Rethinking the soil core microbiome
Year: 2026
Type: article
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.
Source: New Phytologist
DOI: 10.1111/nph.71509
Authors: Jaejin Lee, Bolívar Aponte Rolón, Phillip de Lorimier, Jean‐Michel Ané, Gian Maria Niccolò Benucci, Alyssa A. Carrell, Yen Ning Chai, Janith Chandrasoma, Nicole Geerdes, Valentina Infante, Brandon Kristy, Stanton Martin, Imani Pascoe, Rounak Patra, Lorien Radmer, Tomás Allen Rush, Ndenum Suzzy Shita, Andie Suratt, Patrick F. Suthers, Melissa A. Cregger, Adina Howe, Sarah Lebeis, Henrik Vibe Scheller
Institutions: University of Illinois Urbana-Champaign, Iowa State University, Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin–Madison, Great Lakes Bioenergy Research Center, Michigan State University, Oak Ridge National Laboratory, Center for Bioenergy Innovation, Lawrence Berkeley National Laboratory, Joint BioEnergy Institute, Carl R. Woese Institute for Genomic Biology, University of Georgia, Pennsylvania State University
Language: English
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
SDG: Life on land
Open Access status: hybrid
Estimated APC paid: $5,790
OpenAlex ID: W7203650741