are fairly clearly defined.

In the first instance, some organisms appear to be wholly harmful to the plant; among them are parasitic eelworms and fungi, and bacteria causing disease.

Control of these organisms can be brought about by partial sterilisation, and of all methods heat is the most effective, but it is costly, and attempts are now being made to replace it by chemical treatment. The results are promising, but the investigation is laborious; the organisms show specific relationships, and in finding a sufficiently potent and convenient poison it is necessary in each case to make an investigation into the relationship between chemical constitution and toxicity to the particular organism concerned. Formaldehyde is usually potent against fungi, and the cresols, and particularly their chlor- and chloronitro-derivatives, are potent against animals (eelworms, etc.).

One group of organisms is wholly beneficial, those associated with leguminous plants. Attempts have been made to increase their activities by inoculating the soil with more vigorous strains. The practical difficulties still remain very considerable, but there is hope that they may be overcome.

It is also possible to shift the balance of the soil population in certain directions. Special groups of soil organisms can be caused to multiply temporarily, if not permanently, by satisfying their particular requirements. Thus, when a soil has been heated above 100° C. it becomes specially suited to the growth of fungi, and quite unsuited to certain bacteria such as the nitrifying organisms and others; if this heated soil is infected with a normal soil population the fungi develop to a remarkable extent. The nodule organisms appear to be stimulated by addition of farmyard manure and of phosphates, and the phenol-destroying organisms by successive small additions of phenol.

Finally, quite apart from the control of disease organisms, it is possible to alter the soil population considerably by partial sterilisation, using a temperature of only about 60° C., or a poison like toluene that favours few of the soil organisms. This problem has already been discussed in Chapter I.

The control of the soil population is still only in its infancy, but it already promises useful developments. It cannot, however, be too strongly insisted that the only sure basis of control is knowledge, and we cannot hope to push control further till we have learned much more about the soil population than we know at present.