Characterising plant interactions with bacteria that promote the uptake of nitrogen and sulphur from organic sources

EU-funded researchers investigated the interactions between plants and microbes to improve the uptake of nitrogen (N) and sulfur (S).

In the near future, plant-microbe associations that work to each other’s benefit could be incorporated into crops to give high-performing plant genotypes. The microbial populations are expected to improve nutrient use efficiency and help reduce the need for fertiliser application.

Currently, there is only a limited understanding of the precise biochemical transformations and exchanges that occur between plants and microbes. It is still unclear which species are most effective in supporting plant growth and nutrition uptake. However, there is evidence that plant genotypes exhibit differing capacities to influence the narrow region of soil directly affected by root secretions known as the rhizosphere.

A Marie Skłodowska-Curie Individual Fellowship award, the Horizon 2020 PINBAC project addressed these gaps in scientific knowledge by investigating plant-microbe nutrient exchange in the rhizosphere, using cutting-edge proteomic and metabolomic techniques integrated with metabolic modelling.

New approach for studying plant-microbe interactions

Researchers showed that quantitative proteomics, the large-scale study of proteins, can be successfully applied to taxonomically diverse rhizosphere bacterial strains. “We also successfully integrated growth phenotype and proteomics data with computational models of bacterial metabolism,” says project coordinator Dr Stanislav Kopriva, a Marie Curie fellow.

The project also discovered that a rhizosphere Pseudomonas strain exhibited evidence of metabolic flexibility via large-scale proteome remodelling in response to different organic nitrogen sources.

Furthermore researchers developed a novel liquid chromatography-mass spectrometry methodology for studying plant-microbe nutrient exchange. This exometabolomics approach also known as 'metabolic footprinting' allowed them to study specific extracellular metabolites and to what degree microbial strains differ in their substrate consumption patterns. According to Dr Kopriva: “We successfully tested an exometabolomics approach in combination with proteomics and modelling.” Results of the work were published in Molecular Plant-Microbe Interactions.

In the proteomic study of nitrogen metabolism, PINBAC provided detailed new knowledge about microbial nitrogen metabolism in the rhizosphere. Soon to be published, Dr Richard Jacoby and Dr Kopriva defined the metabolic pathways that diverse rhizosphere bacterial strains utilise to metabolise organic sources of nitrogen.

A review of the interaction of plants and root associated bacteria enhancing plant mineral nutrition has been published in Frontiers in Plant Science. ‘The Role of Soil Microorganisms in Plant Mineral Nutrition—Current Knowledge and Future Directions’ summarises the current knowledge in several research fields that can converge to improve understanding of the molecular mechanisms underpinning the composition of rhizospheric microbiomes and their dynamics.

Plant growth and nutrient efficiency boosted

PINBAC also provided a set of proteins and metabolic pathways that are involved in plant-microbe nutrient exchange. “The genes linked to these proteins can potentially be targeted by future crop breeding approaches aiming to boost recruitment of desired microbial strains into the plant microbiome, or otherwise by rhizosphere engineering approaches aiming to manipulate the microbiome to support plant growth and resource use efficiency,” comments Dr Kopriva.

Methodological approaches developed during the project will have significant potential benefits for future European studies aimed at generating mechanistic information about the metabolic interactions occurring at the plant-microbe interface. Dr Kopriva concludes: “PINBAC results can therefore help to underpin development of agricultural practices aiming at lowering the use of mineral fertiliser and improving agricultural sustainability.”

Reference source: Characterising plant interactions with bacteria that promote the uptake of nitrogen and sulphur from organic sources