411. Introductory Considerations.—The estimation of oxidized nitrogen in the soil would properly find a place in the preceding part; but on account of the late progress in our knowledge of the source of this indispensable and costly plant food it has become necessary to give it especial attention. The present part will, therefore, be devoted to a brief statement of our present knowledge in respect of the origin of oxidized nitrogen, a description of the nitrifying ferments and methods for their isolation and determination and finally the most approved methods of estimating the ammonia, nitrous, and nitric acids formed thereby both in the soil and the waters pertaining thereto or proceeding therefrom. It is scarcely necessary to caution the reader not to consider this part in any sense a treatise on the bacteria active in soil chemistry. Its object is rather to place in the hands of the soil analyst data which will enable him to intelligently study the soil phenomena depending on these organisms and to determine the extent and character of their biological and chemical functions. These are matters which, up to the present time, have found no place in manuals dedicated to agricultural analysis.

412. Organic Nitrogen in the Soil.—With the exception of the small quantities of nitric acid added to the soil directly by rain water, the whole of the supply of this substance is derived from the products of the oxidation of nitrogenous bodies. These products are either stored as the results of past nitrification or are formed synchronously with their consumption by the growing plant. Nitrogenous compounds are present as organic vegetable or animal remains and as humus. All vegetable and animal material deposited in or on the soil contains more or less of these proteid or nitrogenous matters while the amount of nitric acid supplied in this way is probably represented entirely by the quantity in the organism of the plant or animal and unabsorbed at the time of its death. In other words it is not demonstrated that nitrates or nitrites are in any sense a special product of plant growth save in the case of nitrifying organisms themselves which are supposed to be of a vegetable nature. Animal organisms do not in any sense assimilate nitric nitrogen.

With most plants, the quantity of proteid nitrogen which they can deliver to the soil is in no case greater than the sum of organic and nitric nitrogen supplied in their food and they can therefore be regarded only as the carriers and conservers of this substance. On the other hand there are some plants notably those belonging to the leguminous family which permit of the development on their rootlets of colonies of bacteria which have the faculty of rendering atmospheric nitrogen available for plant growth. Whether or not there exist plants other than the micro-organisms mentioned which are capable of directly oxidizing and fixing atmospheric nitrogen is still an unanswered question. It is not probable, however, that the difficult task of oxidizing atmospheric or free nitrogen would be accomplished in nature in only one way. In fact it has already been established that organisms do exist which are capable of oxidizing free nitrogen in a manner wholly independent of other plant life and to produce weighable quantities of nitric acid when developed in media of mineral matters and pure carbohydrates to which free nitrogen has access. It is, therefore, fair to assume that the fixation of free nitrogen is a function of chemical activity quite independent of ordinary plant life and that the leguminous plants take no further part in this process than that of providing in their radical development a favorable nidus for the growth of the nitrifying organism.

By the action of denitrifying organisms a portion of the nitrogen of nitric acid is constantly restored to a free state, a far larger portion, perhaps, than is fixed in the atmosphere itself by the action of electricity. Were it not, therefore, for the activity of the nitrifying ferments the stores of nitrogen available for growing plants would constantly become less. Instead of this being the case, however, it is probable that the contrary is true and that, by a wise system of agriculture, the total nitrogen at the disposal of plants may become greater and greater in quantity.

413. Development of Nitric and Nitrous Acids in Soils.—Owing to the solubility of nitrates there can be but little accumulation of them in soils in those countries where there is any considerable amount of rain-fall. On the other hand in arid regions there may be found extensive deposits of nitrates. The occurrence of a certain quantity of nitrates in the soil, however, is essential to the growth of plants. Until within a few years little was known of the origin of nitric acid in the soil. The presence of nitrates in drainage waters was well established, likewise the consumption of nitric acid by the growing plant, but the method of its supply was unknown. In a general way it was said that the nitric acid came from electrical action and the oxidation of the albuminous bodies in the soil, but without specifying the manner in which this change takes place. The researches of Schloesing and Müntz, of Springer, Winogradsky, Frankland, Warington and others have demonstrated the fact that this oxidation is caused by means of bacteria and that the nitrates formed can be consumed and destroyed by other species of this organism. In the one case the process has been called nitrification and in the other denitrification.^[274]

The influence of these low organisms both in producing fertility in a soil and maintaining it in a state of fertility is of the highest importance.

414. Conditions Necessary for Nitrification.—In order to properly understand the reasons for many of the steps in investigating a soil for nitrifying organisms, it will be useful to state the general conditions on which nitrification depends.

The nitrifying organism, like every other one, first of all feels the necessity for food. In general, food which is given to microbes of all kinds consists of some organic matter together with the addition of mineral substances necessary to growth. These substances in general are phosphoric acid, potash, and lime. Of these articles of bacterial food phosphoric acid seems to be the most important. With the nitrifying organisms, however, it has been found that the organic matter can be omitted. In fact, as will be seen further on, the omission of organic matter supplies the best condition for the proper isolation of the organisms. In other words some forms of the nitrifying organisms have the property of subsisting wholly on mineral substances, i. e., are true vegetables.

The presence of oxygen is also necessary to the growth of the common nitro-organisms. In an atmosphere deprived of oxygen or in which the oxygen is reduced to a very low percentage, the process of nitrification is retarded or stopped as the oxygen diminishes or disappears.

The presence of a base with which the nitrous or nitric acid formed may unite is also essential to the proper conduct of the process. For this reason the nitrification should take place in a solution which is feebly alkaline or in the presence of a base which can be easily decomposed so that no acidity can take place. Calcium carbonate is a base well suited to favor the nitrifying process and its presence in a soil favors the rapid oxidation of proteid matter. The mistake must not be made, however, of supposing that an excess of alkali would favor nitrification. The contrary is true. A slight excess of alkali may prevent nitrification altogether when it is due to the common organisms present in an arable soil. It may be that in soils charged with alkali a different organism exists which is capable of exercising its functions when the alkali is in excess.

The temperature to which the nitrifying body is subjected is also a matter of importance. The nitrifying organisms have the property of remaining active at lower temperatures than most bodies of their class. On the contrary their action is retarded and destroyed by high temperatures. The most favorable temperature for nitrification is about that of blood heat; viz., 37°. At 50° the organism shows very little activity and at 55° its activity ceases altogether. Nitrification, however, according to Warington, cannot be started in a solution if the initial temperature is 40°.

Desiccation has the same retarding influence on nitrification that a high temperature has. Even thoroughly air-drying a soil may destroy its nitrifying qualities.

Darkness is also necessary to the proper progress of nitrification. In a strong light, the activity of the organism is very much diminished or destroyed altogether. A bright light like sunshine may even stop nitrification which has set in.

415. Effect of Potassium Salts on Rate of Nitrification.—Dumont and Crochetelle have described some experiments to determine the effect of potassium salts alone and in combination with lime on nitrification.^[275]

Soil rich in vegetable mold (18.5 per cent of humus and 0.29 per cent of lime) was treated with varying amounts of potassium sulfate and carbonate and kept for twenty days at 25°. In the untreated soil the amount of nitric acid produced was twenty-five parts per million. When potassium carbonate was applied in quantities of from one-tenth to six per cent the amount of nitric acid increased from forty-seven parts per million to 438 parts when four and one-half per cent of the potassium salt were used. Larger quantities caused a decrease in the amount of nitric acid produced. Very little effect, on the contrary, was produced by the action of potassium sulfate. When one-half per cent was employed the quantity of nitric acid formed rose to fifty parts per million, while with quantities as high as five per cent it fell below the normal; viz., twenty-five parts per million.

When calcium carbonate was added to the soil in conjunction with potassium sulfate there was a marked increase in the amount of nitrogen oxidized. The activity of potassium sulfate in promoting nitrification is therefore increased by the presence of the calcium salt, potassium carbonate and calcium sulfate being formed.

416. Production of Nitrous and Nitric Acids.—In the following pages the study of the methods of isolating the nitrous and nitric ferments will be considered as one process, the final isolation of the two classes of bodies being the result of their synchronous cultivation in appropriate media. The special process of the production of ammonia by oxidation is not so well-known, and will therefore be described in brief.

It is now generally conceded that the action of the nitrous organism is precedent to that of the nitric, but the two processes go on so nearly together as to prevent the accumulation of any large quantities of the lower salt in the soil.

Whether or not the formation of ammonia precedes that of nitrous acid is still a subject for experimental demonstration. Chemically, both nitrous acid and ammonia may be produced by the reduction of nitric acid. In nature, the reverse of this process may be the customary method.

417. Production of Ammonia in the Soil by the Action of Microbes.—It is highly probable that organic nitrogen in the soil in passing into the form of nitric acid exists at some period of the process in the form of ammonia.

Marchal has isolated and studied some of these ammonia-making bacteria.^[276] Bacillus mycoides is the most active of these organisms. It occurs constantly in surface soils and is present in the air and in natural waters. In decomposing albumen it produces a strongly alkaline solution due to ammonium carbonate. Organic carbon, during this process, is converted chiefly into carbon dioxid, but small quantities of formic, propionic, and butyric acids are also produced. Any organic sulfur which is present is converted into acid. No hydrogen or nitrogen is eliminated in a free state. While slight alkalinity is favorable to the development of this bacterium, yet it may be propagated in a feeble sulfuric acid solution when the acid is less than one per cent.

The greatest activity of this organism is manifested at 30°. Below 5° and above 42° no ammonia is produced. The bacillus will not develop in an atmosphere of hydrogen or carbon dioxid, except in solutions of organic matter and nitrate. In addition to its action on egg albumen it decomposes other proteid bodies as well as leucin, tyrosin, creatin, and asparagin. It, however, does not oxidize urea, nor does it develop in solutions of ammonium salts and nitrates, except as mentioned above. When soluble carbohydrates are present, acids are formed. It is concluded from these experiments that the final oxidation of organic nitrogenous matter is preceded by its conversion into ammonium carbonate.

418. Summary of Statements.—All nitrogenous matters which would be naturally present in the soil may become subject to nitrification when the proper conditions are supplied. Munro has also succeeded in nitrifying ethylamin, thiocyanates, and gelatin, urea, asparagin, and the albuminoids of milk and rapeseed.

The products of nitrification are ammonia, nitrous or nitric acid, carbon dioxid, and water. The ammonia and nitrous acid may not appear in soils as the final products of nitrification, as the nitric organism attacks the latter at once and converts it into nitric acid. Nitrous acid and ammonia may also be produced in soils as one of the retrograde steps in denitrification.

To summarize the conditions necessary for nitrification it may be said that first, the proper material must be supplied; viz., an organic or inorganic nitrogenous compound capable of oxidation. In the second place, the medium must be faintly alkaline, the temperature must not be too high, the nitrifying organisms must have abundant food, and the process must take place in the dark.

419. Order of Oxidation.—It is quite definitely determined that activity of the ammoniacal and nitrous organisms is the first step in the process, since the nitric organism appears to have no power whatever to oxidize proteid compounds; while, on the other hand, the nitrous organism can not, in any case, complete the conversion of nitrous into nitric acid.

The conditions which permit certain organisms to oxidize free nitrogen have not been definitely determined. The presence of such bodies in the tubercles attached to the rootlets of certain leguminous plants has been established. Lately, Winogradsky has isolated from the soil a nitrifying organism which is capable of converting free nitrogen into forms suited to nourish plant growth. This organism is cultivated in dextrose with careful exclusion of all nitrogen, save that which exists in the air carefully freed of every trace of ammonia or oxidized nitrogen.

Under the influence of the growth of this organism the sugar undergoes a butyric fermentation, and nitrogen in an oxidized form is assimilated in an amount apparently equal to about one five-hundredth of the sugar consumed.

This result leads Warington^[277] to remark that it is a fact of extraordinary interest, both to the physiologist and chemist, that a vegetable organism should be able to acquire from the air all the nitrogen it needs.

420. The Nitrification of Ammonia.—The same organism which converts organic nitrogen into nitrous acid acts also on ammonia and its compounds with a similar result. In fact, the formation of ammonia may be regarded as one of the stages on the road from albuminoid to nitric nitrogen.

Data have been collected by Schloesing on the nitrification of ammonia taking place in arable soil, tending to show that this phenomenon is accomplished without appreciable loss of nitrogen in the gaseous state.^[278] This, however, does not hold good when the quantity of ammonium carbonate introduced into the earth is largely increased. In two experiments, conducted by Schloesing, with a larger quantity of ammonium carbonate, the loss of nitrogen was very notable. In certain conditions the production of nitrous acid may take place, and it is interesting to know whether the appearance of nitrites has any influence on the disengagement of free nitrogen. In order to determine this question a solution of calcium nitrite was prepared by decomposing silver nitrite with calcium chlorid. From the results of the experiments made it was seen that the nitrites were only the results of a retarded and partially incomplete nitrification. They are, moreover, thus an obstacle to the normal work of the nitrifying organisms. It is also established that when they are present a disengagement of gaseous nitrogen takes place, whether the nitrites are formed during the progress of the experiment, or whether they were originally present. However, it is not best to say that the nitrites themselves have been the cause of the disengagement of the nitrogen. It may happen that the disengagement of the nitrogen and the presence of nitrites are simply simultaneous and due to one and the same cause. The destruction of nitrates in the midst of reducing agents furnishes, according to the nature of these bodies and the circumstances, nitrous acid, nitrogen dioxid, nitrogen protoxid, free nitrogen, and even ammonia.

This destruction of nitrates and the appearance of oxids of nitrogen and of free nitrogen are more likely to be due to the presence of a separate denitrifying ferment as pointed out by Springer than to have arisen in the manner mentioned above by Schloesing. In the present state of our knowledge, moreover, we can hardly regard the presence of nitrites as an obstacle to complete nitrification. On the other hand, it seems to be well established that the production of nitrites or ammonia is a necessary step between organic nitrogen and nitric acid.

421. Occurrence of Nitrifying Organisms.—According to the observations of Schloesing and Müntz the nitrifying organisms are widely distributed.^[279] Arable soil containing considerable humus seems to be the medium in which they grow most freely and in which they accomplish their most important functions. Sewage waters are also rich in nitrifying ferments, and, in fact, all waters containing organic matter. They are also found in running waters but not in great numbers. They affect chiefly the surface of bodies, and especially are found on the bottom of culture-flasks.

These authors have not found the nitrifying organisms in normal air. They could not seed sterilized flasks by admitting air freely. The absence of these ferments from the air is explained by reason of their sensitiveness to desiccation.

The method used by Schloesing and Müntz for the separation of the organism consisted in the preparation of original and subcultures in sterilized solutions containing nitrifiable matters. The proof of isolation was assumed when a given subculture contained only one kind of organism as seen with the microscope. The appearance of this organism, as described by the authors, was that of the later isolations by Warington and Winogradsky, but the method used could hardly now be regarded as decisive.

422. Determination of Nitrifying Power of Soils.—In studying the distribution of the nitrifying organisms in a soil the general method of procedure is based on the production of nitrification in a convenient solution by the organisms present in a given sample of soil. If the solution seeded with the given portion of soil remain unaffected, it will show that there were no nitrifying organisms present in the seed used. On the other hand, the vigor of the nitrifying process when once it is started, may be taken as an evidence of the number and activity of the organisms in the soil, a sample of which was used for seed.

423. Composition of the Culture Medium.—The solution recommended by Warington for the culture and isolation of the nitrifying ferments has the following composition:

424. Apparatus and Manipulation.—The experiments are conducted in short, wide-mouthed bottles. The initial volume of the solution in each bottle is 100 cubic centimeters, and the bottle should be of such size as to give a depth of liquid of from three to five centimeters.

The neck of the bottle is closed with a plug of cotton and this is protected from dust by tying over it a cap of filter paper. Arranged in this way, filtered air has free access to the solution. The bottle with the solution thus protected is placed in a water-oven and kept near the temperature of boiling water for six to eight hours to destroy any organisms present. When cool, the solution is ready for use.

The calcium carbonate used should be prepared by precipitation and added in a moist state. The calcium carbonate solution should be added after the sterilization of the liquid, the precipitated carbonate being boiled just before it is added.

Preparation of Seed.—The seed employed to start the nitrification should be a small quantity of fresh soil, usually about one-tenth of a gram. If a previously nitrified solution be used for seed it should be thoroughly shaken and about one cubic centimeter of the solution removed for seeding the new bottle.

In introducing the nitrifying liquor into the bottle the plug should be lifted slightly and a small pipette inserted by means of which the liquor is added. The operation should be carried on in a room perfectly free from dust and to which no one but the operator has access. The greatest care should be exercised to prevent any particles of matter entering the solution except that which is purposely added. In withdrawing the liquor from the nitrifying solution cotton wool should be pressed around the top of the pipette so that the entering air may be filtered before admission to the interior of the bottle. The pipette which is used should be kept in boiling water until it is required for use. After use it should be washed and replaced in boiling water until again required.

After seeding, the bottles should be placed in a dark cupboard and exposed to the ordinary temperature of the laboratory. If a higher or stated temperature be desired, the bottle should be placed in a metal box the temperature of which can be regulated to any degree.

Test of the Commencement of Nitrification.—The beginning of the nitrification can be determined in a solution by testing it with diphenylamin. One cubic centimeter of the solution withdrawn as above indicated, is placed in a small beaker, a drop of solution of diphenylamin sulfate in sulfuric acid added, and then two cubic centimeters of concentrated sulfuric acid and the contents of the beaker well shaken. The development of a violet-blue color shows the presence of nitric or nitrous acid. This test will detect one part of nitric nitrogen in twenty million of water.

Determining the Progress of Nitrification.—The progress of nitrification is determined by repeated examinations for ammonia by nesslerizing, and for nitrous acid with metaphenylenediamin. Each experiment is made with five cubic centimeters of the solution withdrawn as above indicated and placed in test-tubes, always of the same size. The reaction with the nessler solution is then made by adding it in the usual way. The colorations are recorded as, trace, small, moderate, considerable, large, and abundant.

If the change produced by the organism consisted in the formation of nitrites only, the ammonia in the original solution would fall from large to trace, while the nitrous acid would increase from trace to large. If the nitrification consisted in the production of nitrates only, the ammonia would diminish without any corresponding production of nitrous acid. In mother solutions which contain ammonium carbonate instead of sulfate, it should not be forgotten that the ammonia might gradually disappear owing to the volatilization of the carbonate without any corresponding production of free nitrites or nitrates. The complete disappearance of the ammonia in the above experiments shows the completion of the process.

425. To Determine the Distribution of the Nitrifying Organism in the Soil.—The principle on which the determination of the distribution of the nitrifying organism in the soil depends, rests upon seeding the growth solutions with samples of soil taken at different depths and carefully protected from the time of sampling until the time of seeding from any admixture of accidental organisms.

The method of Warington is the simplest and best to follow.^[280] The samples of soil are taken by digging a pit of convenient depth usually from eight to ten feet. A fresh surface is then cut on one of the sides of the pit at the spot selected for sampling. This surface is scraped with a freshly ignited platinum spatula. The spatula should then be washed, re-ignited, and cooled, and a small portion of the soil, at the depth required, detached with the spatula and transferred at once into one of the growth bottles already described.

The growth solution best suited for the purpose contains four cubic centimeters of urine per liter. Each bottle should also contain some freshly precipitated calcium carbonate. In sterilizing urine solutions the calcium carbonate should be added before the heating instead of afterwards. The quantity of soil taken for each seeding should be about one-tenth of a gram.

Inasmuch as the cotton stopper has to be lifted to introduce the soil, opportunity is given for the entrance of any organisms floating in the air. Experience, however, has shown that air free from soil dust very seldom contains nitrifying organisms. The seeded bottles are placed in a dark cupboard of moderate temperature as already described.

426. Sterilized Urine Solution.—The sterilized urine solution used for the determination of the distribution of the nitrifying organisms in the soil, is made by taking four cubic centimeters of healthy urine, diluting to one liter, adding some freshly precipitated calcium carbonate, stoppering with cotton wool and heating for several hours at the boiling temperature of water.

As a result of Warington’s experiments it was shown that the nitrifying organism in the soil did not exist, at least in portions of one-tenth of a gram, to a greater depth than eighteen inches. In only one case was nitrification produced from a sample of soil taken at a greater depth and this may have been due to the accidental introduction of organisms from other sources. It may be assumed that any long delay in the commencement of nitrification under favorable conditions, implies the presence of a very limited quantity of organisms in the solution. Thus a comparative study of the period of incubation and the progress of nitrification in solutions seeded with soils taken at different depths or at different places, becomes a fair index of the number and vitality of the nitrifying organisms contained therein.

427. Depth to Which Micro-Organisms are Found.—Koch states that at the depth of about one meter, the soil is nearly free from every kind of bacteria.^[281] These observations have been corroborated by Pumpelly and Smyth who find that no infection of a bacterial nature is produced in a sterilized solution from samples of clay taken at the depth of nine feet below the surface.^[282]

It is evident from the nature of the experiments above described that the nitrifying processes go on almost exclusively in those portions of the soil which are subject to cultivation, while in the subsoil and below the processes of nitrification are either retarded or arrested. Any stores of nitrogenous matter, therefore, in an insoluble state, resting in the subsoil, are preserved from oxidation and consequent waste until such time as they may be removed to near the surface.

428. Isolation of the Nitrous and Nitric Organisms in the Soil.—The action of the organisms which produce nitrification either in form of nitrites or nitrates, having been thoroughly established, and the method of testing the soil therefor given, it remains to describe a method by means of which these organisms in the soil may be isolated and obtained in a state of purity. The difficulties attending this process are extremely great on account of the similarity of the two organisms. All earlier attempts to make pure cultures of the two separate organisms were attended with but little success.

According to Winogradsky the method of culture on gelatin so long practiced is not to be relied upon.^[283] It is very difficult to eliminate by this process the organisms which grow rapidly in gelatin and which mature their colonies in two or three days, but where they require eight or ten days to produce a colony the method is successful. In fact, by the gelatin process as it was at first practiced, a good deal was owing to chance, but sometimes by a happy accident a pure nitro-bacterium might be isolated.

Formerly it was considered that a liquid could be regarded as sterile if it gave no growth upon gelatin. It has, however, now been demonstrated that a liquid may contain large numbers of nitro-bacteria and still produce no growth upon gelatin. However, for the organisms which accompany the nitro-bacteria in soils, it is regarded as certain that if no growth on gelatin is produced by them they are absent. Therefore in the case of a solution which has been seeded with a soil, if it can be brought to such a state as to produce no growth on gelatin, it may be safely assumed that it contains no bacterial organisms save those which are capable of producing nitrites or nitrates. Therefore if such a solution produce nitrification and at the same time no growth upon gelatin, it may be considered as a proof of the isolation of the nitro-organisms from all others.

This method was also worked out independently by Mr. and Mrs. Frankland.^[284]

Winogradsky says further he confesses that he has advanced these views only provisionally and without being convinced of their infallibility. Strictly speaking, the proof of seeding gelatin is not sufficient alone because the absence of growth can not be regarded as the exclusive privilege of the nitro-bacteria. Such might be the case sometimes for an accidental mixture of microbes, introduced with any given sample of soil into the cultures, but the criterion is not absolute. Microbes, for example, of a sulfurous or ferruginous nature may be cited, for which the gelatin layer is not only unfavorable but even fatal. It may thus happen that there may be eliminated from the solution all that will grow upon gelatin without freeing it from some special kinds of cultures, refractory like the nitro-bacteria, but which might reappear if they should be resown in some favorable nutritive solution. On account of this fault in the process, Winogradsky has been impressed with the necessity of bringing out a better method.

In using the gelatin media it is necessary to find the one that is suited to nourish these organisms, which would evidently be the way promising the greatest success. This having been found, and those organisms which produce colonies being easily recognizable, a great step towards the solution of the problem will have been made and the more so as the medium would be at the same time absolutely unfavorable to other forms of microbes. On account of the slow degree of development of the nitro-organisms, all others would probably have opportunity to grow and strengthen to their exclusion, unless these interfering organisms could be completely removed.

429. The Culture Solution.—The culture-solution, first proposed by Winogradsky, had the following composition:

To ten grams of gelatin or one part of agar-agar in 100 cubic centimeters of water add potassium phosphate, one-tenth of a gram; magnesium sulfate, five-hundredths of a gram; calcium chlorid, trace; and sodium carbonate, half a gram. The solution being sterilized in the usual way by heating, there are added to it a few cubic centimeters of a sterilized solution containing two-tenths per cent of ammonium sulfate. Such a solution has been proved to be very favorable to nitro-organisms. Nevertheless the experiments with such solutions gave no definite results and they were abandoned.

The non-success of this method led Winogradsky to adopt a nitrifying solution which absolutely excluded all organic substances. Instead of using an animal or vegetable gelatinous substance he used one of a mineral nature, first proposed by Graham and Kühne.^[285] Two of these gelatinous mineral substances were considered; viz., the aluminum hydroxid and the hydrate of silica. The latter was chosen.

430. Preparation of the Mineral Gelatinous Solution.—The soluble glass which is found in commerce is generally of a thick, sirupy consistence. It is first diluted with three times its volume of water. One hundred cubic centimeters of this liquid are poured with constant stirring into fifty cubic centimeters of dilute hydrochloric acid and the mixture placed in a dialyzer. It is useless to employ a standard solution of silica. All that is necessary is to submit to dialysis a liquid with an excess of acid and sufficiently dilute not to be exposed to the danger of being spontaneously gelatinized in the dialyzer. The dialyzer is left for one day in running water and two days in distilled water, often renewed. The solution is then ready for use. This is the case when it is no longer rendered turbid on the addition of silver nitrate, showing that the hydrochloric acid has been entirely extracted. The solution is then to be sterilized by boiling, and preserved in a glass flask closed with a plug of cotton.

More recent instructions by Winogradsky for preparing the gelatinous silica recommend dialyzing the soluble glass after treatment with hydrochloric acid in a parchment tube.^[286] The proportions of silicate and acid are 100 cubic centimeters of the silicate solution (1.06 specific gravity) and 100 cubic centimeters of hydrochloric acid (1.1 specific gravity). With a dialyzing tube placed two days in running water and one day in distilled water frequently changed it will be found that the acid is completely removed. One hundred cubic centimeters of the residual liquor giving no reaction for hydrochloric acid are concentrated to twenty cubic centimeters. When cold there is added one cubic centimeter each of a solution of ammonium sulfate and of sodium carbonate, together with corresponding quantities of the other nutrient salts commonly employed. The ammonium sulfate should never exceed two to two and a half, and the sodium carbonate four parts per thousand. To the flask containing the above substances is added one drop of the seed-liquor, which may be a soil water or a drop from some previous culture. The flask is shaken and the mixture poured into a low circular glass dish which is covered by one slightly larger in diameter (Petri double dish). To the liquid in the dish is added a drop of a cold saturated solution of common salt, and it is then stirred with a platinum spatula. The addition of the salt greatly favors the setting of the jelly. The jelly may set in from two to three hours, but a longer time secures better results in the end.

In employing these preparations as seed, after the organisms have grown, it is absolutely necessary to use the isolated cellules and not the aggregated masses (zoöglœæ). The latter are rarely free of foreign germs which adhere to their gelatinous envelope. Since the zoöglœæ can not be broken up by any artificial means it is necessary to await their spontaneous disintegration in order to separate the mobile monads. The opalescence of the culture-liquid is a sure index of this separation.

The particles of mineral gelatin to be used as seed for nitrifying are best taken as follows:

A glass tube is drawn out immediately preceding the operation, until the end is as fine as a hair. The surface of the mineral gelatin is magnified by means of a dissecting microscope magnifying 80 to 100, to the proper degree and the preparation table is so arranged as to give a perfect support to the right hand which should hold the filament of glass. The smallest colony is then pricked with the needle and the end of the glass is broken and dropped into the flask which is to be seeded. The seed is thus selected in as small a particle as may be desired, only a few cells, but it can always be ascertained with certainty that some of the particles have been obtained by this operation.

The method of cultivation on mineral jelly is considered by Winogradsky an important resource in the study of the nitrifying organisms. It removes the chief difficulties heretofore existing in discovering and characterizing these organisms among the innumerable micro-organisms of the soil. The long series of cultures necessary to separate the organisms are rendered nugatory. By directly introducing a little of the earth into the silicic jelly the active organisms in nitrification can be at once discovered. It is preferable, however, as indicated below, to previously produce a nitrification in an aqueous solution by a trace of earth and to take from it the seed for impregnating the solid medium. In order to show at once a proof of its nitrifying character, it is only necessary to take a small bit of the mineral jelly, the size of a grain of rye, and to throw it into a little sulfuric acid which has been treated with diphenylamin. There is at once formed a blue spot equal in intensity to a saturated solution of anilin blue.

In regard to the growths which nitro-organisms make in a medium of the kind described, they are far from being so marked as are those produced by ordinary micro-organisms.

A nitro-bacterium is not capable of the energy of growth which is recognized for the greater number of microbes. The colonies contained in the gelatin always remain small. The largest among them are just visible to the naked eye like white points. Along the striae, on the contrary, there is formed quite a thick white crust. To the naked eye, in general, there is nothing very characteristic in the formation of colonies in a medium of this nature. But this impression changes altogether when the placques are examined with a low magnifying power. The colonies, especially those of the interior surface, reveal then an aspect so curious as to be well remembered when once seen.

This mineral gelatin, as has already been noticed, is very unfavorable to the growth of microbes other than nitro-bacteria and becomes altered only under the action of the air. If the placques be carefully preserved from desiccation the culture of these organisms can be continued for several weeks. Although they do not seem to increase, the colonies, as well as the jelly, are still in a good condition at the end of that time. Nevertheless the expectation that this medium would prevent the formation of any foreign organism has not been realized. Some of the organisms which accompany the nitro-bacteria in soil, also grow upon the silicic jelly; but they do not form colonies, properly so-called, and their growth is extremely slow. They generally make their appearance before the nitro-bacteria and spread exclusively upon the surface in form of white spots, so transparent that without careful examination they would not be discovered. Having reached a certain size the spots do not change during entire weeks. This circumstance renders the operations of isolation somewhat delicate, but does not prevent them.

431. Preparation and Treatment of the Solution to be Nitrified.—The organisms having been grown on the siliceous gelatin in the manner described they are tested for their nitrifying power as follows:

The mineral solution which is to be nitrified with the above preparation is composed of ammonium sulfate, four-tenths gram; magnesium sulfate, half a gram; potassium phosphate, one-tenth gram; calcium chlorid, trace; sodium carbonate, six-tenths to nine-tenths gram; and distilled water, 100 cubic centimeters. The sulfates with the calcium chlorid on the one hand, and the phosphate and carbonate on the other, are dissolved separately and the two solutions sterilized separately and mixed after cooling. The seeding is then done as described above.

432. Isolation of the Nitrous and Nitric Organisms.—Instead of proceeding immediately to the isolation of special organisms in the soil, the preliminary period of purification is prolonged by Winogradsky by allowing the free growth to take place of all the organisms which can be maintained in the ordinary medium.^[287]

The composition of the culture solution employed is as follows: Distilled water, 1,000 parts; potassium phosphate, one part; magnesium sulfate, half a part; calcium chlorid, trace. Each flask receives besides this some magnesium carbonate, freshly washed with boiling water and added in slight excess.

The flasks thus charged are sterilized, and after sterilization there are added two cubic centimeters of a solution of two per cent of ammonium sulfate, which, when added to fifteen or twenty cubic centimeters of liquid give from two to two and a half parts per thousand.

They are then seeded with soil. The reasons for this preliminary treatment are as follows: First, all the observations upon the enfeeblement of the oxidizing power of these organisms have been made upon cultures seeded simply by the fresh soil, and in cultures derived therefrom. In the second place, the existence of the two forms, one nitrous and the other nitric, prevents at once the isolation of a single organism.

Samples of soil from Europe, Africa, Asia, Australia, and America, were used for seed for the experiments. First, the cultures were made by seeding with a small quantity of each of these samples of soil, and each one of these cultures served as a point of departure for a series of subcultures. The temperature of the cultures should be kept constantly at 30°.

The method of following the nitrification adopted by Winogradsky is essentially that of Warington, the percentage of ammonia remaining at any time being determined by nesslerizing. To detect the presence of nitric acid the nitrous acid is decomposed by boiling with ammonium chlorid in excess, or with urea, and then diphenylamin is used as a reagent. By treatment with ammonium chlorid and boiling, the ammonium nitrite is resolved into free nitrogen and water as indicated by the equation NH₄NO₂ = N₂ + 2H₂O. Or the total oxidized nitrogen may be estimated by the Schloesing method or by any of the standard methods hereafter given. The nitrous acid is then determined by potassium permanganate and the nitric acid by difference.

A great difference is to be noted between freshly taken earth and that which has been kept for a long while, especially when sealed. With fresh earth taken near the surface a mere trace is sufficient to produce nitrification. With samples of earth which have been kept for a long while and thoroughly dried, several grams must be added in order to secure perfect nitrification. The period of incubation with the samples of earth ranges from three to twenty days. The beginning of the phenomenon is revealed by the appearance of nitrous acid, of which the quantity is increased very rapidly, but in the end it disappears and is transformed into nitric acid.

433. Statement of the Results.—The method of stating the results of examination of soils for nitrifying organisms is illustrated by the following example:

Soil from Zurich. The culture was seeded on the 11th of October, one gram of soil being taken. On the 20th of October the nitrous acid had reached its maximum of intensity and there was no ammonia left. On the 29th of October the nitrous acid remained almost stationary and there was hardly any nitric acid present. On the 1st of November the reaction for nitrous acid began to decrease. On the 5th of November the reaction for nitric acid was very intense. On the 11th of November the nitrous acid had all disappeared except a mere trace.

The above order of phenomena was observed with all the samples of soil tried, from which it is concluded with certainty that nitrifying organisms transplanted directly from their natural medium in the soil into a liquid easily nitrifiable produce at once nitrous acid in abundance. The phenomenon of nitrification is divided into two periods therefore, of which the first is devoted to the production of nitrites, and the second consists in the oxidation of the nitrites, and this does not commence until the total disappearance of the ammonia. Occasionally the formation and oxidation of the nitrites practically go on together, but never equally, the oxidation of the nitrites being always sensibly behind their formation.

434. Method for Subcultures.—From the mother cultures described above, Winogradsky makes subcultures as follows:

The solution to be nitrified is prepared as in the mother cultures. The seeding is accomplished by adding a small quantity of the liquor of the mother culture after shaking. Subcultures can be made in this way to the seventh generation.

In respect of the oxidation of the nitrites the results may be entered as negative if they have not disappeared at the end of two months.

To determine whether the process of oxidizing the nitrites is in progress or not the total nitrous acid is estimated, and the process repeated at the end of eight or ten days. Should there be no diminution of the nitrous acid within this time it may be considered that the further oxidizing action is not taking place.

435. Use of a Solid Medium.—It may be justly claimed that the action of nitrifying organisms in a liquid is not to be compared with their action in a solid medium, such as a soil which is their natural habitat. It might be, therefore, that the inability of the nitrous organism to produce nitrates is due to the nature of the medium in which it is cultivated. Winogradsky in order to determine this question cultivated the organism in a solid medium of two kinds, first a silicate gelatin impregnated with an ammonium salt and second in sterilized earth. The silicate jelly is prepared as follows:

Mix a jelly of silica containing some ammonium sulfate with sterilized soil. The seeding is done with one of the subcultures which no longer has the power of producing nitrates.

In the case of the jelly the seeding is accomplished as follows:

A minute drop of a culture liquid is taken with a capillary glass tube and applied in striae to different parts of the solid jelly; or a minute drop of the culture liquid may be mixed with the jelly before solidification. The Petri dishes in which these cultures are made can be preserved in a moist atmosphere and thus the desiccation be easily prevented for a long time. From time to time small pieces of the jelly as large as a pea can be taken and tested for the progress of nitrification.

Results.—The nitrous reaction, both in the prepared jelly and in sterilized soil, will appear in a few days. At the end of from seven to twelve days it will have attained its maximum intensity and will then remain stationary indefinitely. Sterilized soil has no power to generate the nitric from the nitrous ferment. The two organisms are, therefore, of different species.

After a few generations the power of producing nitrates seems to be lost although the nitrous ferment may still be active. This suppression of the power to oxidize the nitrites is not due to any pernicious influence of the culture-medium but to the condition of the successive solutions at the time of taking the seeding samples.

436. Microscopic Examination.—A small particle of the deposit in the culture-liquid is spread on a glass slide and dried. There is then added a drop of very dilute perfectly transparent malachite green solution. Malachite green is Bittermandelölgrün, or tetramethyldiamidotriphenylcarbinol. Use the zinc chlorid double salt or oxalate. In about half a minute it is washed and colored by a very dilute solution of gentian violet which is left to act for some time. The cells then appear distinctly colored on a colorless background.

In examining in this way nitrous cultures under a moderate enlargement there are seen particles of material covered with scattered groups and massive zoöglœæ composed of cells which are, doubtless, identical.

By their round or roundish forms, by their relative size and especially by their numbers and uniformity they are at once distinguished from the other vegetations which are generally of a purely bacillus shape.

With the exception of some shreds of mycelium coming from some oidium in the soil the microscope reveals nothing but the organisms described. The microscopic appearance^[288] of the nitrous ferment is shown in Fig. 69.