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The role of drought on root-associated bacterial communities across diverse cereal grass species and over a developmental gradient

  • Author(s): Naylor, Daniel Torres
  • Advisor(s): Coleman-Derr, Devin
  • Hake, Sarah
  • et al.
Abstract

Plant roots represent a unique environmental niche within which diverse assemblages of bacteria come to flourish. Over the course of evolution, co-evolution between plant hosts and their associated bacterial communities have resulted in an intimate association between these two, such that plant health is highly dependent on presence and composition of these communities. It is known that plant tolerance to abiotic stresses is at least partially mediated by responses in belowground root communities – however, the community response to drought, perhaps the most agronomically important abiotic stress, remains largely unexplored.

While the response to moisture limitation in soil bacterial communities and plant physiology have been detailed, synthesizing the existing literature to explore how these responses pertain to root community responses reveals a number of specific limitations in the current knowledge base for the droughted root microbiome. The dissertation presented here addresses important questions remaining in this area, including how community responses to drought are similar and different between a broad-ranging phylogenetic framework of plant hosts, how community profiles correspond to host relatedness and the effect drought may have on this relationship, and the response community profiles exhibit during host development with concurrent drought exposure.

To explore common and distinct trends in the root microbiome under drought, eighteen grass lineages were planted in a common field and exposed to drought conditions, after which bacterial community profiles were examined. These results indicated a number of environmental and host factors exert a sigificant influence on bacterial community diversity. These factors included not only watering regime, but also compartment, species, and time point. The most striking drought-related trend was elevated relative abundance for lineages belonging to class Actinobacteria, a lineage of Gram-positive, monoderm bacteria. This enrichment was conserved across all examined plant host species and compartments, though especially pronounced in roots. As genomic analysis of enriched bacterial OTUs revealed sporulation is unlikely to account for elevated presence of Actinobacteria, we hypothesize a number of potential alternatives for this enrichment, such as the ability to degrade plant cell walls or putative plant growth-promotion abilities.

This same work also investigates a potential correlation between host phylogeny and microbiome dissimilarity. While previous studies have looked at the role of genotype in microbiome community composition, limitations in experimental methodologies have precluded the ability to make inferences about how closely related plant species may harbor more similar root microbiota; furthermore, no studies as of yet have investigated whether drought affects this relationship. Using statistical tests, we confirm that a significant positive correlation exists between host phylogenetic distance and microbiome dissimilarity. This correlation is strongest in root-associated communities; however, effect size is smaller and less significant in compartments with increasing distance from the roots, and is weaker in drought treatments. We propose that there may be a conserved drought response shared between grass species that circumvents species-specific enrichment trends. Further research into the species effect on the microbiome reveals the existence of a drought core grass microbiome that includes a diverse array of bacteria.

There is little knowledge available about how root communities change over the course of plant development, especially in response to abiotic stress, as plants are expected to take an active role in recruiting a beneficial microbiome upon stress exposure. Growing two cultivars of the grass Sorghum bicolor with distinct drought susceptibilities in a common field revealed that host plant developmental stage is a significant factor influencing microbiome composition. With respect to abundance trends, in replicates exposed to drought, relative abundance of class Actinobacteria increased with duration of drought at the expense of classes Sphingobacteria and multiple classes belonging to phylum Proteobacteria, a trend largely reversed upon rewetting. Replication of this experiment at an additional field site, incorporating pre- and post-flowering drought treatments and a full time series from emergence to senescence, allowed for further investigation of developmental trends. We observed that the root microbiome experiences an initial period of flux under control conditions but reaches an approximate steady state after roughly 3-5 weeks. Under pre-flowering drought stress, perturbations such as drought imposition or rewetting induce bacterial communities to echo this pattern of stability followed by flux, although this trend is not seen under post-flowering drought. Similarly, bacteria enrichment and depletion trends under drought from the initial pilot experiment were confirmed from results in this main experiment, but they were dependent on what developmental stage drought was imposed on plants, as community responses were far more pronounced for pre-flowering compared to post-flowering drought. We propose that a stable root microbial community is related to the plant’s acclimatization to the surrounding water conditions, and will continuously change under continuous application of a consistent watering treatment before reaching equilibrium after 3-5 weeks. Furthermore, as developmental stage was a significant factor in abundance trends, we hypothesize that plant establishment and maturity by post-flowering developmental stages allows for a microbiome more resistant to drought stress.

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