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Frontiers in Microbiology - V. Microbe Communities

When we think of microbes we typically envision them as free-living cells swimming in water or resting in the soil. Scientists have learned most of what they know about microbes by isolating them and growing cultures of homogeneous populations in the laboratory. This approach has taught us a great deal but also leaves out some of the more interesting and important aspects of microbial life. In nature, microbes don't often lead a solitary existence. Instead their populations often reside in or on other organisms. They may share an environment with other species of microbes with which they compete. It has been estimated that approximately 99 percent of bacteria live in microbial communities and not in a free-living state. This fact alone illustrates why it is critical to study microbial communities.

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Bacteria within a population can communicate with each other by sending and receiving chemical signals. One important type of microbe community is called a biofilm. Unless the population of bacteria is sufficiently large, forming a biofilm doesn’t benefit the individual cells. Bacteria can detect the presence of their neighbors through a process called quorum sensing. This process works through secreted molecules called autoinducers. When the concentration of autoinducers reaches a threshold, the formation of a biofilm begins.

To form a biofilm, the bacteria first attach to a surface that has nutrients. They next secrete a glue that secures their attachment. During this time gene expression is changing. Since the need for movement is no longer important, genes associated with the flagellum are turned off and genes associated with pili are turned on. The bacteria begin to pile up on each other. Clusters of cells become separated from each other by channels of water. This arrangement is in some ways similar to a rudimentary circulatory system. Nutrients make their way to cells of the biofilm through these channels while waste products are removed via the same channels. Some cells in the biofilm are not located near these channels and rely instead on diffusion to obtain nutrients and expel waste. Cells buried deep within the biofilm may be deprived of oxygen and remain dormant. Under these conditions, the bacteria comprising the biofilm express different subsets of their genome depending on their local environment. In this way, a biofilm can be compared to a multicellular organism.

Figure 6.

Understanding biofilms is important for recognizing how bacteria interact with our bodies and how to treat infections by pathogenic bacteria. Some biofilms are relatively innocuous. They form coatings on our teeth and even on contact lenses. Other biofilms are life-threatening. Patients with the disease cystic fibrosis cannot properly regulate the passage of salt in and out of their cells. A mucus forms in the lung tissue, which provides a breeding ground for bacteria. Some species such as Pseudomonas aeruginosa can form biofilms in lung tissue.

It is much more difficult to rid the body of bacteria organized into a biofilm as compared to those in the free-living state. First, the sheer size of the biofilm is too large for the macrophages of the immune system to cope with. Second, treatment with antibiotics can be problematic. It is more difficult for antibiotics to reach and destroy cells deep within the biofilm. The drug may kill cells on the outer surface, leaving the dormant cells of the interior to reactivate the infection once the antibiotics are gone. Bacteria such as Escherichia coli and Pseudomonas aeruginosa have been shown to form biofilms upon exposure to low levels of antibiotics (Hoffman et al., 2005). Presumably this response evolved as a result of microbial competition.

Biofilms can be helpful or harmful. Biofilms have been harnessed to treat sewage and decontaminate ground water. They have also been used to produce biochemicals used in medicines, cleaning products, and food additives. On the other hand, biofilms cost water-based industries billions of dollars per year in lost productivity and damage to product and capital infrastructure. Industries that are seriously impacted by biofilms include

medicine (devices and implants);
food processing;
paper manufacturing;
oil recovery;
drinking water;
cooling water; and
shipping (from biofilms forming on the hulls of ships).

The reductionism that has characterized microbiology for decades has greatly enhanced our understanding of microbes. As discussed in this section, however, there are limits to how far this approach can take us toward understanding microbial communities. The genomes of many microbes have been completely sequenced. We are now in a position to study microbiology using a more holistic perspective. The complexity of microbial communities and their relationships to other organisms and the environment requires scientists to adopt a multidisciplinary systems-biology approach.

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