Metabolomics in the Rhizosphere: Tapping into Belowground Chemical Communication

The rhizosphere is densely populated with a variety of organisms. Interactionsbetween roots and rhizosphere community members are mostly achieved viachemical communication. Root exudates contain an array of primary and sec-ondary plant metabolites that can attract, deter, or kill belowground insectherbivores, nematodes, and microbes, and inhibit competing plants. Metabo-lomics of root exudates can potentially help us to better understand thischemical dialogue. The main limitations are the propersampling ofthe exudate,the sensitivityofthemetabolomicsplatforms,andthemultivariatedataanalysisto identify causal relations. Novel technologies may help to generate a spatiallyexplicit metabolomeoftherootanditsexudatesatascalethatisrelevantfortherhizosphere community.Communication in the Rhizosphere

https://www.cell.com/trends/plant-science/pdf/S1360-1385(16)00009-1.pdf

Metabolomics in the Rhizosphere: Tapping into Belowground Chemical

Legume growing has many benefits. Indeed legumes provide plant proteins for animal feed and human food. Legumes fix atmospheric N2 and, in turn, provide cheap and green N fertilisers. Additionally, legumes are used as diversification crops in rotations based on oilseed rape and cereals. Despite those benefits, legume crops in Europe represent less than 4 % of arable lands, and European legume seeds are underused for animal and human nutrition. Nonetheless, European authorities are now fostering the development of legume crops for sustainable agriculture. Here, we analyse forage and grain legume-producing systems since 1950 in order to identify the actual constraints of legume development. We show that legumes can contribute to the agroecological transition for sustainable agriculture, food and energy and for sustainable agri-food systems. Then, we point out that high added-value niche markets are required for supporting legume production. The major research needs identified are (1) analysing the constraints of the current systems and identifying ways of moving towards systems that include more legumes, (2) identifying new and diversified uses for legumes in a sustainable food chain, (3) assessing and improving the ecosystem services provided by legumes at cropping system and territory scales and (4) promoting agroecology through and for legume crop management.

/pdf/legumes-for-feed-food-biomaterials-and-bioenergy-in-europe-a-3kub50tlpv.pdf

Legumes for feed, food, biomaterials and bioenergy in Europe: a review

An intensive agricultural production is necessary to satisfy food requirements for the growing world population. However, its realization is associated with the mass consumption of non-renewable natural resources and with the emission of greenhouse gases causing climate changes. The research challenge is to meet sustainable environmental and economical issues without compromising yields. In this context, exploiting the agro-ecosystem services ofsoil microbial communities appears as a promising effective approach. This chapter reviews the research efforts aimed atimproving a sustainable and healthy agricultural production through the appropriate management of soil microorganisms.First, the plant-associated microbiome is briefly described. Then, the current research technologies for formulation and application of inocula based on specific beneficial plant-associated microbesare summarized. Finally, the perspectives and opportunities to manage naturally existing microbial populations, including those non-culturable, are analyzed. This analysis concerns: (i) a description of the already available, culture-independent, molecular techniques addressed at increasing our understanding of root-microbiome interactions; (ii) how to improve the ability of soil microbes for alleviating the negative impacts of stress factors on crop productivity; and (iii) whether plants can structure their root-associated microbial communities and, leading on from this, whether the rhizosphere can be engineered (biased) to encourage beneficial organisms, while prevent presence of pathogens.

/pdf/future-challenges-and-perspectives-for-applying-microbial-3dgor9ss1o.pdf

Future challenges and perspectives for applying microbial biotechnology in sustainable agriculture based on a better understanding of plant-microbiome interactions

Although yield and total biomass produced by annual legumes remain major objectives for breeders, other issues such as environment-friendly, resource use efficiency including symbiotic performance, resilient production in the context of climate change, adaptation to sustainable cropping systems (reducing leaching, greenhouse gas emissions and pesticide residues), adaptation to diverse uses (seeds for feed, food, non-food, forage or green manure) and finally new ecological services such as pollinator protection, imply the need for definition of new ideotypes and development of innovative genotypes to enhance their commercialization. Taken as a whole, this means more complex and integrated objectives for breeders. Several illustrations will be given of breeding such complex traits for different annual legume species. Genetic diversity for root development and for the ability to establish efficient symbioses with rhizobia and mycorrhiza can contribute to better resource management (N, P, water). Shoot archit...

/pdf/breeding-annual-grain-legumes-for-sustainable-agriculture-3uudro9fsm.pdf

Breeding Annual Grain Legumes for Sustainable Agriculture: New Methods to Approach Complex Traits and Target New Cultivar Ideotypes

Combining Molecular Microbial Ecology with Ecophysiology and Plant Genetics for a Better Understanding of Plant–Microbial Communities' Interactions in the Rhizosphere

Soil microorganisms play a key role in both plants nutrition and health. Their relation with plant varies from mutualism to parasitism, according to the balance of costs and benefits for the two partners of the interaction. These interactions involved the liberation of plant organic compounds via rhizodeposition. Modification of atmospheric CO2 concentration may affect rhizodeposition and as a consequence trophic interactions that bind plants and microorganisms. Positive effect of elevated CO2 on plants are rather well known but consequences for micoorganisms and their interactions with plants are still poorly understood. A gnotobiotic system has been developed to study the interaction between Medicago truncatula Jemalong J5 and the mutualistic bacteria Pseudomonas fluorescens strain C7R12 under two atmospheric CO2 concentrations: ambient (365 ppm) versus enriched (750 ppm). Costs and benefits for each partner have been determined over time by measuring plant development and growth, the C and N contents of the various plant parts and the density of the bacteria in rhizosphere compartments. Following the increase in CO2, there was a beneficial effect of P. fluorescens C7R12 on development, vegetative growth, and C/N content of M. truncatula. Concerning plant reproduction, an early seed production was noticed in presence of the bacterial strain combined with increased atmospheric CO2 conditions. Paradoxically, this transient increase in seed production was correlated with a decrease in bacterial density in the rhizosphere soil, revealing a cost of increased CO2 for the bacterial strain. This shift of costs-benefits ratio disappeared later during the plant growth. In conclusion, the increase in CO2 concentration modifies transiently the cost-benefit balance in favor of the plant. These results may be explained either by a competition between the two partners or a change in bacterial physiology. The ecosystem functioning depends on the stability of many plant-microbe associations that abiotic factors can disrupt.

/pdf/interaction-between-medicago-truncatula-and-pseudomonas-1lusi4s6mk.pdf

Clémentine Lepinay

Papers

Combining Molecular Microbial Ecology with Ecophysiology and Plant Genetics for a Better Understanding of Plant–Microbial Communities' Interactions in the Rhizosphere

Interaction between Medicago truncatula and Pseudomonas fluorescens: Evaluation of Costs and Benefits across an Elevated Atmospheric CO2