Microbes as hidden or prominent players in plant life

To maintain food security, we must enhance our ability to protect crop plants without harming the environment with potentially toxic synthetic chemicals. This research centres on plant resistance and resilience to drought stress. It utilises an evolutionary systems biology approach, focusing on the plant hologenome (the genomes of the plant and its associated microbiome). The overall objective is to better understand and harness holobiont adaptation and evolution mechanisms to improve, within a single or a few generations, the resistance and resilience of plants to abiotic stress, preventing yield losses. Here, we evaluated how drought stress alters resource allocation and mediates the trade-off between plant nutrient uptake and growth dynamics. We focused on how carbon and nitrogen utilisation and the abundance of microbial functional genes contribute to plant physiological performance and modulate holobiont dynamics under drought stress. Microbial abundance/diversity and nutrient cycling were strongly correlated with increased phenotypic plasticity under simulated drought treatments. Distinct community assembly processes were observed for each drought treatment, suggesting that the mode of stress influences microbiome composition, which in turn shapes holobiont performance and plant adaptive responses. By reframing crop improvement through a holobiont lens, this research provides a blueprint for climate-smart agriculture.

The bacterial genus Sphingomonas is a common colonizer of major crop leaves and roots. It is non-pathogenic and often provides growth-promoting benefits to plants, making it a promising candidate for agricultural inoculants. To enable targeted applications, we aim to uncover the genetic basis of Sphingomonas’ beneficial interactions with plants. To pinpoint essential genes for plant colonization, we are performing large-scale mutant screens on the Sphingomonas genome. We have generated a pool of ~85,000 mutants for the model beneficial strain Sphingomonas melonis FR1. In our mutagenesis process, we use method known as RB-TnSeq, which allows for identifying mutants in a population simply by amplicon sequencing of their unique barcodes. We are applying these mutant populations to in-vitro and in-planta conditions to identify differentially represented mutants across conditions. Those mutants missing in-planta may represent genes critical for plant colonization. In parallel, we are using a CRISPR RNA-guided integrase-based reverse genetics system to disrupt specific genes that we believe may play an essential role in plant interactions or bacterial colonization, and also to introduce genetic barcodes for easily quantifying mutants and wild-type strains by amplicon sequencing. The expected outcome will be genes required for Sphingomonas' success on plants

Biography

Ezgi Mehmetoglu Boz was the poster prize winner at Microbes as hidden or prominent players in plant life