The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes

Abstract

All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.

FIG 1

Microphotographs of endophytes showing (arrows) endophytic fungi in Sphagnum sp. (Alex Fluor 488-wheat germ agglutinin [WGA]) (A), endophytic fungi in a fern stem (Alex Fluor 488-WGA) (B), endophytic fungi in a stem of a Pinus sp. (Alex Fluor 488-WGA) (C), fungal endophytes in a stolon of a Trifolium sp. (Alex Fluor 488-WGA) (D), and mycorrhiza colonizing Eleutherococcus sieboldianus (toluidine blue) (E). (F and G) Bacterial endophytes in Sphagnum magellanicum (fluorescence in situ hybridization [FISH] with probes targeting Alphaproteobacteria [F] and Planctomycetes [G]). (H and I) Bacterial endophytes in fern leaves (double labeling of oligonucleotide probes-fluorescence in situ hybridization [DOPE-FISH] with EUBMIX-FLUOS probe for all bacteria [H] and with NONEUB-FLUOS probe [I]). (J and K) Colonization of Scots pine seedling by green fluorescent protein-tagged Methylobacterium extorquens DSM13060. (L) Bacterial endophytes in flowers of grapevine plants (FISH with EUBMIX-Dylight488 and LGC-Dylight549 probes, targeting all bacteria and Firmicutes, respectively). (M) Bacterial endophytes in the xylem of grapevine plants (DOPE-FISH with EUBMIX-FLUOS and HGC69a-Cy5 probes, targeting all bacteria and Actinomycetes, respectively). (N and O) Bacterial endophytes in a nodule of Medicago lupulina (DOPE-FISH with EUBMIX-FLUOS probe targeting all bacteria [N] and with NONEUB-FLUOS probe [O]). (Panel E reprinted from reference . Panels F and G reprinted from reference by permission from Macmillan Publishers Ltd. [copyright 2011]. Panels J and K reprinted from reference with kind permission from Springer Science and Business Media. Panel L reprinted from reference with kind permission from Springer Science and Business Media. Panel M reprinted from reference by permission of the Society for Molecular Biology and Evolution.) All photographs show environmental samples, except those in panels J and K. Note that Alexa Fluor 488-WGA can also detect microbes other than fungi.

FIG 2

Beneficial properties of endophytes. The left panel shows plants inoculated (In) with beneficial microorganisms that significantly improve plant growth compared to noninoculated (Ni) plants. Various microorganisms, in particular bacteria (orange) and fungi (purple), can colonize the internal tissues of the plant (middle panel). Once inside the plant, the endophytic bacteria and fungi interact intimately with the plant cells and with surrounding microorganisms (large panel). Endophytic fungi, represented here as arbuscular mycorrhizal fungi (AMF) (lilac), might form specialized structures, called arbuscules, where plant-derived carbon sources, mainly sucrose (Su), are exchanged for fungus-provided phosphate (Pi), nitrogen (NH₄⁺), and potassium (K⁺) elements (blue). Plant cytoplasmic sucrose is transported to the periarbuscular space, where it is converted to hexose (HEX) to be assimilated by the fungus. Hexose is finally converted to glycogen (G) for long-distance transport. Phosphate and nitrogen are transported inside the fungal cytoplasm as polyphosphate granules (Poly-P), which are converted to Pi and arginine (Arg) in the arbuscule. Pi is transported to the host cytoplasm, whereas Arg is initially converted to urea (Ur) and then to ammonium (NH₄⁺). Fungal and bacterial plant hormones, such as auxins (IAA), gibberellins (GAs), cytokinins (CKs), volatile organic compounds (VOCs), and polyamines (Poly-NH₂), as well as secondary metabolites (SMs), are transferred to the host (violet). Various bacterial structures, such as flagella, pili, secretion system machineries (e.g., TIV SS and SEC), and lipopolysaccharides, as well as bacterium-derived proteins and molecules, such as effectors (EF), autoinducers, and antibiotics, are detected by the host cells and trigger the induced systemic resistance (ISR) response (red). ACC, the direct precursor of ethylene (ET), is metabolized by bacteria via the enzyme ACC deaminase (ACCd), thus ameliorating abiotic stress (light green). A range of reactive oxygen species detoxification (ROS detox) enzymes might also ameliorate the plant-induced stress (orange). Diazotrophic bacterial endophytes are capable of fixing atmospheric nitrogen (N₂) and might actively transport NH₄⁺ and nitrate (NO₃⁻) to the host (dark green). Bacterial processes of siderophore production (Sid) and uptake (Fe) that are involved in plant growth promotion, biocontrol, and phytoremediation are shown in brown. Examples of various substrates on which the transmembrane proteins are enriched among endophytes are shown in yellow. Transcriptional regulators (TR) are also shown (orange). Communications and interactions between cells of microorganisms dwelling inside the plant tissues are promoted by growth factor (GF), antibiotic (A) (fuchsia), and autoinducer molecules.

FIG 3

Colonization of endosphere tissues by clinical bacterial strains. Volume renderings are shown for confocal laser scanning micrographs for FISH analyses of stained Stenotrophomonas maltophilia cells (red signal) within the emerging lateral root of a tomato plant (beige signal) (A to C) and stained Escherichia coli cells (red signal) invading a lettuce leaf via a stoma (green signal) (D and E). (Panels A to C reprinted from reference with kind permission from Springer Science and Business Media. Panel E reprinted from reference .)