Large-scale replicated field study of maize rhizosphere identifies heritable microbes

Authors: WALTERS, WILLIAM - Max Planck Institute Of Molecular Plant Physiology; JIN, ZHAO - Cornell University; YOUNGBLUT, NICHOLAS - Max Planck Institute Of Molecular Plant Physiology; WALLACE, JASON - University Of Georgia; SUTTER, JESSICA - Max Planck Institute Of Molecular Plant Physiology; ZHANG, WEI - Cornell University; GONZÁLEZ-PEÑA, ANTONIO - University Of California; PEIFFER, JASON - Cornell University; KOREN, OMRY - Cornell University; SHI, QIAOJUAN - Cornell University; KNIGHT, ROB - University Of Georgia; GLAVINA DEL RIO, TIJANA - Department Of Energy Joint Genome; TRINGE, SUSANNAH - Department Of Energy Joint Genome; Buckler, Edward - Ed; DANGL, JEFFRY - University Of North Carolina; LEY, RUTH - Max Planck Institute Of Molecular Plant Physiology

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/23/2018
Publication Date: 7/10/2018
Citation: Walters, W.A., Jin, Z., Youngblut, N., Wallace, J.G., Sutter, J., Zhang, W., González-Peña, A., Peiffer, J., Koren, O., Shi, Q., Knight, R., Glavina Del Rio, T., Tringe, S.G., Buckler IV, E.S., Dangl, J.L., Ley, R.E. 2018. Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Proceedings of the National Academy of Sciences. 115(28):7368-7373.

Interpretive Summary: Plants grow in soils with a complex array of micro-organisms that surround and interact with their roots. In this very large-scale, longitudinal field study of the maize (or corn) root-microbe interaction, we evaluated the importance of field location, maize variety, weather, and time. The largest effects were attributable to time and location, but the genetics of maize does a play a more modest but significant role in all environments. This suggests that maize diversity and breeding could be used to change a part of the microbiome. What needs to be determined next is whether the microbes that are affected by maize genetics are beneficial to soil health or maize productivity. If beneficial, this suggests a new target for sustainable maize breeding.

Technical Abstract: Soil microbes that colonize plant roots and are responsive to differences in plant genotype remain to be ascertained for agronomically important crops. From a very large-scale longitudinal field study of 27 maize inbred lines planted in three fields, with partial replication 5 y later, we identify root-associated microbiota exhibiting reproducible associations with plant genotype. Analysis of 4,866 samples identified 143 operational taxonomic units (OTUs) whose variation in relative abundances across the samples was significantly regulated by plant genotype, and included five of seven core OTUs present in all samples. Plant genetic effects were significant amid the large effects of plant age on the rhizosphere microbiome, regardless of the specific community of each field, and despite microbiome responses to climate events. Seasonal patterns showed that the plant root microbiome is locally seeded, changes with plant growth, and responds to weather events. However, against this background of variation, specific taxa responded to differences in host genotype. If shown to have beneficial functions, microbes may be considered candidate traits for selective breeding.