Seed Endophytes for Sustainable Agriculture: An Inheritance-Function-Engineering Framework for Climate-Resilient Agriculture

Abstract

Agriculture is increasingly challenged to maintain yield stability under climate variability while reducing reliance on synthetic agrochemicals. Plant-associated microbiomes represent a promising strategy for sustainable intensification, yet the practical application of beneficial microbes remains inconsistent and poorly scalable. Seed endophytes are a unique, understudied fraction of the plant microbiome due to their early colonization and potential vertical transmission across generations. However, insufficient understanding of their intergenerational stability, functional reliability, and field applicability has restricted their agronomic translation. Here, we performed a systematic synthesis of 2,065 publications from 1999 to 2025 to characterize the evolution of seed endophyte research and identify bottlenecks limiting practical deployment. Bibliometric analyses revealed a progressive shift from descriptive diversity surveys to mechanistic studies on microbial inheritance, functional validation, and application-oriented strategies. Four core research themes emerged: (I) Taxonomy and Diversity; (II) Vertical Transmission and Colonization Mechanisms; (III) Ecological Functions and Action Mechanisms; (IV) Applications in Sustainable Agriculture. We identified critical gaps in evidence for consistent vertical transmission, functional stability, and scalable deployment. We then propose an integrated Inheritance-Function-Engineering framework to unify heritability, functional relevance, and practical design, alongside standardized evaluation metrics. This review clarifies the research trajectory, establishes evidence benchmarks for vertical transmission, summarizes key functional mechanisms, and provides a structured roadmap to improve the reliability of seed endophyte-based solutions for sustainable agriculture.