This work is published
Chodkowski JL and A Shade. 2024. Bioactive exometabolites drive maintenance competition in simple bacterial communities. mSystems. [https://journals.asm.org/doi/10.1128/msystems.00064-24]
Genomics, metabolomics, and transcriptomics data are available at Joint Genomes Institute Portal (https://genome.jgi.doe.gov/portal/) under JGI Proposal ID 502921
mSystems Volume 9, Number 4 16 April 2024
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
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SUPPLEMENTAL MATERIAL
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ABSTRACT During prolonged resource limitation, bacterial cells can persist in metabolically active states of non-growth. These maintenance periods, such as those experienced in stationary phase, can include upregulation of secondary metabolism and release of exometabolites into the local environment. As resource limitation is common in many environmental microbial habitats, we hypothesized that neighboring bacterial populations employ exometabolites to compete or cooperate during maintenance and that these exometabolite-facilitated interactions can drive community outcomes. Here, we evaluated the consequences of exometabolite interactions over the stationary phase among three environmental strains: Burkholderia thailandensis E264, Chromobacterium subtsugae ATCC 31532, and Pseudomonas syringae pv. tomato DC3000. We assembled them into synthetic communities that only permitted chemical interactions. We compared the responses (transcripts) and outputs (exometabolites) of each member with and without neighbors. We found that transcriptional dynamics were changed with different neighbors and that some of these changes were coordinated between members. The dominant competitor B. thailandensis consistently upregulated biosynthetic gene clusters to produce bioactive exometabolites for both exploitative and interference competition. These results demonstrate that competition strategies during maintenance can contribute to community-level outcomes. It also suggests that the traditional concept of defining competitiveness by growth outcomes may be narrow and that maintenance competition could be an additional or alternative measure.
This material is based upon work supported by the National Science Foundation under Grant No DEB##1749544, by Michigan State University, and by a DOE-JGI Community Science Program award (Proposal ID 502921). The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231. J.C. was supported by the Eleanor L. Gilmore Fellowship from the Department of Microbiology and Molecular Genetics.