Elevated carbon dioxide reduces a common soybean leaf endophyte

Abstract Free‐air CO 2 enrichment (FACE) experiments have elucidated how climate change affects plant physiology and production. However, we lack a predictive understanding of how climate change alters interactions between plants and endophytes, critical microbial mediators of plant physiology and ecology. We leveraged the SoyFACE facility to examine how elevated [CO 2 ] affected soybean ( Glycine max) leaf endophyte communities in the field. Endophyte community composition changed under elevated [CO 2 ], including a decrease in the abundance of a common endophyte, Methylobacterium sp. Moreover, Methylobacterium abundance was negatively correlated with co‐occurring fungal endophytes. We then assessed how Methylobacterium affected the growth of co‐occurring endophytic fungi in vitro. Methylobacterium antagonized most co‐occurring fungal endophytes in vitro, particularly when it was more established in culture before fungal introduction. Variation in fungal response to Methylobacterium within a single fungal operational taxonomic unit (OTU) was comparable to inter‐OTU variation. Finally, fungi isolated from elevated vs. ambient [CO 2 ] plots differed in colony growth and response to Methylobacterium , suggesting that increasing [CO 2 ] may affect fungal traits and interactions within the microbiome. By combining in situ and in vitro studies, we show that elevated [CO 2 ] decreases the abundance of a common bacterial endophyte that interacts strongly with co‐occurring fungal endophytes. We suggest that endophyte responses to global climate change will have important but largely unexplored implications for both agricultural and natural systems.