Has plant domestication decoupled beneficial Plant-microbe interactions in wheat?

Abstract

Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars by selecting for high-yielding dwarf crops which are reliant on unsustainable levels of inorganic fertilizer. This transition from natural to agricultural systems has played an important role in the development of agriculture over the last 10,000 years but may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Plant growth-promoting rhizobacteria (PGPR) are essential for plant health and fitness and play an important role in the sustainable intensification of agriculture. This thesis assesses the impacts of domestication on beneficial plant-microbial interactions in wheat with a view to developing robust microbial inocula for enhanced crop growth. Culture dependent and independent approaches were used to explore the influence of widely used nitrogen-phosphate-potassium (NPK) fertilizer on the abundance of wheat rhizobacterial genera with plant growth-promoting traits. Putative plant growth-promoting rhizobacteria (PGPR) were reduced in fertilized wheat plants. Approximately 1,500 bacterial isolates were amassed from the rhizosphere and rhizoplane of Cadenza wheat plants grown in low nutrient soil either supplemented with or without fertilizer in pot greenhouse experiments, representing an inherently more controlled design than many literature field studies. PGPR were taxonomically identified by Sanger sequencing of the 16S rRNA gene and functionally characterized using single colony functional bioassays (nitrogen, phosphate, potassium, iron, and zinc solubilization) and subsequently identified in high throughput 16S rRNA gene amplicon sequence derived culture-independent community datasets, which revealed a significantly lower abundance of nutrient-solubilizing rhizobacteria in fertilized plants. The same methods were applied to rhizoplane samples from 19 ancestral and domesticated wheat genotypes grown in the same conditions which resulted in isolation of approximately 15,000 bacterial isolates. Notably, there was a significantly lower abundance of PGPR isolated from unplanted control pots (bulk soil) compared to plants and no difference between fertilization conditions. Moreover, differences in the abundance of PGPR under contrasting fertilization conditions were more pronounced in domesticated wheat, which we hypothesize is due to a loss of plant-microbe signalling pathways as the wheat genome underwent expansion. Key genera differentially more abundant in non-fertilized wheats included members of the phylum Cyanobacteria (Nostoc) and Proteobacteria (Bradyrhizobium, Pseudomonas) compared to fertilized wheats which were richer in Actinobacteria (Arthrobacter, Catenulispora, Leifsonia, and Streptomyces). Introduction of the Reduced height (Rht) genes during the Green Revolution has been hypothesized to reduce PGPR selection due to their influence on the plant hormone gibberellin (GA). 16S rRNA gene amplicon sequencing revealed a markedly different rhizosphere microbiome in severe Cadenza wheat Rht dwarf mutants which became more pronounced with mineral fertilizer addition. There was a higher differential abundance in Acidobacteria, Chloroflexi and Gemmatimonadetes, phyla more commonly associated with bulk soil, in Rht mutant cultivars compared with a higher differential abundance of Bacteroidetes, Firmicutes and Proteobacteria, phyla more commonly associated with plant growth promotion, in wildtype Cadenza wheat. The research presented in this thesis contributes to our understanding of the impact domestication has had on plant-microbe interactions in the presence and absence of agriculturally important but potentially environmentally deleterious chemicals, as well as presenting a method for functional characterization of microbiomes. This knowledge will benefit the development of more targeted ecologically benign biofertilization strategies.