From teosinte to modern maize: domestication and crop improvement reshape the endophytic microbiome

Every plant carries a hidden world within its tissues, a bustling community of bacteria and fungi that live inside its roots and leaves. These microscopic neighbors are not merely passengers; they are essential partners that help the plant gather nutrients, withstand stress, and defend against disease. For centuries, humans have shaped the evolution of crops, selecting plants for traits like larger seeds or higher yields. This process, known as domestication, has transformed wild ancestors into the modern varieties we eat today. But as the plant's genetics changed, a critical question remained: what happened to the invisible communities living inside them? Did the same forces that bred better corn also alter the microbial partners that help it survive? Understanding this relationship is vital, because if modern farming has inadvertently stripped crops of beneficial microbes, we may be missing a key tool for building more resilient and sustainable agriculture.

A team of researchers set out to trace this invisible history by comparing the internal microbial life of maize, from its wild ancestor to the high-yield hybrids found in fields today. They gathered seeds representing the full spectrum of maize evolution: the wild grass known as teosinte, traditional varieties grown by farmers for generations, and modern, scientifically bred lines. To ensure a fair comparison, they grew all these different types in the same greenhouse, using identical soil and care, so that any differences in their internal microbes could be attributed to the plants' own genetics rather than their environment. They carefully collected leaves and roots from each plant, sterilized the surfaces to ensure they were only studying the microbes living inside, and then sequenced the DNA of the bacterial and fungal communities to see who was present and how diverse they were.

The results revealed a clear pattern of loss and change as maize moved from the wild to the modern field. The wild teosinte and the traditional landraces hosted the richest and most diverse communities of microbes, particularly fungi. In contrast, the modern, improved maize lines carried significantly fewer types of microbes inside their tissues. Interestingly, a hybrid created by crossing a traditional landrace with a modern line showed a surprising boost in fungal diversity, suggesting that mixing genetic backgrounds might help restore some of the microbial richness lost during centuries of breeding. The researchers found that the location within the plant mattered most; the communities living in the roots were fundamentally different from those in the leaves, forming distinct groups regardless of the plant type. However, even within these specific locations, the type of maize mattered. The wild plants were home to bacteria and fungi known for helping with nutrient cycling and growth, while the modern varieties were dominated by different groups of microbes often found in managed agricultural soils.

This shift was not just a change in who was present, but also in what the community was likely capable of doing. The microbes inside the wild maize appeared better equipped to produce compounds that help the plant interact with its environment and manage stress naturally. The microbes in modern maize, however, showed a functional profile more aligned with surviving in a human-managed world, with a higher presence of organisms that can be pathogenic or that thrive in disturbed environments. The study suggests that while the physical location of the plant tissue is the strongest force shaping these communities, the history of the plant itself—whether it is a wild grass or a modern hybrid—has quietly reshaped the diversity and function of its internal ecosystem. The findings point to wild relatives and traditional varieties as valuable reservoirs of microbial diversity, offering a potential path forward for breeders who wish to restore beneficial partnerships between crops and their microscopic allies.