Multiomic Analysis of Sorghum Microbiome

Microbial community analysis was conducted as in the study by Naylor et al. (13 (link)) on soil, rhizosphere, and root endosphere samples of two sorghum cultivars collected from field-grown plants in Parlier, California (36.6008°N, 119.5109°W). Metatranscriptome profiling, metabolomics, qPCR, HPLC analysis, bacterial isolation and conjugation, inoculation experiments, and confocal microscopy were performed as described in SI Appendix, Material and Methods. A combined assembly of the metatranscriptome can be accessed and downloaded via integrated microbial genomes (IMG)/expert review (ER) (https://img.jgi.doe.gov/) using the IMG ID 3300017790.

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Xu L., Naylor D., Dong Z., Simmons T., Pierroz G., Hixson K.K., Kim Y.M., Zink E.M., Engbrecht K.M., Wang Y., Gao C., DeGraaf S., Madera M.A., Sievert J.A., Hollingsworth J., Birdseye D., Scheller H.V., Hutmacher R., Dahlberg J., Jansson C., Taylor J.W., Lemaux P.G, & Coleman-Derr D. (2018). Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria. Proceedings of the National Academy of Sciences of the United States of America, 115(18), E4284-E4293.

Publication 2018

Bacterial Confocal microscopy Hplc Inoculation Isolation Microbial community Microbial genomes Plants Rhizosphere Root Sorghum

Corresponding Organization :

Other organizations : University of California, Berkeley, Plant Gene Expression Center, Pacific Northwest National Laboratory, University of Nebraska at Kearney, Lawrence Berkeley National Laboratory, University of California, Davis

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Protocol cited in 23 other protocols

Variable analysis

independent variables

Sorghum cultivars (two cultivars)

dependent variables

Microbial community composition and structure (via metatranscriptome profiling)
Metabolite profiles (via metabolomics)
Gene expression (via qPCR)
Metabolite profiles (via HPLC analysis)
Bacterial isolation and conjugation
Inoculation experiment outcomes
Microbial localization (via confocal microscopy)

control variables

Soil, rhizosphere, and root endosphere samples
Field-grown plants in Parlier, California (36.6008°N, 119.5109°W)

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

Annotations

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