Chemical-biogeographic survey of secondary metabolism in soil

Proc Natl Acad Sci U S A. 2014 Mar 11;111(10):3757-62. doi: 10.1073/pnas.1318021111. Epub 2014 Feb 18.


In this study, we compare biosynthetic gene richness and diversity of 96 soil microbiomes from diverse environments found throughout the southwestern and northeastern regions of the United States. The 454-pyroseqencing of nonribosomal peptide adenylation (AD) and polyketide ketosynthase (KS) domain fragments amplified from these microbiomes provide a means to evaluate the variation of secondary metabolite biosynthetic diversity in different soil environments. Through soil composition and AD- and KS-amplicon richness analysis, we identify soil types with elevated biosynthetic potential. In general, arid soils show the richest observed biosynthetic diversity, whereas brackish sediments and pine forest soils show the least. By mapping individual environmental amplicon sequences to sequences derived from functionally characterized biosynthetic gene clusters, we identified conserved soil type-specific secondary metabolome enrichment patterns despite significant sample-to-sample sequence variation. These data are used to create chemical biogeographic distribution maps for biomedically valuable families of natural products in the environment that should prove useful for directing the discovery of bioactive natural products in the future.

Keywords: antibiotics; bioprospecting; eDNA; metagenomics.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cluster Analysis
  • Genetic Variation*
  • Geographic Mapping
  • Metabolome / genetics*
  • Microbiota / genetics*
  • Multigene Family / genetics
  • New England
  • Phylogeography
  • Secondary Metabolism / genetics
  • Soil / chemistry*
  • Soil Microbiology*
  • Southwestern United States


  • Soil