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Peer-reviewedCC BY 4.0The New Phytologist

Rethinking the soil core microbiome

  • Jaejin Lee1,2
  • Bolívar Aponte Rolón1,2
  • Phillip de Lorimier1,2
  • Jean‐Michel Ané3,4,5
  • Gian Maria Niccolò Benucci3,6
  • Alyssa A. Carrell7,8
  • Yen Ning Chai9,10
  • Janith Chandrasoma2,11
  • Nicole Geerdes1,2
  • Valentina Infante3,5
  • Brandon Kristy3,12
  • Stanton Martin7,8
11 more authors
  • Imani Pascoe3,13
  • Rounak Patra2,11
  • Lorien Radmer1,2
  • Tomás Allen Rush7,8
  • Ndenum Suzzy Shita8,14
  • Andie Suratt2,11
  • Patrick F. Suthers2,8,15
  • Melissa A. Cregger7,8
  • Adina Howe1,2
  • Sarah Lebeis3,6,13,16
  • Henrik Vibe Scheller9,10
16 affiliations
  1. 1Department of Agricultural and Biosystems Engineering Iowa State University Ames IA 50011 USA
  2. 2DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois Urbana‐Champaign Urbana IL 61801 USA
  3. 3The Great Lakes Bioenergy Research Center University of Wisconsin‐Madison Madison WI 53726 USA
  4. 4Department of Bacteriology University of Wisconsin‐Madison Madison WI 53706 USA
  5. 5Department of Plant and Agroecosystem Sciences University of Wisconsin‐Madison Madison WI 53706 USA
  6. 6Department of Plant, Soil and Microbial Sciences Michigan State University East Lansing MI 48824 USA
  7. 7Biosciences Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA
  8. 8The Center for Bioenergy Innovation Oak Ridge TN 37831 USA
  9. 9Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
  10. 10Joint BioEnergy Institute Berkeley CA 94608 USA
  11. 11Carl R. Woese Institute for Genomic Biology University of Illinois Urbana‐Champaign Urbana IL 61801 USA
  12. 12Department of Integrative Biology Michigan State University East Lansing MI 48824 USA
  13. 13Department of Microbiology, Genetics, and Immunology Michigan State University East Lansing MI 48824 USA
  14. 14Department of Genetics University of Georgia Athens GA 30602 USA
  15. 15Department of Chemical Engineering The Pennsylvania State University University Park PA 16802 USA
  16. 16Plant Resilience Institute Michigan State University East Lansing MI 48824 USA
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Abstract

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.

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Cite

BibTeXRIS
BibTeX
@article{lee2026rethinking,
  title = {{Rethinking the soil core microbiome}},
  author = {Jaejin Lee and Bolívar Aponte Rolón and Phillip de Lorimier and Jean‐Michel Ané and Gian Maria Niccolò Benucci and Alyssa A. Carrell and Yen Ning Chai and Janith Chandrasoma and Nicole Geerdes and Valentina Infante and Brandon Kristy and Stanton Martin and Imani Pascoe and Rounak Patra and Lorien Radmer and Tomás Allen Rush and Ndenum Suzzy Shita and Andie Suratt and Patrick F. Suthers and Melissa A. Cregger and Adina Howe and Sarah Lebeis and Henrik Vibe Scheller},
  journal = {The New Phytologist},
  year = {2026},
  month = aug,
  doi = {10.1111/nph.71509},
  url = {https://doi.org/10.1111/nph.71509},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Rethinking the soil core microbiome
AU  - Jaejin Lee
AU  - Bolívar Aponte Rolón
AU  - Phillip de Lorimier
AU  - Jean‐Michel Ané
AU  - Gian Maria Niccolò Benucci
AU  - Alyssa A. Carrell
AU  - Yen Ning Chai
AU  - Janith Chandrasoma
AU  - Nicole Geerdes
AU  - Valentina Infante
AU  - Brandon Kristy
AU  - Stanton Martin
AU  - Imani Pascoe
AU  - Rounak Patra
AU  - Lorien Radmer
AU  - Tomás Allen Rush
AU  - Ndenum Suzzy Shita
AU  - Andie Suratt
AU  - Patrick F. Suthers
AU  - Melissa A. Cregger
AU  - Adina Howe
AU  - Sarah Lebeis
AU  - Henrik Vibe Scheller
PY  - 2026
DA  - 2026/08/17
JO  - The New Phytologist
DO  - 10.1111/nph.71509
UR  - https://doi.org/10.1111/nph.71509
AB  - 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.
SN  - 0028-646X
SN  - 1469-8137
ER  -