Elevated carbon dioxide reduces a common soybean leaf endophyte

Abstract

Free‐air CO2 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 [CO2] affected soybean (Glycine max) leaf endophyte communities in the field. Endophyte community composition changed under elevated [CO2], 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 [CO2] plots differed in colony growth and response to Methylobacterium, suggesting that increasing [CO2] may affect fungal traits and interactions within the microbiome. By combining in situ and in vitro studies, we show that elevated [CO2] 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.

Phylogenetic and spatial determinants of leaf endophyte microbiomes in the flowering plant genusHeuchera(Saxifragaceae)

“…Proteobacteria, Bacteroidetes, and Actinobacteria have consistently been reported as dominant and prevalent members of endophytic bacterial assemblages within plant tissues (Hardoim et al, 2015;Zarraonaindia et al, 2015;Coleman-Derr et al, 2016;de Souza et al, 2016;Ding and Melcher, 2016;Aydogan et al, 2018;Wemheuer et al, 2019;Mina et al, 2020;Yang et al, 2023). At the genus level, Pseudomonas, Sphingomonas, Methylobacterium, and Hymenobacter were also found to be relatively abundant in leaves of both cultivated (Hallmann et al, 1997;Rosenblueth and Martínez-Romero, 2006;Miliute et al, 2015;Afzal et al, 2019;Christian et al, 2021) and non-cultivated plants (Ding and Melcher, 2016;Afzal et al, 2019). On the other hand, the majority of leaf endophytic fungi in Heuchera belonged to Ascomycota and Basidiomycota, similarly reported as two of the most dominant fungal endophyte classes in its close relative, Saxifraga (Zhang and Yao, 2015) and across a variety of host plants (Zimmerman and Vitousek, 2012;Jin et al, 2013;Fan et al, 2020;Pang et al, 2022).…”

Microbial communities of Schisandra sphenanthera Rehd. et Wils. and the correlations between microbial community and the active secondary metabolites

“…These two bacteria were not only dominant bacteria, but also beneficial microorganisms. Achromobacter can use aromatic compounds as the only carbon source, and Methylobacterium protects plants from pathogens ( Christian et al, 2021 ; Ho, Hsieh & Huang, 2013 ). In addition, Rhodoplanes , Candidatus Solibacter, and Gemmata were also the dominant flora in the below-ground parts ( Table S5 ).…”

Community composition and differential analysis of rhizosphere soil microorganism and endophytes in Schisandra sphenanthera Rehd. et Wils.

“…Achromobacter can inoculate into vetiver grass (Chrysopogon zizanioides) which utilizes aromatic compounds as a sole carbon source (Ho et al, 2013). Methylobacterium protects soybean (Glycine max) against pathogens by inducing endophytic community changes (Christian et al, 2021). Propionibacterium is a kind of bacterial microorganism in stem that can synthesize propionic acid using special carboxylic enzymes, and the study shows that Propionibacterium is widely used in the production of vitamin B12, four pyrrole compounds and propionic acid, acid, as well as probiotics and cheese industry (Ames et al, 2012;Guyomarc'h et al, 2020).…”