Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2025 Aug 4;14(15):2421.
doi: 10.3390/plants14152421.

Harnessing Seed Endophytic Microbiomes: A Hidden Treasure for Enhancing Sustainable Agriculture

Affiliations
Review

Harnessing Seed Endophytic Microbiomes: A Hidden Treasure for Enhancing Sustainable Agriculture

Ayomide Emmanuel Fadiji et al. Plants (Basel). .

Abstract

Microbes perform diverse and vital functions in animals, plants, and humans, and among them, plant-associated microbiomes, especially endophytes, have attracted growing scientific interest in recent years. Numerous plant species thriving in diverse environments have been shown to host endophytic microbes. While endophytic bacteria commonly colonize plant tissues such as stems, roots, and leaves, seed-associated endophytes generally exhibit lower diversity compared to those in other plant compartments. Nevertheless, seed-borne microbes are of particular importance, as they represent the initial microbial inoculum that influences a plant's critical early developmental stages. The seed endophytic microbiome is of particular interest due to its potential for vertical transmission and its capacity to produce a broad array of phytohormones, enzymes, antimicrobial compounds, and other secondary metabolites. Collectively, these functions contribute to enhanced plant biomass and yield, especially under abiotic and biotic stress conditions. Despite their multifaceted roles, seed microbiomes remain underexplored in plant ecology, and their potential benefits are not yet fully understood. This review highlights recent advances in our understanding of the diversity, community composition, mechanisms of action, and agricultural significance of seed endophytic microbes. Furthermore, it synthesizes current insights into how seed endophytes promote plant health and productivity and proposes future research directions to fully harness their potential in sustainable agriculture.

Keywords: plant growth and health; plant–microbe interactions; seed endophytes; stress amelioration.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Overview of vertical and horizontal transmission of seed-borne endophytes.
Figure 2
Figure 2
Overview of the beneficial roles of seed microbiomes in plant growth improvement.

Similar articles

References

    1. Malfanova N., Lugtenberg B.J., Berg G. Bacterial endophytes, who and where and what are they doing there? In: De Bruijn F.J., editor. Molecular Microbial Ecology of the Rhizosphere. Wiley-Blackwell; Hoboken, NJ, USA: 2013. pp. 391–403.
    1. Fadiji A.E., Babalola O.O. Exploring the potentialities of beneficial endophytes for improved plant growth. Saudi J. Biol. Sci. 2020;27:3622–3633. doi: 10.1016/j.sjbs.2020.08.002. - DOI - PMC - PubMed
    1. Truyens S., Weyens N., Cuypers A., Vangronsveld J. Changes in the population of seed bacteria of transgenerationally Cd-exposed Arab. Thaliana. Plant Biol. 2013;15:971–981. doi: 10.1111/j.1438-8677.2012.00711.x. - DOI - PubMed
    1. Thomas P., Sahu P.K. Vertical transmission of diverse cultivation-recalcitrant endophytic bacteria elucidated using watermelon seed embryos. Front. Microbiol. 2021;12:635810. doi: 10.3389/fmicb.2021.635810. - DOI - PMC - PubMed
    1. Nelson E.B. Microbial dynamics and interactions in the spermosphere. Annu. Rev. Phytopathol. 2004;42:271–309. doi: 10.1146/annurev.phyto.42.121603.131041. - DOI - PubMed

LinkOut - more resources