Plants face ongoing biotic stresses from microbial populations, pathogens, and pests, which challenge their growth and survival (Mishra et al., 2024; Raza et al., 2025). To address these challenges, plants have evolved sophisticated molecular monitoring systems that detect stress-related signals and initiate defense responses (Alonso Baez and Bacete, 2023; Bender and Zipfel, 2023; Wolf, 2022). These adaptive processes involve reprogramming physiological functions, with a key strategy being the activation of disease resistance mechanisms against pathogens. However, this defense strategy incurs significant energetic costs, requiring resources such as signaling molecules and antimicrobial compounds (Ma et al., 2024; Uddin et al., 2024b). This trade-off can negatively impact plant growth, reproduction, and overall fitness (Karasov et al., 2017; Monson et al., 2022). To balance defense with development, plants use regulated resistance mechanisms, including cellular monitoring systems that detect pathogen invasions and modulate the intensity and duration of their responses (Bender and Zipfel, 2023; Wolf, 2022).

A crucial system in plant defense is the cell wall, which surrounds and encloses all plant cells. Beyond its mechanical support role, the cell wall is dynamic and multifunctional, regulating cell growth, influencing differentiation, and shaping the overall architecture of the plant (Delmer et al., 2024; Wolf, 2022). Importantly, the cell wall also acts as a key defensive barrier against biotic and abiotic stresses, which can alter its composition and structure, thereby impacting its integrity (Baez et al., 2022; Gigli-Bisceglia et al., 2022; Molina et al., 2021). In plant-microbe interactions, pathogens attempt to compromise this barrier by secreting cell wall-degrading enzymes, which disrupt the cell wall integrity (Zheng et al., 2021). In response, plants activate a signaling cascade mediated by specific receptors and sensors that detect these alterations, triggering adaptive defense mechanisms. These responses include the de novo synthesis or remodeling of cell wall components to reinforce its structural integrity (Bacete et al., 2022; Gigli-Bisceglia et al., 2022; Wolf, 2022; Zheng et al., 2021). Genetic and chemical approaches, such as modifying the expression of cell wall-related genes in Arabidopsis thaliana, have provided valuable insights into the role of cell wall modifications in both plant development and disease resistance (Ogden et al., 2024).

In addition to monitoring cell wall integrity, plants have developed sophisticated immune recognition systems to detect microbial threats. These systems perceive conserved pathogen-derived molecular signatures, known as microbe-associated molecular patterns (MAMPs), through plasma membrane-anchored pattern recognition receptors (PRRs), which primarily consist of receptor kinases and receptor-like proteins (Bender and Zipfel, 2023). PRRs can also recognize damage-associated molecular patterns (DAMPs), which are endogenous signals released in response to pathogen-induced tissue damage (De Lorenzo and Cervone, 2022). The recognition of MAMPs and DAMPs triggers pattern-triggered immunity (PTI), the first line of defense against infection. In addition, plants can detect specific microbial effectors, such as avirulence (Avr) proteins, through intracellular receptors often encoded by resistance (R) genes, activating effector-triggered immunity (ETI) (DeFalco and Zipfel, 2021). A recent study showed that PTI and ETI function synergistically, contributing to a more robust and effective immune response against pathogens (Yuan et al., 2021).

This review examines the molecular regulation of cell wall biosynthesis, immune signaling, and biotechnological advances with a focus on lignocellulosic biomass. It explores the transcriptional and epigenetic regulation of lignin biosynthesis and secondary cell wall (SCW) formation, and their interplay with immune signaling pathways mediated by PRRs. Furthermore, the review highlights the role of biotechnological innovations such as CRISPR/Cas genome editing, synthetic regulatory circuits, and field-trial-driven trait prediction in enhancing biomass engineering. These innovations contribute to improved saccharification efficiency, pathogen resistance, and stress resilience. Despite these advancements, challenges remain in translating these technologies to practical applications. We propose integrated strategies to improve lignocellulosic feedstocks' scalability and industrial applicability as renewable alternatives to fossil resources, contributing to a sustainable bioeconomy.