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.
Jaejin Lee, Bolívar Aponte Rolón, Phillip de Lorimier et al.· New Phytologist· 1 citation
Exposure to abiotic stress is one of the primary factors limiting crop productivity with drought stress is the most prevalent. Under drought, plants can produce osmolytes that increase water retention and prevent severe drought symptoms. Plant responses by extension also impact their associated root microbiomes through altered root metabolite concentrations and exudation. For example, myo-inositol (MI) serves as a precursor to osmolytes and also serves as a mediator for plant-microbe interactions in Arabidopsis thaliana (Arabidopsis). Here, we inoculated plants with Pantoea sp. R4 (R4), an isolate that can catabolize MI, and subjected them to drought. We observed that R4 colonized plants experiencing drought maintained their leaf relative water content while uninoculated planted did not, and that this colonization coincided with enrichment of MI in the shoots and depletion of MI in the roots. Interestingly, exogenous MI alone rescued water retention in wild-type Col-0, but not in int1 mutants, which lack the tonoplast MI transporter. Together, our results show that R4 colonization under drought conditions increases MI in the shoots, that this accumulation is associated with increased leaf water retention, and that INT1-mediated MI transport is required for this protection. Our results suggest that microbial colonization can alter how MI is localized in plants, which can inform future development of treatments to protect plants from drought.
T. Tran, Kevin D. Santiago-Morales, B. O'Banion et al.· bioRxiv· 0 citations
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