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Contributed Talk

Session: Biogeochemistry: Linking Community Structure And Ecosystem Function 1

COS 227-2 - Directed plant-microbiome evolution to improve crop performance under drought

Thursday, August 18, 2022

10:15 AM – 10:30 AM EDT

Location: 513B

Coauthor(s)

SS

Sanna Sevanto

Earth and Environmental Sciences Division, Los Alamos National Laboratory, United States

Presenting Author(s)

DM

Dea Musa

Los Alamos National Laboratory, United States

Coauthor(s)

KC

Kelsey R. Carter, PhD

Post doc
Los Alamos National Laboratory
Los Alamos, New Mexico, United States
EM

Eric R. Moore, n/a

Los Alamos National Laboratory
Los Alamos, New Mexico, United States
AN

Abigael Nachtsheim

Los Alamos National Laboratory, United States
AK

Anastasiia Kim

Los Alamos National Laboratory, New Mexico, United States
JM

Joshua Mitchell

Los Alamos National Laboratory
Los Alamos, New Mexico, United States
JH

Jack Heneghan

Los Alamos National Laboratory, United States
LD

L. Turin Dickman

Los Alamos National Laboratory
Los Alamos, New Mexico, United States
AS

Anthony Sabella

Los Alamos National Laboratory, United States
EG

Estella Gomez

Los Alamos National Laboratory
Los Alamos, New Mexico, United States
ER

Eliana Rodriguez

Los Alamos National Laboratory
Los Alamos, New Mexico, United States
SN

Sangeeta Negi

Los Alamos National Laboratory, United States
GP

George Perkins

Los Alamos National Laboratory
Los Alamos, New Mexico, United States
RH

Rose Harris

Los Alamos National Laboratory
Los Alamos, New Mexico, United States
OM

Oana Marina

Los Alamos National Laboratory
Los Alamos, United States
BN

Brent Newman

Los Alamos National Laboratory, United States
JH

Jeffrey Heikoop

Los Alamos National Laboratory, United States
CA

Christine Anderson-Cook

Los Alamos National Laboratory
Los Alamos, United States
NL

Nicholas Lubbers

Los Alamos National Laboratory, United States
ST

Scott Twary

Los Alamos National Laboratory
Los Alamos, United States
CY

Chris M. Yeager

Los Alamos National Laboratory, United States
LC

Louise Comas

Agricultural Research Service, USDA, United States
DM

Dan Manter

Research Scientist
USDA ARS
Fort Collins, Colorado, United States
CS

Christina Steadman

Los Alamos National Laboratory, United States
MA

Michaeline Albright

Los Alamos National Laboratory, United States
JD

John Dunbar

Los Alamos National Laboratory
Los Alamos, United States

Background/Question/Methods

Microbiome optimization could improve the performance of biological systems, from humans to plants and ecosystems. Yet, owing to challenges in finding and cultivating microbiomes that maintain their function in field conditions, use of microbes to improve plant productivity and crop stress tolerance has not become widespread despite years of trials. Based on the strong interactions and interdependency of rhizosphere microbes and plants, directed plant-microbiome evolution has been suggested as a means for developing microbiomes for these purposes. To test the feasibility of this method in developing microbial communities that improve plant performance under reduced irrigation, we cultivated Zea mays from seed in an artificial soil inoculated with soil microbiomes originating from a pine forest or a historically-droughted maize field. In the initial generation, water use efficiency (WUE) and stomatal closure point (SCP) were measured once the plants grew 10 leaves. The microbiomes of three plants demonstrating the best or worst WUE or SCP values for each microbiome source were selected for propagation to the next generation, and the process was repeated for two additional generations. Microbiome composition was analyzed after each generation using Illumina MiSeq sequencing, and microbial groups affecting plant performance were identified using Latent Dirichlet Allocation.

Results/Conclusions

Our results show that, in three generations, the microbiome originating from the forest soil was able to consistently influence plant SCP, while the microbiome from the agricultural field had no significant effect on either WUE or SCP. The forest and agricultural microbiomes remained distinct from one another throughout the evolutionary process, but the microbiomes adapted to the greenhouse experiment such that the parent and offspring microbiomes became progressively more similar in subsequent generations. Interestingly, we also found that the microbiome originating from forest soil consistently produced faster growing plants than the microbiome from the agricultural field. This microbiome contained more bacteria related to the nitrogen cycle than the agricultural microbiome, while the agricultural microbiome had a higher abundance of bacteria commonly found in dry soils. We were able to consistently identify consortia of bacteria related to different plant traits using a dimension reduction method called Latent Dirichlet Allocation (LDA). Our experiment demonstrates that, in only a few generations (3 as opposed to 6-10 in previous studies), directed evolution can produce soil microbiomes that influence important functional drought tolerance traits in maize, but not all soils may have the microbial diversity or species structure needed to optimize plant traits.