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Climate change presents new challenges for managing plant health. Simultaneously, the revolution in sequencing technologies offers an exciting new perspective on whole microbial communities – and on both microbial responses to climate and microbial effects on plant health. There is still the need for a comparable revolution in experimental approaches to understand the functional roles of microbial taxa within these communities. Two approaches leveraging advances in genomics tools and analyses may contribute. First, new soil mixing experiments may be developed, where analyses of quantitative trait taxa (QTT) may be analogous to analyses of quantitative trait loci (QTL). Second, new approaches for characterizing the extended phenotype or phenome of soil microbial communities may be developed, leveraging genomic tools for Arabidopsis and other model plant species through the construction of plant genotype panels in an ‘Arabidopsitron’.