A recent study in Microbiological Research reveals that plant-protecting bacteria like Bacillus subtilis, which protects from bacterial infections, viruses and fungi, possess memory, which they can pass down through generations.

The research highlights how memory allows bacteria to recolonize plant hosts efficiently and enhance their symbiotic relationships by “activating the stress response system, giving them an advantage in competition.” This discovery paves the way for innovations in probiotics and agricultural biotechnology, potentially boosting resilience and performance in plants and human gut microbiomes.

“Our work demonstrates a bacterial memory manifested by multigenerational reversible adaptation to plant hosts in the form of activation of the stressosome, which confers an advantage to symbiotic bacteria during competition,” details the study.

Symbiotic Futures connects with Dr. Ilana Kolodkin-Gal, Head of Microbiome and Synthetic Microbiology Lab, and Senior lecturer at Scojen Institute of Synthetic Biology, Reichman University, to learn about the discovery:

How does the multigenerational memory of beneficial bacteria like Bacillus subtilis enhance their symbiotic relationships with plant hosts and contribute to more stable colonization?

In optimal conditions, B. subtilis cells divide rapidly (30 mins). Therefore, if detached from their host, the signals for symbiosis will dilute with generations. A plant host life span is significantly longer, and the margins are between months and years. Therefore, maintaining the signals for the host for multiple bacterial generations allows them to rapidly recolonize the same host, fostering a sense of “loyalty” between the plant and symbiotic bacteria.

How might the multigenerational inheritance patterns observed in Bacillus subtilis inform our understanding of similar mechanisms in probiotic bacteria within the human gut? 

We found that Bacillus subtilis, an effective probiotic bacterium and efficient plant biofertilizer and biopesticide, changes almost 25% of its gene expression when interacting with a host. However, once the host signal is removed, most of the gene expression changes induced by the plant decrease rapidly. Nonetheless, around 5% of the genes continue to be expressed at similar levels in the bacteria’s descendants that interact with the plant, just like in their parent cells. This host-dependent pattern was consistent for over eight generations of bacteria. We may have pinpointed the essential set of genes needed for host colonization, which might also be relevant for interactions with the gastrointestinal tract. We are now looking to further explore these questions.

What potential applications and ethical implications could arise from manipulating the genes identified in this study to create synthetic circuits with memory for agricultural and industrial purposes?

The research work with beneficial strains does not raise any ethical considerations. Our work has two potential applications: incorporating purified plant signals with the strains to improve their symbiosis with crop hosts in the field, which requires no significant adjustments to existing protocols, or creating genetically modified strains with more beneficial genes, including memory. The ethical discussion surrounding the introduction of genetically modified strains into agriculture is complex and challenging. Our findings support the idea that symbiotic interactions are tightly regulated, and we can manipulate them with chemical signals as well as genetic modifications, which also applies to mammalian hosts. 

The application of this work extends beyond agriculture: The bacterium B. subtilis plays multiple roles in medicine and nutrition as a probiotic, in biotechnology as a producer of metabolites and enzymes, and as a bio-cement additive, and in agriculture as an efficient biopesticide and biofertilizer. Delving into the components and networks of B. subtilis epigenetic machinery presents interesting opportunities for creating synthetic circuits with memory. Understanding the epigenetic inheritance of B. subtilis will enable us to enhance its performance across a wide range of applications, while potentially revolutionizing our understanding of bacterial evolution, adaptation, and inheritance.

What role do stress resistance and other defense mechanisms play in the successful colonization and symbiosis of beneficial bacteria with their hosts, and how might this understanding be applied to enhance interspecies communication and relationships?

Most research on symbiosis tends to focus on metabolic interactions and the host’s immune response to bacteria. This study, however, sheds light on how the “immune” system of firmicutes aids in neutralizing host defenses to promote colonization. The stressosome, a cluster of proteins that mitigates general stressors, is identified as a vital component of bacterial immunity, enabling efficient colonization by overcoming host defenses. Therefore, our results indicate that competition to neutralize host defenses may hold greater significance than any other symbiotic mechanism. 

Interview by Venya Patel