Outer Membrane Vesicles Help Bacteria Digest Lignin-Derived Compounds

Bacterial cells exude specialized enzymes to extract nutrients locked within plant cell walls.

The Science

Fungi are thought to be the primary organisms that break down tough, woody matter called lignin in plants, but bacteria also play a role that isn’t fully understood. A study of three bacterial species reveal a key mechanism for breaking down lignin in one particular strain, Pseudomonas putida KT2440. Its cells release an abundance of enzymes in the presence of lignin-derived compounds, selectively packaging those enzymes in pouches called outer membrane vesicles that leave the main cell body of the bacteria and digest lignin outside the cell.

The Impact

While lignin is found in most plants, the molecular composition of lignin varies from one type of plant to another. The discovery of this specialized bacterial process and how the cells exude enzymes via outer membrane vesicles offers new insight into how bacteria might work with fungi in the soil to break down lignin. Understanding this cellular strategy eventually could help inform approaches to process lignin for biofuels and other products.


The study builds on previous work showing that multiple organisms are capable of breaking down lignin oligomers, even though such oligomers are unlikely to pass through a bacterial cell membrane. To find out how such a feat might be accomplished, a multi-institutional team of scientists studied three of these aromatic-catabolic soil bacteria, comparing how they interacted with lignin-rich media and with lignin-free media. They analyzed the exoproteome, which is the protein content released by bacterial cells in response to lignin and found that all of the strains— P. putida KT2440, Rhodoccocus jostii RHA1, and Amycolatopsis sp. ATCC 39116— exhibited exoproteomes that were distinct from the intracellular proteins. P. putida displayed an extraordinarily complex exoproteome when exposed to lignin-derived compounds. A microscopic view of P. putida cells revealed outer membrane vesicles (OMVs), which are spherical bodies secreted from the cell membranes that contain enzymes capable of breaking down lignin-related compounds. Scientists from the Environmental Molecular Sciences Laboratory (EMSL) conducted the exoproteome analysis as part of EMSL’s Functional Omics and Cellular Dynamics Integrated Research Platforms. The team also included scientists from the National Renewable Energy Laboratory, Oak Ridge National Laboratory, and Argonne National Laboratory. Further work will be needed to fully decipher the role of OMVs and the exoproteome in carbon cycling and in conversion of waste organic carbon into valuable chemical products.

Principal Investigator(s)

Robert L. Hettich
Oak Ridge National Laboratory


This work was funded by the Bioenergy Technologies Office within the U.S. Department of Energy (DOE) Office of Energy Efficiency and Renewable Energy; DOE’s Office of Science to the Center for Bioenergy Innovation, a DOE Bioenergy Research Center and the Environmental Molecular Sciences Laboratory user facility (both within the Office of Biological and Environmental Research Program); and the Center for Nanoscale Materials user facility within the the DOE Office of Science’s Office of Basic Energy Sciences. Additional funding was provided by the Laboratory Directed Research and Development Program at Argonne National Laboratory.


Salvachúa, D., Werner, A.Z., Pardo, I. et al. “Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440.” Proceedings of the National Academy of Sciences USA 117(17) 9302–9310 (2020). [DOI:10.1073/pnas.1921073117]