Microorganisms embedded in plant tissues may be defined as "internalized," derived from "internal," meaning located inside the plant surface. Functionally, internalized microbes cannot be washed off the plant, they are protected from environmental stresses, and they cannot be inactivated by contact bio-cides or other surface disinfectants. Inside the plant, most microorganisms are located in spaces between cells called intercellular spaces, whereas plant viruses and certain other pathogens are inside host cells. Microbes in the intercellular spaces are bathed in nearly saturated relative humidity with a gas composition that enables aerobic metabolic activities . The main threat to the survival of internalized microorganisms appears to be mechanisms that protect the plant against microbial attack . As such, the microbe must either evade, counteract, or not induce its host's defenses. Plant pathogenic microorganisms, which by nature harm plant tissues, have developed ways to cope with host defense reactions. In contrast, nonplant pathogens usually do not harm living tissues and, as a consequence, appear unlikely to stimulate plant defenses. Moreover, the absence of tissue damage reduces the likelihood that nonpathogens will be exposed to preformed antimicrobial chemicals, which would be compartmentalized in the cytoplasm or specialized cells.
Microorganisms that are resistant to washing, surface disinfectants, or environmental stresses are not always internalized. Romantschuk et al.  noted that washing leaves, with or without sonication, does not remove all bacteria that live entirely on the plant surface, perhaps because portions of this population may embed in surface biofilms or other attached aggregates (see Chapter 2). Additionally, bacteria have been observed partially buried in surface waxes  and in cracks in the cuticle . Microorganisms embedded in aggregates, biofilms, surface waxes or ruptures in the cuticle are somewhat protected against environmental stresses  and surface treatments. However, truly internalized organisms, which are located beneath layers of plant cells, would have much greater protection.
Proof that microorganisms exist inside healthy, unblemished fruits and vegetables was provided by Samish et al. . Using special surface sterilization procedures, her group isolated Gram-negative, motile, and rod-shaped bacteria frequently from tomatoes, cucumbers, English peas, and green beans sampled from farm fields. Populations were found less frequently in melons and bananas, whereas successful isolations were infrequent in grapes, citrus fruits, olives, and peaches. Internal populations of microorganisms would likely be highest in root tissues  and lowest in the acidic environment within certain fruit tissues .
Internalized microorganisms are part of a complex microbial ecosystem associated with plants [8,9]. Epiphytic microorganisms survive and multiply on the plant surface, whereas endophytes colonize the interior of plants without causing noticeable damage . Those that grow on or in plants and cause damage are plant pathogens . Epiphytes, endophytes, and plant pathogens may be considered resident microorganisms because they compose the plant-associated microbial ecosystem. Individual species that fail to establish a presence in this ecosystem despite one or more introductions are called casual microorganisms . Casual microbes are usually ill-suited to survive on the plant surface. Once inside the plant, however, casuals can survive for prolonged periods of time depending on their ability to adapt to an environment that is high in humidity but low in available nutrition. However, under certain conditions, internalized casuals multiply. For example, Dong et al.  observed endophytic growth of Escherichia coli and Salmonella enterica (strains of Cubana, Typhimurium, and Infantis serovars) in alfalfa and barrel medic seedlings grown in test tubes. Young  noted that water congestion of leaf tissues enabled a wide range of bacteria to multiply. King and Bolin  reported that severe tissue water congestion caused plant cell membranes to leak minerals and metabolites, which supported the growth of saprophytes. Furthermore, the development of large populations of microorganisms on fresh-cut vegetables could produce nonspecific spoilage, likely because plant defense mechanisms were compromised by anoxia.
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