The plant endomicrobiome: Structure and strategies to produce stress resilient future crop

Abstract

Plants have a microbiome, a diverse community of microorganisms, including bacteria, fungi, and viruses, living inside and on their tissues. Versatile endophytic microorganisms inhabited in every plant part without causing disease and develop endophytic microbiome or endo-microbiome. Plant endo-microbiome are drawn by the nutrient rich micro-environment, and in turn some microbes mutualistically endorse and protect plant from adverse environmental stresses. Plant endo-microbiome interact within well-designed host equilibrium containing xylem, phloem, nutrients, phytohormones, metabolites and shift according to environmental and nutritional change. Plant endo-microbiome regulate and respond to environmental variations, pathogens, herbivores by producing stress regulators, organic acids, secondary metabolites, stress hormones as well as unknown substances and signalling molecules. Endomicrobiome efficiently synthesizes multiple bioactive compounds, stress phytohormones with high competence. The technological innovation as next generation genomics biology and high-throughput multiomics techniques stepping stones on the illumination of critical endo-microbiome communities and functional characterization that aid in improving plant physiology, biochemistry and immunity interplay for best crop productivity. This review article contains deeper insight in endomicrobiome related research work in last years, recruitment, niche development, nutrient dynamics, stress removal mechanisms, bioactive services in plant health development, community architecture and communication, and immunity interplay in producing stress resilient future crop.

Keywords: Community; Environmental change; Future crop; Plant microbiome; Stress management.

Graphical abstract

Fig. 1

The keywords cooccurrence network, obtained from the articles extracted by PUBMED, selecting three keywords: “endophytic” (or "endophyte"), “stress” and “agriculture” in the all-available literature. The resent review is specifically addressed to the publications of the last 5 years (from 2018 to 2023). The network map highlights the most frequency used bibliographic terms to understand the most active research fields that are grouped into three clusters.

Fig. 2

Different sites of endophytes recruitment in plants from aerial part (shoot) and hidden part (roots).

Fig. 3

Endophytes mediated immunity evolving different MAMPs/PAMPs and components of cell wall. Endophytes interface with host immune signalling components by developing receptor proteins, effectors, phytohormones, cytosolic calcium, reactive oxygen species and strengthen immune response of plants to pathogens and facilitates niche development. Abbreviations: exopolysaccharides (EPS), microbial associated molecular patterns (MAMPs), pathogen-associated molecular patterns (PAMPs), receptor-like kinases (RLKs), receptor-like proteins (RLPs), pattern recognition receptors (PRRs), apoplastic proteins (APPs), ethylene (ET), jasmonic acid (JA), salicylic acid (SA), cytosolic calcium (Ca²⁺), reactive oxygen species (ROS).

Fig. 4

Proposed model exhibiting the plant endomicrobiome services in stress resilient future crops and NbS.