DOE OSTI · 3484855
Rethinking the soil core microbiome
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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Lee, Jaejin [Iowa State University, Ames, IA (United States); University of Illinois Urbana-Champaign, IL (United States)] (ORCID:0000000297939473), Rolón, Bolívar Aponte [Iowa State University, Ames, IA (United States); University of Illinois Urbana-Champaign, IL (United States)] (ORCID:0000000225444551), de Lorimier, Phillip [Iowa State University, Ames, IA (United States); University of Illinois Urbana-Champaign, IL (United States)] (ORCID:0009000035439644), Ané, Jean‐Michel [University of Wisconsin-Madison, WI (United States)] (ORCID:0000000231289439), Benucci, Gian Maria Niccolò [University of Wisconsin-Madison, WI (United States)] (ORCID:000000031589947X), Carrell, Alyssa A. [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); The Center for Bioenergy Innovation, Oak Ridge, TN (United States)] (ORCID:0000000311424709), Chai, Yen Ning [Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Joint BioEnergy Institute, Berkeley, CA (United States)] (ORCID:0000000224379524), Chandrasoma, Janith [University of Illinois Urbana-Champaign, IL (United States)] (ORCID:000000026357500X), Geerdes, Nicole [Iowa State University, Ames, IA (United States); University of Illinois Urbana-Champaign, IL (United States)] (ORCID:0009000159049533), Infante, Valentina [University of Wisconsin‐Madison, WI (United States)] (ORCID:0009000967051754), Kristy, Brandon [University of Wisconsin‐Madison, WI (United States); Michigan State University, East Lansing, MI (United States)] (ORCID:0000000324217143), Martin, Stanton [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); The Center for Bioenergy Innovation, Oak Ridge, TN (United States)], Pascoe, Imani [University of Wisconsin‐Madison, WI (United States); Michigan State University, East Lansing, MI (United States)] (ORCID:0000000187843542), Patra, Rounak [University of Illinois Urbana-Champaign, IL (United States)] (ORCID:000000025822466X), Radmer, Lorien [Iowa State University, Ames, IA (United States); University of Illinois Urbana-Champaign, IL (United States)] (ORCID:0000000325005062), Rush, Tomás Allen [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); The Center for Bioenergy Innovation, Oak Ridge, TN (United States)] (ORCID:0000000232071466), Shita, Ndenum Suzzy [The Center for Bioenergy Innovation, Oak Ridge, TN (United States); University of Georgia, Athens, GA (United States)] (ORCID:0000000285327146), Suratt, Andie [University of Illinois Urbana-Champaign, IL (United States)] (ORCID:0000000277683693), Suthers, Patrick F. [University of Illinois Urbana-Champaign, IL (United States); The Center for Bioenergy Innovation, Oak Ridge, TN (United States); The Pennsylvania State University, University Park, PA (United States)] (ORCID:0000000255609986), Cregger, Melissa A. [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); The Center for Bioenergy Innovation, Oak Ridge, TN (United States)] (ORCID:000000018329366X), Howe, Adina [Iowa State University, Ames, IA (United States); University of Illinois Urbana-Champaign, IL (United States)] (ORCID:000000027705343X), Lebeis, Sarah [University of Wisconsin‐Madison, WI (United States); Michigan State University, East Lansing, MI (United States)] (ORCID:0000000194179678), Scheller, Henrik Vibe [Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Joint BioEnergy Institute, Berkeley, CA (United States)] (ORCID:0000000267023560). 2026-08-17. Rethinking the soil core microbiome. https://doi.org/10.1111/nph.71509
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