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A global atlas of the dominant bacteria found in soil

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Science  19 Jan 2018:
Vol. 359, Issue 6373, pp. 320-325
DOI: 10.1126/science.aap9516
  • Fig. 1 Abundance and composition of dominant soil bacterial phylotypes across the globe.

    (A) Percentage of phylotypes and relative abundance of 16S rRNA genes representing the dominant versus the remaining bacterial phylotypes. (B) Relative abundance (mean ± SE) of dominant phylotypes across continents and ecosystem types. Ecosystem type classification followed the Köppen climate classification and the major vegetation types found in our database. Grasslands include both tropical and temperate grasslands. Shrublands include polar, temperate, and tropical shrublands. The number of samples in each category is indicated in parentheses. (C) The taxonomic composition of the dominant phylotypes. The phylotypes assigned to the least abundant phyla are not shown (including Armatimonadetes = 0.08%, TM7 = 0.05%, and WS2 = 0.03%). Details on the top 511 dominant phylotypes are shown in table S1.

  • Fig. 2 Phylogenetic tree including the taxonomic information on dominant soil bacterial phylotypes.

    (A) Histogram showing the percentage 16S rRNA gene sequence similarity between the 511 dominant phylotypes and the most closely related available reference genome for each phylotype. (B) Phylogenetic distribution of the 511 dominant phylotypes. Black shading on the innermost and middle rings indicates, for each phylotype, whether there is a representative isolate and a genome match at the ≥97% 16S rRNA gene sequence similarity level. The coloring on the outermost ring highlights the distribution of environmental preferences for all phylotypes (n = 511). For the few phylotypes where taxonomic assignment did not correspond to tree topology, no manual corrections were made. Betaproteo., Betaproteobacteria; Alphaproteo., Alphaproteobacteria; Deltaproteo., Deltaproteobacteria; Plancto., Planctomycetes; Firmic., Firmicutes.

  • Fig. 3 Identified habitat preferences for dominant soil bacterial phylotypes.

    (A) Relationships between the relative abundance of the phylotypes assigned to each ecological cluster and their major environmental predictors (statistical analyses and identity of phylotypes within each cluster are presented in table S1). (B) Network diagram with nodes (bacterial phylotypes) colored by each of the five major ecological clusters that were identified, highlighting that the phylotypes within each ecological cluster tend to co-occur more than expected by chance (statistical analyses presented in fig. S12).

  • Fig. 4 A global atlas of the dominant bacteria found in soil.

    (A to D) Predicted global distribution of the relative abundances of the four major ecological clusters of bacterial phylotypes sharing habitat preferences for high pH, low pH, drylands, and low plant productivity. R2 (percentage of variation explained by the models) as follows: (i) high-pH cluster, R2 = 0.53, P < 0.001; (ii) low-pH cluster, R2 = 0.36, P < 0.001; (iii) drylands cluster, R2 = 0.64, P < 0.001; and (iv) low-productivity cluster, R2 = 0.40, P < 0.001. The scale bar represents the standardized abundance (z-score) of each ecological cluster. An independent cross-validation for these maps is available in (20).

Supplementary Materials

  • A global atlas of the dominant bacteria found in soil

    Manuel Delgado-Baquerizo, Angela M. Oliverio, Tess E. Brewer, Alberto Benavent-Gonzílez, David J. Eldridge, Richard D. Bardgett, Fernando T. Maestre, Brajesh K. Singh, Noah Fierer

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S14
    • Appendix S1
    • Caption for table S1
    • References
    Table S1
    List of identified dominant bacterial phylotypes from soils across the globe. This list contains information on the taxonomic identity of each phylotype, the ecological cluster it was assigned to, and the most closely related reference genome, cultivated strain and isolate.
    Correction (31 January 2018):
    1. In Table S1, a minor typographical error in two of the reference sequences was corrected. The errors did not affect the validity of information for these two sequences.
    2. Reference 22 has been corrected.
    The original PDF is accessible here and the original table is accessible here.

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