Genome-scale fitness profile of Caulobacter crescentus grown in natural freshwater

• Published in: The ISME Journal Vol. 13; no. 2; pp. 523 - 536
• Main Authors: Hentchel, Kristy L., Reyes Ruiz, Leila M., Curtis, Patrick D., Fiebig, Aretha, Coleman, Maureen L., Crosson, Sean
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.02.2019; Nature Publishing Group
• Subjects: 45; 45/23; 631/326/171/1878; 704/158/855; Amino acids; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Biomedical and Life Sciences; Biosynthesis; Caulobacter crescentus; Caulobacter crescentus - genetics; Cell density; Cell surface; Culture media; Ecology; Ecosystems; Evolutionary Biology; Fitness; Flagella; Flagella - genetics; Flagella - metabolism; Fresh Water - microbiology; Freshwater ecosystems; Freshwater environments; Gene disruption; Gene Expression Regulation, Bacterial; Gene sequencing; Genes; Genetic Fitness; Genome, Bacterial; Genomes; Heterogeneity; Lakes; Life Sciences; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Microfiltration; Peptones; Replication; Reproductive fitness; Substrates; Sugar; Transposons
• ISSN: 1751-7362; 1751-7370
• DOI: 10.1038/s41396-018-0295-6

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.