Embracing the unknown: disentangling the complexities of the soil microbiome

Nat Rev Microbiol. 2017 Oct;15(10):579-590. doi: 10.1038/nrmicro.2017.87. Epub 2017 Aug 21.


Soil microorganisms are clearly a key component of both natural and managed ecosystems. Despite the challenges of surviving in soil, a gram of soil can contain thousands of individual microbial taxa, including viruses and members of all three domains of life. Recent advances in marker gene, genomic and metagenomic analyses have greatly expanded our ability to characterize the soil microbiome and identify the factors that shape soil microbial communities across space and time. However, although most soil microorganisms remain undescribed, we can begin to categorize soil microorganisms on the basis of their ecological strategies. This is an approach that should prove fruitful for leveraging genomic information to predict the functional attributes of individual taxa. The field is now poised to identify how we can manipulate and manage the soil microbiome to increase soil fertility, improve crop production and improve our understanding of how terrestrial ecosystems will respond to environmental change.

Publication types

  • Review

MeSH terms

  • Bacteria / classification
  • Bacteria / genetics
  • Eukaryota / classification
  • Eukaryota / genetics
  • Fungi / classification
  • Fungi / genetics
  • Microbiota / genetics*
  • Soil / parasitology*
  • Soil Microbiology*


  • Soil