The Invisible Farmers: Microbes That Shape the Future of Seeds

Germination: The Start of Something Big

When thinking about agriculture, we often talk about plant diseases, crop yields and soil health. These topics usually concern the young or fully grown plant. Nonetheless, there is an earlier phase where it all begins—a moment that sets the tiny seed bursting open to begin its journey: germination! Apart from the fascinating process itself, this moment is crucial for plant growth and, ultimately, for our food supply.

Why Germination Matters More Than You Think

Germination is vital for numerous plants we rely on. Just think about tomatoes, potatoes or soybeans— they are all grown from seeds! You may be wondering, are there plants that are not grown from seeds? This is true for some economically and nutritionally important trees, like the olive tree. But even in that case, the process is still key in breeding programs, where new varieties with better traits to face environmental challenges are produced.

Despite its importance, many questions about germination remain unanswered. For example: How do seeds process multiple signals—like temperature, light, and water availability—to decide the best germination time? Why do some seeds remain dormant for decades, even under ideal conditions? How do plant hormones interact to regulate germination?

A process with such complexity can face several difficulties. From seed-borne pathogens to dormancy, many factors can unexpectedly lower germination rates, threatening food production and plant survival. To address these problems, researchers and farmers combine physical, chemical, and biological methods. However, these approaches come with potential drawbacks, including reduced seed vitality and long-term effects on plant health.

But the mystery surrounding seeds and germination has another hidden layer: microorganisms. If bacteria and fungi are so important for plant health, colonising nearly every environment on Earth, what about plant seeds? And what roles can they play in seed germination?

A single sprout thriving in microbial-rich soil – nature's invisible farmers at work. Image by vecstock on Freepik

How Microbes Help or Harm Germination

Seed microbiota consists of microorganisms that inhabit both the inside (endosphere) and the outer layer and surrounding soil (spermosphere) of seeds. Researchers have found that seed microbial communities can prevent pathogenic fungi from colonizing the seed surface. Moreover, it has been shown that rice seeds treated with antibiotics face a reduction in their germination rate. But when researchers reintroduced beneficial bacteria like Enterobacter asburiae and Pantoea dispersa, seedling growth and development were restored. Similarly, studies showed that the bacteria Sphingomonas melonis helps suppress the seed-borne pathogen Burkholderia plantarii and promote the growth of seedlings.

A New Study: Can Microbes Make or Break Germination?

With the growing recognition of the seed microbiome, multiple research are being published on this topic. However, most studies in this area are descriptive. Experimental evidence that supports our understanding of their role and mechanisms in seed germination is still scarce. That’s why I was very interested in a recent paper published in Microbiome. A team of researchers studied a medicinal plant—Asparagus—which often struggles with germination. Their question was simple but powerful: Do seeds that germinate harbour different microbes than those that don’t? And if so, could those microbes play a role in the process?

Digging Deeper: What’s Hiding Inside the Seed?

To explore this, the researchers looked closely at the microbial communities colonising both germinated and ungerminated seeds. They used a technique called amplicon sequencing that involves reading a tiny part of the microbe's DNA to identify its taxonomic group. This gave the researchers a broad view of the microbes living inside the seed (the endosphere) and those living in the soil around it (the spermosphere).

With this analysis, they found a relationship between germination and the presence of some fungal and bacterial groups. Germinated seeds had a higher abundance of Pantoea and Pseudomonas, bacteria that could potentially help the plant grow. Interestingly, seeds that failed to germinate had more abundance of Fusarium, a fungal group known for their pathogenic potential.

So the next question was clear, are these microbes linked with the germination process?

What’s hidden inside seeds? An exploration of the microbes essential for plant development.

Can Microbes Actually Control Germination?

Armed with this information, the researchers wanted to put their hypothesis to the test in real life. They crushed ungerminated seeds, diluted them in water and grew them in a nutrient-rich source.

I'm sure the researchers were thrilled to discover that their isolates belonged to the fungal group Fusarium! They cultivated this strain to test whether applying it to sterilized seeds would reduce germination. The results were clear: inoculating Astragalus seeds with the strain's conidia significantly lowered both the germination rate and the germination index.

So it looks like seeds can harbour microorganisms that hinter germination. But is the opposite also possible? Could beneficial microbes be helping the seeds germinate?

Beneficial Microbes for Germination

To find out, the team also isolated microbes from seeds that had already germinated. Of the 26 bacterial strains they found, 21 could break down cellulose—a key process for germination. Cellulose makes up the seed coat, and breaking it down helps water and nutrients reach the embryo, promoting successful germination.

And of the 26 bacterial isolates, 16 of them actively inhibited the growth of another microbe… guess who? You’re right! They were able to fight off the Fusarium isolate that undermines germination! Moreover, 12 out of the 26 bacterial isolates were linked with higher germination rates.

Three of these beneficial strains—Pae, Bac_1, and Bac_2—were selected for further testing. When these microbes were added to seeds in pot experiments, they didn’t just improve germination rates. They also made the plants grow taller and their underground biomass.

The Takeaway: Microbes Might Be the Key to Better Crops

These results are crucial in developing our understanding of seed germination. Their findings suggest that seeds may actively recruit beneficial microorganisms during germination, helping them combat pathogenic fungi.

This new understanding of the seed microbiome opens the door to new ways we can support plant health, improve germination, and ultimately boost crop growth.

In short, the tiny, invisible world inside a seed could hold the key to the future of agriculture. By working with these microorganisms, we might be able to make our crops stronger, more resilient, and better able to face the challenges ahead.

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References

Li, D., Chen, W., Luo, W., Zhang, H., Liu, Y., Shu, D., & Wei, G. (2025). Seed microbiomes promote Astragalus mongholicus seed germination through pathogen suppression and cellulose degradation. Microbiome, 13(1), 23.