The Maize Rhizosphere Microbiome

Abstract

The rhizosphere microbiome, which is the microbial community living in close proximity to plant roots, is important for plant growth and development. Besides environmental factors, plant genetic control is key in cultivating the rhizosphere microbiome. Whether the genetic variation influences the taxonomy or function of the rhizosphere microbiome remains equivocal. I approached this question by culturing and sequencing 48 Pseudomonas isolates from two maize genotypes grown at two different fields, and analyzing the Pseudomonas genomes to identify components under maize genetic control. I observed a small but significant association of maize genotypes with the variation in the metabolic genes of the Pseudomonas isolates, while I did not see an association of maize genotypes with the abundance of the isolates. Plant age is another important factor in shaping the rhizosphere microbiome, as plant age reflects changes in plant genetic control. Treating the rhizosphere microbiome as a quantitative trait, the proportion of this phenotypic variation attributable to plant genetic control can be measured as the heritability of the rhizosphere microbiome. To address how much variation in the maize rhizosphere microbiome is accounted for by maize genotypic variation, and to monitor how the heritability of the maize rhizosphere microbiome changes as maize grows and develops, we sampled the maize rhizosphere microbiome from 27 diverse maize lines grown in three different fields over the entire maize growing season. I followed the temporal dynamics of the microbiome, and estimated the proportion of variation in the beta diversity of the rhizosphere microbiome samples at each time point explained by maize genotypes, fields, and genotype by field interactions. I found that the maize genotype effect starts to increase at week 2 after planting, suggesting that the maize genetic control is taking effect. I observed the strongest maize genotype effect around flowering time. I also identified some potential heritable taxa as well as OTUs whose abundances vary over maize developmental stages. In addition, I observed increased species loss starting at week 2, which corresponds to the time point when maize genetic control starts to take effect, whereas species loss peaks at flowering time when maize imposes the strongest genetic control on the rhizosphere microbiome. Metagenomes are full of microbial "dark matters" that may harbor vast functional capacities. To optimize the function and decipher a functional region in a plant-growth promoting bacterial protein from the maize rhizosphere, I retrieved the rhizosphere bacterial protein regions and swapped them into E. coli to construct variant libraries, and selected the variant libraries for several rounds using nitrogen source limitation. I observed the fixation of known essential active site residues before the selection, and the fixation of several residues after selection, suggesting they are important for protein function. My results showed successful optimization and functional characterization of a region in this maize rhizosphere enzyme.