Plant root systems typically contain diverse microorganisms. Researchers have observed a rare exception to this rule, in which the root microbiome is dominated by a single bacterial genus.
Sorghum bicolor, also known as sorghum, is an important bioenergy crop in the United States and staple in other parts of the world. Sorghum is often planted on poor agricultural land and arid climates due to its ability to grow with minimal irrigation.
Plant root systems are home to a variety of microorganisms, referred to as the plant microbiome, that can interact with their hosts to change plant fitness and health. These microbial communities are typically quite diverse throughout a plant’s life span, containing many thousands of different species. A new study in the root system of Sorghum bicolor, a DOE-mission relevant bioenergy crop, discovered an exception to this rule. In this pilot experiment part of a larger sorghum field study, it was observed that in the early season, the microbiome of the soil directly surrounding the root was predominately comprised of members belonging to the genus of bacteria Pseudomonas. Single molecule long read technology combined with shotgun metagenomics demonstrated that several Pseudomonas lineages were enriched in sorghum. The Pseudomonas bloom was recapitulated using specific carbon compounds added to field soil brought back to the lab. Understanding the cause of this phenomena may be important for efforts to shape plant health, as members of this genera are known to be both pathogenic and plant beneficial organisms.
There is a growing interest in improving crop performance in agricultural systems by adding to or modifying the microbial partners within the plant microbiome. To use these ‘bioinoculants’ effectively, an improved understanding of how the plant microbiomes shift and change over time is needed. Specifically, it will be important for us to identify the forces that cause certain members of the microbiome to out compete other members of the community. The research in this study suggests that the bloom of Pseudomonas that only appears in the early field season may be the result of a combination of the plant developmental stage, the right environmental conditions, and selective carbon root exudates. This discovery may help us create beneficial microbiome habitats in crop root systems through alterations in plant metabolism.
Researchers have discovered a time-dependent shift in the root-associated microbiomes, or ‘rhizospheres’, of field grown sorghum. Through 16S rRNA amplicon sequencing, the team compared the root-associated microbiomes of ten sorghum genotypes grown in eastern Nebraska. It was observed that early rhizospheres were dominated by Pseudomonas species in a manner that was independent of the type of sorghum or the amount of fertilizer used. Deeper characterization of this trend using a combination of higher-resolution analytic tools and improved sequencing techniques, it was shown that this bloom was comprised of a wide variety of individual Pseudomonas species. To confirm this unexpected finding, and to help identify the underlying cause, the team used a lab-based approach to see which plant produced sugars and carbon sources might lead to this bloom. It was discovered that a select group of carbon sources have the ability to enrich for Pseudomonas in a manner similar to that observed in the field. Collectively, this work suggests a possible connection between the enrichment of Pseudomonas species and a plant-driven exudate profile and provides an opportunity for developing new tools for microbiome-manipulation in the agricultural sector.
Link to paper:
Chiniquy, D. et al. Microbial Community Field Surveys Reveal Abundant Pseudomonas Population in Sorghum Rhizosphere Composed of Many Closely Related Phylotypes. Front. Microbiol. 12, 598180 (2021). [DOI: 10.3389/fmicb.2021.598180] https://www.frontiersin.org/articles/10.3389/fmicb.2021.598180/full