Using a new approach to shine a light on hidden plant microbes

Despite there being more microbes on Earth than stars in our galaxy, only a tiny fraction have been discovered. An approach called metagenomics—a type of DNA sequencing—may help scientists learn more about these elusive organisms, according to Penn State researchers.

With leaves holding up to 100 million bacterial cells per gram and the space around a plant’s roots containing up to 1 trillion bacteria, microbes have ample opportunity either to help or harm a plant’s health, said Verónica Román-Reyna, assistant professor of global change pathology in the College of Agricultural Sciences at Penn State. However, the vast majority of these microbes cannot be examined via traditional methods.

Román-Reyna—along with Sharifa Crandall, assistant professor of soilborne disease dynamics and management at Penn State—recently published a paper about using metagenomics in Frontiers in Plant Science. Penn State News spoke with Román-Reyna about why uncovering these microbial communities is important and how metagenomics can help.

Why is it important to identify and learn about these microbial communities?

Plant pathogens pose a threat to all plants, including food crops, which can potentially exacerbate food insecurity around the globe. For example, fungal pathogens alone can lead to crop losses of 10% to 20%, according to the U.S. Department of Agriculture.

When studying plant pathology, we typically want to identify the microorganisms that are responsible for the disease—the pathogens. However, it’s equally important to consider the broader context, because the pathogen is interacting not only with the plant but also with the plant’s microbiome.

How the pathogen and broader microbial community interact can either support the pathogen’s ability to infect the plant or, conversely, create competition that limits disease severity.

Therefore, understanding the microbial communities present in the host environment can provide valuable insights into the dynamics of disease development and potential strategies for disease control.

What is metagenomics?

Usually, microbes such as bacteria and fungi are studied by isolating and culturing each organism individually in the lab. However, most microbes can’t be studied in this way for various reasons and have remained invisible and unstudied.

Metagenomics—the study of genetic material, specifically DNA, obtained directly from every organism in environmental samples such as leaves, soil, air or even rainwater and analyzed for diversity, structure and function—is a way for us to uncover and understand this vast, previously unknown microbial presence in the environment.

This approach enables researchers to simultaneously analyze multiple microorganisms from one bulk sample, offering a view of the entire microbial community in a given environment without the need to culture each organism individually.

Why is there a need to incorporate this approach into plant science research?

In plant pathology, there’s an opportunity to incorporate metagenomics from two perspectives: microbial ecology and disease diagnostics.

From a microbial ecology standpoint, it helps us understand the microbial interactions and functions involved in disease, including how microbes communicate and exchange genes, such as those associated with antibiotic resistance.

From a diagnostic perspective, metagenomics empowers us to assess pathogen diversity, track pathogens and compare them across different locations with similar diseases. It also enables the rapid detection of pathogens that are difficult to culture, offering a powerful, unbiased tool to identify all potential pathogens in a sample.

What can metagenomics help achieve?

In plant pathology, metagenomics can help us understand the reasons behind plant disease outbreaks, such as the emergence of new species, reemergence of known microbes, pathogen adaptation to the host or changes affecting plant microbial communities.

It has expanded our capacity to digitally record the causal agents of plant disease and the diversity of pathogens. Metagenomics also allows us to investigate plant diseases without prior knowledge of the pathogens, overcoming the limitations associated with unculturable organisms.