Putrefying Agents

Putrefying bacteria

Lactococcus lactis

Lactobacillus sp.

Yeast and molds

Putrefying bacteria

Time (days)

Figure 30.4 Growth of Microbial Populations in Unpasteurized Raw Milk at Room Temperature Production of acid causes souring and encourages growth of fungi. Eventually bacteria digest the proteins, causing putrefaction.

Time (days)

Figure 30.4 Growth of Microbial Populations in Unpasteurized Raw Milk at Room Temperature Production of acid causes souring and encourages growth of fungi. Eventually bacteria digest the proteins, causing putrefaction.

and then a third. An example of such a microbial succession is the one that occurs in unpasteurized milk. Most of the microorganisms involved are destroyed by pasteurization.

Unpasteurized milk usually contains various species of bacteria, yeasts, and molds, which are derived mainly from the immediate environment around the cow. Initially, the dominant organism is the bacterium Lactococcus (Streptococcus) lactis, which breaks down the milk sugar lactose, forming lactic acid as an end-product (figure 30.4). The resulting acid inhibits the growth of most other organisms in the milk, and eventually enough acid is produced to prevent even the further growth of L. lactis. The acid sours the milk and also curdles it, a result of denaturation of the milk proteins. Bacterial species such as Lactobacillus casei and Lactobacillus bulgaricus can multiply in this highly acidic environment. These species metabolize any remaining sugar, forming more acid until their growth is also inhibited. Yeasts and molds, which grow very well in this highly acidic environment, then become the dominant group and convert the lactic acid into non-acidic products. Because most of the sugar has already been used, the streptococci and lactobacilli cannot resume multiplication since they require this substrate. Milk protein (casein) is still available and can be utilized for energy by bacteria of the spore-forming genus Bacillus, and some other bacteria, all of which secrete proteolytic enzymes that digest the protein. This breakdown of protein, known as putrefaction, yields a completely clear and very odorous product. The milk thus goes through a succession of changes with time, first souring and finally putrefying.

Microbial Communities

Microorganisms most often grow in communities attached to a solid substrate or at air-water interfaces. General aspects of biofilms were described in detail in chapter 4. In this section,

Figure 30.5 A Microbial Mat A microbial mat is a thick, dense, highly organized structure composed of distinct layers of different groups of microorganisms.

we focus on a specific type of biofilm, a microbial mat. ■ biofilms, p. 104

A microbial mat is a thick, dense, highly organized structure composed of distinct layers. Frequently they are green, pink, and black, which indicate the growth of different groups of microorganisms (figure 30.5). The green layer is the uppermost and is typically composed of various species of cyanobacteria. The color is due to the photosynthetic pigments of these microbes. The pink layer directly below consists of purple sulfur bacteria. The light-harvesting pigments of these anoxygenic phototrophs can use wavelengths of light not collected by the cyanobacteria. The black layer at the bottom results from iron molecules reacting with hydrogen sulfide produced by a group of bacteria called sulfate-reducers. These obligate anaerobes oxidize the organic compounds produced by the photosynthetic bacteria growing in the upper layers of the mat, using sulfate as a terminal electron acceptor. ■ cyanobacteria, p. 278 ■ photosynthetic pigments, p. 156 ■ purple sulfur bacteria, p. 276 ■ sulfate-reducers, p. 274 ■ terminal electron acceptor, p. 134

Although microbial mats can be found in a variety of areas, those near hot springs in Yellowstone National Park are some of the most intensively studied. The mats in these extreme areas are undisturbed by grazing eukaryotic organisms and, consequently, they provide an important model for the study of microbial interactions.

Studying Microbial Ecology

Because so few microorganisms can be successfully cultured in the laboratory, investigating only those that have been isolated may give some essential insights into their activities but often does not portray an accurate picture of what actually occurs in nature. Molecular techniques are now complementing the traditional

30.1 Principles of Microbial Ecology 769

methods such as culture and microscopy, enabling researchers to better understand complex microbial communities.

Microscopic methods, which allow researchers to observe individual cells, can now be used to examine the composition of microbial populations. For example, certain dyes are made fluorescent by metabolic activities carried out only by living cells, and therefore can be used to observe only those cells that are viable (see figure 3.19a). A different technique, fluorescence in situ hybridization (FISH), uses nucleic acid probes that are labeled with a fluorescent molecule to observe only cells that contain specific nucleotide sequences. By employing a probe that binds to a specific 16S rRNA sequence that characterizes a certain domain, genus, or species, FISH allows an investigator to enumerate members of that particular phylogenetic group. Confocal scanning laser microscopes enable researchers to observe sectional views of a three-dimensional specimen such as a biofilm (see figure 3.8). ■ fluorescent dyes, p. 49 ■ FISH, p. 226 ■ 16S rRNA, p. 255 ■ confocal scanning laser microscope, p. 43

Polymerase chain reaction (PCR) can be used to detect certain organisms and assess population characteristics. To detect a specific organism, primers are selected that amplify only DNA unique to that organism (see figure 9.11). To study the composition of a population, total 16S rRNA gene segments can be amplified. Individual fragments can then be cloned and studied. Alternatively the set of amplified sequences can be separated and examined using a technique called denaturing gradient gel electrophoresis (DGGE). This procedure gradually denatures double-stranded nucleic acid during gel electrophoresis and, as a consequence, separates fragments of similiar size according to their melting point, which is related to the nucleotide sequence. Using DGGE, a mixture of 16S rRNA fragments with different sequences will resolve into a distinct pattern of bands. PCR and DDGE studies have confirmed that standard culture techniques can be poor indicators of the composition of natural microbial populations. Based on these molecular techniques that can show the relative abundance of specific nucleotide sequences in the sample, the species that predominate in culture often represent only a minute portion of the total population. ■ polymerase chain reaction, pp. 229,239 ■ gel elec-trophoresis, p. 236

Genomics is also advancing the study of microbial ecology because sequence information gleaned from one organism can be applied to others. For example, researchers found that variations of a gene coding for bacterial rhodopsin, a lightsensitive pigment that provides a mechanism for harvesting the energy of sunlight, are widespread in marine bacteria. This gene provides bacteria with a mechanism for phototrophy that does not require chlorophyll and might be an important mechanism for energy accumulation in ocean environments. ■ genomics, p. 180 ■ bacterial rhodopsin, p. 223

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