SOIL BACTERIA.
_A._ OCCURRENCE AND METHODS OF STUDY.
To understand the development of our knowledge of soil bacteria, it
must be remembered that bacteriology is under the disadvantage that
it started as an applied science. Although bacteria were first seen
by Leeuwenhoeck about the middle of the seventeenth century, and
some of their forms described by microscopists of the eighteenth and
early nineteenth centuries, it was only with the work of Pasteur on
fermentation, and of Duvaine, Pasteur, and their contemporaries on
disease bacteria, that bacteriology may be said to have started.
From the outset, therefore, attention has been directed mainly to
the bacteria in their specialised relationship to disease or to
fermentation and similar processes. As a result, little research was
done on the pure biology of the bacteria, so that even now many of the
most fundamental and elementary problems concerning them are quite
unsolved.
In their work on fermentations and disease bacteria, the earlier
workers were assisted by the fact that under both sets of conditions
the causative bacteria exist, as a rule, either in practically pure
culture, or else in preponderating numbers. The study and elucidation
of such a mixed micro-population as exists in the soil, became possible
only when methods had been devised for isolating the different kinds
of bacteria, and thus studying them apart from each other. It was the
development of the gelatine plate method of isolating pure cultures by
Koch[36] in 1881 that made the study of the soil bacteria practicable.
The plating method opened up two lines of research. In the first
place, it provided a simple means of isolating organisms from the mixed
population of the soil, and thus enabled a qualitative study to be made
of each organism in pure culture, and, in the second place, from it was
developed a counting technique for estimating differences in bacterial
numbers between samples of soil, from which has sprung much of our
knowledge of the quantitative side.
The earliest studies of the soil bacteria consisted of such estimations
of numbers, and showed that the soil contained a very numerous
population of bacteria. About 20,000,000 bacteria per gram of soil
is now considered a fair average number. The number and variety of
bacteria existing in the soil is so enormous that the method of
separating out all the different forms, and of discovering their
characters and functions, has proved impracticable. In practice,
therefore, the problem has been approached from the biochemical
standpoint. That is to say, the special chemical changes that the
bacteria produce in the soil have first been investigated, and this
has been followed by the isolation and study of the various groups of
bacteria that bring about the changes under investigation.
The method commonly employed in isolating the organisms that produce a
given chemical change in the soil is called the “elective” method. The
soil is inoculated into a culture medium that will especially favour
the group of bacteria to be isolated, to the exclusion of others.
For example, if it is desired to isolate the organisms that attack
cellulose, a medium is made up containing no other organic carbon
compounds except cellulose. Such a selective medium encourages the
growth of the group of organisms to be investigated, so that after
several transfers to fresh medium a culture is obtained containing
only two or three different types of organisms. These are separated by
plating and pure cultures obtained.
Another difficulty which has not yet been completely overcome is
that of adequately describing an organism when it is isolated. The
morphology of bacteria is not the constant thing that is seen in
the more stable higher organisms. In many cases the appearance of a
single strain is entirely different on different media, and may be
quite altered by such conditions as changes in acidity of the medium
or temperature of incubation. Even on a single medium remarkable
changes in morphology occur, at any rate, in some bacteria. This is
well seen in a cresol-decomposing organism under investigation at
Rothamsted. In cultures a few days old this organism develops as bent
and branching rods; these rods then break up into chains of cocci and
short rods, which separate, and in old cultures all the organisms
may be in the coccoid form (Fig. 1). It is claimed by Löhnis[47_b_]
that the possession of a complex life-cycle of changing forms is a
universal character in the bacteria. The instability of shape in many
bacteria makes it necessary to standardise very carefully the cultural
conditions under which they are kept when their appearance is described.
[Illustration:
Culture 15 hours old.
Culture 3 days old.
FIG. 1.--Change in appearance, in culture, of a cresol decomposing
bacterium.]
The inadequacy of mere morphology as a basis for describing bacteria
led to the search for diagnostic characters, based on the biochemical
changes that they produced in their culture media, and the appearance
of their growth in the mass on various media. These characters
unfortunately have also proved to be very much influenced by the exact
composition of the medium and other conditions of culture. Recently
an attempt has been made by the American Society of Bacteriologists to
standardise the diagnostic characters used in describing bacteria, and
also the media and cultural conditions under which they are grown for
the purpose of description. The need for such precautions, however,
was not sufficiently realised by the early workers, many of whose
descriptions cannot now be referred to any definite organism.
The large number of organisms found in the soil, and the difficulty
and labour of adequately describing them, is such that even now we
have no comprehensive description of the common soil bacteria that
appear on gelatine platings. A careful study based on modern methods of
characterisation has been made of certain selected groups of bacteria,
and it is hoped that the laborious systematic work of describing the
common forms will gradually be completed.
Several attempts have been made to classify the bacteria that appear
commonly on gelatine platings. This work was commenced by Hiltner and
Stormer in Germany, and continued by Chester, Harding, and Conn in
America. Conn[10],[14] found that the common organisms fell into the
following main groups:--
(1) Large spore-forming bacteria, related to _Bacillus subtilis_, which
form about 5-10 per cent. of the numbers. He adduced evidence[12],[13]
that these organisms exist in the soil mainly as spores, so that they
may not form an important part of the active soil population.
(2) Short non-sporing organisms, related to _Pseudomonas fluorescens_,
that are rapid gelatine liquefiers. These form another 10 per cent. of
the numbers.
(3) Short rod forms that liquefy gelatine slowly or not at all, and
develop colonies very slowly. These form 40-75 per cent. of the
numbers, and may therefore be of considerable importance in the soil.
(4) A few micrococci also occur.
These groups comprise the larger portion of the bacterial flora of the
soil, but, in addition to these organisms, that develop on the media
commonly used for plating, there are special and important groups
that appear only on special media, either owing to their being unable
to grow on ordinary media or because they get swamped by other forms.
Examples of such groups are the ammonia and nitrite oxidising bacteria,
the nitrogen fixing groups, the cellulose decomposing organisms, and
the sulphur bacteria.
In order that we may apply the results of the study of a definite
organism to other localities, a knowledge of the geographical
distribution of the soil bacteria is clearly needed. We have,
unfortunately, very little knowledge of the distribution of soil
organisms. The common spore-forming groups appear to be universally
distributed. Thus Barthel, in a study of the bacterial flora of soils
from Greenland and the island of Disko, obtained soil organisms
belonging to the groups of _Bacillus subtilis_, _B. amylobacter_, _B.
fluorescens_, _B. caudatus_, and _B. Zopfii_, which are common groups
in European soil, indicating that the general constitution of the
bacterial flora of the soil in arctic regions is not widely different
from that of Western Europe. Bredemann, who made an extensive study of
the _Bacillus amylobacter_ group, obtained soil samples from widely
scattered localities, and found these organisms in soil from Germany,
Holstein, Norway, Italy, Morocco, Teneriffe, Russia, Japan, China,
the East Indies, Samoa, Illinois, Arizona, German East Africa, and
the Cameroons. Some soil organisms, on the other hand, are apparently
absent from certain districts. This may be due to the conditions,
such as climatic environment, being unfavourable to them. A study has
recently been made at Rothamsted of the distribution over Great Britain
of a group of bacteria that are capable of decomposing phenol and
cresol. One of these organisms, apparently related to the acid-fast
_B. phlœi_, has an interesting distribution. It has been found in 50
per cent. of the soils samples examined from the drier region, where
the annual rainfall is less than 30 inches, but in only 20 per cent.
of the samples in the wetter parts of Britain. Another example of
limited distribution is found in the case of _Bacillus radicicola_,
the organism that produces tubercles on the roots of leguminous plants.
The distribution of the varieties of this organism follows that of
the host plants with which they are associated, so that when a new
leguminous crop is introduced into a country, nodules may not appear
on the roots unless the soil be specially inoculated with the right
variety of organism. In cases where a group of soil organisms is widely
distributed over the globe, it may yet be absent from many soils
owing to the soil conditions not suiting it. Thus, phenol decomposing
bacteria, though abundant in the neighbourhood of Rothamsted, are yet
absent from field plots that have been unmanured for a considerable
period. The occurrence of the nitrifying organisms and the nitrogen
fixing _Azotobacter_ is also very dependent on the soil conditions.
Owing to the method by which our knowledge of soil bacteria has been
acquired, by studying first the chemical changes in the soil and then
the bacteria that produce them, it is natural for us to divide them
into physiological groups according to the chemical changes that they
bring about. This grouping is the more reasonable since so little is
known as to the true relationships of the different groups of bacteria
that a classification based on morphology is well-nigh impossible. In
considering the activities of bacteria in the soil, it is convenient to
group the changes which they bring about into the two divisions into
which they naturally fall in the economy of the organisms.
In the first place, there are the changes that result in a release of
energy, which the bacteria utilise for their vital processes.
In the second place, there are the processes by which the bacteria
build up the material of their bodies. These building up processes
involve an intake of energy for their accomplishment.
It will be convenient to deal first with the release of energy for
their own use by bacteria, and its consequences.
_B._ ACTIVITIES CONNECTED WITH THE ACQUIREMENT OF ENERGY.
Unlike the green plants, most bacteria are unable to obtain the energy
that is required for their metabolism from sunlight. They must,
therefore, make use of such chemical changes as will involve the
release of energy.
As an example of the acquirement of energy in this way may be taken the
oxidation of methane by _B. methanicus_. This organism, described by
Söhngen, obtains its energy supply by the conversion of methane into
CO₂ and H₂O.
CH₄ + 2O₂ = CO₂ + 2H₂O 220 Cal.
A further example is the acetic organism that obtains its energy
through the oxidation of alcohol to acetic acid.
C₂H₆O + O₂ = C₂H₄O₂ + H₂O 115 Cal.
The decomposition processes brought about by micro-organisms in
obtaining energy are usually oxidations, but this is not necessarily
so, as can be seen in case of the fermentation of sugar into alcohol.[E]
C₆H₁₂O₆ = 2C₂H₆O + 2CO₂ 50 Cal.
[E] These examples are from Orla-Jensen (Centralblatt f. Bakt., II.,
Bd. 22, p. 305).
By far the greater part of the decomposition of organic matter is
brought about by bacteria in the process of acquiring energy. In the
soil, nearly the whole of the material utilised by bacteria as a source
of energy is derived ultimately from green plants. The energy materials
left in the soil by the plant fall into two groups, the non-nitrogenous
compounds, which are mainly carbohydrates and their derivatives, and
the nitrogenous compounds, principally derived from proteins.
(1) _Decomposition of Non-nitrogenous Compounds._
The simpler carbohydrates and starches are attacked and decomposed by
a large variety of bacteria. The addition of such substances to soil
causes a rapid increase in bacterial numbers. In nature the sugars are
in all probability among the first plant constituents to be destroyed
during the decay processes.
A large proportion of plant tissues consist of cellulose and its
derivatives. These compounds are consequently of great importance
in the soil. Unfortunately our knowledge of the processes by which
cellulose is broken down in the soil is very inadequate. The early
experimental study of cellulose decomposition, such as that of
Tappeiner[60] and Hoppe-Seyler,[33] was mostly carried out under
conditions of inadequate aeration, and the products of decomposition
were found to include methane and CO₂, and sometimes fatty acids and
hydrogen. The bacteriology of this anaerobic decomposition was studied
by Omelianski,[54] who described two spore-bearing organisms, one of
which attacked cellulose with the production of hydrogen, and the other
with the production of methane. Both species also produce fatty acids
and CO₂. It is probable that these organisms operate in the soil under
conditions of inadequate aeration. In swamp soils, in which rice is
grown, it has been shown that methane, hydrogen, and CO₂ are evolved
in the lower layers. In these soils, however, the methane and hydrogen
are oxidised when they reach the surface layers. This oxidation is
also effected by micro-organisms. Bacteria capable of deriving energy
by the oxidation of hydrogen gas have been isolated and studied by
Kaserer,[37] and by Nabokich and Lebedeff,[52] while Söhngen[57] has
isolated an organism which he named _Bacillus methanicus_, that was
capable of oxidising methane.
Under normal conditions in cultivated soils, however, the decomposition
of cellulose takes place in the presence of an adequate air supply,
and so follows a different course from that studied by Omelianski. Our
knowledge of this aerobic decomposition is very scanty. A number of
bacteria, capable of decomposing cellulose aerobically, are known. A
remarkable organism was investigated by Hutchinson and Clayton,[30]
who named it _Spirochæta cytophaga_. This organism, which they isolated
from Rothamsted soil, though placed among the _Spirochætoidea_, is
of doubtful affinities. During the active condition it exists for
the most part as thin flexible rods tapered at the extremities. This
form passes into a spherical cyst-like stage, at first thought to be
a distinct organism (Fig. 2). _Spirochæta cytophaga_ is very aerobic,
working actively, only at the surface of the culture medium. It is
very selective in its action. It appears unable to derive energy from
any carbohydrate other than cellulose. Indeed, many of the simple
carbohydrates, especially the reducing sugars, are toxic to the
organism in pure culture. An extensive study of aerobic cellulose
decomposition by bacteria was made by McBeth and Scales,[50] who
isolated fifteen bacteria having this power. Five of these were
spore-forming organisms. Unlike _Spirochæta cytophaga_, they are all
able to develop on ordinary media such as beef agar or gelatine, and
are thus not nearly so selective in their food requirements.
[Illustration: FIG. 2.--_Spirochæta cytophaga._ Changes occurring in
culture. (After HUTCHINSON and CLAYTON.)]
We are at present ignorant as to which organisms are most effective
in decomposing cellulose in the soil under field conditions, or what
are the conditions best suited to their activity. It is possible that
fungi also help in the decomposition of cellulose to a great extent.
This subject of the decomposition of cellulose offers one of the most
promising fields of research in soil bacteriology. The difficulty
of the subject is further increased by our present ignorance of the
chemical aspect of cellulose decomposition. It has been supposed that
the early decomposition products are simpler sugars, but these are
not found under conditions in which cellulose is being decomposed by
pure cultures of the bacteria mentioned above. Hutchinson and Clayton
found that their organism produced volatile acids, mucilage, and a
carotin-like pigment. The organisms isolated by McBeth and Scales also
produce acids, and in some cases yellow pigments. It is known, however,
that the decomposition products of cellulose can be utilised as energy
supply for other organisms, such as nitrogen fixing bacteria.
When plant remains decompose in the soil there are ultimately produced
brown colloidal bodies collectively known as humus. The processes by
which this humus is produced are not yet properly understood. Humus is
of great importance in the soil, in rendering the soil suitable for
the growth of crops. It affects the physical properties of the soil
to a great extent. In the first place, it improves the texture of the
soil, making heavy clay soils more friable, and loose sandy soils more
coherent. Secondly, it has great water-retaining powers, so that soils
rich in organic matter suffer comparatively little during periods of
drought. And lastly, it exerts a strong buffering effect against soil
acids. Now, it is one of the problems of present-day farming that
soil is becoming depleted of its humus. This is due to the increasing
scarcity of farmyard manure in many districts, and the consequent use
of mineral fertilisers to supply nitrogen, potash, and phosphate to
the crop. A need has therefore arisen for a substitute for farmyard
manure, by means of which the humus content of soils may be kept up in
districts where natural manure is scarce.
[Illustration: FIG. 3.--Cellulose decomposed by _S. cytophaga_ in media
with increasing amounts of nitrogen. (After HUTCHINSON and CLAYTON.)
X-axis: Milligrams of nitrogen supplied as sodium-ammonium phosphate.
Y-axis: Milligrams of cellulose decomposed in 21 days.]
It is well known that if fresh unrotted manure or straw be added to
the soil, it often produces harmful effects on the succeeding crop.
The problem, therefore, was to develop a method by which fresh straw,
before application to the soil, could be made to rot down to a mixture
of humus compounds such as occur in well-rotted farmyard manure. The
solution of this problem came as a result of an investigation by
Hutchinson and Richards,[30_b_] at Rothamsted, into food requirements
of the cellulose decomposing bacteria. They realised that since more
than 10 per cent. of the dry weight of bacteria consists of nitrogen,
it would be necessary to supply the cellulose decomposing bacteria with
a supply of nitrogen, in order that they should attain their greatest
activity. Experiments with cultures of _Spirochæta cytophaga_ showed
that the amount of cellulose decomposed depended upon an adequate
supply of nitrogen for the organism (Fig. 3). Similarly, materials such
as straw will scarcely decompose at all if wetted with pure water. An
adequate supply of nitrogen compounds is needed to enable decomposition
to take place. Hutchinson and Richards tested the effect of ammonium
sulphate, and discovered experimentally the proportion of ammonia to
straw that produced the most rapid decomposition. They found that if
a straw heap was treated with the correct proportion of ammonia, it
decomposed into a brown substance having the appearance of well-rotted
manure. This has resulted in the development of a commercial process
for making synthetic farmyard manure from straw. The method of
manufacture is as follows: A straw stack is made and thoroughly wetted
with water. The correct amount of ammonium sulphate is then sprinkled
on the top and wetted, so that the solution percolates through the
straw. The cellulose bacteria attack the straw, breaking it down
and assimilating the ammonia. This ammonia is not wasted, as it is
converted into bacterial protoplasm that eventually decays in the soil.
Field trials of this synthetic manure show that it produces an effect
closely similar to that of natural farmyard manure.
While cellulose and related carbohydrates are by far the most
important non-nitrogenous compounds left in the soil by plants, there
are other compounds whose destruction by bacteria is of special
interest. Such, for example, is the case of phenol. This compound is
produced by bacterial action as a decomposition product of certain
amino-acids. It occurs in appreciable amounts in cow urine. It is
probable that it forms a common decomposition product in soil and
also in farmyard manure. If this phenol were to persist in the soil,
it would eventually reach a concentration harmful to plant growth. It
does not, however, accumulate in the soil; indeed, if pure phenol or
cresol be added to ordinary arable soil, a rapid disappearance occurs.
This disappearance is of some practical importance, since it limits
the commercial use of these compounds as soil sterilising agents.
The cause of the disappearance has been to some extent elucidated at
Rothamsted,[58] where it was found to be in part a purely chemical
reaction with certain soil constituents, and partly due to the activity
of bacteria capable of decomposing it. A large number of soil bacteria
have now been isolated that can decompose phenol, meta-, para-, and
ortho-cresol, and are able to use these substances as the sole sources
of energy for their life processes. These organisms have a wide
distribution, having been found in soil samples taken from all over
Great Britain, from Norway, the Tyrol, Gough Island, Tristan da Cunha
and South Georgia. Soil bacteria have also been isolated that are able
to decompose and derive their energy from naphthalene and from toluene.
The ability of the bacteria to break up the naphthalene is very
remarkable, and all the more so since they can hardly have come across
this compound in the state of nature. The naphthalene organisms have a
distribution as world-wide as the phenol group.
(2) _Ammonia Production._
The second main group of products left in the soil by higher plants
are the nitrogen-containing compounds, such as the proteins and
amino-acids. Plant remains are not the only source of organic nitrogen
compounds available to soil bacteria. There are, in addition, the dead
bodies of other soil organisms, such as protozoa and algæ. The relative
importance of these sources of nitrogen is not known, but almost
certainly varies greatly with the state of activity of the various
groups of the soil population. Bacteria are able to utilise organic
nitrogen compounds as energy sources, as can be exemplified in the
oxidation of a simple amino-acid:--
H O
| //
H--C--C + 3O = 2CO₂ + H₂O + NH₃ + 152 Cal.
| \
NH₂ OH
It will be seen that, in the acquirement of energy from such a
compound, ammonia is released as a by-product. It is not certainly
known what is the exact course of the reactions brought about by
bacteria in soil during the breaking-down of organic nitrogen
compounds, but they result in the splitting off of most of the nitrogen
as ammonia. Herein lies the great importance of the process, for the
production of ammonia is an essential stage in the formation of nitrate
in the soil, and on the supply of nitrate the growth of most crops
largely depends.
[Illustration: FIG. 4.--Quantities of ammonia produced by pure cultures
from 5 grams of casein in the presence of varying quantities of
dextrose. (After DORYLAND.)
X-axis: Percentage of dextrose added.
Y-axis: Milligrams of NH₃ produced.]
It is very important to note that the production of this ammonia is
only a by-product in the economy of the bacteria, the benefit that they
derive from the reactions being due to the release of energy involved
in the decomposition. The common ammonia-producing bacteria in the
soil have been found equally capable of deriving their energy by the
oxidation of sugars and similar non-nitrogenous compounds. Fig. 4
shows an experiment by Doryland,[17] in which cultures of common soil
bacteria were grown in peptone solution, to which increasing quantities
of sugar were added. One can see that, as the amount of sugar is
increased, the production of ammonia is lowered, since the bacteria
are obtaining energy from the sugar instead of from the nitrogen
compound, peptone. Consequently, if soil contains a quantity of easily
decomposible carbohydrate material, bacteria will derive their energy
from this source, and the production of ammonia and nitrate will be
lowered. Thus the addition of sugar or unrotted straw to the soil often
lowers the nitrate production, and consequently reduces the crop yield.
If the soil is sufficiently rich in carbohydrate material, the bacteria
may multiply until the supply of organic nitrogen is used up, and
then will actually assimilate some of the ammonia and nitrate already
existing. There is thus a balance of conditions in the soil due to
varying proportions of nitrogenous and non-nitrogenous energy material.
When nitrogen compounds are the predominant energy source, the bacteria
utilise them, and ammonia is released. When a non-nitrogenous energy
source predominates, this is utilised and little or no ammonia is
released, and in extreme cases ammonia may be assimilated.
Although a large number of the common organisms in the soil produce
ammonia in culture media containing peptone, the relative importance
of these in the soil has yet to be decided. It was supposed that the
spore-forming organisms related to _Bacillus mycoides_ were of chief
importance. This supposition dates from the work of Marchal,[49] who
studied the production of ammonia by an organism of this group in
culture solution, and found it to be a very active ammonifier. As
already mentioned, however, there is some doubt as to whether the large
spore-forming organisms are very active under soil conditions.[12],[13]
The existence of rapid fluctuations in nitrate content, found to exist
in soil, may in the future indicate which are the most active of the
common bacteria in the soil itself by enabling us to observe which
types increase during periods of rapid ammonia and nitrate formation.
(3) _Nitrate Production._
The ammonia produced in the soil under normal field conditions is
rapidly oxidised successively to nitrite and to nitrate, a process
known as nitrification. The process of nitrification is more rapid than
that of ammonia production, with the consequence that no more than
traces of ammonia are able to accumulate. The rate at which nitrate is
formed in the soil is consequently set by the slower process of ammonia
production.
The work of Schloesing and of Warington showed that the oxidation
of ammonia was the work of living organisms. It is, however, to
Winogradsky’s isolation and study of the causative organisms that we
owe our present knowledge of the biology of the process. By a new
and ingenious technique, he isolated from soil two remarkable groups
of bacteria that bring about nitrification. The first group oxidises
ammonium carbonate to nitrite, and was divided by Winogradsky into
the two genera, _Nitrosomonas_, a very short rod-like organism bearing
a single flagellum, and _Nitrosococcus_, a non-motile form found in
South America. The second group oxidises nitrites to nitrates. They are
minute pear-shaped rods to which he gave the name _Nitrobacter_.
Winogradsky found that the first, or nitrite-producing group, would
live in a culture solution containing:--
2·25 grams ammonium sulphate,
2·0 „ sodium chloride,
1·0 „ magnesium carbonate,
to the litre of well water.
Nitrobacter would grow in a similar medium containing sodium nitrite
instead of ammonium sulphate. There being no organic carbon in these
media, the organisms had no source of carbon for their nutrition,
except the CO₂ of the air, or possibly that of bicarbonate in solution.
It therefore followed that the organisms must obtain their carbon
supply from one of these sources. Unlike green plants, the nitrous and
nitric organisms are able to carry on this carbon assimilation in the
dark, and must therefore obtain the energy needed for the process from
some chemical reaction. The only sources of energy in Winogradsky’s
solutions were the nitrogen compounds, and it consequently followed
that the organisms must derive their energy supply by the oxidation
of ammonia and nitrite respectively. The release of energy obtained
by these two reactions has been calculated by Orla-Jensen to be as
follows:--
(NH₄)₂CO₃ + 3O₂ = 2HNO₂ + CO₂ + 3H₂O + 148 Cals.
KNO₂ + O = KNO₃ + 22 Cals.
The exact process by which ammonium carbonate is converted into nitrite
is not at present known. The two groups of organisms are extremely
selective in their source of energy. The nitrous organisms can derive
their energy only by the oxidation of ammonia to nitrite, and the
nitric organisms only by the oxidation of nitrite to nitrate. In
culture media they are, indeed, inhibited by soluble organic compounds
such as sugars. Under natural conditions, however, they appear to
be less sensitive, since ammonium carbonate is readily nitrified
in substrata rich in organic matter. The rapid nitrification that
takes place during the purification of sewage is an example of this.
The conditions in culture, with regard to aeration and the removal
of metabolic products from the neighbourhood of the organisms, are
very different from those in the soil, and perhaps account for the
discrepancies found.
The oxidation of ammonium carbonate by nitrosomonas results in the
formation of nitrous acid. The organisms are very sensitive to acidity,
and can only operate if the nitrous acid produced is neutralised by an
available base. In normal soils calcium carbonate supplies this base,
and in acid soils the formation of nitrite is, as a rule, increased
by the addition of lime, or of calcium or magnesium carbonate. There
is evidence that in the absence of calcium carbonate, other compounds
can be used as a base. It was found by Hopkins and Whiting[32] that
in culture solution the nitrifying organisms could use insoluble rock
phosphate as a base, producing therefrom the soluble acid phosphate.
There is evidence, however, that in ordinary soil containing calcium
carbonate very little solution of phosphate takes place in this way.
The further oxidation of nitrite to nitrate by _Nitrobacter_ does not
produce acid, and requires no further neutralising base.
The nitrate produced in this way is the main source of nitrogen supply
to plants under normal conditions. Experiments have shown that a number
of plants are capable of utilising ammonia as a source of nitrogen, and
Hesselmann[34] has found forest soils in Sweden where no nitrification
was proceeding, and where, therefore, plants would presumably obtain
their nitrogen in this way, but such cases must be regarded as
exceptional.
Another group of bacteria capable of deriving their energy from
an inorganic source exists in the soil. This comprises the sulphur
bacteria, which are able to derive energy by the oxidation of sulphur,
sulphides, or thiosulphates to sulphuric acid:--
S + 3O + H₂O = H₂SO₄ + 141 Cals.
One organism studied by Waksman and Joffe[63] is able to live in
inorganic solution, deriving its carbon from carbon dioxide. The
sulphur bacteria have recently come into prominence in America owing to
their faculty for producing acid. Thus Thiospirillum will increase the
acidity of its medium to a reaction of P_{H} 1·0 before growth ceases.
The potato scab disease in America is now treated by composting with
sulphur. This treatment depends on the production of sulphuric acid by
the sulphur oxidising bacteria, which renders the soil too acid for the
parasite. There is some evidence also that acid thus produced can be
used to render insoluble phosphatic manures more available in the soil.
Analogous to the sulphur organisms are certain bacteria isolated from
sheep dig tanks in South Africa by Green,[28_b_] which can derive
energy by the oxidation of sodium arsenite to arsenate.
(4) _Anaerobic Respiration._
As is seen in the examples mentioned, energy is commonly obtained by
bacteria through an oxidation process in which free oxygen is utilised.
In water-logged soil, however, or in soil overloaded with organic
matter, anaerobic bacteria may develop, which obtain their oxygen
from oxidised compounds. Thus there are soil organisms described by
Beijerinck[2] and others which can obtain oxygen by reducing sulphates
to sulphides.
A more important source of oxygen under these conditions is nitrate,
which can supply oxygen to a larger number of bacteria. The stage to
which the reduction can be carried varies according to the organism.
A very large number of bacteria are capable of reducing nitrates to
nitrites. Many can reduce nitrate to ammonia, and some can produce
an evolution of nitrogen gas from nitrate. The effects of nitrate
reduction, therefore, appear under water-logged conditions in soils.
For example, in swamp soils in which rice is grown, it has been found
by Nagaoka,[53] in Japan, that treatment with nitrate of soda depresses
the yield, probably owing to the formation of poisonous nitrites by
reduction.
Under normal conditions of well aerated soil, however, it is unlikely
that the reduction of nitrate is of great importance. In such soils the
activities through which bacteria acquire their energy are, as we have
seen, of vital importance to the plant, resulting in the disintegration
of plant tissues, with the ultimate formation of humus, and in the
production of nitrate.
In their activities connected with the building up of their protoplasm,
bacteria may, on the other hand, compete with the plant. These
activities and their consequences will be reviewed in the following
chapter.