Manipulating plant microbiomes for crop security

The human body is home to trillions of microbes that help us digest food, boost our immunity and influence our metabolism. So why wouldn’t the same hold true of plants and the soil around them?

Often overshadowed by research on the human microbiome, the bustling community of microbes nestled within plant roots is critical to a plant's vitality and ecosystem health.

“If you think about plants being healthy, and those plants also producing nutritional foods, microbes are essential players in that,” explains Penn State microbiologist and assistant professor of plant phytobiomes, Francisco Dini-Andreote.

When plants have an unhealthy microbiome, it can lead to detrimental effects. An imbalanced microbiome can result in poor nutrient absorption, stunted growth and increased susceptibility to diseases. For example, plants with a compromised microbiome may struggle to fend off pathogens like Fusarium or Pythium, leading to root rot and other infections.

Additionally, such plants may fail to thrive in suboptimal soil conditions, ultimately decreasing crop yields and destabilizing the ecosystem.

The balance of microbiomes in and around plants is influenced by a multitude of factors. Root hairs and root anatomical traits, for example the size and density of cortical cells, can affect the secretion of chemicals along the roots, says Dini-Andreote. This in turn affects the type of microorganisms that take up residence around those roots. Environmental conditions like soil type, soil pH, moisture levels and nutrient availability also impact the microbial community.

By understanding such interactions, Dini-Andreote’s “main quest” is to harness the function of plant microbiomes to maximize the benefit of what they already do naturally, he says.  

The witchweed problem

“Microbes provide nutrients to plants, but also protect them against biotic and abiotic stresses such as drought, nutrient deficiency and pathogens that we have in the systems and even parasitic plants,” says Francisco. One such parasitic plant is the witchweed.

This silent weed parasite lurks in the heart of agricultural landscapes in many countries in Sub-Saharan Africa, threatening the livelihood of farmers and the security of food supplies. With its insidious tendrils, witchweed, also known as Striga, stealthily siphons nutrients from the roots of vital crops like sorghum and millet. By some estimates, Striga causes crop yield losses ranging from $7 to $10 billion each year (1).

As part of his post-doc research at the Netherlands Institute of Ecology (NIOO-KNAW), Dini-Andreote was involved in a collaborative project to study ways to use the microbiome to control the impact of Striga. The researchers learned that Striga seed germination is triggered by chemical molecules exudated by host plants. Most interestingly, they found that many types of soil bacteria naturally produce compounds that affect this chemical communication between the parasite and host plants.

Drought resistance and carbon storage

Striga is just one example of how Dini-Andeote is trying to harness understanding of the plant microbiome to solve an agricultural problem affecting millions of people. But with the microbiome being such a perfect research subject, it is no wonder that this is just one of multiple projects.

“If I want to manipulate 100 different microbial species over a given number of generations, I can do it. Microbiomes are kind of the ideal experimental units,” says Dini-Andeote.

Other ongoing projects include studying the root architecture of maize plants to make them more drought-tolerant and perhaps better able to sequester carbon for long term soil C storage.

Maize and wheat plant varieties vary in the density, size, and composition of their root cells, Dini-Andreote explains. He uses laser ablation tomography to quantify the cell density and then study how distinct root anatomical composition affects the type of microorganisms that take up residence in the roots.

He and his colleagues are also studying how specific root traits of maize plants affect the composition of the root tissue with implications for long-term carbon storage in soil.

“In general, if roots are more lignified and angled in a more vertical manner, they can grow deeper into the soil,” says Dini-Andreote. One question he is trying answer is whether these more lignified roots take longer to decompose in crop systems. “That may not seem important, but when you think of the extent of maize cultivation in the US, that can be a huge source of carbon sequestration.”

His lab is also collaborating on projects focused on mitigating soil-borne diseases or boosting plant immunity by engineering plant-associated microbiomes.

Tech makes research possible

Dini-Andreote has been using QIAGEN DNA and RNA soil extraction kits to study plant microbiomes since he began his scientific career. In his lab today, he uses DNeasy Plant Pro and to prepare his samples for study, and QIAquick Gel Extraction Kits to purify them. He also uses qPCR assays to amplify, quantify and analyze microbial nucleic acids.

“QIAGEN soil extraction kits were a large part of the investment in starting up my lab,” he says. “The major advantages are the consistency of results and the ease of use of QIAGEN protocols.” Dini-Andreote has tried other kits in the past, but they often yielded inconsistent results. “I never had any issues with QIAGEN kits.”

Despite promising results thus far, the complexity of the microbiome poses a continuous challenge. “We're talking about 10 to the ninth power of bacterial cells per gram of soil. That doesn’t even include fungi, protists, archaea, and viruses,” he says.

Sometimes, trying to tease apart how individual microorganisms contribute to a plant’s health and the surrounding ecosystem can feel like a mouse trying to climb Mt. Everest, he quips.

Nevertheless, the Striga project shows that it is possible to better understand how microbes contribute to a plant’s overall growth and health, even if “we’re still learning how to properly manipulate and engineer their function at the plant-soil interface.”