Research Project: Discovery of Plant Genetic Mechanisms Controlling Microbial Recruitment to the Root Microbiome

Location: Plant Gene Expression Center

2021 Annual Report

Objectives
The goal of this research is to generate a better understanding of the interrelationship between crop plant genetics and plant microbiomes. Collectively, the experiments described in the Objectives below will provide for direct testing of a priori hypotheses regarding the genetic pathways associated with plant microbiome recruitment (Objective 2), which we define in this proposal as the assembly and maintenance of plant-associated microbiome, as well as unbiased genome wide analyses that may capture genes previously unsuspected to be involved in this phenotype (Objectives 1 and 3). Integration of the results from this multifaceted approach may allow for corroboration of key findings from individual Objectives. For instance, loci identified in Objective 1 from the association-based analysis of host genes will be cross-referenced with the genes identified as part of the transcriptional analyses described in Objective 3. In Objective 2, genes confirmed through mutant analysis to have direct effects on plant microbiome phenotypes can potentially serve as positive controls for analyses carried out in Objective 1. While the Objectives differ in terms of experimental methodology, as well as the precise question being addressed, the broader goal of each is the identification of elements involved in host control of the microbiome, and we anticipate that this diversified approach in a single host system and by a single investigative team will provide valuable insight addressing this key knowledge gap in the field of plant-biotic interactions. Objective 1: Identify the host genetic elements (genes and other functional sequences) associated with microbiome recruitment through genome wide association studies in Sorghum bicolor using microbial community analysis as the scoreable phenotype. Objective 2: Create sorghum mutants in cell wall biosynthesis pathway genes, and other target plant processes, that are critical for the recruitment of microbes during drought stress; characterize the microbiomes and abiotic stress tolerance of these lines. Objective 3. Use an established microbial culture collection for sorghum to test the changes in the sorghum root following exposure to root endophytes and abiotic stress to establish causality with stress tolerance.

Approach
Obj. 1: We aim to identify loci that contribute to the plant bacterial microbiome phenotype in sorghum through Genome-wide association studies (GWAS) analysis using a mapping panel of diverse sorghum lines. GWAS represent a powerful approach to detect variants at genomic loci associated with complex traits in a genetically diverse population. We will use the Sorghum Association Panel (SAP), grown in a randomized block design. Root samples will be harvested and separated into root endosphere and rhizosphere samples and bacterial communities for target plant samples will be assessed via amplicon-based next-generation, and the relative abundance of specific bacterial taxa showing large differential abundance across our genotypes, or overall microbial community composition using individual component axes of principal coordinate analyses with the broader dataset, will be used as phenotypic inputs in the GWAS. Should our analysis of the root endosphere microbiome be unsuccessful, alternate sample types including rhizospheres and leaf epispheres, and alternate phenotypes, can be investigated. Obj. 2: We aim to test whether suberin deposition within roots of sorghum during drought stress acts to recruit and support specific bacterial taxa, namely Actinobacteria, to the root microbiome, and to promote drought tolerance. We will develop a protocol for CRISPR/Cas9 delivery into sorghum roots via Agrobacterium rhizogenes, and utilize this system to create engineered lines with alterations in the suberin biosynthesis pathway. The engineered genotypes along with wildtype will be grown in the greenhouse in field soil under two watering regimes, and sampled, phenotyped, and assayed for root suberin content via fluorescence microscopy with a suberin specific stain and subjected to 16S rRNA and ITS2 metagenomic analysis to investigate changes in the bacterial and fungal microbiome. Should the construction of CRISPR lines prove challenging, we will obtain mutants from a TILLING mutant population in sorghum. Obj. 3: We aim to identify the physiological and molecular consequences of colonization by endophytic isolates on gnotobiotically-grown sorghum through phenotypic and transcriptional analysis in the plant root. Sorghum roots will be grown in a sterile system filled with autoclaved soil medium. Select Actinobacteria and non-Actinobacterial isolates from our collection will be introduced individually to the roots of 7-day-old sorghum plants. One week following inoculation, we will induce drought stress in half of the gnotobiotic systems, and collect roots of inoculated and control plants. Plant samples will be phenotyped and used to isolate high-quality total RNA for preparation of RNA-Seq libraries for Illumina sequencing. An analysis of the datasets will determine differentially expressed genes between drought and control treatments, inoculated and uninoculated roots, and between the individual microbial treatments used in our experiment. Should the induction of drought prove challenging, we have an alternative gnotobiotic system that will allow for longer periods of sorghum growth, which has been achieved in other grass systems by our collaborators.

Progress Report
For Objective 1, research continued on identifying loci that contribute to the plant bacterial microbiome phenotype in sorghum through genome-wide association studies (GWAS) analysis using a mapping panel of diverse sorghum lines. A full field-scale GWAS experiment was evaluated following prior field data using the plant microbiome as a phenotype, and the results were published in the International Society of Microbial Ecology Journal in fiscal year (FY) 2021. For Objective 2, research continued on generating sorghum mutants that have altered metabolism in pathways suspected to affect microbiome composition. Transformed lines have been identified and currently we are searching for lines with edits in the target genes. We anticipate identifying edits in three target genes in FY 2022. For Objective 3, research continued on the role of synthetic communities and individual isolates on plant performance under drought stress. Specific experiments on Streptomyces and related taxa were implemented in the field and growth chamber, yielding evidence that Streptomyces can promote root growth in crops during drought stress. Additional isolate generation and characterization is ongoing through use of a new instrument, the GALT Prospector. Use of a transgenic maize line with a loss of function mutation in the iron transporter TOM1 was used to show iron metabolism in plants plays a role in shaping microbiome composition in the rhizosphere.

Accomplishments
1. Identification of novel plant pathway controlling microbiome development under drought stress. Understanding the role of plant genetics in shaping microbiome composition under environmental stress is critical to ongoing efforts to develop microbial products for use in agriculture. ARS researchers in Albany, California, have successfully implemented an holo-omics approach combined with genome-resolved metagenomics to identify a new role for iron metabolism in shaping the crop microbiome. This strategy provides new evidence that crop genetics related to nutrient status is related to microbiome management. This is a valuable breakthrough for understanding plant microbiomes in the rhizosphere.

Review Publications
Wipf, H., Xu, L., Gao, C., Spinner, H., Taylor, J., Lemaux, P., Mitchell, J., Coleman-Derr, D.A. 2021. Agricultural soil management practices differentially shape the bacterial and fungal microbiome of Sorghum bicolor. Applied and Environmental Microbiology. 87(5). https://doi.org/10.1128/AEM.02345-20.
Zhang, X., Peng, H., Zhu, S., Xing, J., Li, X., Zhu, Z., Zheng, J., Wang, L., Wang, B., Chen, J., Ming, Z., Yao, K., Jian, J., Luan, S., Coleman-Derr, D.A., Liao, H., Peng, Y., Peng, D., Yu, F. 2020. Nematode-encoded RALF peptide mimics facilitate parasitism of plants through the FERONIA receptor kinase. Molecular Plant. 13:214-216. https://doi.org/10.1016/j.molp.2020.08.014.
Willing, C., Pierroz, G., Coleman-Derr, D.A., Dawson, T. 2020. The generalizability of water-deficit on bacterial community composition; Site-specific water-availability predicts the bacterial community associated with coast redwood roots. Molecular Ecology. 29:4721–4734. https://doi.org/10.1111/mec.15666.
Wipf, H., Bui, T., Coleman-Derr, D.A. 2021. Distinguishing between the impacts of heat and drought stress on the root microbiome of Sorghum bicolor. Applied and Environmental Microbiology. 5(2):2471-2906. https://doi.org/10.1094/PBIOMES-07-20-0052-R.
Mishra, L., Kim, S., Caddell, D.F., Coleman-Derr, D.A., Funk, C. 2021. Loss of Arabidopsis matrix metalloproteinase-5 affects root development and root bacterial communities during drought stress. Physiologia Plantarum. 172(2):1045-1058. https://doi.org/10.1111/ppl.13299.
Xu, L., Pierroz, G., Wipf, E., Gao, C., Taylor, J., Lemaux, P., Coleman-Derr, D.A. 2021. Holo-omics for deciphering plant-microbiome interactions. Microbiome. 9:69. https://doi.org/10.1186/s40168-021-01014-z.
Xu, L., Dong, Z., Chiniquy, D., Pierroz, G., Deng, S., Gao, C., Diamond, S., Simmons, T., Wipf, H.M., Caddell, D.F., Varoquaux, N., Madera, M.A., Hutmacher, R., Deutschbauer, A., Dahlberg, J., Guerinot, M., Purdom, E., Banfield, J.F., Taylor, J.W., Lemaux, P.G., Coleman-Derr, D.A. 2021. Genome resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics. Nature Communications. 12. Article 3209. https://doi.org/10.1038/s41467-021-23553-7.
Wipf, H., Coleman-Derr, D.A. 2021. Evaluating domestication and ploidy effects on the assembly of the wheat bacterial microbiome. PLoS ONE. 16(3). Article e0248030. https://doi.org/10.1371/journal.pone.0248030.
Deng, S., Caddell, D.F., Xu, G., Dahlen, L., Washington, L., Wang, J., Coleman-Derr, D.A. 2021. Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome. The ISME Journal: Multidisciplinary Journal of Microbial Ecology. Available: https://doi.org/10.1038/s41396-021-00993-z.
Li, X., Panke-Buisse, K., Yao, X., Coleman-Derr, D.A., Ding, C., Wang, X., Ruan, H. 2019. Peanut plant growth was altered by monocropping-associated microbial enrichment of rhizosphere microbiome. Plant and Soil. 446:655–669. https://doi.org/10.1007/s11104-019-04379-1.