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Prokaryotes are well recognized as essential members of the biosphere. They inhabit all possible locations in which life exists from those offering ideal conditions for growth and reproduction to those representing extreme environments at the borderline of abiotic conditions.

The ubiquity of microorganisms is based on three major properties: their small size for easy dispersal by air and water, their metabolic versatility and flexibility, and their ability to tolerate unfavorable conditions. A predominant population is commonly composed of species able to grow under the particular conditions of a habitat. Many other species may also be present but in low numbers of individuals. As a rule, ecosystems of indistinct physicochemical and nutritional characteristics, such as many soils or sea water, which neither suppress nor specifically support microbial growth, usually carry low numbers of microorganisms but a high diversity of species. In contrast, ecosystems of strong environmental characteristics, such as acid mine waters, salt brines, and hot springs, commonly contain high cell numbers of very few species.

Experimental enrichment procedures bring about the predominance of certain species by controlling the supply of specific nutrients or the use of certain physicochemical conditions. If the growth conditions of a particular microorganism are known and reproducible, enrichment and isolation usually pose no problem. But if the particular requirements for growth of an organism are unknown, isolation procedures may be difficult to discover (; ). For that reason, a number of organisms long known from microscopical observations, such a or , have not yet been isolated in pure culture. Furthermore, organisms that have hitherto unknown growth characteristics and that are too small and inconspicuous for easy microscopical recognition have often escaped detection. An excellent example is ().

In characterizing an ecosystem microbiologically, it is important to distinguish between 1) organisms introduced incidentally by air, soil runoff, etc., physiologically just making the best of it, and 2) organisms typically adapted to the particular habitat and not occurring in any other except in the form of survival stages. An example of the former is , as frequently found in polluted waters. An example of the latter is the above-mentioned sp., whose need for dissolved oxygen and hydrogen sulfide at the same time requires a high motility combined with chemotactic orientation in an aquatic oxic/anoxic interface.

Although their morphological differentiation is limited, prokaryotes have evolved a number of structural and chemical mechanisms that enable them to inhabit various extreme environments. The presence of a specified pigment, for instance, protects a cell against detrimental radiation or may provide for the absorption of light energy at specific wavelengths encountered in deeper water. Some filamentous cyanobacteria show a certain degree of cell differentiation, a feature that permits the fixation of elemental nitrogen concomitantly with oxygenic photosynthesis in oligotrophic environments. More importantly, however, the metabolic versatility of the prokaryotes, which reflects the development of metabolism during the evolution of life, enables them to live in many parts of the biosphere, including several where eukaryotes are not able to exist.

The vegetative microbial cell, with its relatively large reactive surface, responds quickly to changing physicochemical conditions of its immediate surrounding. As a consequence, the effective habitat of a microorganism is its microhabitat, the immediate surrounding of the cell in a compatible scale of space and time as determined by the radius of its metabolic action and interaction.

Naming microorganisms for their occurrence in certain characteristic macrohabitats, for example, soil and water bacteria, is of limited use. The two apparently very different habitats, soil and water, can be characterized as representing different proportions of the two phases, solid surface and water. The continuum of habitats ranges from highly arid desert soil with no or firmly bound pore water to offshore pelagic sea water containing a minimum of suspended particulate matter. Within the range of suitable physicochemical conditions, the abundance of microorganisms in an ecosystem is determined by the availability of the required energy and carbon sources and essential nutrients. All the more or less specific environments—e.g., the surface of leaves or skin, intestinal tracts, and symbiotically or parasitically invaded tissues—conform to this general description.

The concept of microenvironments eliminates the sharp dividing lines between aquatic, terrestrial, and even medical microbiology. Indeed, in ecological research the distinction between these academic disciplines is now more and more deemphasized by encompassing them under the label of environmental or biogeochemical microbiology. This chapter does not try to cover all the habitats of all organisms treated in this Handbook; the individual habitats and their characteristics are considered chapter by chapter for single species or physiological groups of prokaryotes. This chapter reviews the versatility of prokaryotic metabolism in relation to a few principles that determine the distribution of prokaryotes in nature.

The principal methods for the enrichment and isolation of the major metabolic types of microorganisms were discovered within a relatively short time. Details of the techniques developed by Winogradsky and Beijerinck are dispersed through the journals. Their collected papers (; ) are treasure troves for microbiologists; only one contemporary compilation exists (). Since the enrichment principles and methods were the subject of a symposium (), several reviews have appeared (; ; ).

The aim of this Handbook is to encourage biologists to continue and intensify the search for bacteria in their natural environments, define habitats and ecological niches, and understand the flux of matter and energy through the biosphere. One may remember that in many soil and water samples there are more kinds of bacteria present than we can cultivate. Furthermore, much data on the flux of carbon and of trace gases through ecosystems cannot yet be accounted for by the bacteria cultivated so far. The gaps need to be filled by laboratory and field studies.

“Well, in country,” said Alice, still panting a little, “you’d generally get to somewhere else—if you ran very fast for a long time, as we’ve been doing.”

“A slow sort of country!” said the Queen, “Now, , you see, it takes all the running can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!”

—Lewis Carroll, , (1872)

“Well, in country,” said Alice, still panting a little, “you’d generally get to somewhere else—if you ran very fast for a long time, as we’ve been doing.”

“A slow sort of country!” said the Queen, “Now, , you see, it takes all the running can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!”

—Lewis Carroll, , (1872)

“Well, in country,” said Alice, still panting a little, “you’d generally get to somewhere else—if you ran very fast for a long time, as we’ve been doing.”

“A slow sort of country!” said the Queen, “Now, , you see, it takes all the running can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!”

—Lewis Carroll, , (1872)

I have spent a lot of time discussing the rise of FSR and there is much more to come. I think that is justified, because after all FSR has been one of the defining features of tropical agricultural science in the second half of the twentieth century. But FSR is software, it deals with methodologies, approaches and attitudes. The hardware is agricultural production: farming practices used by farmers and of course improved technologies invented by scientists. To maintain good balance I will devote the next three chapters to that, before continuing with the FSR story.

The aim of characterization (in the present context) is to obtain a complete collection of data describing the properties of a prokaryotic pure culture, i.e., to develop a description. The aim of “identification” is to equate the properties of a pure culture with those of a well-characterized and accepted species. When identification in this sense cannot be accomplished, the aim of identification must shift to characterization of a new species, i.e., to a new description.

It is clear that the amount of data required for the identification of an isolate with an established species is usually lower than the amount of data collected for characterization. And it is also clear that the final aim of characterization, as mentioned above, is never reached because continuing progress in scientific and technological methods allows the study of an ever-increasing number of characters or properties of a species. Although this continuous progress results in a higher reliability in identification, the practical aim of identification is to base it upon the smallest possible number of characteristics. Therefore, identification in many cases (especially with pathogenic organisms) is a compromise between accuracy and speed. The selected characteristics used for identification usually are weighted and are those that have proved to be significant in distinguishing one organism from another.

Prokaryotes are well recognized as essential members of the biosphere. They inhabit all possible locations in which life exists from those offering ideal conditions for growth and reproduction to those representing extreme environments at the borderline of abiotic conditions.

The ubiquity of microorganisms is based on three major properties: their small size for easy dispersal by air and water, their metabolic versatility and flexibility, and their ability to tolerate unfavorable conditions. A predominant population is commonly composed of species able to grow under the particular conditions of a habitat. Many other species may also be present but in low numbers of individuals. As a rule, ecosystems of indistinct physicochemical and nutritional characteristics, such as many soils or sea water, which neither suppress nor specifically support microbial growth, usually carry low numbers of microorganisms but a high diversity of species. In contrast, ecosystems of strong environmental characteristics, such as acid mine waters, salt brines, and hot springs, commonly contain high cell numbers of very few species.

Experimental enrichment procedures bring about the predominance of certain species by controlling the supply of specific nutrients or the use of certain physicochemical conditions. If the growth conditions of a particular microorganism are known and reproducible, enrichment and isolation usually pose no problem. But if the particular requirements for growth of an organism are unknown, isolation procedures may be difficult to discover (; ). For that reason, a number of organisms long known from microscopical observations, such a or , have not yet been isolated in pure culture. Furthermore, organisms that have hitherto unknown growth characteristics and that are too small and inconspicuous for easy microscopical recognition have often escaped detection. An excellent example is ().

In characterizing an ecosystem microbiologically, it is important to distinguish between 1) organisms introduced incidentally by air, soil runoff, etc., physiologically just making the best of it, and 2) organisms typically adapted to the particular habitat and not occurring in any other except in the form of survival stages. An example of the former is , as frequently found in polluted waters. An example of the latter is the above-mentioned sp., whose need for dissolved oxygen and hydrogen sulfide at the same time requires a high motility combined with chemotactic orientation in an aquatic oxic/anoxic interface.

Although their morphological differentiation is limited, prokaryotes have evolved a number of structural and chemical mechanisms that enable them to inhabit various extreme environments. The presence of a specified pigment, for instance, protects a cell against detrimental radiation or may provide for the absorption of light energy at specific wavelengths encountered in deeper water. Some filamentous cyanobacteria show a certain degree of cell differentiation, a feature that permits the fixation of elemental nitrogen concomitantly with oxygenic photosynthesis in oligotrophic environments. More importantly, however, the metabolic versatility of the prokaryotes, which reflects the development of metabolism during the evolution of life, enables them to live in many parts of the biosphere, including several where eukaryotes are not able to exist.

The vegetative microbial cell, with its relatively large reactive surface, responds quickly to changing physicochemical conditions of its immediate surrounding. As a consequence, the effective habitat of a microorganism is its microhabitat, the immediate surrounding of the cell in a compatible scale of space and time as determined by the radius of its metabolic action and interaction.

Naming microorganisms for their occurrence in certain characteristic macrohabitats, for example, soil and water bacteria, is of limited use. The two apparently very different habitats, soil and water, can be characterized as representing different proportions of the two phases, solid surface and water. The continuum of habitats ranges from highly arid desert soil with no or firmly bound pore water to offshore pelagic sea water containing a minimum of suspended particulate matter. Within the range of suitable physicochemical conditions, the abundance of microorganisms in an ecosystem is determined by the availability of the required energy and carbon sources and essential nutrients. All the more or less specific environments—e.g., the surface of leaves or skin, intestinal tracts, and symbiotically or parasitically invaded tissues—conform to this general description.

The concept of microenvironments eliminates the sharp dividing lines between aquatic, terrestrial, and even medical microbiology. Indeed, in ecological research the distinction between these academic disciplines is now more and more deemphasized by encompassing them under the label of environmental or biogeochemical microbiology. This chapter does not try to cover all the habitats of all organisms treated in this Handbook; the individual habitats and their characteristics are considered chapter by chapter for single species or physiological groups of prokaryotes. This chapter reviews the versatility of prokaryotic metabolism in relation to a few principles that determine the distribution of prokaryotes in nature.

The principal methods for the enrichment and isolation of the major metabolic types of microorganisms were discovered within a relatively short time. Details of the techniques developed by Winogradsky and Beijerinck are dispersed through the journals. Their collected papers (; ) are treasure troves for microbiologists; only one contemporary compilation exists (). Since the enrichment principles and methods were the subject of a symposium (), several reviews have appeared (; ; ).

The aim of this Handbook is to encourage biologists to continue and intensify the search for bacteria in their natural environments, define habitats and ecological niches, and understand the flux of matter and energy through the biosphere. One may remember that in many soil and water samples there are more kinds of bacteria present than we can cultivate. Furthermore, much data on the flux of carbon and of trace gases through ecosystems cannot yet be accounted for by the bacteria cultivated so far. The gaps need to be filled by laboratory and field studies.

“Well, in country,” said Alice, still panting a little, “you’d generally get to somewhere else—if you ran very fast for a long time, as we’ve been doing.”

“A slow sort of country!” said the Queen, “Now, , you see, it takes all the running can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!”

—Lewis Carroll, , (1872)

“Well, in country,” said Alice, still panting a little, “you’d generally get to somewhere else—if you ran very fast for a long time, as we’ve been doing.”

“A slow sort of country!” said the Queen, “Now, , you see, it takes all the running can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!”

—Lewis Carroll, , (1872)

“Well, in country,” said Alice, still panting a little, “you’d generally get to somewhere else—if you ran very fast for a long time, as we’ve been doing.”

“A slow sort of country!” said the Queen, “Now, , you see, it takes all the running can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!”

—Lewis Carroll, , (1872)