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

Periodic Reporting for period 1 - PINBAC (Characterising plant interactions with bacteria that promote the uptake of nitrogen and sulphur from organic sources)

Reporting period: 2016-07-01 to 2018-06-30

1.1 What is the problem being addressed?
There is increasing research interest in enhancing agricultural sustainability via targeted manipulation of plant-microbe interactions, but there is an incomplete scientific knowledge about how plants interact with their microbiome at the metabolic level. Therefore, PINBAC (Characterising Plant INteractions with BACteria that promote the uptake of nitrogen and sulphur from organic sources) aimed to deepen the molecular knowledge of plant-microbe nutrient exchange in the rhizosphere

1.2 Why is it important for society?
In contemporary agriculture, the vast majority of nitrogen is delivered via application of mineral fertilisers, which have undesirable environmental consequences such as waterway eutrophication and greenhouse gas production. There is increasing research interest in designing agricultural systems based on the nitrogen dynamics found in natural ecosystems, where nitrogen compounds are cycled between plants and soil, with microbes playing a crucial role in this process. However, this will require a better scientific understanding of how microbial metabolism can best support plant nutrition, and also of how plants recruit favourable microbial strains to their root microbiome.

1.3 What are the overall objectives?
Using advanced scientific techniques, the PINBAC project aimed to gain new scientific knowledge about the metabolic mechanisms of nutrient exchange between plants and microbes. Specific aims included: 1) To define the specific metabolites are produced by plant roots and transferred to root-associated microbes for consumption as growth sources; 2) To define the specific microbial genes that are expressed to mobilise soil nutrients for boosting plant nutrition.
2.1 What work was performed during the project?
The scientific content of PINBAC was divided into three Work Packages. The Work Package 1 involved reviewing the scientific literature, to summarise the role of soil microorganisms in plant mineral nutrition. Work Package 2 used modern experimental methods to analyse how rhizosphere bacterial strains metabolise different nitrogen sources. Work Package 3 developed and implemented a novel methodological approach for studying the bacterial consumption of root-derived metabolites.

2.2 What were the main results achieved?
In the literature review (Work Package 1), members of the PINBAC project collated the scientific literature from several different disciplines to summarise how plants can shape their rhizosphere microbiome via root exudates, and also which microbial genes are linked to enhancing plant nutrition. In the proteomic study of nitrogen metabolism (Work Package 2), PINBAC provided detailed new knowledge about microbial nitrogen metabolism in the rhizosphere, by defining the metabolic pathways that diverse rhizosphere bacterial strains utilise to metabolise organic sources of nitrogen. In the exometabolomic study of how bacteria consume plant root metabolites (Work Package 3), PINBAC developed a novel methodological approach for studying nutrient exchange between plants and microbes, as well as defining the specific root metabolites that rhizosphere bacterial strains consume as growth substrates.

2.3 How were the results communicated and disseminated?
The primary communications aim of the PINBAC project was to publish open-access papers in peer-reviewed journals. This has been achieved, with publications detailing the results of Work Package 1 (Jacoby et al, 2017, Front Pla Sci: 8) and also Work Package 3 (Jacoby et al, 2018, Mol Plant Microbe In: 31; 803). A manuscript summarising the results of Work Package 2 is in preparation and expected to be submitted in the next few months. Both published articles are open-access, and the third manuscript will be submitted to an open-access journal. Furthermore, all primary metabolomics data associated with Deliverable 3 are publicly available via deposition in the MetaboLights repository, while the proteomics data associated with Deliverable 2 will be deposited in the ProtemeXchange repository upon submission. To communicate the results of PINBAC to a general audience, one avenue was the ‘Planter’s Punch’ contributed by Dr Jacoby in October 2017. The Planter’s Punch is a series of online articles that summarise CEPLAS research to a non-scientific readership. Another avenue for public engagement was the series of public lectures given by Prof. Kopriva as part of UoC’s Competence Area for Food Security, where a broad range of topics were discussed, including the role of plant science in shaping environmental sustainability and human nutrition.
3.1 What progress was achieved beyond the state of the art?
The ability of microorganisms to use root-derived metabolites as growth substrates is a key trait for success in the rhizospheric niche. However, few studies describe which specific metabolites are consumed, or to what degree microbial strains differ in their substrate consumption patterns. Therefore, the methodological approach developed in Work Package 3 of the PINBAC project represents a major achievement beyond the state of the art, because the data derived from this workflow provide detailed new information about which root-derived metabolites are consumed by rhizosphere bacterial strains. Regarding microbial nitrogen metabolism, the vast majority of previous research studied model laboratory strains such as E. coli, but there was little knowledge about how nitrogen nutrition is mediated in the rhizosphere microbiome. Therefore, the data generated in Work Package 2 of PINBAC also represents progress beyond the state of the art, because it provides detailed mechanistic information about the metabolic pathways involved in the metabolism of organic-N molecules by non-model bacterial strains isolated from field-grown plant roots.

3.2 What are the potential impacts (including the socio-economic impact and the wider societal implications of the project)?
The work achieved by the PINBAC project has impacts relating to the challenges of food security, sustainable agriculture, and resource efficiency. There is increasing research interest in enhancing agricultural sustainability via targeted manipulation of plant-microbe interactions, and the PINBAC project has deepened the molecular knowledge of plant-microbe nutrient exchange in the rhizosphere. Specifically, PINBAC has defined a set of proteins and metabolic pathways that are involved in plant-microbe nutrient exchange. The genes linked to these metabolic phenomena can potentially be targeted by future crop breeding approaches aiming to boost recruitment of desired microbial strains into the plant microbiome, or by rhizosphere engineering approaches aiming to manipulate the microbiome to support plant growth and resource use efficiency. Furthermore, the methodological approaches developed during the PINBAC project have significant potential for future studies aiming to generate mechanistic information about the metabolic interactions occurring at the plant-microbe interface.
Key research questions investigated by PINBAC