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Microbes communicate by excreting simple and complex molecules called metabolites that interact with, talk to, and manipulate their local environment and neighboring cells in a process known as metabolic exchange. Understanding the timing and distribution of these molecular exchanges will be useful for interpreting and potentially manipulating microbial communities for applications ranging from bioremediation to drug discovery.

An exciting and novel technique developed at EMSL now allows researchers to characterize, with high sensitivity and in time and space, the metabolite profile of living microbial communities grown on a soft agar surface. The new method combines EMSL’s nanospray desorption electrospray ionization (nanoDESI) mass spectrometry (MS) and a new bioinformatics technique called molecular networking, which was developed by EMSL users from the University of California, San Diego.

NanoDESI allows for the direct chemical analysis of microbial communities in space and time. Molecular networking is a new way to analyze, organize, and visualize MS data, such as from nanoDESI. During high-resolution MS analysis, thousands of molecules are detected, and structural information is gathered about these molecules by breaking them into fragments. Molecular networking assigns each molecule to a family with shared structural characteristics based on the observed fragmentation patterns—in this case, revealing insights about how microbial communities communicate.

The combined nanoDESI and molecular networking approach was validated by studying Pseudomonas sp. strain SH-C52, a bacterium that protects plants from fungal infection. It successfully allowed researchers to detect and partially characterize the antifungal Pseudomonas agent thanamycin, a lipopeptide that is undetectable using traditional methods. The sensitivity afforded by nanoDESI coupled with molecular networking along with the potential for the broad implementation of the combined technique provide a significant gain toward characterizing complex microbial interactions by directly observing metabolic exchange processes—a long-sought breakthrough in the microbiology field.