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Information for Researchers No. 66 | 5 October 2020
Priority Programme “Deconstruction and Reconstruction of the Plant Microbiota: DECRyPT” (SPP 2125)

In 2017, the Senate of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) established the Priority Programme “Deconstruction and Reconstruction of the Plant Microbiota: DECRyPT” (SPP 2125). The programme is designed to run for six years. The present call now invites proposals for the second three-year funding period.

In nature, the roots and leaves of plants engage in intimate associations with an enormous diversity of microbes including bacteria, fungi, algae, oomycetes and protists. Collectively, the microbial assemblage of a plant is called the “plant microbiota” and the sum of the plant-inhabiting microbial genomes the “plant microbiome”. Previous studies have demonstrated not only adverse, but also beneficial functions of individual members of these microbial assemblages for plant hosts, including nutrient mobilisation and uptake, protection against plant pathogens, or abiotic stress tolerance. However, the current shortage of fundamental knowledge on principles underlying community establishment and functions conferred by microbe-microbe and/or microbe-host interactions in these assemblages makes it difficult to predict whether individual members of the microbiota retain their beneficial or detrimental activities in a microbial community context.

The central scientific objectives of this Priority Programme are to obtain a deep and more predictive understanding of plant-microbiota associations and to develop pioneering reductionist approaches towards a molecular understanding of plant microbiota functions. This Priority Programme aims to elucidate genetic factors underlying plant microbiota establishment, to test presumed community adaptation in ecological contexts and to define community-associated emergent properties. Computational and genomic tools will guide hypothesis testing and the design of microbiota reconstitution experiments in controlled environments.

This Priority Programme aims at a pragmatic understanding of the plant microbiota by application of systematic reductionist approaches, including the deconstruction and reconstruction of microbial assemblages. The deconstruction phase involves establishment of model microbial culture collections from plants grown in contrasting natural environments and microbial whole-genome sequencing of pure strains. The reconstruction phase includes microbiota reconstitution experiments using gnotobiotic plant systems to test the impact of different microbes and defined environments on plant fitness parameters such as disease resistance, nutrient acquisition, resource allocation and abiotic stress tolerance under laboratory conditions, to help us understand their roles in nature. One challenge is to determine how the manipulation of specific host and microbial pathways affects microbiota composition, their protective effects and consequently plant health. The ultimate goal is to validate inferences from the reductionist approaches in natural or agricultural ecosystems.

To maximise the potential for synergies and cross-referencing of data, three model plants will be employed in this Priority Programme, the dicotyledonous model Arabidopsis thaliana (and related sister species), the legume symbiosis model Lotus japonicus (and related Lotus corniculatus) and the cereal crop model Hordeum vulgare. Participants of the Priority Programme are encouraged to use a standardised natural substrate and characterised microbiota culture collections. Projects, which move from exploratory to mechanistic studies over the course of this Priority Programme, are particularly encouraged. For accurate and high-resolution analysis of microbiome data, the programme has established a central platform providing members with computational and genomic tools and will establish mutant libraries. It also provides access to comprehensive microbe culture collections. The Priority Programme will not cover binary interactions between host plants and a single microbe, the virome of plants, or studies focusing on soil biophysics or soil geochemistry, as this would dilute the focus of the programme on understanding the molecular basis and ecological relevance of plant-associated microbial assemblages.

Research areas addressed in this Priority Programme:

Ecological and molecular mechanisms of community establishment, community dynamics, including disease resistance and resilience, and microbial physiology in a community context. Goals are:

  • to identify keystone species and key processes involved in the assembly of plant microbiota
  • to test the contribution of plant-microbe and microbe-microbe interactions to community assembly and microbiota-influenced host traits
  • to test assembly of plant microbiota under a broad range of environmental conditions in controlled experiments
  • to identify mechanisms underlying plant-microbiota resilience to genetic, nutritional and/or environmental perturbations
  • to elucidate processes by which plants discriminate between pathogens and beneficial microbes in a community context
  • to establish how variation in innate immunity recognition and signalling influences microbial community structure and function
  • to test whether microbe-microbe interactions and community patterns observed in simplified systems are reflected in observations from natural or agricultural systems

Collective toolkit development. Goals are:

  • to expand the toolkit for computational pipelines for meta-genomics, meta-transcriptomics, network construction and genome mining
  • to expand the toolkit for examining responses to biotic and abiotic stresses
  • to establish plant and microbial mutant libraries for mechanistic studies

Proposals must be submitted in English via the DFG’s electronic submission system “elan” by 15 January 2021.

Please be aware that all CVs need to be prepared in English as well.

If you are using the “elan” portal for the first time, please note that you need to register yourself and your institutional address before submitting a proposal to the DFG. If you have not yet registered, please note that you must do so by 5 January 2021 to submit a proposal under this call. You will normally receive confirmation of your registration within the next two working days. You will be asked to select the appropriate Priority Programme call during both the registration and the proposal submission process.

Those applicants who already have an elan-account are asked to check their institutional data and update them if necessary prior preparing your electronic proposal. Elan updates will be processed within the next two working days.

For new proposals: If you would like to submit a proposal for a new project within the existing Priority Programme, please go to Proposal Submission – New Project – Priority Programmes – Selection of “SPP 2125/2 – DECRyPT”.

For renewal proposals: Previous applicants can submit a proposal for the renewal of an existing project under Proposal Submission – Proposal Overview/Renewal Proposal. Please note that you need to select your previous project first from the proposal overview in order to get access to submit a renewal proposal. The aforementioned SPP selection does not apply because your project is already linked to the Priority Programme.

In preparing your proposal, please review the programme guidelines (form 50.05, section B) and follow the proposal preparation instructions (form 54.01). For your proposal it is mandatory to use the up-to-date Project Description form (form 53.01, 04/20). These forms can either be downloaded from the DFG website or accessed through the elan portal.

Up to now, it is planned that all submitted proposals will be evaluated by a review panel in the course of a colloquium, which is anticipated to take place in May or June 2021 in Bonn. All principal investigators will receive formal invitations in due course.

The envisaged start of funding is October 2021.

Further Information

More information on the Priority Programme is available at:

The elan system can be accessed at:

Proposal guidelines, preparation instructions, the DFG rules for publication lists and the current project description for your proposal are outlined in the DFG forms 50.05, 54.01, 1.91 and 53.01, which can be found either in elan or on the DFG’s website at:

For scientific enquiries please contact the Priority Programme coordinator:

Further instructions on submitting a proposal are supplied by the DFG:


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