Abstract
While the root-associated microbiome is typically less diverse than the surrounding soil due to both plant selection and microbial competition for plant derived resources, it typically retains considerable complexity, harboring many hundreds of distinct bacterial species. Here, we report a time-dependent deviation from this trend in the rhizospheres of field grown sorghum. In this study, 16S rRNA amplicon sequencing was used to determine the impact of nitrogen fertilization on the development of the root-associated microbiomes of 10 sorghum genotypes grown in eastern Nebraska. We observed that early rhizosphere samples exhibit a significant reduction in overall diversity due to a high abundance of the bacterial genus Pseudomonas that occurred independent of host genotype in both high and low nitrogen fields and was not observed in the surrounding soil or associated root endosphere samples. When clustered at 97% identity, nearly all the Pseudomonas reads in this dataset were assigned to a single operational taxonomic unit (OTU); however, exact sequence variant (ESV)-level resolution demonstrated that this population comprised a large number of distinct Pseudomonas lineages. Furthermore, single-molecule long-read sequencing enabled high-resolution taxonomic profiling revealing further heterogeneity in the Pseudomonas lineages that was further confirmed using shotgun metagenomic sequencing. Finally, field soil enriched with specific carbon compounds recapitulated the increase in Pseudomonas, suggesting a possible connection between the enrichment of these Pseudomonas species and a plant-driven exudate profile.
Highlights
The plant microbiome is a dynamic landscape, shifting both over plant development and under environmental change (Edwards et al, 2018; Xu et al, 2018; Zhalnina et al, 2018)
Large scale surveys using 16S rRNA gene amplicon sequencing of the maize rhizosphere collected from field grown plants across two growing seasons in New York revealed that just three Pseudomonas operational taxonomic unit (OTU) accounted for ∼44% of the maize rhizosphere amplicon reads beginning after week 8 in one of these seasons (Walters et al, 2018)
In wild populations of Arabidopsis thaliana collected in Southwestern Germany, a single Pseudomonas OTU accounted for ∼50% of amplicon sequences in the phyllosphere (Karasov et al, 2018)
Summary
The plant microbiome is a dynamic landscape, shifting both over plant development and under environmental change (Edwards et al, 2018; Xu et al, 2018; Zhalnina et al, 2018). Large scale surveys using 16S rRNA gene amplicon sequencing of the maize rhizosphere collected from field grown plants across two growing seasons in New York revealed that just three Pseudomonas OTUs accounted for ∼44% of the maize rhizosphere amplicon reads beginning after week 8 in one of these seasons (Walters et al, 2018). This enrichment was not seen in the surrounding soil, indicating that plant selection, possibly combined with the opportunistic nature of these microbes, was driving their increased abundance. These studies present instances of Pseudomonas dominance within different plant compartments, soil types, plant hosts, and geographic locations, and highlight the need for improved understanding of the community dynamics and plant microbe interactions that produce them
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