Phenylpropanoid methyl esterase unlocks catabolism of aromatic biological nitrification inhibitors

Authors: WILSON, ANDREW - Pacific Northwest National Laboratory; VAN FOSSEN, ELISE - Pacific Northwest National Laboratory; SHRESTHA, RITU - Pacific Northwest National Laboratory; FRANK, ANDREW - Pacific Northwest National Laboratory; TROTTER, VALENTINE - Lawrence Berkeley National Laboratory; BALDINO, HENRI - Pacific Northwest National Laboratory; POIRIER, BRENTON - Pacific Northwest National Laboratory; KIM, YOUNG-MO - Pacific Northwest National Laboratory; NELSON, WILLIAM - Pacific Northwest National Laboratory; SIMMONS, TUESDAY - University Of California Berkeley; Coleman-Derr, Devin; DEUTSCHBAUER, ADAM - Lawrence Berkeley National Laboratory; EGBERT, ROBERT - Pacific Northwest National Laboratory; ELMORE, JOSHUA - Pacific Northwest National Laboratory

Submitted to: The ISME Journal: Multidisciplinary Journal of Microbial Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/5/2025
Publication Date: 11/13/2025
Citation: Wilson, A., Van Fossen, E., Shrestha, R., Frank, A., Trotter, V., Baldino, H., Poirier, B., Kim, Y., Nelson, W., Simmons, T., Coleman-Derr, D.A., Deutschbauer, A., Egbert, R., Elmore, J. 2025. Phenylpropanoid methyl esterase unlocks catabolism of aromatic biological nitrification inhibitors. The ISME Journal: Multidisciplinary Journal of Microbial Ecology. 19(1). Article wraf251. https://doi.org/10.1093/ismejo/wraf251.
DOI: https://doi.org/10.1093/ismejo/wraf251

Interpretive Summary: Agriculture is a major source of greenhouse gases (GHG) on the planet. Although application of N-fertilizers increases crop yields, a large proportion of applied N-fertilizer is ultimately lost to the atmosphere as N2O, a potent GHG. Nitrifying microbes catalyze the oxidation of reduced forms of nitrogen into nitrate and NO3- is converted to the potent greenhouse gas N2O by denitrifying bacteria that are widely prevalent in soil. One approach to reduce nitrification in agriculture is the co-application of chemical nitrification inhibitors with fertilizers. Here we work to solve this problem by identifying bacterial genes that can help with this process.

Technical Abstract: Agriculture is one of the largest sources of greenhouse gases (GHG) on earth. Conversion of nitrogen fertilizers into more oxidized forms by microbial nitrification drives GHG production, proliferation of toxic algal blooms, and increases the costs of crop production. Some plants exude biological nitrification inhibitors (BNIs) that prevent ammonium-oxidizing microbes from performing nitrification. Applying synthetic biology to transfer BNI production into food and bioenergy crops is a promising approach to reduce nitrification, but the success of this strategy depends on improving our limited understanding of BNI mechanisms and degradation in soil. Here we address this gap by characterizing a previously unknown route through which phenylpropanoid methyl esters (PPMEs), a prominent class of aromatic BNI, is degraded by microbes. We used a combination of transcriptomics and high-throughput functional genomics to identify genes of unknown function that are required for PPME degradation. Using genetic and biochemical analyses we found that two of these genes encode previously uncharacterized enzymes, including a novel phenylpropanoid methyl esterase, that funnel PPMEs into phenylpropanoid catabolism. Transfer of these two genes into bacteria capable of using other phenylpropanoids enabled them to use PPMEs as carbon sources. This work provides avenues to better understand the catabolism of BNI compounds and is a first step towards development of model in vivo plant-microbe systems for studying BNI mechanisms under well controlled conditions.