Monday, 25 June 2012

Secrets Beneath the Ground

Of all the mysteries in the natural world, probably the most mysterious and least understood are the ecosystems which lie hidden beneath the ground. Not only are these ecosystems hidden under a layer of leaves and twigs, they are also hidden from us because their size is far below our level of sensory perception. There are billions of individual fungi, protozoa and bacteria in every handful of soil. By far the greatest number are the bacteria. Microbiologists have estimated that there are more than 10,000 different species of these tiny organisms in that little pile of soil! Most of them are so small that a line of 1000 of them, end to end, will only stretch for a distance of a millimetre.

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! It is also twice as many species of bacteria than are described in Bergey’s Manual.

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.

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