PNNL

The Science 

In nature, microbes often grow in complex molecular environments created by other organisms such as plants and fungi. Researchers investigated how the molecular environment influences microbial phenotypes by developing a growth medium inspired by compounds that beneficial soil fungi release. They discovered that the mixture of compounds produced a unique growth phenotype in the soil bacterium and synthetic biology workhorse Pseudomonas putida that could not be reproduced with any individual substrate. By integrating experiments with metabolic modeling, they also predicted how the bacterium coordinated the use of multiple nutrients over time during growth.

The Impact 

This work shows that the composition of the molecular environment, not just the amount of nutrients (total carbon or nitrogen), is a key factor in determining bacterial growth and metabolism. The study integrated experiments with metabolic modeling as a framework to interpret and predict microbial responses under environmentally relevant conditions. These findings can inform the design of improved microbial growth media and biosystems for biotechnology and environmental applications. The work highlights the importance of studying microbes in ecologically realistic molecular environments, where mixtures of molecules may produce microbial behaviors that cannot be predicted from individual substrates alone.

Summary 

Researchers used a media mimicking a fungal exudate to investigate how an ecologically realistic mixed molecular environment influences the soil bacterium Pseudomonas putida. Compared with individual substrates, the mixed molecular environment produced an emergent growth phenotype characterized by faster growth initiation, earlier attainment of maximum biomass, and high biomass accumulation. The fungal exudate-inspired growth medium enabled bacteria to initiate growth at least twice as fast as any individual substrate even under the same total carbon and nitrogen. Time-resolved measurements of substrate utilization showed that the bacterium first prioritized the organic acid malate before coordinating the use of multiple additional substrates. Researchers then integrated these measurements with genome-scale metabolic modeling and proteomics to accurately predict both substrate utilization dynamics and metabolic pathway activity and to provide mechanistic insight into how the molecular environment shapes microbial growth and metabolism. Together, these findings demonstrate that the composition of a molecular environment strongly influences microbial behavior and presents an approach for interpreting and predicting microbial responses under chemically realistic conditions.

Contact 

Sneha Couvillion, Pacific Northwest National Laboratory, sneha.couvillion@pnnl.gov 

Funding 

The work was supported by the Predictive Phenomics Initiative at Pacific Northwest National Laboratory and conducted under the Laboratory-Directed Research and Development Program. Pacific Northwest National Laboratory is a multiprogram national laboratory operated by Battelle for the Department of Energy under Contract No. DE-AC05-76RL01830. Undergraduate interns in the research team were supported in part by the U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists under the Science Undergraduate Laboratory Internships program.