Bacteria, fungi interact far more often than previously thought

Los Alamos National Laboratory researchers have screened a diverse collection of fungal strains from all over the globe for potential bacterial partners. Credit: Los Alamos National Laboratory
Researchers using bioinformatics to assess bacterial-fungal interactions found that fungi can host an extraordinary variety of bacteria. This makes bacterial-fungal interactions more common than ever before.

Aaron Robinson, a Los Alamos National Laboratory biologist and the lead author of a paper that describes his research in Nature's Communications Biology journal, said, "Until now, examples bacterial-fungal interaction were pretty limited in numbers and diversity." It was assumed that bacterial-fungal interactions might not be very common. We found many bacteria species that were associated with fungi and detected them at a high frequency."

This research contributes to an understanding of fungal bacteriome. It is the existence of bacteria within and in close association to a fungal host. This opens up opportunities to study the interactions and connects that research with issues like ecosystem functioning and climate change impact.

Robinson stated that this research is a good starting point for further investigation of mechanisms of bacterial-fungal interaction at a deeper level. This research will help us understand how bacteria can associate with fungi and how we can best use that information to achieve our goals at the Laboratory, the Department of Energy and society as a whole. It is extremely valuable to understand how these organisms interact and contribute to larger systems. This knowledge can be used to model climate change or to benefit society by utilizing microbes in agricultural or industrial applications.

Researchers tested 294 fungal isolates from four cultures from Europe, North America and South America to identify potential bacterial partners. Researchers were able to visualise many of these associations through collaborations with the Center for Integrated Nanotechnologies (Los Alamos).

These fluorescence microscopy inspections were used in conjunction with the screening to confirm the presence of bacterial partners among various fungal isolates, and even within the fungal host's hyphae.

Collaboration with the Center for Integrated Nanotechnologies. A visualization of potential bacterial partners (green) in fungal hyphae by fluorescence-in situ hybridization (FISH). Credit: Los Alamos National Laboratory

The research team screened culture collections and also reviewed 408 fungal genome sequencing project from the MycoCosm portal. This portal contains fungal genome projects that have been developed by the Department of Energy Joint Genome Institute.

In 79 percent, bacterial signatures were found in fungal genomes. Multiple cases yielded complete or near-complete genomes for these bacterial partners. These fungal-associating bacteria genomes were able to be compared with free-living and fungal-associating bacteria.

The research team found bacterial associates in 88 percent of the 702 fungal isolates. This is a surprising detection rate compared to other, less thorough studies. These results revealed the complexity and diversity in the fungal bacteriome throughout the fungal tree.

This study provides a foundation for further understanding of fungal-bacterial relationships. Further analysis of these interactions will help to better understand the environmental microbiome processes, including fungal and bacteria contributions to nutrient cycle, plant health, and climate modeling.

Understanding how bacteria-fungal interactions affect plants, animals, ecosystem functioning, and the environment in which they occur is crucial to understanding the changing climate. This will help us predict and possibly manipulate the effects of these interactions.

Further Ecological drivers of decoupled patterns in latitudinals in bacterial diversity gradients

Additional information: Aaron J. Robinson and colleagues, Widespread Bacterial Diversity within the Bacteria of Fungal, Communications Biology (2021). Information from Communications Biology Aaron J. Robinson and colleagues, Widespread Bacterial Diversity within the bacteriomeof fungi. (2021). DOI: 10.1038/s42003-021-02693-y