Leaf Surface RNA: A Hidden Influencer of Microbial Ecosystems

The research, Diverse plant RNAs coat Arabidopsis leaves and are distinct from apoplastic RNAs, was published on January 3, 2025, in the Proceedings of the National Academy of Sciences. The principal authors are Lucía Borniego and Meenu Singla-Rastogi, postdoctoral researchers at the Indiana University Department of Biology within the College of Arts and Sciences. The lead author is Roger Innes, Distinguished Professor of Biology.

“What thrills us most about this finding is that it implies plants may regulate their microbiomes, at least in part, by modulating gene expression in microbes through cross-kingdom RNA interference, also referred to as RNAi,” stated Innes. “RNA interference is a widely recognized form of gene regulation whereby cells can diminish the expression of a gene by synthesizing a small RNA that can pair with the RNA of the target gene. This type of gene regulation appears to be prevalent across nearly all living organisms, but it has only recently been demonstrated that RNAs produced by one organism can be assimilated by another organism and subsequently interact with RNAs in the recipient organism.”

RNA is incredibly delicate and consequently degrades swiftly if not safeguarded. This study provides some of the earliest evidence that plants can release functional RNA onto the surfaces of their leaves.

The research identified that there are plentiful RNAs on leaf surfaces that exhibit an unexpected level of stability. Data presented in the paper indicate that this stability may be linked to the capacity of the RNA to create condensates with polysaccharides, such as pectin. By revealing that plant leaves are coated with RNA, this study demonstrates that the microbes colonizing the leaf surfaces are exposed to plant RNA and are likely to engage with this RNA. Consequently, this interaction may affect gene expression within these microbes, influencing which microbes prosper on the surfaces of the leaves.

“The alteration of microbial communities by environmental RNA is probably occurring in our own intestines as well, with RNA being secreted by our intestinal epithelial cells,” noted Innes. “It is also quite feasible that RNA present on the surfaces of leaves, like those found in salads, could impact our gut microbiomes.”

Additional contributors to the publication include Megha Hastantram Sampangi-Ramaiah and Hana Zand Karimi from the Indiana University Department of Biology, Patricia Baldrich and Blake C. Meyers from the University of California — Davis, and Madison McGregor from the Donald Danforth Plant Science Center.