Rethinking the soil core microbiome
The concept of a core microbiome emerged from host-associated research to describe microbial members or functions conserved across clearly defined spatial, temporal, and biological boundaries. In soil- and plant-associated microbiome research, however, the term has increasingly shifted toward analytically defined subsets selected using study-specific thresholds or criteria. Synthesizing recent literature and cross-site analyses of bioenergy crop field soils, we show that the original biological meaning of the core microbiome has been blurred by dataset-specific analytical criteria. Taxa designated as 'core' were highly sensitive to methodological choices and often reflected explanatory value rather than conserved biological membership. Moreover, many studies that identify taxonomic 'core' members interpret their significance in functional terms, suggesting that functional conservation may be the biological interest. Taxonomic conservation may not be the most biologically meaningful target in highly heterogeneous soil and rhizosphere systems, where functional conservation may persist despite taxonomic turnover. Accordingly, 'core microbiome' should be reserved for microbial components explicitly demonstrated to be conserved across defined spatial, temporal, and environmental dimensions and linked to conserved ecological functions, while taxa selected for explanatory value are better described as 'explanatory subsets of taxa'. Greater terminological precision will improve cross-study comparability and strengthen ecological inference in plant-soil microbiome research.
Authors
- Tomás A. Rush (ORCID: https://orcid.org/0000-0002-3207-1466)
- Janith Chandrasoma (ORCID: https://orcid.org/0000-0002-6357-500X)
- Jean‐Michel Ané (ORCID: https://orcid.org/0000-0002-3128-9439)
- Henrik Vibe Scheller (ORCID: https://orcid.org/0000-0002-6702-3560)
- Yen Ning Chai (ORCID: https://orcid.org/0000-0002-2437-9524)
- Valentina Infante (ORCID: https://orcid.org/0009-0009-6705-1754)
- Ndenum Suzzy Shitta (ORCID: https://orcid.org/0000-0002-8532-7146)
- Brandon Kristy (ORCID: https://orcid.org/0000-0003-2421-7143)
- Sarah L. Lebeis (ORCID: https://orcid.org/0000-0001-9417-9678)
- Gian Maria Niccolò Benucci (ORCID: https://orcid.org/0000-0003-1589-947X)
- Alyssa A. Carrell (ORCID: https://orcid.org/0000-0003-1142-4709)
- Melissa A. Cregger (ORCID: https://orcid.org/0000-0001-8329-366X)
- Phillip De Lorimier
- Bolívar Aponte Rolón (ORCID: https://orcid.org/0000-0002-2544-4551)
- Patrick F. Suthers (ORCID: https://orcid.org/0000-0002-5560-9986)
- Adina Howe (ORCID: https://orcid.org/0000-0002-7705-343X)
- Lorien Radmer
- Jae‐Jin Lee (ORCID: https://orcid.org/0000-0002-9793-9473)
- Rounak Patra (ORCID: https://orcid.org/0000-0002-5822-466X)
- Andie Suratt (ORCID: https://orcid.org/0000-0002-7768-3693)
- Nicole Geerdes
- Imani Pascoe
- Stanton Martin
Institutions
- Oak Ridge National Laboratory (US)
- Pennsylvania State University (US)
- University of Wisconsin–Madison (US)
- Lawrence Berkeley National Laboratory (US)
- University of Illinois Urbana-Champaign (US)
- University of Georgia (US)
- Iowa State University (US)
- Great Lakes Bioenergy Research Center (US)
- Bioenergy Life Science (United States) (US)
- Joint BioEnergy Institute (US)
- Michigan State University (US)
Publication Details
- Journal
- New Phytologist
- Published
- 2026-08-17
- DOI
- https://doi.org/10.1111/nph.71509
- Primary Topic
- Microbial Community Ecology and Physiology
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Great Lakes Bioenergy Research Center