**3. Plants as microbial habitats**

The plant microbiome is highly dynamic and diverse. Plant-associated microbial communities are deeply influenced by environmental conditions (pH, moisture, temperature, and nutrient availability) and host genotypes. Plants harbor microbial communities in above- and below-ground tissues (**Figure 1**). Below ground, the rhizosphere (soil region in intimate contact with roots) is the environment most densely populated by microorganisms [31]. The root endosphere is another important belowground region that hosts a vast diversity of microbial communities. The endosphere is the region encompassing the apoplastic spaces in the root cortex (inside the roots). The host genotype strongly influences the microbial communities of the rhizosphere and endosphere, and this can be considered an "extended root phenotype" (i.e., a manifestation of the effects of plant genes on their environment inside and/or outside the organism) [32].

*Perspective Chapter: Microorganisms and Their Relationship with Tree Health DOI: http://dx.doi.org/10.5772/intechopen.110461*

#### **Figure 1.**

*Interactions between microorganisms and trees. Microorganisms present in the bulk soil that roots can recruit via organic molecule exudation (1). Microorganisms in the rhizosphere and endosphere. The presence of root exudates (sugars, lipids, proteins, and secondary metabolites) stimulates the recruitment of specific microbial taxa. The rhizosphere microbiota is strongly influenced by the physicochemical profile of the exudates of this niche (2). Endophytic microorganisms can inhabit internal regions of the plant without causing disease. Bacteria that inhabit the root endosphere can be translocated via the xylem to other regions of the plant above ground (3). The phyllosphere is the compartment that houses associated microorganisms above ground, and this niche is mainly represented by the leaves (4). Other above-ground compartments may harbor associated microorganisms, such as the outer surface of fruits (carposphere), flowers (anthosphere), and the stem (caulosphere) (5). Microorganisms can be dispersed from one plant to another or from the soil to the phyllosphere by wind, rain, insects, and animals (6). The composition of the microbial community of the phyllosphere is significantly influenced by environmental factors, including solar radiation, temperature, and humidity (7).*

Between the volume of soil not occupied by roots and the endosphere region, there is a selection degree of microorganisms. Various studies have demonstrated that microbial species richness is the highest in the bulk soil and that it decreases in the rhizosphere and endosphere (**Figure 1**). In contrast, the population density of specific microorganisms increases from the soil toward the root surface, indicating favorable conditions for the selected microbial species [5]. This phenomenon is called the rhizospheric effect, that is, the composition of root exudates (sugars, oligosaccharides, vitamins, nucleotides, flavones, auxins, and secondary metabolites) modulates the physicochemical conditions of the rhizosphere region and, thus, the plant can recruit and select groups of microorganisms that can proliferate in the specific physicochemical conditions of the root zone [33]. Estimates have indicated that up to 40% of the carbon reserves fixed by photosynthesis are provided in

the rhizosphere, indicating the active role of plants in recruiting microbial communities. Although the root zone harbors a wealth of biodiversity, the rhizosphere and endosphere microbial communities are dominated by four bacterial phyla: Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria [5, 34]. In the bulk forest soil, the dominant fungal group is Basidiomycota, while Ascomycota is the most prevalent group in plant tissues [9].

Evidence suggests that plants adapt to biotic stress by altering their root exudate chemistry to assemble health-promoting microbiomes [35]. This phenomenon is termed the "cry-for-help" hypothesis, and it posits that plants modulate the chemistry of root exudates to recruit partner microorganisms capable of increasing the plants tolerance to a given stress condition, such as insect herbivory, pathogen attack, or nutrient shortage. Therefore, the chemical composition of root exudates influences the metabolism of rhizosphere microbial taxa while the recruited microbiota assists plant homeostasis by encoding functionalities that extend the plant genome [36]. For example, a study with the model plant *Arabidopsis thaliana* and inoculated with the Gram-negative pathogen *Pseudomonas syringae* demonstrated that subsequent generations of *A. thaliana* subjected to inoculation with the pathogen were able to modulate the root exudation profile, alter the composition of the rhizosphere microbial community, and increase the disease suppressive response [37].

Above ground, there is also an important plant compartment that hosts microorganisms; it is called the phyllosphere and refers mainly to the leaves. However, there are also other important plant sub-compartments above ground, such as the anthosphere (external environment of flowers), caulosphere (environment of the plant stem), carposphere (external surface of fruits), and spicosphere (niche formed in plants with spikes) [38–39]. The phyllosphere is an oligotrophic environment subject to severe modifications in a short period of time (temperature, humidity, and radiation fluctuations); despite being disconnected from the soil, this environment indirectly influences the phyllosphere. Dust particles from the soil can be dispersed by the wind and deposited in the above-ground plant compartments and thus provide nutrients for the microbial communities of the phyllosphere. In addition, microorganisms can be dispersed from the soil to the above-ground part of the plant by wind or colonize the phyllosphere after being recruited in the rhizosphere and systematically translocated to the above-ground part via the xylem. Microorganisms that can colonize plant tissues internally or translocate via the xylem to different tissues of the plant above ground without causing disease are called endophytes. These microorganisms may live part of their life cycle associated with the root endosphere region or translocated to plant tissues above ground. Furthermore, as in the rhizosphere, the bacterial communities of the phyllosphere are dominated by the taxa Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria [40].

The phyllosphere is an open environment where the arrival and departure of taxa are constant [41]. The phyllosphere generally consists of microorganisms that are dispersed mainly from the soil and reach the surface of leaves and stem through rain, wind, and insects (**Figure 1**). The survivability and colonization of these microorganisms depend on several factors, such as host genotype and health (since both modulate the chemical composition of leaves), water availability, temperature fluctuation, UV exposure, chemical applications (i.e., fertilizers and pesticides), and inter- and intraspecific microbial competition [41–43]. Although several factors influence microbial communities, it is recognized that environmental conditions are the key factors that determine population structure in microbial communities of the phyllosphere. For instance, a recent study revealed that the microbial community

#### *Perspective Chapter: Microorganisms and Their Relationship with Tree Health DOI: http://dx.doi.org/10.5772/intechopen.110461*

composition of the phyllosphere of spruce trees was influenced by seasonal changes, whereas the bacterial and fungal communities of the rhizosphere of these same trees were influenced by anthropogenic nutrient availability [44].

Because it is an environment with harsh conditions, many microorganisms have evolved and developed survival strategies to colonize the phyllosphere. Thus, to colonize niches in the phyllosphere, some microorganisms can alter the chemistry of the leaf surface or use specialized cellular structures to increase their ability to compete. For example, the bacterium *P. syringae* (an important plant pathogen) releases surfactants that increase mobility and local water availability on leaf surfaces. In addition, this microorganism has flagella that favor bacterial motility on the leaf surface. In the case of *P. syringae*, these strategies are related to its virulence [41]. Nonetheless, characteristics of the host plant's aerial part structures also influence the successful colonization of the phyllosphere. One study evaluated the bacterial functional diversity in the phyllosphere of different tree species in a Neotropical forest and found evidence suggesting an adaptive correspondence between phyllosphere microorganisms and their tree hosts [40]. The authors demonstrated that tree characteristics, such as leaf morphology and leaf metal contents (copper, manganese, and zinc), are correlated with phyllosphere microbial community composition [40].
