The tripartite interplay between plants, bacteria, and fungal endophytes, such as Epichloë , is recognized as vital

The gap

Evidence profile

Sourced from the future work and abstract of the source papers, classified as general, spanning 5 journals. Those papers have been cited 1 times in total.

Supporting evidence — 5 representative gaps

• What do we know about the seed microbiome? (2026) · Microbiome · cited 1× · doi

  The seed microbiome occupies a unique niche charac- terized by low microbial biomass, spatial isolation, and generational stability, distinguishing it from other plant compartments. Optimizing the composition of seed endophytes through microbiome engineering holds sig- nificant implications for sustainable agriculture. Recent research advances on the seed microbiome have uncovered its taxonomic composition and diversity across different plant species, its transmission mecha- nisms, and its multifunctional roles in seed germination, seedling establishment, growth promotion, and stress resistance. As a dynamic, vertically transmitted microbial community, the seed microbiome not only supports early plant development but also contributes to long-term plant adaptation through nutrient mobilization, hormone regulation, pathogen suppression, and intergenerational stability. Despite these advances, fundamental gaps remain in our understanding of this critical compartment. Key uncertainties include the specific paths and regulatory mechanisms that allow microbes to enter and survive within seeds; the physiological and molecular basis for microbial dormancy and reactivation during germina- tion; host and microbial traits determining core com- munity assembly and intergenerational stability; and developmental drivers of internal compartmentalization within seeds and seedlings. Methodological challenges, such as low microbial biomass, host DNA contamina- tion, taxonomic bias, and the need for single-seed resolu- tion, still hinder progress in linking microbial community composition to functional outcomes. Resolving these unanswered questions requires a com- prehensive approach, such as integrating multi-omics technologies with spatially resolved techniques, lever- aging large-scale datasets from various resources, and conducting synthetic community experiments to explore the underlying principles. Recent discoveries in plant microbiome research indicate that Microbiome genes (M genes) are promising breeding targets in plants that allow microbiome optimization via host genetics [106]. These genes regulate either host immunity or chemical signaling in plants to recruit specific microbial taxa. By Qi et al. Microbiome (2026) 14:106 Page 9 of 12 developing plant varieties that shape their seed-endo- phytic communities via M genes, new avenues for practi- cal applications could emerge due to the transformative potential for sustainable agriculture. In addition, targeted inoculation with beneficial seed endophytes, bio-prim- ing, or advanced seed coatings could reduce reliance on chemical inputs, enhance resilience to climate stresses, improve nutrient use efficiency, and ultimately boost crop yields, quality, and food security. Finally, by filling the remaining knowledge gaps, future research will posi- tion the seed microbiome as a powerful tool for devel- oping resilient, resource-efficient cropping systems in a changing climate.

  generalfuture work
  Keywords: seed microbiome microbial plant tion host genes stability composition community biomass endophytes sustainable agriculture recent
• Endophytes Across the Plant Life Cycle: Potential Roles in Plant Protection, Litter Decomposition, and Nutrient Cycling (2026) · Plants · doi

  6.1. Major Conclusions Plant endophytes have long been studied in living tissues to explore their effects on plant growth, stress tolerance, and disease resistance. Based on the accumulated evidence, it is proposed that the ecological relevance of some endophytes may extend to senescent tissues and litter-associated microbial succession. Therefore, endophytes should be viewed as plant-associated microorganisms that may also influence various links in the plant-tissue- litter-soil-microbe-nutrient cycle and other processes. During the living plant stage, endophytes can contribute to plant growth, stress tol- erance, and disease resistance through multiple mechanisms. However, the expression and ecological consequences of these functions depend on microbial identity, host iden- tity, tissue niche, developmental stage, and environmental conditions. Plant–endophyte relationships may therefore shift among mutualistic, commensal, latent pathogenic, and conditionally deleterious states. After senescence or tissue death, a subset of endophytes or endophyte-derived pop- ulations may persist in litter and influence early microbial succession, decomposition, and localised nutrient transformations. Current evidence is stronger for effects on early community assembly, litter carbon transformation, and localised phosphorus mobilisation, whereas sustained regulation of litter nitrogen mineralisation, soil carbon sequestration, and ecosystem-scale nutrient cycling remains uncertain. Vertical transmission, horizontal acquisition, environmental dispersal, and renewed host filtering may link living-tissue colonisation, post-senescence persistence, and the formation of plant-associated communities in subsequent generations. Therefore, we put forward an open and non-linear continuum connecting “endophytic colonisation in living plants—saprotrophic persistence—potential recolonisation of new hosts.” This framework integrates related but incomplete cross-stage processes. A complete same-strain life-history loop should therefore be regarded as a testable hypothesis rather than an established general pattern. This framework may guide the development of microbial strategies for plant defence, sustainable agriculture, environmental remediation, and ecological restoration. However, the beneficial functions in life cannot be assumed to continue after the host dies, and post-senescence effects may be beneficial, neutral, or detrimental. Accordingly, potential applications should be based on stage-specific functional verification rather than taxonomic identity or in vitro performance alone. 6.2. Future Research Directions Although considerable progress has been achieved, the persistence, functional tran- sitions, dispersal, and establishment of endophytes across living plants, litter, soil, and new hosts remain insufficiently resolved, particularly whether the same taxa or strains persist continuously from seed-associated stages through senescence and into litter. Futur

  generalfuture work
  Keywords: plant litter endophytes living associated microbial tissue stage senescence effects ecological soil nutrient host environmental
• Endophytic bacteria and fungi as a source of polysaccharides: production and characterization techniques (2026) · Frontiers in Microbiology · doi

  Despite the significant advances in research on endophyte- limitations remain. A major derived polysaccharides, several challenge is the accurate isolation and identification of true endophytes. Because microorganisms can associate themselves with senescent or dead parts of plants as epiphytes or saprophytes, it is difficult to distinguish between true endophytes and external colonizers. Additionally, most existing research work covers only a limited number of culturable isolates obtained from a single host species or location, which may not adequately represent the true diversity of polysaccharide-producing endophytes. Many endophytic microorganisms remain unculturable under conventional laboratory isolation conditions, leaving a significant fraction of their biosynthetic potential unexplored. Despite many reported studies showing promising biological activities, the detailed structural characterization is often incomplete, with limited information about their glycosidic linkage, branching architecture, molecular conformation, and structure- activity relationship. The absence of standardized methods for plant surface sterilization, extraction, purification and characterization limits reproducibility and comparisons between studies. In addition, most research work remains confined to in vitro assays, whereas mechanistic studies, toxicity evaluation, in vivo validation, and scalable production strategies are still scarce. isolation, polysaccharide endophyte

  generalfuture work
  Keywords: isolation true endophytes despite signi cant endophyte remain cation microorganisms limited polysaccharide characterization advances limitations
• Dynamic Assembly and Multifunctional Roles of Plant Endophytic Microbiomes (2026) · Microorganisms · doi

  Extensive surveys of key crops and plant species have generated preliminary insights into their dominant bacterial and fungal endophytes. Nevertheless, substantial plant- associated microbial diversity, core microbiome assemblies, and the host physiological functions mediated by these microbiomes remain to be uncovered in most plant species. Systematic frameworks for profiling microbiomes of ecologically and economically valu- able plants are urgently required to characterize core endophytic microbiomes and the beneficial host functions they confer. Such standardized strategies enable comprehensive assessment of the interaction between root endophytic microorganisms and their host plants. Two major directions merit further investigation: the regulatory factors govern- ing endophytic microbial assembly and community establishment at the plant–microbe interface, as well as the assembly rules and symbiotic patterns formed by crop-associated microbial communities. High-throughput sequencing technology can be applied to identify the recruitment mechanisms of core endophytic microorganisms across diverse host species. Besides community-level investigations, further mechanistic studies are needed to decode the molecular crosstalk between endophytes and plant immune signaling. For instance, how endophytic strains fine-tune PTI and ETI responses via phytohormones, volatile or- ganic compounds, and small RNAs remains largely unresolved for most crop-endophyte systems. Dissecting such multilayered signaling events will reveal how immunity serves as a host-selection filter and governs the functional output of endophytic communities. By evaluating plant–root endophytic interactions under various biotic and abiotic stresses, researchers can screen functional synthetic microbial consortia capable of activating plant systemic resistance and boosting crop productivity. Further large-scale microbiome surveys covering diverse native crop germplasm and locally adapted wild relatives are urgently required. Most current studies focus on a small set of model or widely cultivated crop accessions, whereas the endophytic microbiomes of wild plant relatives remain largely unexplored. Exploring these genetic resources may uncover valuable core endophytic taxa with superior stress-resistance and plant-beneficial traits. Meanwhile, advanced in-situ https://doi.org/10.3390/microorganisms14092118 Microorganisms 2026, 14, 2118 11 of 16 and live-cell imaging techniques should be further adopted to resolve the spatial coloniza- tion patterns of endophytes inside plant tissues. Such visual approaches help disentangle physical niche partitioning and microbe–microbe interactions within the host internal microenvironment, which cannot be fully captured by bulk sequencing alone. Moreover, future synthetic-consortia design should move beyond simple strain combination and prioritize the ecological compatibility among constituent members. Rational design needs to consider native soil background, host genotype, and fluctuating field environments to improve in planta persistence of inoculated microbes. Optimizing synthetic consortia for better ecological fitness will greatly narrow the gap between laboratory mechanistic findings and practical agricultural application of endophyte-based products. Similar to conventional crop breeding, plant microbiota serve as critical modulators of plant pheno- types. Targeted screening of favorable plant–microbe symbiosis facilitates the breeding of disease-resistant crop varieties. Therefore, harnessing microbiota to enhance crop disease resistance and yield is of great practical significance. Author Contributions: Conceptualization, J.S. (Jie Song) and Q.Y.; resources, W.L., J.S. (Jinfeng Shi), Y.S. and M.L.; data curation, J.S. (Jinfeng Shi), W.L., Y.S. and Y.D.; writing—original draft preparation, J.S. (Jie Song); writing—review and editing, J.S. (Jie Song), Q.Y. and Y.Z.; visualization, J.S. (Jinfeng Shi), Y.D. and M.L.; supervision, Q.Y. and Y.Z.; funding acquisition, J.S. (Jie Song) and Q.Y. All authors have read and agreed to the published version of the manuscript. Funding: This research was funded by the Heilongjiang Plant Protection Society of China (HT-2026-01- 003), Talent Introduction Project of Heilongjiang Bayi Agricultural University (XYB202010, XYB202005), and Research Project on Ecological Environment Protection in Heilongjiang Province (HST2025TR008). Institutional Review Board Statement: Not applicable. Informed Consent Statement: Not applicable. Data Availability Statement: No new data were created or analyzed in this study. Data sharing is not applicable to this article. Conflicts of Interest: The authors declare no conflicts of interest.

  generalfuture work
  Keywords: plant endophytic crop host microbial core microbiomes microorganisms further microbe song species endophytes synthetic consortia
• Unlocking the power of Pseudomonas : network-guided isolation enhances plant growth on Achnatherum inebrians (2026) · mSystems · doi

  IMPORTANCE Although the tripartite interplay between plants, bacteria, and fungal endophytes, such as Epichloë , is recognized as vital for host fitness, the specific mechanisms through which these endophytes shape associated bacterial communities, particularly in ecologically significant grasses, such as Achnatherum inebrians , remain poorly understood.

  generalabstractevidence 3/5
  Keywords: endophytes importance tripartite interplay plants bacteria fungal epichlo recognized vital host fitness specific mechanisms shape

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