Microbial Ecology

The basic concept behind the discipline of Microbial Ecology is that the microorganisms which inhabit any particular environmental niche do so in dynamic relationship with all the other living things which may enter, reside within or leave that niche. The immediate surroundings of any particular living organism is the sum total of all physical, chemical and biological aspects which go to make up that "environment". Physical aspects include soil type, elevation, ground water, microclimate and temperature. Chemical aspects include such things as dissolved minerals and gasses in water which in turn determines soil pH (acidity/basicity), soil mineral compounds and organic compounds produced by plants, animals and microorganisms. Biological aspects are the other living organisms residing in the same environment. The relationships which these living organisms make with one another are called ecosystems. Ecosystems are composed of communities of like organisms. Many communities go to make up any one ecosystem. Microorganisms which conduct complementary physiological processes interact to form these communities.

Communities in turn are formed by metabolically related microorganisms called guilds. Thus, sets of guilds form a community. Guilds in turn are formed by populations of one type of microorganism. The number of different populations of microorganisms in any guild will vary depending upon the environment. Populations cause significant changes in the environment in which they are found due to the results of their metabolic processes. Thus, the sum of all the various metabolic processes of the microorganisms in any environmental niche is such as to transform the physical, chemical and biological aspects of the ecosystem which makes up the environment. The Earth as we know it today is the result of the workings of microorganisms throughout the ages. As the relationships between microorganisms have developed over millions of years, the aspects of those relationships are complex and when studied yield a fascinating array of competitive stratagems for growth and development.

All present life on this Earth is dependent upon energy derived from the Sun or the residual heat of the Earth due to the compression of the force of gravity. As I am not going to deal with the microorganisms present in hydrothermal vents and the like, I will reserve my comments to those dependent upon the insolation of the sun.

Plant life transforms the energy from the Sun into organic compounds such as simple sugars, simple fatty acids and amino acids. These simple compounds are then used to build other more complex organic compounds such as starch, oils and proteins; to name a few. Life as we know it is dependent upon this transformation by plants.

As the saying goes, "Life abhors a vacuum". Thus, where there is energy available for use, living entities will find a way for it to be exploited and used for their own purposes. Where the energy is used by plants to build organic compounds, animal life uses the energy bound up in organic compounds to build themselves and what is left over is excreted as waste. The waste of plants is metabolic (carbon dioxide and water) and structural components(mostly shed leaves, flowers and branches). The waste of animals is metabolic(carbon dioxide and water) and structural components (shed skin cells, hair, exoskeleton, chitin, etc.) as well as excreted by-products of digestion as feces. It is the microflora in the large intestine which is of interest to us as they utilize what we do not use (and some of what we do use) and hereby make more of themselves and the vitamins, effector and cofactors which we require and are not able to make for ourselves. In this respect, we are feeding our own microflora in much the same manner as ruminants and other herbivores.

Much in the same manner that we have altered the kinds of microflora which we encounter in our diet, we have also altered the diet and microorganisms in the animals which we keep as livestock. The microflora commensal and symbiotic with our livestock have evolved along with the changing circumstances of husbandry. The feedlot where cattle are raised is a far, far cry from the open range. The small cages where chickens are raised is a far, far cry from the jungle also. Thus, you may be aware that the meat which you eat is a far, far cry from that which our ancestors ate.

The way in which the monoculture of food crops is managed with the use of artificial fertilizer, pesticides and herbicides is also a far, far cry from that which our ancestors ate. All these factors combine to seriously dilute the quality of our food and to make even more imperative the consumption of "live" foods. Hence the phrase, "Don't panic, there’s organic", to which I would like to add, "To survive, eat it live!"

Perhaps this is a good place to discuss just what I mean when I say live. Plant tissue used for salad and fruit are alive when eaten. Sashimi (raw fish) and raw oysters are alive also. What I am referring to in relation to food is any raw(non-pasteurized) foods prepared by the action of viable microorganisms which contain the microorganisms and their products as an integral part of that food.

Just as we live in communities with and relate to one another, all life relates to other life on this planet in some manner whether readily observable or not. Just as we compete for resources and seek a niche for ourselves in society, microorganisms microorganisms also have to compete for resources and seek out a niche to which their evolutionary development has been honed for optimum growth and development. Microorganisms have to compete for resources among their own kind and with the myriad of other species. The end result is always to make more of the same as fast as possible. As the availability of resources is spread unevenly in time and space, most microorganisms face a feast or famine type of existence. The doubling time for Escherichia coli in your intestinal tract is about 12 hours where the availability of resources is excellent as compared to soil microorganisms. Unless a pulse of nutrient makes itself available, most environmental conditions afford very low rates of growth.

If I want the same as what everyone else wants, how do I ensure that I get what I want? Well, you may be sure that microorganisms do not think in the same manner that we do. But, the possibilities of genetic evolution in living systems works for us all, no matter what the species. Mankind makes the use of constructs for what is perceived as the real world and this allows manipulation the world around us as we see fit. All life does this by means of genetic evolution or it passes away from being a viable, living organism. Microorganisms under ideal conditions have complete lives in 20 minutes. It is possible for mankind to procreate in the early teens. Thus genetic evolutionary processes occur much faster in microorganisms and the means by which these processes work allow for much experimentation. Most genetic changes are not enhancing, most are detrimental.

If(as a dynamic, living organism) I am able to do something to enhance my survival, to decrease the survival of other organisms or to combine activities with another organism which increases my survivability: my progeny have a better chance of surviving at this point in the evolution of my kind. Let us delineate the many kinds of activities which we know about that will enhance a microorganisms survivability.

Competition for nutrients by microorganisms is intense. Outcomes depend upon rates of growth which are dependent upon rates of nutrient uptake and rates of inherent metabolic processes. If there is enough energy available, microorganisms might secrete a compound which will inhibit the physiological activities of other organisms. These compounds we call antibiotics and use for suppressing microbial infections in microorganisms other than the one producing it.

If I am able to combine my activities in conjunction with another or others of like kind to accomplish what I alone am not able to do but as a group are capable of accomplishing, then I, we, are better able to survive and prosper in an environment lacking in nutrients. Some of us move electrons between inorganic compounds, usually metals and complexes of various degrees of oxidation(nitrite to nitrate and sulfate to elemental sulfur as examples). Some of us have one enzyme and others another so that in toto a series of electron transferees occur which will allow us to accumulate high energy bonds which we may use to make ATP(adenosine-tri-phosphate) which the currency of metabolism and required for all organic life.

Some microorganisms survive simply because they have the ability to accomplish one reaction which no other microorganism is yet capable of performing. Others survive because no other microorganism is able to do so under their living conditions. Somehow life respects their ability and does not intrude.