Working Groups
Coherence and Effectiveness Of The Working Plan
Description Of The Working Groups, Tasks And Activities
To address the challenges, four Working Groups (WG) have been identified. WG1 will focus mainly on methodologies to characterize the functional diversity of beneficial root-associated micro organism populations, with an emphasis on meta-analyses of currently available data and coordination of future resource/tools development. WG2 will focus on molecular mechanisms underlying the interactions with the beneficial root-associated microorganisms, with an emphasis on the effect of multi-partite interactions and resilience towards stressful environmental conditions.WG3 will focus on the ecological and economic services provided by beneficial root-associated microorganisms. WG4 will focus in identifying levers to improve services provided by beneficial root-associated microorganisms in agriculture.The WG1, 2 and 3, addressing questions on beneficial root-associated microorganisms at different levels, will provide results/knowledge/meta-analyses to feed the WG4. The WG4 will integrate all Action results and link them to stakeholder needs and requests.
The WG1, 2 and 3, addressing questions on beneficial root-associated microorganisms at different levels, will provide results/knowledge/meta-analyses to feed the WG4. The WG4 will integrate all Action results and link them to stakeholder needs and requests.
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WG1: Functional characterization of beneficial microorganism diversity
Advances in sequencing and computational approaches have provided the scientific community with unprecedented insights into the taxonomic composition and encoded functions of the microbial community associated with plants, among which the beneficial root-associated microorganisms are of particular interest for both basic science and translational applications. However, this research field remains essentially “fragmented”: individual studies often focus on specific combinations of plants and microorganisms, making it difficult to define common principles regarding the recruitment of the different beneficial microorganisms. This WG will tackle this knowledge gap by retrieving and reanalyzing sequencing data present in the current literature of the plant root microbiota using a common computational framework to focus on services provided by beneficial root-associated microorganisms.This approach will shed new light on the ecological coherence of beneficial microorganisms and identify whether any taxa and functions could be conserved across plant lineages.
The specific objectives of WG1 are:
Objective 1.1. To develop a curated database of sequencing studies describing beneficial root- associated microorganisms. Objective 1.2. To reconstruct the taxonomic affiliation of plant beneficial root-associated microorganisms across plant lineages. Objective 1.3. To infer the functional potential of beneficial root-associated microorganisms by interrogating large-scale genomic datasets, and evaluate the efficiency of the services they provide.
These objectives will be achieved by using the following methods and means:
To achieve objective 1.1, the current literature for studies describing beneficial microorganisms will be mined using ad hoc search terms. Cut-off dates as well as the following criteria will be included in the survey: a) primary literature (e.g., not review manuscripts), b) quantitative and replicated measurements of a plant growth/health parameters must be present and c) availability of a sequencing dataset. The selected manuscripts will be further classified according to the type of host species (e.g., cereals,legumes, horticultural crops, model species and others), as well as the primary beneficial effects exerted by microorganisms (e.g., growth promotion per se and/or pathogen protection). In addition, soil-basedand lab-based (axenic) experimental designs will be discriminated. Finally, for each study, the cognateraw sequencing datasets will be retrieved.
For objective 1.2, these raw sequencing data will be processed according to an established pipeline depending on the nature of the primary information (e.g., individual genomes, amplicon survey and metagenomics) in order to create so-called observation/count matrices and implement descriptive statistical approaches to characterise these studies. Using open source tools, the contribution of defined factors, namely host species and types of services will be evaluated, and the distribution of beneficial root-associated microorganisms, their taxonomic affiliations and their encoded functions (the latter for individual genome and metagenomics data) will be investigated.
For objective 1.3, as amplicon sequencing surveys are anticipated to represent a significant proportion of our activity, data gathered from objective 2 will be used to interrogate existing genomic collections ofplant-associated microorganisms. The gathered taxonomic information will be used to predict in silicometagenomic composition and process obtained data as indicated in the objective 1.2. A focus will bemade on barcodes that could allow intragenus/species identification, with the ultimate objective to definemarkers relevant to evaluate the functional efficacy of the services provided.
Photo credit : Marcela Mendoza, Louis Mercy, Jan
WG2: Molecular mechanisms associated with beneficial interaction networks
The objective of WG2 is to define similarities and differences of molecular mechanisms regulating the establishment and functioning of beneficial root-associated microorganism interactions, and crossregulations occurring during complex interactions, and more specifically, to determine how these interactions co-exist, compete or have synergistic effects on plant growth and protection against diseases and abiotic stress. The interaction between expert researchers in the field will allow reviewing the relevant scientific literature, mining databases, and performing meta-analysis studies of published data on different plant species and microorganisms. At first, efforts will be devoted to the two best-knownplant beneficial associations (i.e., AM fungi and N-fixing rhizobia), which will then be extended to other beneficial plant- microorganism associations (e.g. plant growth promoting (PGP) bacteria/fungi). These collaborative studies will identify gaps in knowledge and propose future research lines and management strategies for the use of these microorganisms, either individually or in consortia, in agriculture. In addition, a focus will be made on studies related to on-going climate change challenges, to highlight the potential of using beneficial root-associated microorganisms in a context of fast evolving environmentalconditions.
The specific objectives of WG2 are:
Objective 2.1. To summarize knowledge on specific and common molecular and cellular mechanisms controlling beneficial root-associated microorganism interactions Objective 2.2. To provide a comprehensive analysis of the molecular mechanisms that govern and/orare modulated during multiple beneficial root-associated microorganism interactions. Objective 2.3. To evaluate how these molecular mechanisms are regulated by environmental factorsin the frame of agricultural practices and climate change contexts.
These objectives will be achieved by using the following methods and means:
The evolutionary relationship between AM and rhizobial symbioses has revealed that the genetic program of the more ancient mycorrhizal symbiosis was recruited for the rhizobial interaction. To achieve objective 2.1 and 2.2, a literature review will first be performed on genetic factors involved in beneficial root-associated microorganism interactions, both on the plant and on the microbial side.Quantitative parameters will be collected with the aim of using this knowledge to facilitate further comparative studies of complex beneficial root-associated microorganism interactions. The synergistic exchange of knowledge among the different research groups involved in ROOT-BENEFIT will be critical to reach these objectives.
To address the objective 2.3, meta-analysis studies will focus on the effect of different agricultural factors, such as fertilization, cropping systems, and soil type, as well as of environmental climatechange-related stress factors (high CO2, drought, temperature, light and radiation), on the formation and functioning of beneficial root-associated microorganism interactions. The impact of these environmental conditions on key molecular mechanisms identified as relevant in the objective 2.1 will be addressed.The knowledge generated in objectives 2.1 and 2.2 will be used to publish focused reviews in peer-reviewed open access journals as a useful resource for researchers, companies and end-users. Targeta nd quantitative parameters identified will fuel the WG3 analyses.
Photo credit : Louis Mercy, Jan
WG3: Ecological and economical services provided by the root beneficial interaction networks
The objective of the WG3 is primarily to establish concepts and frameworks to assess and quantify services provided regarding plant/crop growth, yields and nutritional quality, beneficial root-associated microorganisms, their functional diversity, multi-functionality and synergism/antagonism between the different microorganisms, taking into account their environmental dependency. In coordination with theWG2, the published literature will be used for meta-analyses to propose/quantify ecological and economic values of these beneficial interaction networks, reflecting their contribution towards securing agricultural production base upon stable, changing, or fluctuating climatic conditions, maintenance and improving of ecosystem services and human well-being.
The specific objectives of WG3 are:
Objective 3.1. To provide a comprehensive meta-analysis of benefits (mineral nutrition, abiotic and biotic stress tolerance/resistance, soil, water and air quality) conferred by beneficial13microorganisms/microbiomes, considering the different methodologies and approaches to assess the benefits directly or indirectly (e.g. through molecular proxies).Objective 3.2. To propose a framework to determine economic value(s) of the benefits, taking into account different aspects such as values for socio-economic actors, including end-users and citizens.Objective 3.3. To analyse previously published literature for modulation of the services caused by changing environmental conditions, including agricultural management and/or global climate changes.Objective 3.4. To estimate the potential of beneficial interaction networks to help secure agricultural production based upon stable, changing, or fluctuating climates.
These objectives will be achieved by using the following methods and means:
To address objective 3.1, meta-analyses of the published literature and expert discussions will be conducted in close interaction with WG2 to identify known benefits, their modes of action, and appropriate detection tools, with regards to agro-ecosystem health and resilience.
The objective 3.2 will be tackled mainly by interdisciplinary discussions including ecologists, biologists,sociologists and economists. Furthermore, ideas will be subject to expert scrutiny during a peer review process upon submitting manuscripts to scientific journals.
The objective 3.3 will be mainly achieved by meta-analyses considering studies in both agricultural management contexts and in future climate change scenarios. Direct and indirect (collateral) effects will be considered and available models will be used to allow theoretical predictions of future development upon known environmental and external resource constraints. Results will be confronted to those of theWG2 dealing with symbiotic molecular signals and pathways.
The objective 3.4 will be addressed by using previously generated knowledge, modeling platforms with diversifying possible future scenarios as to changing and/or fluctuating climatic conditions, and/or geopolitical situations affecting external resource (fossil energy, fertilizers, manpower) availability and/or prices.
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WG4: Managing and improving beneficial interaction networks under field conditions
The objective of WG4 is to facilitate the implementation of scientifically well-supported strategies for improvement of beneficial root-associated microorganism interactions, as well as the introduction of beneficial root-associated microorganisms in agriculture. Levers for improvement of crop benefits gained from root-associated microorganism interactions are mainly related to crop management, crop breeding, and microbial inoculation. However, beneficial root-associated microorganism interactions are often overlooked in analyses of cropping system performance and in breeding programs. In addition,environmental and agronomical factors explaining the variability of the inoculation impact on crop performance are not well understood. Crop genetic diversity and strain competitiveness are also often not taken into consideration in the process of microorganism selection and evaluation for inoculant production. Finally, there was up to now no effort targeted on the simultaneous co-selection of efficient plants and beneficial root-associated microorganisms. ROOT-BENEFIT will identify barriers limiting the implementation of beneficial root-associated microorganisms in agriculture, among which are the stakeholder knowledge and the lack of tools to evaluate crop responses to these microorganisms at the field level. ROOT-BENEFIT will also propose recommendations and strategies for inoculant selection and breeding, and methodologies to evaluate their potential in field conditions.
The specific objectives of WG4 are:
Objective 4.1. To identify barriers limiting the use of beneficial root-associated microorganisms under field conditions.
Objective 4.2. To propose recommendations on beneficial root-associated microorganism inoculant properties and quality.
Objective 4.3. To propose methodologies for evaluation of the effect of beneficial root-associated microorganisms in field conditions.
Objective 4.4. To propose strategies for co-selection of plants and microorganisms.
These objectives will be achieved by using the following methods and means:
To address objective 4.1, ROOT-BENEFIT participants will study the relevant literature and conduct a survey among plant breeders, agricultural advisers and farmers to collect their input on the state of the art of beneficial root-associated microorganism use, and on key open questions that remain to bead dressed for a more widespread application.
The objective 4.2 will be addressed by analysing the literature on the impact of inoculation on the native soil microbiota, as well as on inoculated strain persistence in soils. Criteria for strain selection based on 14 their competitiveness, persistence and plant response efficacy, will be proposed. Moreover, inoculant quality criteria will be discussed. Finally, evolutions of European and national legislations will be evaluated to provide feedback to policy-makers and end-users. Inoculant producers will be strongly involved of this objective, to take into account not only the scientific relevance, but also economic and practical constraints that may limit the implementation of the proposed strategies and methodologies.
To address the objective 4.3, the knowledge and methodologies identified as relevant in previous WGs will be assessed to determine the potential of their use in large-scale field conditions. Agronomical technical institutes, inoculant producers, breeders and companies proposing soil microbial diagnostics will be specifically integrated for evaluating how realistic could be the implementation of such methodologies in field conditions, taking also into account economical parameters (running costs,equipment needed, etc.)
To address the objective 4.4, plant and microorganism geneticists will propose conceptual strategies for the simultaneous co-selection of adapted and responsive crop and microorganism genotypes. Inoculant producers, breeders will be specifically integrated in this process, to evaluate the feasibility of such approaches. Proof of concept studies will be designed and proposed for funding in future European ortranslational calls.
Photo credit : Marcela Mendoza, Louis Mercy
The Management Committee (MC) will be in charge of the tasks not covered by the four scientific WGs, including
- Coordination of the different WG activities to stimulate WG interactions;
- Organization of annual meetings;
- Organization of STSM calls;
- Organization of the workshops dedicated to socio-economic actor needs;
- Implementation of the dissemination plan described in 3.2.2
Writing reports
Regular interactions between the different WGs about work progress will be ensured by the MC. In addition, the MC will ensure the dissemination and secure dataset storage even after the COST Action ends. Finally, the MC will supervise during the whole course of the Action gender, age and geographical balances among participants. The MC will be assisted by executive dissemination, STSM committees and any other leadership roles/committee that will be appointed by the MC.
