Similarly, lateral roots are associated with distinct microbial communities, differing between tips and bases, as well as between different types of lateral root . One trait influencing the differential microbial colonization of root tissues could be the differential exudation profiles of the distinct root parts. This is illustrated in the following example. Clusterroots are densely packed lateral roots formed by some plants growing on extremely nutrient-poor soils; these roots exude high amounts of organic acids and, in some cases, protons, to solubilize phosphate. The low pH and carboxylate-rich rhizosphere of cluster roots is associated with a specialized rhizobiome, dominated by Burkholderia species that metabolize citrate and oxalate. Besides organic acids, mature cluster roots also exude isoflavonoids and fungal cell wall degrading enzymes, leading to a decrease in bacterial abundance, as well as fungal sporulation. Taken together, cluster root exudates not only solubilize phosphate, but also regulate microbes in such a way that they do not interfere with phosphate uptake. Beyond this example, spatial patterns ofmetabolite exudation are largely unexplored.We hypothesizethat such patterns exist in all root systems forthe following reasons: spatially distinct organic acid exudation is atrait of all root systems ; spatially distinct exudation was similarly detected for strigolactones, amino acids, and sugars;and root nutrient uptake,hydroponic net pots which is sometimes coupled with proton transport, can also exhibit spatial patterns.
Overall, spatially defined metabolite exudation by distinct root parts is likely an important factor in structuring the rhizobiome. Future studies should aim at characterizing spatially distinct rhizobiomes and their functional traits, and at investigating spatially distinct root exudation.Roottips are not only associated with high numbers of bacteria , but also produce border cells and mucilage , crucial for plant–microbe interactions. Depending on the root meristem organization,border cells are released into the rhizosphere either assingle cells or as border-like cells.Single maize border cells stayed alive in soil for months, likely due to the presence of starch deposits, whereas arabidopsis border-like cells survived for only 2 weeks. Border cells have a transcriptional profile distinct from root tip wells, with overall lower primary and higher secondarymetabolism. ABC transporters constitute a large fraction of differentially expressed genes, which is consistent with transport of secondary metabolites. Secondary metabolites are likely central to the role of border cells in defense against pathogens. Pathogen attack can result not only in higher border cell production and release, but also in higher mucilage production by border cells and root tip cells. Mucilage contains proteins with antimicrobial functions , as well as extracellular DNA involved in defense against fungi and certain bacteria. Importantly, mucilage is also produced under nonpathogenic conditions, serving as a lubricant for the root environment and stabilizing soil particles. Interestingly, mucilage also provides distinct carbon sources for microbes, thus influencing rhizobiome composition. Border cells similarly interact with nonpathogenic microbes : they release flavonoids that attract rhizobia, uncharacterized compounds that induce branching of mycorrhizal hyphae, and arabinogalactans that trigger biofilm formation of specific beneficial bacteria . The full extent of how border cells and mucilage shape root–microbe interactions remains unclear.
It is tempting to speculate that the specialized metabolism of the border cells results in a distinct exudation profile of not only proteins and mucilage, but also low molecular-weight compounds that could serve as microbial nutrients or as signaling compounds. Further research should focus on the genetic and physiological differences between border cells and border-like cells, as well as on the transport proteins involved in exudation of low-molecular-weight compounds, DNA, and proteins.Plant–microbe interactions are not only defined by plant root morphology and plant-derived exudates, but also by microbe–microbe interactions . Thus, we focus further here on microbial communities. Specifically, we discuss: how plant exudates influence microbial diversity; how plant-responsive microbes are identified; how microbes interact and how mycorrhizal fungi influence root–bacteria interactions. The rhizosphere serves as carbon-rich niche for the establishment of microbial communities, in contrast to bulk soil, which is rapidly depleted in carbon and other nutrients by heterotrophic microbes. Given that the ability of microbes to metabolize plant-derived exometabolites might determine their success in the microbial community, several studies have investigated whether the diversity of plant exudates correlates with microbial diversity. Some studies found higher plant diversity was associated with higher microbial diversity, and that the addition of a diverse exudate mix to plant monocultures increased microbial diversity. Interestingly, isolates from soils with a diverse plant community consistently exhibited less-narrow niches and displayed less resource competition than did isolates from low plant diversity environments. Although on a global scale, environmental factors had a larger impact on microbial diversity than did plant diversity, we can conclude that, on a local scale, high plant diversity likely promotes a diverse microbial community.
The large diversity of microbial communities is a current challenge for plant–microbe research, because it is impractical to study questions such as how members of a community interact, and what specific traits a microbial community has. Therefore, many studies currently aim at identifying the subset of microbes responsive to plants. Strikingly, only 7% of bulk soil microbes increased in abundance in the rhizosphere compared with bulk soil, which reduces the number of taxa to investigate from thousands to hundreds. Other approaches to identifying plant-responsive microbes have focused on transcriptional profiling. Compared with soilabundant microbes, plant-associated microbes exhibited distinct transcriptional responses to plant exudates and, intriguingly, displayed distinct phylogenetic clustering. Network analyses further revealed that rhizosphere microbes displayed higher levels of interactions than did bulk soil microbes. These studies illustrate the potential for the identification of a distinct set of plant-responsive microbes. The above points highlight how plants influence microbial communities. However, the members of microbial communities also interact with each other. Compellingly, it is still unclear whether microbe–microbe interactions are predominantly positive or negative. Network analyses reported predominantly positive intrakingdom interactions. By contrast, laboratory growth assays identified competition as the major factor in shaping isolate communities, and cooperation could only be detected for 6–10% of the isolates. One major difference between the two experimental approaches is that the former investigates a natural system, whereas the latter is based on the ability to culture microbes. Isolation of microbes introduces a bias, since it can select against cooperators, precluding obligate syntrophs. Further evidence that at least some microbes avoid competition was provided by co-cultivation experiments. Environmental isolates: displayed high substrate specialization; did not necessarily take up the compound with the highest energy; and diverged in substrate use when cultivated for several generations. In addition, some metabolites exuded by microbes could be metabolized by others,blueberry grow pot suggesting potential cross-feeding between community members. The above findings suggest complex interactions of microbes. It remains to be resolved in which situation competition or cooperation dominates communities. However, it is evident that microbial interactions are based on altered gene expression. Microbes responded to competing bacteria or even close relatives by differentially regulating genes involved in metabolite exudation and transport processes, making the study of microbial transporters a compelling topic for future studies. Thus, metabolite uptake, release, and sensing are important factors in shaping microbial communities. Metabolite turnover in soil is influenced not only by plants, but also by functionally diverse bacteria, fungi, and animals. Plant–fungal and plant–animal interactions in the rhizosphere go beyond the scope of this review, and are discussed elsewhere. Here, we provide a few brief examples focusing on the impacts of mycorrhiza on rhizobiomes and exometabolite turnover. Endomycorrhizal fungi receive a significant fraction of the carbon fixed by plants . Interestingly, these fungi also exude sugars,shaping a distinct bacterial community. Likewise, Ectomycorrhiza receive carbon from plants, and form a dynamic bacterial community; they even participate in plant-to-plant carbon transport. The field of fungal microbiomes is nascent: if and how fungi control exudation, whether fungal microbiomes have beneficial functions, and how plant and fungal microbiomes influence each other are all unknowns. Although many questions remain, these recent findings already suggest that a holistic view of rhizosphere nutrient cycling and signaling exchange via exometabolites requires a whole-community approach including all domains of life.Plant exudates shape microbial communities. Overall, plants exude up to 20% of fixed carbon and 15% of nitrogen, which includes an array of simple molecules, such as sugars, organic acids, and secondary metabolites, as well as complex polymers, such as mucilage.
Although every plant produces exudates, the amount and composition of root exudates varies. First, exudation is defined by the genotype of the host, as observed in the distinct exudation patterns of 19 arabidopsis accessions. Strikingly, the amount of variation between the accessions depended on the metabolite class investigated. Glucosinolates displayed most, flavonoids medium, and phenylpropanoids low variability. Second, exudation changes with plant developmental stage: with increasing age, arabidopsis sugar exudation decreased, and amino acid and phenolic exudation increased. Third, exudation is modulated by abiotic stresses: the amounts of exuded amino acids, sugars, and organic acids changed in maize grown in phosphate-, iron-, nitrogen-, or potassium-deficient conditions. In addition, phosphate-deficient arabidopsis plants increased coumarin and oligolignol exudation, heavy metal-treated poplar induced organic acid exudation, and zinc-deficient wheat increased phytosiderophore exudation. Differential exudation is a plausible mechanism by which plants could modulate their interaction with microbes, as exemplified by the correlation between exudation patterns and rhizobiome variation reported for eight arabidopsis accessions. Differential exudation modulated by transport proteins is discussed below.Plant-derived exometabolites need to cross at least one membrane to transit from the cytoplasm of root cells into the rhizosphere. There is considerable discussion as to what degree plants are able to regulate this transport. In general, different modes of transport could be envisioned. First, small, hydrophilic compounds could diffuse from the root into the rhizosphere, driven by the large concentration gradient. Second, channel proteins could facilitate such diffusion. Third, active or secondary active transporters could shuttle compounds across membranes against a concentration gradient. Diffusion of compounds can only be relevant in young root tissue, which is still devoid of Casparian strips or suberized endodermis that both block apoplasmic flow in adult tissues. Transport proteins involved in exudation are mostly elusive. From a conceptual point of view, plasma membrane-localized exporters likely have a direct, and vacuolar transporters an indirect effect on exudation. The vacuole is a major storage organelle for many metabolites detected in exudates, such as sugars, organic acids, and secondary metabolites. Alteration of vacuolar transporter levels impacts vacuolar and cytosolic concentrations and, thus, can influence metabolite exudation into the rhizosphere. The few characterized transporters involved in exudation are essential for the transport of specific compounds, and are presented in Table 1. Since only a few transporters involved in exudation have been characterized, we suggest additional families that might be involved in the process. To complete the picture of metabolite exchange between roots and soil, Table 1 additionally contains a few important plasma membrane-localized metabolite uptake systems. Below, we discuss the evidence for transport processes involved in the import and exudation of compounds detected in root exudates, such as sugars, organic acids, and secondary metabolites.Sugars constitute a significant fraction of exudates, and are a main carbon source for microbes. Interestingly, many more sugar uptake than release systems have been described. Sugar Transport Proteins utilize high extracellular proton levels to import sugars, and mutation of STPs leads to higher external sugar levels. Sugars Will Eventually Be Exported Transporters are sugar uniporters, and all root-expressed members localize to the vacuole. Due to an alteration of root sugar homeostasis, SWEET mutant plants exhibited higher sugar export from roots compared with wild-type plants, and were more susceptible to disease. Intriguingly, no transporters directly exporting sugars into the rhizosphere have been characterized so far, and it is debated whether sugar exudation is a transport-driven process at all. Potential evidence for passive sugar efflux was supported by the observation of higher sucrose concentrations around young, permeable root tissue than around older, less-permeable root tissue. However, because sugars are synthesized in leaves, they still need to be unloaded either from phloem or from root cells to be exuded into the rhizosphere, a process likely depending on transporters due to the hydrophilic nature of sugars. A further indication of the presence of elusive transporters is the differential sugar exudation in various environments, as shown, for example, for maize grown in potassium-, phosphate-, or iron-deficient conditions.