Trans. and Proc. of the Botanical Society of Pennsylvania (1911)
Bacteria and other Fungi in Relation to the Soil

Thesis presented to the Faculty of the Graduate School of the University of Pennsylvania, in partial fulfillment of the requirements for the Degree of Doctor of Philosophy.
D. RIVAS, M. S., M. D., Ph. D.
University Research Fellowship in Biology, University of Pennsylvania.


Mycology has reached its development within the last fifty years. Until the end of the nineteenth century the knowledge of the bacteria was incomplete, and spontaneous generation was believed to explain the origin of the micro-organismal world. The classification of the fungi was gradually elaborated by Linneaus in 1707, and by Persoon in 1822. The brothers René and Charles Tulasne, of Paris, in 1861, made a most important contribution upon the comparative morphology of these microscopic plants and described in detail the life history of Claviceps purpurea (ergot fungus), while De Bary discovered the intermediate host of Puccinia graminis (wheat rust). Saccardo in 1882 published a work of eighteen volumes (Sylloge Fungorum omnium hucusque Cognitorum) in which 50,000 species are described.

A new conception as to the action of bacteria was introduced by the genius of Pasteur in his classic work on fermentation, which settled once and for all that each fermentation depends upon a specific micro-organism. Further, his important contributions upon the pathogenic properties of Bacillus anthracis and the bacillus of symptomatic anthrax, followed by the discoveries of Koch, Nicolaier, Kitasato, Klebs, Loeffler, Behring, Ducleaux, Roux, Calmette, Winogradsky, Pfeffer, etc., opened a new era in bacteriology, a new era in medicine, surgery, industrial fermentations, agriculture, serotherapy, etc., while a more thorough conception was sought as to the role which this microscopic world plays in nature. So the study of mycology at present is divided into four main branches, namely: (1) Morphology; (2) Life Cycle and Sexuality; (3) Saprophytism or Parasitism; (4) Biologic Characters.

(1) Morphology: Though based on the theory of evolution, it is difficult and sometimes almost impossible to identify a distinct and constant type for each species. Under careful observation of the life cycle and environment it will be found that like the changes of an egg into larva, pupa and imago, so also the different forms of bacteria and fungi represent phylogenetic stages in a common group, hence their subdivision into Myxomycetes, Schizomycetes and the groups of the higher fungi.

(2) The Life Cycle and Sexuality: The division of the vegetable kingdom into Phanerogamae and Cryptogamae belongs wholly to the past, when the sexuality of the lower forms was not recognized. After Hofmeister's discoveries of sexuality amongst the so-called cryptograms, followed by similar contributions from others along this line, sexuality has been recognized as extending from the Alga and Fungi through Pteridophyta to the Angiospermae amongst plants.

(3) Saprophytism or Parasitism: The line of separation between saprophytes is not well marked, because the conception that a parasite is an organism incapable of living as saprophyte, or that a parasite implies the life of an organism upon another, in which the parasite is detrimental to the host, admits many exceptions. As our technique improves, numbers of well-known parasitic forms are found to thrive as saprophytes, and many forms living apparently as parasites are not only harmless, but of use to the host. The algal and fungal elements in lichens, the commensalism between the Leguminosae and the bacteria, the mycorrhiza in the roots of higher plants, etc., may serve as some of the many examples to illustrate how difficult it is to determine where saprophytism ends and parasitism begins. This difficulty, no doubt, arises from our attempt to mould things according to our way of conceiving them, and not according to the universal manifestations of nature. Many plants would doubtless have ceased to exist were it not for the aids given in the elaboration of their food by fungi in their roots, while the detrimental effects of what may be regarded as a parasite are in most cases, if not in all, secondary. Parasitism in the true sense would imply the life of an organism upon the living tissues of the host, but who has shown that from the most pathogenic forms of bacteria found in the tissues of plants and animals to the harmless fungi found in the roots of plants thrive upon the healthy living cell of the host? Commensalism on the one hand and saprophytism on the other, that is, the disintegration and absorption of dead matter, are at the base of and constitute one fundamental manifestation of nature, while parasitism as conceived at present belongs to individual cases, the number of which gradually diminishes with the advancement of science and the perfection of our technique.

(4) Biologic Characters: As frequently interpreted, the morphologic features, parasitism and the life cycles all belong to the biologic characters which make up a complete study of any one organism. But the rapid progress made in recent years has expanded so considerably our knowledge of mycology that, for convenience, the biologic characters are here considered as relating especially to the cultural characteristics of bacteria and the higher fungi.

The continuous changes in the organic world, which exhibit themselves in the constant alternation of synthesis and analysis, is due to the elaboration of organic material and subsequent decay of the same. The whole may be viewed as a process of oxidation on the one hand and of reduction on the other, so that a balance is constantly maintained. As our knowledge advances, much of this change is being attributed to the agency of the bacteria and fungi. That each soil has its own bacterial flora, upon which its richness depends, is a fact at present generally admitted. But this view has been considered as explaining the nature of the soil by mycologists, agriculturists and biologists in general, only after the chemic analysis of the soil was found unsatisfactory to explain the phenomena of soil fertility. Likewise the physical analysis has not given much aid; but in search of new light, after attention had been directed to the role of the bacteria in the soil, the most fruitful results have been reached in recent years, and a better conception has been obtained as to the maintenance of the equilibrium in nature by considering the activity of living organisms in the soil.

In the year 1888, Hellriegel and Wilfarth demonstrated the assimilation of nitrogen by bacteria (Bacillus radicicola or Rhizobium leguminosarum) found in the tubercles of leguminous plants; but it was due to Winogradsky's epoch-making discovery of the Clostridium Pasteurianum in the soil. This anaerobic bacterium produces butyric and acetic acid, carbon dioxide and hydrogen in the presence of sugar. It is capable of assimilating nitrogen from the air in such abundance that no addition of this element is necessary; ammonia is formed.

Side by side with C. Pasteurianum, Winogradsky also found in the soil the presence of nitrifying organisms (Nitrosomonas, Nitrococcus) concerned in the oxidation of ammonia into nitrous acid, from which nitrites are formed, whereas another organism (Nitrobacter) oxidizes nitrous acid into nitric acid or nitrite into nitrate. The importance of these bacteria can be readily understood, since through their agency a constant supply of nitrate is given to the soil.

Beside the existence of certain fungi living symbiotically in the roots of plants (Mycorrhiza), which supply nitrogenous food to the plant and receive in return carbohydrates for their nutrition, plants require the action of certain complex substances, enzymes or ferments for the metabolism of a great part of their food. The best known of these ferments acts on the carbohydrates, the oils, the glucosides or the protein compounds.

As to the action of ferments, most of them are hydrolytic, as shown in the formation of sugar from starch. A katalytic action is also attributed to them, which, if compared in this respect to the formation of ether by the aid of sulphuric acid, may induce molecular combinations; hence of importance in synthetic processes. Ferments also can be regarded as stimulating or accelerating agents, whether they are vehicles for the transmission of molecular movements or act by means of dissociatory power, generating a series of actions and reactions directed along particular channels. Whatever the case may be, the action of ferment serves both to digest food substances and to render them capable of absorption, as well as to prepare them for assimilation by the protoplasm, hence the important role which they play in the economy of the plant and their use to vegetation in general. It is with these facts in view that the present work is presented. The soil from which vegetation derives its nourishment, being always invaded by bacteria, special attention is given to the different ferments produced by them, and the changes which they produce upon the organic matter of the soil in which they thrive. A monthly quantitative and qualitative study of the bacteria of the soil has been made at different seasons of the year. The results comprise a description of the material for the work (pp. 248-250), the methods employed in the research (pp. 250-256). The biologic characters of the bacteria and fungi isolated are especially considered. A general consideration of them, and the conclusions in which an attempt is made to show that the autotrophic nutrition or photosynthesis in the economy of the plant, is probably not the only means for the elaboration of their food, and that for its nutrition the plant most probably is dependent upon the root system for absorption of the elaborated food previously digested and rendered assimilable through the action of the ferments produced by the bacteria and fungi of the soil. The writer is of the belief that with the remarkable and successful advances in bacteriology, the time is approaching in which a return to the HUMUS THEORY, long forgotten, would not be out of place, and it is hoped that the results here given will at least suggest investigations along this line.