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Chance and pleiotropy dominate genetic diversity in complex bacterial environments

Abstract

How does environmental complexity affect the evolution of single genes? Here, we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase mutants across 19 different environments—from phenotypically homogeneous single-cell populations in liquid media to heterogeneous biofilms, plant roots and soil populations. The effects of individual gene mutations on organismal fitness were highly reproducible in liquid cultures. However, 84% of the tested alleles showed opposing fitness effects under different growth conditions (sign environmental pleiotropy). In colony biofilms and soil samples, different alleles dominated in parallel replica experiments. Accordingly, we found that in these heterogeneous cell populations the fate of mutations was dictated by a combination of selection and drift. The latter relates to programmed prophage excisions that occurred during biofilm development. Overall, for each condition, a wide range of glutamate dehydrogenase mutations persisted and sometimes fixated as a result of the combined action of selection, pleiotropy and chance. However, over longer periods and in multiple environments, nearly all of this diversity would be lost—across all the environments and conditions that we tested, the wild type was the fittest allele.

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Fig. 1: Selection versus chance-dominated conditions.
Fig. 2: The pleiotropic effects of alleles across different conditions.
Fig. 3: Genetic sweeps in colony biofilms and soil and the dominance of the wild-type allele.
Fig. 4: The combined action of selection and chance in colony biofilms and soil colonization.
Fig. 5: Programmed genomic excisions drive GudB’s drift in colony biofilms.

Data availability

The data that support the findings of this study are available from the corresponding author on request.

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Acknowledgements

L.N.-G. was supported by CONACYT grant no. 203740 and the Martin Kushner Fellowship at the Weizmann Institute of Science. D.S.T. is the Nella and Leon Benoziyo Professor of Biochemistry. Financial support from the Kahn Centre for Systems Biology at the Weizmann Institute of Science is gratefully acknowledged. We thank R. Milo, S. Fleishman, Z. Livneh and F. Kondrashov for their support and critical advice and E. Segev and A. de Visser for their critical and insightful comments on the manuscript. We appreciate the help of M. Hershko with script development for data processing and of Y. Bar-On and S. Gleizer with the analysis of genomic sequences. We are grateful to R. Rotkopf from Weizmann Life Sciences Core Facilities for his guidance on the statistical analysis. We are thankful for the services provided by the Crown Genomics Institute of the Nancy and Stephen Grand Israel National Centre for Personalized Medicine, Weizmann Institute of Science.

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Authors

Contributions

L.N.-G. and D.S.T. designed the experiments and wrote the manuscript. L.N.-G., D.D. and D.S.T. analysed the data. L.N.-G. performed all experiments, except the selection of the soil colonization that was performed in collaboration with E.K. and A.A. D.D. and A.E. wrote the scripts used for the data analysis and visualization. E.P. applied the machine learning classification.

Corresponding author

Correspondence to Dan S. Tawfik.

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Supplementary information

Supplementary Information

Supplementary Figures 1–12, Supplementary Tables 1–10 and legends for Supplementary Datasets.

Reporting Summary

Supplementary Dataset 1

Illumina raw counts for all alleles measured in each experiment. All codons that encode for the wild-type amino acid were summed under ‘WT’ and are shown in bold numbers. Sheet no. 1 shows the Illumina reads raw counts for the selection conditions that were initiated from Initial Mix 1 and 2: liquid, pellicle biofilms, colony biofilms, spores and germinated spores. Sheet no. 2 shows the Illumina reads raw counts for the conditions initiated from Initial mix 3: bulk soil. For each condition, three replica experiments were performed except for the bulk soil condition, where five replica experiments were performed.

Supplementary Dataset 2

FC values for all alleles and experiments. The codes assigning the individual conditions and experiments are described in Supplementary Tables 2 and 3. Sheet no. 1 shows the FC values for all conditions initiated from Initial Mix 1 and 2: liquid, pellicle biofilms, colony biofilms, spores and germinated spores. Sheet no. 2 shows the FC values for all conditions initiated from Initial Mix 3: bulk soil.

Supplementary Dataset 3

Analysis of SNPs and mobile elements in the sequenced genomes of various populations. The position in the genome, the mutations, their frequency and the mutated gene/protein (if applicable) are shown. Sheet no. 1 provides a description of all sheets in this file.

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Noda-García, L., Davidi, D., Korenblum, E. et al. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nat Microbiol 4, 1221–1230 (2019). https://doi.org/10.1038/s41564-019-0412-y

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