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Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution

Abstract

Natural bacterial populations can display enormous genomic diversity, primarily in the form of gene content variation caused by the frequent exchange of DNA with the local environment. However, the ecological drivers of genomic variability and the role of selection remain controversial. Here, we address this gap by developing a nationwide atlas of 1,854 Listeria isolates, collected systematically from soils across the contiguous United States. We found that Listeria was present across a wide range of environmental parameters, being mainly controlled by soil moisture, molybdenum and salinity concentrations. Whole-genome data from 594 representative strains allowed us to decompose Listeria diversity into 12 phylogroups, each with large differences in habitat breadth and endemism. ‘Cosmopolitan’ phylogroups, prevalent across many different habitats, had more open pangenomes and displayed weaker linkage disequilibrium, reflecting higher rates of gene gain and loss, and allele exchange than phylogroups with narrow habitat ranges. Cosmopolitan phylogroups also had a large fraction of genes affected by positive selection. The effect of positive selection was more pronounced in the phylogroup-specific core genome, suggesting that lineage-specific core genes are important drivers of adaptation. These results indicate that genome flexibility and recombination are the consequence of selection to survive in variable environments.

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Fig. 1: Nationwide distribution and ecological drivers of Listeria.
Fig. 2: Biogeography, pangenome openness and recombination across Listeria phylogroups.
Fig. 3: Stronger positive selection in more cosmopolitan phylogroup.
Fig. 4: Impact of selection differs between Listeria core genes and phylogroup-specific core genes.

Data availability

Trimmed paired-end reads for the 594 Listeria isolates used in this study were deposited to the National Center for Biotechnology Information’s (NCBI) Sequence Read Archive (SRA) and assembled genomes were deposited to NCBI GenBank under the accession numbers listed in Supplementary Table 2. Metadata collected in this study including sampling date, latitude, longitude, elevation, soil physiochemical data, climate data and land-use data are provided in Supplementary Table 1.

Code availability

Codes for sigB allelic typing, negative sample selection, core SNPs detection and Listeria phylogroup detection are available at https://github.com/JingqiuLiao/listeria-biogeography. The code for land-use proportion calculation is available at https://github.com/wellerd2/Calculating-land-use-land-cover-and-landscape-structure-parameters.

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Acknowledgements

This work was supported by the Center for Produce Safety (award number 2018CPS13) through the Florida Department of Agriculture and Consumer Services (under agreement number 024842) (M.W.) and Simons Foundation Collaboration: Principles of Microbial Ecosystems (PriME) award # 542395 (O.X.C.). The contents do not necessarily reflect the views or policies of the Center for Produce Safety the United States Department of Agriculture nor does mention of trade names, commercial productions, services or organization imply endorsement by the U.S. Government. We are grateful for A. Harrison, A. Snyder, A. Curtis, A. Shed, A. Alles, A. Andrus, A.a Ho Watson, A. Edwarthy, A. King, A. Roberts, A. Carroll, A. Ferrero, A. Buehler, B. Perkins, C. Casou, C. Ajua, C. Metzger, C. Rock, C. Day, C. Burnham, C. Mauck, C. Cox, C. Fitzegerald, C. Robinson, D. Koziol, D. Bryan, D. Trudelle, D. van De Grift, D. Baumler, D. Murphy, D. Sue, D. Brasill, Debarah Weller, Donald Weller, D. Thomas, E. White, E. Wilson, F. Becker, G. Gandhi, G. Bulnhem, H. Zhang, H. Duong, H. Deng, J. Zimmerman, J. Lunsford, J. Kovac, J. Adams, J. Goettig, J. Moreira, J. Perkins, J. David, J. Eggers, J. Jenkins, J. Steffan, J. Bejeck, K. Kniel, K. Kharel, K. Kruckow, K. Cobb, K. Schmidt, K. Gall, K. Kemp, K. Jordan, L. Sun, L. Carroll, L. Gorski, L. Goddik, L. Adams, L. Nelther, M. Scawartz, M. Schwart, M. Yeung, M. Levandowski, M. Nelther, M. Stasiewicz, M. Watterson, M. Jin, M. Cao, M. Theriault, N. Brassill, R. Nuir, R. Vgas, R. Smith, R. Wallar, S. Cimowsky, S. Beno, S. Murphy, S. Duerr, S. Ahn, S. Morquez, S. Clark, T. Cobb, T. Denes, T. Lan, T. Autry, T. Peters, V. Gund, V. Lappi, V. Chherri, X. Cheng, Y. Han, Y. Hu, Z. Raposo and Z. Xiong for helping with the sample collection.

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Authors

Contributions

J.L., M.W. and O.X.C. designed the study. J.L., D.L.W. and M.W. designed the sample collection plan. J.L. coordinated the sample collection processes. J.L. and X.G. processed soil samples and performed Listeria isolation and molecular characterization. J.L. analysed the data with input from S.P., D.H.B. and O.X.C. J.L. and O.X.C. wrote the manuscript with input from S.P., D.H.B. and M.W.

Corresponding authors

Correspondence to Martin Wiedmann or Otto X. Cordero.

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The authors declare no competing interests.

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Peer review information Nature Microbiology thanks the anonymous reviewers for their contribution to the peer review of this work. Peer reviewer reports are available.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Density of samples positive and negative for Listeria based on spatial, soil, and climate variables.

“***”, “**”, and “*” indicates a significant difference between positive and negative samples at P level of 0.001, 0.01, and 0.05, respectively, in two-sided Mann–Whitney tests with a Benjamini and Hochberg (BH) false discovery rate (FDR) correction.

Extended Data Fig. 2 Pairwise Pearson correlation between spatial, soil, climate, and land-use variables.

r is the Pearson coefficient. “*” indicates that variables are significantly correlated at two-sided P level of 0.05 with a BH FDR correction. TN: total nitrogen; TC: total carbon; OM: organic matter; Developed A: developed open space (< 20% impervious cover); Developed B: developed open space (>20% impervious cover).

Extended Data Fig. 3 Variable importance in predicting the presence of Listeria based on the Mean Decrease Gini index in a random forest model.

The 24 environmental variables (13 soil, 3 climate, and 8 land-use variables) and 2 spatial variables are sorted in ascending order according to the median Mean Decrease Gini value of 1,000 repetitions. Minimum and maximum values are depicted by short vertical lines of whiskers; the box signifies the upper and lower quartiles, and the short line within the box signifies the median. Points above and below the whiskers indicate outliers. Developed A: developed open space (< 20% impervious cover); Developed B: developed open space (>20% impervious cover).

Extended Data Fig. 4 Clusters in networks of recent horizontal gene transfer among Listeria genomes.

Nodes represent clonal clusters and edges represent the inferred amount of gene flow between them. Node size indicates the size of clonal cluster, which represents a group of too closely related genomes (<0.035% divergence). Nodes are color-coded by phylogroups.

Extended Data Fig. 5 Distribution of each Listeria phylogroup across the US.

Circles indicate samples positive for each Listeria phylogroup. Polygon indicates the distribution of each phylogroup.

Extended Data Fig. 6 Prevalence of the 12 Listeria phylogroups.

Prevalence is indicated by the proportion of sampling sites positive for one phylogroup among all 1,004 sampling sites. Populations are sorted by the prevalence in descending order. The mean prevalence is 3.35%. The standard deviation is 3.08%.

Extended Data Fig. 7 The accumulation curves of core genomes and pangenomes of Listeria phylogroups.

The blue and red line is showing the mean pan and core genome sizes of 100 repetitions of subsampling an increasing number of genomes, respectively. The vertical bars indicate the standard deviations of 100 repetitions. The formula of the power law function cNγ predicting the pangenome size (npan) is shown, where c is the size of the core genome, N is the number of genomes and γ is a scaling exponent with between 0 and 1.

Extended Data Fig. 8 Relationship between prevalence and average nucleotide diversity of phylogroup core genes.

R is the two-sided Spearman’s rank correlation coefficient, R2 indicates the variability explained by the linear regression model, and the line and the shaded area depict the best-fit trendline and the 95% confidence interval (mean + /− 1.96 SEM) of the linear regression, respectively.

Extended Data Fig. 9 Spearman’s rank correlation between the average r2N/r2S of core genes of Listeria phylogroups and the variance of soil, climate, and land-use variables for their samples.

R is the two-sided Spearman’s rank correlation coefficient. The line and the shaded area depict the best-fit trendline and the 95% confidence interval (mean + /− 1.96 SEM) of the linear regression, respectively.

Extended Data Fig. 10 Spearman’s rank correlation between prevalence and average dN/dS of Listeria core genes (orange) and phylogroup-specific core genes (blue) involved in each COG functional category.

R is the two-sided Spearman’s rank correlation coefficient. The line and the shaded area depict the best-fit trendline and the 95% confidence interval (mean + /− 1.96 SEM) of the linear regression, respectively. COG functional categories are descripted as below. C: Energy production and conversion; D: Cell cycle control, cell division, chromosome partitioning; E: Amino acid transport and metabolism; F: Nucleotide transport and metabolism; G: Carbohydrate transport and metabolism; H: Coenzyme transport and metabolism; I: Lipid transport and metabolism; J: Translation, ribosomal structure and biogenesis; K: Transcription; L: Replication, recombination and repair; M: Cell wall/membrane/envelope biogenesis; N: Cell Motility; O: Posttranslational modification, protein turnover, chaperones; P: Inorganic ion transport and metabolism; Q: Secondary metabolites biosynthesis, transport and catabolism; S: Function unknown; T: Signal transduction mechanisms; U: Intracellular trafficking, secretion, and vesicular transport; V: Defense mechanisms; Z: Cytoskeleton.

Supplementary information

Supplementary Information

Supplementary Methods, Figs. 1–5 and Tables 3, 5, 7–8.

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Supplementary Tables File

Supplementary Table 1, metadata summary of 1,004 soil samples; Supplementary Table 2, metadata summary of 594 Listeria isolates selected for whole-genome sequencing; Supplementary Table 4, core genes of Listeria phylogroups undergoing positive selection based on BUSTED model; and Supplementary Table 6, gene type and functional annotation of orthologous genes.

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Liao, J., Guo, X., Weller, D.L. et al. Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution. Nat Microbiol 6, 1021–1030 (2021). https://doi.org/10.1038/s41564-021-00935-7

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