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Sj stems, leaves, flowers, and fruits, each presenting different challenges and rewards to the colonizing bacteria.

The Spermosphere and the Rhizosphere

A single gram of garden soil may contain 109 bacteria, 107 fungi, 104 protozoa, 104 algae, and a diverse array of small animals. Within the vast subterranean ecosystem, nowhere are organisms more numerous than in the soils surrounding a plant. As soon as a seed germinates, it exudes a variety of metabolites into the soil, creating a rich habitat around the seed called the spermosphere. Bacteria borne on the seed and those indigenous to the soil proliferate and thrive in the spermosphere.

As the plant develops, intense microbial activity occurs in the region surrounding the root, known as the rhizosphere. When discussing root function, emphasis is usually placed on nutrient uptake from the soil; however, roots also deposit nutrients into the soil - a function that is often overlooked. Forty to eighty percent of the carbon captured during photosynthesis is released from the roots in a process called rhizodeposition. Nutrients are deposited into the soil as (1) cells sloughed from the root cap, (2) lysates from dying cells, (3) gelatinous mucilage that helps aggregate soil particles, and (4) exudates. Exudates contain sugars, organic acids, amino acids, proteins, vitamins, phenolics, and flavo-noids. One gram of root is estimated to release 50-100 mg of exudate, enough to support 2 x 1010 bacteria. Not surprisingly, the rhizosphere contains 10-100 times more bacteria than bulk soil. Furthermore, the diversity of microbes found in the rhizosphere can be staggering. Analysis of 16S rRNA DNA sequences demonstrates that the bacterial composition of the rhizo-sphere differs significantly from bulk soil. Microbes aggregate in areas where rhizodeposition is plentiful -around the root cap, elongation zone, root hairs, and where lateral roots emerge (Figure 2).

Most rhizosphere bacteria are considered commensals. They thrive in the nutrient-rich habitat provided by the root, but neither benefit nor harm the plant. However, the distinction between commensals, mutualists, and parasites is often murky. For example, Rhizobium species are renowned for mutualism, providing fixed nitrogen to their legume partners, in exchange for carbohydrates. However, in the absence of a legume host, Rhizobium colonizes other plants as a commensal.

Successful colonization of roots requires that bacteria compete with other microbes for resources and space. By improving their competitive fitness, bacteria sometimes benefit the host plant. For example, the most successful colonists efficiently break down and utilize root-derived organic compounds, which cannot be used by plants for nutrition. By degrading those compounds to feed

Figure 2 Confocal laser scanning micrograph of fluorescently labeled bacteria attached to an alfalfa root. The bacteria outline the main and lateral roots. Photograph, courtesy of M. R. Lum.

themselves, bacteria inadvertently provide the plant with usable forms of the nutrient. Some rhizosphere bacteria become successful colonists by secreting antibiotics that kill competitors. Often, this war between microbes does not significantly impact the plant. In some cases, antibiotic production plays an important role in plant defense. For example, Pseudomonas species produce antibiotics that suppress fungal infection of plants.

The Phyllosphere

The phyllosphere is the aerial region of the plant colonized by microbes; its colonists are often called epiphytes. Fungi, algae, protozoa, and nematodes inhabit the leaf and stem surfaces, but the most abundant epiphytes are bacteria (averaging 106-107 cells cm-2).

Perhaps the most famous of the eukaryotic commensals on plants are the wild or indigenous yeasts (species of Hanseniaspora (Kloeckera), Metschnikowia, and Pichia), often associated with the white, waxy coating or 'bloom' found on grape berries. These wild yeasts are thought to impart a spoiled taste to the wine when used for fermentation, and hence are replaced by cultured strains of Saccharomyces cerevisiae, which normally is estimated to be present on only 1 in 1000 berries.

The phyllosphere is considered to be a hostile environment due to rapid changes in temperature and humidity, limited nutrients, and solar irradiation. Yet, phyllosphere commensals have adapted to cope with these conditions. For example, many epiphytic bacteria are pigmented to prevent ultraviolet (UV) damage, and microbial communities preferentially develop along veins, and around trichomes and stomata, where nutrients leak from the plant surface.

Phyllosphere research has mostly focused on understanding pathogenic bacteria. Considerably less is known about the nonpathogenic epiphytes, although commensals appear to play a role in limiting the population size of pathogens. Until recently, traditional culturing assessed the composition of the phyllosphere community, but not all organisms can be grown under laboratory conditions. Using a culture-independent approach, 16S rRNA DNA analyses identified many species that had never been seen before on plants, indicating that phyllosphere communities are more complex than previously thought.

Recently, the presence of human pathogens in the phyllosphere has been linked to outbreaks of food-borne illness. Surveys have identified enteric pathogens such as Salmonella and Shigella on produce. These organisms colonize the phyllosphere as commensals, but in humans, the same microbes can become parasitic.

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