Exploring the Diversity of Endophytic Microorganisms: From Microbial Ecology to Agronomic Applications

1. Introduction

Endophytic microorganisms—bacteria, fungi, and other microbial taxa that colonize the internal tissues of living plants without causing overt disease—play pivotal roles in plant health, development, and resilience. Over the past two decades, advances in culture-independent techniques and high-throughput sequencing have revealed that virtually every plant species hosts a rich and dynamic endophytic community, whose composition is shaped by the host genotype, developmental stage, and environmental conditions. These endophytes contribute to nutrient acquisition, phytohormone modulation, abiotic stress tolerance, and biotic defense, positioning them as key mediators in the soil–plant–microbiome continuum [1,2].

Despite this growing recognition, our understanding of endophytic diversity and function remains underexplored. Many biosynthetic pathways encoded within endophyte genomes remain cryptic under standard laboratory conditions, and the mechanisms governing microbial assembly, interaction networks, and functional shifts under stress are only beginning to be elucidated. Moreover, translating microbial ecology insights into agronomic applications requires integrative studies that couple genomics, network analysis, and field-relevant trials [3]. Addressing these knowledge gaps is essential for harnessing endophytes in sustainable crop production systems and for developing bioinoculants that are both effective and environmentally friendly [4].

This Special Issue, “Exploring the Diversity of Endophytic Microorganisms: From Microbial Ecology to Agronomic Applications”, brings together multidisciplinary investigations spanning genome mining, community profiling, network ecology, induced microbiome assembly, and aerosolized microbiota. The five contributions collected herein employ State-of-the-Art methodologies—from comparative genomics to co-occurrence network modeling and one-health bioaerosol assessments—to advance our conceptual framework of endophytic biology and to chart practical routes for its deployment in agriculture. In the following section, we synthesize each study’s objectives, methodologies, and principal findings, and conclude by outlining the emerging frontiers and research priorities for endophyte-driven agronomic innovation.

2. Summaries of Contributions

Building on the thematic framework outlined above, the studies collected in this Special Issue can be grouped into three interconnected domains: genome mining of cryptic pathways, community assembly under biotic and abiotic drivers, and targeted microbiome engineering for plant health and sustainability.

2.1. Genome Mining and Secondary Metabolism

Coca-Ruiz et al. [5] performed an in-depth comparative genomic analysis of Botrytis deweyae versus its pathogenic relative B. cinerea, employing the antiSMASH platform to predict secondary metabolite gene clusters (SMGCs). They identified 19 SMGCs in B. deweyae, including five nonreducing polyketide synthase clusters (BdPKS22–26) with no close homologs in public databases and one terpene synthase cluster exhibiting less than 40% identity to known enzymes. Phylogenetic conservation across 12 Botrytis species demonstrated that these clusters are uniquely retained in B. deweyae and select endophytic strains, indicative of evolutionary adaptation to an endophytic lifestyle. Preliminary LC-HRMS metabolite profiling under simulated plant tissue conditions provided evidence of polyketide production, underscoring the potential of these cryptic pathways for novel bioactive compound discovery.

To transition from genome-based insights to community-level patterns, the next two contributions examine how the host genotype and environmental stress shape the assembly of endophytic communities in rice.

2.2. Community Assembly Under Host Genotype and Environmental Stress

Two studies on rice endophytes elucidate the continuum from the genetic to environmental modulation of microbial assemblages:

• Cultivar-Specific Assembly

Sokel et al. [6] compared the root endophytic bacterial communities of four Japanese sake rice cultivars and two table rice cultivars at 0, 3, and 6 weeks post sowing. High-throughput sequencing of the V4 region of the 16S rRNA gene, coupled with PERMANOVA analysis, revealed significant community structure differences between sake and table rice at transplant (R² = 0.21, p < 0.001), which persisted through vegetative growth. Co-occurrence network analysis indicated that sake cultivars harbored more densely connected microbial networks (average degree = 4.3) compared to table cultivars (average degree = 3.1), with keystone taxa such as Pantoea agglomerans and Methylobacterium extorquens driving early successional dynamics.

• Effects of Drought Stress

Extending this host-driven perspective, Wu et al. [7] subjected rice plants to controlled drought (40% field capacity) versus well-watered conditions (80% field capacity) and characterized rhizosphere and endosphere microbiomes at panicle initiation. Using SparCC to construct co-occurrence networks from 16S rRNA gene data (~50,000 reads/sample), they observed a 35% increase in the average clustering coefficient and a 22% rise in the positive edge ratio under drought, indicative of enhanced microbial co-operation. Taxonomic profiling revealed enrichments of Actinobacteriota (3.5-fold) and Gemmatimonadetes (2.1-fold), taxa associated with osmoprotectant synthesis. Functional predictions via PICRUSt2 indicated the upregulation of sulfur oxidation (sox pathway) and manganese cycling genes, suggesting microbial mechanisms that mitigate water deficit stress.

These insights into natural assembly processes pave the way for interventions that deliberately steer endophytic communities toward beneficial outcomes.

2.3. Induced Microbiome Assemblages for Disease Resistance

Cui et al. [8] investigated the effect of exogenous poly-γ-glutamic acid (γ-PGA; 100 mg L⁻¹) on the root endophytic microbiota and disease resistance of Chrysanthemum. Treatment with γ-PGA resulted in an 18% increase in Shannon diversity and a significant enrichment of Burkholderiaceae from 5% to 22% relative abundance (p < 0.01). Concurrent assays demonstrated a 2.3-fold rise in salicylic acid levels and a 73% reduction in Fusarium oxysporum colony-forming units compared to controls. Quantitative PCR analysis of SA-responsive genes (PR1, PR5) confirmed the systemic activation of defense pathways. These findings support γ-PGA as a biostimulant that selectively assembles a disease-suppressive endophytic community, offering a sustainable strategy for pathogen management in ornamental crops.

To extend the concept of microbiome shaping beyond the root zone, the final contribution explores the aerial dimension of microbial signaling.

2.4. Bioaerosols as Vectors of Agroecological Signaling

Gashi et al. [9] synthesized over 120 studies on agricultural bioaerosols from a One Health perspective, detailing sampling methodologies (impaction vs. filtration), emission sources (soil, phyllosphere, and manure), and the concurrent transport of volatile organic compounds (VOCs) and living cells. Their meta-analysis implicates bioaerosols in the aerial dissemination of fungal pathogens such as Puccinia spp., and highlights their role in mediating plant–plant communication via airborne beneficial microbes like Trichoderma spp. In one field trial, the adoption of cover cropping reduced the aerobiome index—composite of microbial load, VOC concentration, and pathogen ratio—by 40%, correlating with a lower disease incidence. The authors propose the “aerobiome index”—a composite metric incorporating microbial load, VOC concentration, and pathogen ratio—as a practical indicator for monitoring agroecological interventions. They further advocate for the deployment of portable real-time aerosol sensors integrated with machine learning classifiers to enable the precision surveillance of crop health and environmental quality.

3. Conclusions

The five studies presented in this Special Issue collectively deepen our understanding of endophytic microorganisms and their roles in plant health and productivity. From the discovery of novel secondary metabolite gene clusters in Botrytis deweyae to the elucidation of host- and stress-driven assembly rules in rice, and from the targeted recruitment of disease-suppressive endophytes in Chrysanthemum to the conceptualization of bioaerosols as vectors of agroecological signals, these contributions demonstrate both the ecological complexity and practical relevance of endophyte research. We thank all the authors for their outstanding scientific contributions, the peer reviewers for their insightful evaluations, and the editorial staff for their dedicated support. It is our hope that this collection serves as a valuable reference for researchers and practitioners seeking to integrate endophytic biology into sustainable crop management.