Artificial Selection on Microbiomes To Breed Microbiomes That Confer Salt Tolerance to Plants

• Main Authors: Burns, K.M (Author), Carlson, A.L (Author), Des Marais, D.L (Author), Edwards, J.A (Author), Fang, C.-C (Author), Juenger, T.E (Author), Kardish, M.R (Author), Mueller, U.G (Author), Smith, C.C (Author)
• Format: Article
• Language: English
• Published: American Society for Microbiology 2021
• Subjects: Beneficial microbes; Brachypodium distachyon; Experimental evolution; Host-mediated indirect selection; Microbiome breeding; Microbiome selection; Rhizosphere microbiome; Salt stress; Salt tolerance
• Online Access: View Fulltext in Publisher

 We develop a method to artificially select for rhizosphere microbiomes that confer salt tolerance to the model grass Brachypodium distachyon grown under sodium salt stress or aluminum salt stress. In a controlled greenhouse environment, we differentially propagated rhizosphere microbiomes between plants of a nonevolving, highly inbred plant population; therefore, only microbiomes evolved in our experiment, but the plants did not evolve in parallel. To maximize microbiome perpetuation when transplanting microbiomes between plants and, thus, maximize response to microbiome selection, we improved earlier methods by (i) controlling microbiome assembly when inoculating seeds at the beginning of each selection cycle; (ii) fractionating microbiomes before transfer between plants to harvest, perpetuate, and select on only bacterial and viral microbiome components; (iii) ramping of salt stress gradually from minor to extreme salt stress with each selection cycle to minimize the chance of overstressing plants; (iv) using two nonselection control treatments (e.g., nonselection microbial enrichment and null inoculation) that permit comparison to the improving fitness benefits that selected microbiomes impart on plants. Unlike previous methods, our selection protocol generated microbiomes that enhance plant fitness after only 1 to 3 rounds of microbiome selection. After nine rounds of microbiome selection, the effect of microbiomes selected to confer tolerance to aluminum salt stress was nonspecific (these artificially selected microbiomes equally ameliorate sodium and aluminum salt stresses), but the effect of microbiomes selected to confer tolerance to sodium salt stress was specific (these artificially selected microbiomes do not confer tolerance to aluminum salt stress). Plants with artificially selected microbiomes had 55 to 205% greater seed production than plants with unselected control microbiomes. © 2021 Mueller et al.