Principles of Microbial Ecology

Ecology is the study of the relationships of organisms, plant and animal, large and small, to each other and to their environment. Likewise, microbial ecology is the study of the relationships of microorganisms to each other and to their environment. Living organisms interact with one another in symbiotic relationships, such as commensalism, mutualism, and parasitism, described in chapter 19. Organisms in a given area, the community, interact with each other and the non-living environment, forming an ecological system, or ecosystem. Major ecosystems include the oceans, rivers and lakes, deserts, marshes, grasslands, forests, and tundra. Each ecosystem possesses a certain spectrum of organisms and characteristic physical conditions. The region of the earth inhabited by living organisms is called the biosphere. Within the biosphere, ecosystems vary both in biodiversity (the number of species present and their evenness of distribution) and biomass (the weight of all organisms present). ■ symbiotic relationships, p. 461

Microorganisms play a major role in most ecosystems, and many ecosystems host microbes unique to themselves. The role that an organism plays in a particular ecosystem is called its ecological niche. The environment immediately surrounding an individual microorganism, the microenvironment, is most relevant to that cell, but because microbes are so small the microenvironment is difficult to identify and measure. The more readily measured gross environment, or macroenvironment, may be very different from the microenvironment. Consider a bacterial cell living within a biofilm, a polysaccharide-encased microbial community such as plaque on the surface of a tooth (figure 30.1); growth of aerobic organisms in the biofilm can deplete oxygen and create microzones that will support the survival of

Figure 30.1 Bacteria Within a Biofilm This scanning electron micrograph image of a human tooth surface shows a variety of bacteria within the biofilm of plaque. Growth of aerobic organisms depletes oxygen, creating anaerobic microzones where obligate anaerobes can grow. On teeth, these anaerobes ferment sugars from foods, producing acids.The acids corrode tooth enamel, resulting in cavities.

Figure 30.1 Bacteria Within a Biofilm This scanning electron micrograph image of a human tooth surface shows a variety of bacteria within the biofilm of plaque. Growth of aerobic organisms depletes oxygen, creating anaerobic microzones where obligate anaerobes can grow. On teeth, these anaerobes ferment sugars from foods, producing acids.The acids corrode tooth enamel, resulting in cavities.

obligate anaerobes. Fermenters can produce organic acids that are metabolized by other organisms in the film. Other growth factors can be transferred directly within the microenvironment of the biofilm. Thus, certain microorganisms that might seem unexpected in a given macroenvironment actually thrive there because of microenvironments. ■ biofilm, p. 104 ■ growth factor, p. 91

Nutrient Acquisition

Organisms are categorized according to their trophic level, or their source of food, which is intimately related to the cycling of nutrients. There are three general trophic levels: primary producers, consumers, and decomposers (figure 30.2):

■ Primary producers are autotrophs; they convert carbon dioxide into organic materials. Producers include both photoautotrophs such as plants, algae, cyanobacteria, and anoxygenic phototrophs, which use sunlight for

Dead organic matter

Dead organic matter

Small molecules (including CO2)

Figure 30.2 Relationship Between Producers, Consumers, and Decomposers in an Ecosystem

Small molecules (including CO2)

Figure 30.2 Relationship Between Producers, Consumers, and Decomposers in an Ecosystem

Nester-Anderson-Roberts: I V. Applied Microbiology I 30. Microbial Ecology I I © The McGraw-Hill

Microbiology, A Human Companies, 2003

Perspective, Fourth Edition energy, and chemolithoautotrophs, which oxidize inorganic compounds for energy. Primary producers serve as a food source for consumers and decomposers. ■ photoautotroph, p. 91 ■ cyanobacteria, p. 278 ■ anoxygenic phototrophs, p. 276 ■ chemolithoautotroph, p. 91

■ Consumers are heterotrophs: Because they utilize organic materials, they rely on the activities of primary producers. Herbivores, which eat plants or algae, are primary consumers. Carnivores that eat herbivores are secondary consumers; carnivores that eat other carnivores are tertiary consumers. This chain of consumption is called a food chain. Interacting food chains are called a food web.

■ Decomposers are heterotrophs that digest the remains of primary producers and consumers. The fresh or partially decomposed organic matter used as a food source, including carcasses, excreta, and plant litter, is called detritus. Decomposers specialize in digesting complex materials such as cellulose, converting them into small molecules that can more readily be reused by other organisms. The complete breakdown of organic molecules into inorganic molecules such as ammonia, sulfates, phosphates, and carbon dioxide is called mineralization. Microorganisms, particularly bacteria and fungi, play a major role in decomposition processes owing to their ubiquity and unique metabolic capabilities.

Bacteria in Low-Nutrient Environments

Since low-nutrient environments are common in nature, microorganisms capable of growth in dilute aqueous solutions are also common. Most microbial growth in these environments is in biofilms, and the organisms are shed from the film into the aqueous solution. These organisms are by no means restricted to lakes, rivers, and streams. Indeed, microorganisms even grow in distilled-water reservoirs such as those found in research laboratories and pulmonary mist therapy units used in hospitals. In these environments, the microbes can extract trace amounts of nutrients absorbed by the water from the air or adsorbed onto the biofilm. Although the organisms grow slowly, they can reach concentrations as high as 107 per milliliter. Since this cell concentration is not high enough to result in a cloudy solution, the growth usually goes unnoticed. This can have serious consequences for the health of hospitalized patients and for the success of laboratory experiments that depend on water purity. Organisms that grow in dilute environments contain highly efficient transport systems for moving nutrients inside the cell. Other mechanisms that bacteria use to thrive in dilute aquatic environments are described in chapter 11. ■ transport systems, p. 55 ■ thriving in aquatic environments, p. 286

Microbial Competition and Antagonism

Although many different species may be capable of living in a given microenvironment, only one or a few actually occupy it. The species best adapted to live in a particular microenvironment is the one that inhabits it to the exclusion of others. A large num-

30.1 Principles of Microbial Ecology 767

ber of different species are found, for example, within a particle of soil. If, however, the particle is carefully dissected into squares of about 70 ¡lm per side, only a single species will be found living as a microcolony within any one of these squares.

Perhaps nowhere in the living world is competition more fierce and the results of competition more quickly evident than among microorganisms. The ability of an organism to compete successfully for a habitat is generally related to the rate at which the organism multiplies, as well as to its ability to withstand adverse environmental conditions. The complete takeover of one species by another is especially likely when two species have similar nutrient requirements and one of the nutrients is in limited supply. The organism that multiplies faster will yield the larger population, utilizing more of the limited nutrient supply. Because bacteria often can divide at least once every several hours, any small differences in their generation times will result in a very large difference in the total number of cells of each species after a relatively short time. For example, if 10 cells each of a rod and a coccus are growing in the same natural environment, under conditions in which the generation time of the rod is 100 minutes and that of the coccus is 99 minutes, and if the number of cells reaches about 109, there will be 1.35 times as many cocci as rods. If the cells are then placed in conditions where they can continue to multiply, the ratio of cocci to rods will increase to the point where there are very few rods left (figure 30.3).

Antagonism between groups of organisms also helps determine the make-up of a community. In the soil, for example, some microbes resort to a type of chemical warfare, producing antimicrobial compounds. Bacteriocins, which are proteins produced by bacteria that kill closely related strains, are an example of an antagonistic chemical that plays an important role in microbial ecosystems, promoting biodiversity through competition. It is

Growth

Transfers and more growth

Transfers and more growth

Coccus

Coccus

Figure 30.3 Competition Between Two Bacteria The organism that multiplies faster yields the larger population.

768 Chapter 30 Microbial Ecology tempting to speculate that antibiotics produced by Streptomyces species share a similar function, but their natural role is still poorly understood. In the laboratory, antibiotics are produced along with other secondary metabolites as nutrients become depleted and cells enter late-log phase. This is also when Streptomyces species begin forming spores called conidia, a dormant form capable of withstanding dry conditions. Perhaps antibiotic production allows the cells to fend off the competition for the few remaining nutrients, thereby permitting them to complete the process of sporulation, increasing the species chance of long-term survival. Recently, the genome sequence of S. coelicolor was determined, a development that will hopefully shed light on the answer. ■ the genus Streptomyces, p. 284 ■ secondary metabolite, p. 102 ■ late-log phase, p. 102 ■ DNA microarray, p. 226

Competition and antagonism both probably contribute to the observation that the community of bacteria living in the human intestine tends to remain relatively stable with time. Although humans swallow large numbers of bacteria, including some closely related to those already present, the new strains have great difficulty becoming established. The resident community not only competes successfully for a limited food supply, it also produces toxic substances that inhibit the growth of newcomers. The resident microorganisms thus provide a natural defense mechanism against intestinal pathogens.

Microorganisms and Environmental Changes

Environmental changes often result in changes in a community. Those organisms that have adapted to live several inches beneath the surface of an untilled field will probably not be well adapted to that field if it is plowed, fertilized, and irrigated. If the organisms are to survive under these new conditions, they must adapt to the altered environment. Cells may be able to synthesize different enzymes that help them cope with a new environment. Generally, cells synthesize only the enzymes they absolutely require for growth. Under changed environmental conditions, however, additional or different enzymes may become important. In response to the new stimuli, the microbes are induced to synthesize these enzymes and stop producing others that are no longer useful. For example, some bacteria can produce an enzyme that inactivates mercury, a toxic metal, but the enzyme is only formed when mercury is present. ■ enzyme induction, p. 183

A mutant within a population may be ill adapted to its environment and remain in the minority. It may, however, be especially well adapted to a new changed environment. For example, bacteria that mutate to become resistant to the antibiotic tetra-cycline are at a distinct advantage when tetracycline is added to the environment. As the antibiotic inhibits growth of competing organisms, the tetracycline-resistant bacteria then become the dominant organisms (see figure 21.13).

In addition to external sources of environmental change, the growth and metabolism of organisms themselves may alter the environment dramatically. Nutrients may become depleted, and a variety of waste products, many of which are toxic, may accumulate. In some environments, the changing conditions bring about a highly ordered and predictable succession of bacterial species. First one species becomes dominant, then another,

Acidity i

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