Abstract
Bacterial genomes evolve in complex ecosystems and are best understood in this natural context, but replicating such conditions in the lab is challenging. We used transposon sequencing to define the fitness consequences of gene disruption in the bacterium Caulobacter crescentus grown in natural freshwater, compared with axenic growth in common laboratory media. Gene disruptions in amino-acid and nucleotide sugar biosynthesis pathways and in metabolic substrate transport machinery impaired fitness in both lake water and defined minimal medium relative to complex peptone broth. Fitness in lake water was enhanced by insertions in genes required for flagellum biosynthesis and reduced by insertions in genes involved in biosynthesis of the holdfast surface adhesin. We further uncovered numerous hypothetical and uncharacterized genes for which disruption impaired fitness in lake water, defined minimal medium, or both. At the genome scale, the fitness profile of mutants cultivated in lake water was more similar to that in complex peptone broth than in defined minimal medium. Microfiltration of lake water did not significantly affect the terminal cell density or the fitness profile of the transposon mutant pool, suggesting that Caulobacter does not strongly interact with other microbes in this ecosystem on the measured timescale. Fitness of select mutants with defects in cell surface biosynthesis and environmental sensing were significantly more variable across days in lake water than in defined medium, presumably owing to day-to-day heterogeneity in the lake environment. This study reveals genetic interactions between Caulobacter and a natural freshwater environment, and provides a new avenue to study gene function in complex ecosystems.
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Acknowledgements
This work was supported by UChicago BIG grant to SC and MLC, and NIGMS grant R01GM087353 to SC. KLH was supported by an NIH Ruth Kirschstein Postdoctoral Fellowship (F32 GM122242) and a Chicago Biomedical Consortium Postdoctoral Core Grant (FP064244-01-PR). LMRR was supported by the NIH Molecular and Cellular Biology Training Grant (T32 GM007183). PDC is supported an NSF CAREER award (1552647); he began the Tn5 library construction in the laboratory of Dr. Yves V. Brun at Indiana University. We thank the members of the Crosson laboratory for helpful discussions, Tom Ioerger (Texas A&M) for assistance with TRANSIT, Adam Deutschbauer (University of California-Berkeley) for the E. coli APA752 strain, and David Hershey for construction of the C. crescentus CB15 Himar transposon library. We also thank Pieter Faber and Abhilasha Cheruku from the University of Chicago Genomics Facility for technical advice and helpful discussions, and Kasia Kluszczynska, Xiomy Alejandro-Navarreto, Lydia Varesio, and Olivia Stovicek for help with lake water collection.
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Hentchel, K.L., Reyes Ruiz, L.M., Curtis, P.D. et al. Genome-scale fitness profile of Caulobacter crescentus grown in natural freshwater. ISME J 13, 523–536 (2019). https://doi.org/10.1038/s41396-018-0295-6
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DOI: https://doi.org/10.1038/s41396-018-0295-6
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