Just as the forest has many
different habitats such as streambanks, logs, tree trunks, sunny openings,
etc., so does the soil have many different habitats. Soil habitats, however,
are microscopic ones. Particles which have come from the breakdown of leaves,
wood, bark, insects, minerals and many other sources are all different, and
support their own unique populations of bacteria. Each one forms its own
special ecosystem, an ecosystem with a diameter about one-tenth of a
millimetre. Most of these bacteria have not only never been named, they have
never been seen. So how do scientists know there is this much diversity under
the ground? The people who study genes and molecular biology have extracted DNA
from soil samples and analyzed it. Some of this analysis involves observing how
long it takes for pieces of DNA to recombine with other pieces of DNA. The
longer it takes, the more kinds of different DNA are in the sample. After the
mathematicians have made their calculations, the conclusion is that there are more
than 10,000 strains in a sample of good rich soil. This is more than three
times the number of higher plant species in all of British Columbia
Bergey’s Manual is a multi-volume
set of books that contains information on all the named species of bacteria.
There are about 5000 of these. How can a few grams of soil contain more
bacterial species than this? One of the most significant reasons involves how
we study and grow bacteria. Most kinds of bacteria that are known, are known
because they have been cultured on a Petri dish, a clear plastic dish
containing agar, which is a nutrient-rich jelly substance. The nutrients can be
varied, depending upon what kind of food the particular bacteria like to eat.
If the bacteria like the food they are given they will form great big colonies
on top of the agar. The average bacterium is only a thousandth of a millimetre
long, so there are millions of individuals in such a colony. With this large a
number, the bacteria in question can be studied in detail. To study bacteria in
this way, bacteriologists must be able to grow them. They must be able to give
them the food they like, and they must also be able to grow them in a
monoculture, without other competing organisms. The species that can be
cultured in this way are usually species that like lots of nutrients. Most of
the pathogenic ones fall within this category.
Most bacteria, however, do
not cause disease, and they do not live in habitats with lots of food. The
bacteria we have names for are the ones we can grow. Scientists now believe
that over 99% of species cannot be cultivated. In other words almost all the
bacteria in nature are unknown. About 20 years ago biologists were first able
to study the DNA from soil organisms, and these studies revealed that not only
were there many times more strains of bacteria than had been surmised, but that
the vast majority of these are not closely related to the known ones. Many of those in the soil occur in very small
numbers, in many different micro-ecosystems. Particles from such differing
origins as insect skeletons, tree resin, leaves, wood, animal droppings, or
different kinds of mineral grains will all have their own special types of bacteria,
and there are innumerable kinds of micro-particles. Some bacteria appear to be
dormant almost all the time, waiting in the ground until they receive the
nutrients they require. When the food is exhausted they go back into dormancy
again.
We cannot see the bacteria
within their own environment. Some of them can be cultured in Petri dishes, but
this is micro-agriculture, not nature. To study soil ecosystems themselves they
need to be manipulated and disturbed, as these are worlds beyond our level of perception.
To find individual organisms in this realm is more difficult than looking for a
needle in a haystack, because we can see the needle when we find it. It is more
comparable to clearing a piece of land with a bulldozer, and looking through
the rocks to see what kind of mosses were growing there.
There is also evidence that
bacteria have complex social relations with other bacteria. The majority of
soil species may require contact with other soil bacteria. These requirements
cannot be supplied in a laboratory environment. Bacterial cells talk to each
other through a chemical language called quorum sensing. They produce
substances which diffuse into their surroundings. When a critical level is
reached they cause the individual cells to change their behaviour. They may
tell them it is time to reproduce, or in the case of some disease-causing
strains, there is a message that they have a high enough population to
transform from a harmless state into an invasive, pathogenic one. Some of the
most virulent disease organisms are completely harmless until they reach their
critical density. Future medical treatments may involve neutralizing this
communication system.
The majority of our
antibiotics are produced by soil bacteria, and most of these come from a group
of bacteria called Streptomyces. There are myriads of these compounds, and
bacteriologists have discovered that in nature they do not act as antibiotics.
They are used for chemical communication. The bacteria usually make them when
they are ready to produce spores for reproduction. They, however, produce them
in very small quantities, quantities which are below the minimum inhibitory
concentration. This refers to the minimum amount of substance that is required
to inhibit bacterial growth. The Streptomyces are grown artificially in pure
cultures, which never occurs in nature where they occur with thousands of other
micro-organisms. In large amounts, antibiotics disrupt the growth processes of
other bacteria. That is the reason they can be used to kill disease organisms.
Some researchers have expressed concerns about releasing these naturally
occurring substances in unnaturally large amounts into the environment, which
is what takes place in some agricultural settings.
As you walk through the
woods, even if you can name every plant, animal or mushroom you see, you are
only naming a small percentage of the diversity that surrounds you. Almost all
of it is un-named and unknown, and will remain so for many decades to come.
Scientists are only beginning to fathom the invisible ecosystems which are
common here, and upon which all the larger living things depend. It is the soil
and the secret realities within it that support all the ecology we see around
us.
