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

Zancarini, Anouk; Lepinay, Clémentine; Burstin, Judith; Duc, Gérard; Lemanceau, Philippe; Moreau, Delphine; Munier-Jolain, Nathalie; Pivato, Barbara; Rigaud, Thierry; Salon, Christophe; Mougel, Christophe

doi:10.1002/9781118297674.ch7

Cited by 15 publications

(8 citation statements)

References 191 publications

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“…With respect to environmental and nutritional conditions during the vegetative stage, approximately 20% of the absorbed photosynthetic carbon is released through rhizodeposition [ 67 ]. Moreover, during the reproductive stage, the plants release lower amounts of carbon compounds in their exudates because they devote the majority of their energy to seed production [ 68 , 69 ]. Breidenbach and Conrad [ 7 ] investigated the bacterial community of the soil from rice fields using 16S rDNA amplicon analysis and also profiled the expression level of various taxa throughout the vegetative, reproductive, and maturation stages.…”

Section: Discussionmentioning

confidence: 99%

Bacterial Community of the Rice Floodwater Using Cultivation-Independent Approaches

Pittol

Scully

Miller

et al. 2018

International Journal of Microbiology

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In agricultural systems, interactions between plants and microorganisms are important to maintaining production and profitability. In this study, bacterial communities in floodwaters of rice fields were monitored during the vegetative and reproductive stages of rice plant development using 16S amplicon sequencing. The study was conducted in the south of Brazil, during the crop years 2011/12 and 2012/13. Comparative analyses showed strong differences between the communities of floodwaters associated with the two developmental stages. During the vegetative stage, 1551 operational taxonomic units (OTUs) were detected, while less than half that number (603) were identified in the reproductive stage. The higher bacterial richness observed in floodwater collected during the vegetative stage may have been favored by the higher concentration of nutrients, such as potassium, due to rhizodeposition and fertilizer application. Eighteen bacterial phyla were identified in both samples. Both communities were dominated by Gammaproteobacteria. In the vegetative stage, Alphaproteobacteria and Betaproteobacteria were more abundant and, in contrast, Bacilli and Clostridia were the more dominant classes in the reproductive stage. The major bacterial taxa identified have been previously identified as important colonizers of rice fields. The richness and composition of bacterial communities over cultivation time may contribute to the sustainability of the crop.

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Section: Discussionmentioning

confidence: 99%

Bacterial Community of the Rice Floodwater Using Cultivation-Independent Approaches

Pittol

Scully

Miller

et al. 2018

International Journal of Microbiology

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“…Key information from these that the target plant recruit in its rhizosphere (Hirsch et al, 2013b). Since the root-associated microorganisms, stimulated by rhizodeposition, carry out specific activities impacting on plant nutrition and health, a feedback loop between plant and microorganisms is generated (Zancarini et al, 2013). These authors point out that plant functioning, as affected by the activities of microbial communities, can be analyzed thanks to high throughput plant phenotyping, while the effects of plant genotype on the diversity and functioning of microbial communities can be analyzed thanks to molecular ecology tools (sequencing, meta-"omics", etc.…”

Section: Molecular Ecology Approaches For a Better Understanding Of Rmentioning

confidence: 99%

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

Barea

2015

J. Soil Sci. Plant Nutr.

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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 agroecosystem services of soil microbial communities appears as a promising effective approach. This chapter reviews the research efforts aimed at improving 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 microbes are 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 rootassociated microbial communities and, leading on from this, whether the rhizosphere can be engineered (biased) to encourage beneficial organisms, while prevent presence of pathogens.

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“…and Zabrotes subfasciatus (Say)) is a goal for breeders and some progress has been made by using inhibitors and antibiosis (Fory et al, 1996). Wild accessions and traditional landraces have been recently identified as important sources of resistance against bean weevils (Zaugg et al, 2013). Introgression lines and segregating populations could be used to perform QTL analysis to fine map QTLs and genes that control agronomic features related to resistance to the above-mentioned storage insect pests.…”

Section: Reducing Insecticide Use By Breedingmentioning

confidence: 99%

“…As reviewed by Zancarini et al (2013), the existing genetic variability for root development and for production of root exudates are important traits that breeders should consider in the near future in their ideotype definitions, for positive interactions with total soil microflora, which reciprocally can impact plant yield and health.…”

Section: Improved Efficiency Of the Vesicular And Arbuscularmentioning

confidence: 99%

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

Duc

Agrama²,

Shu

et al. 2014

Critical Reviews in Plant Sciences

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131

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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 architectures and phenologies can contribute to yield and biotic constraint protection (parasitic weeds, diseases or insects) reducing pesticide use. Variable maturity periods and tolerance to biotic and abiotic stresses are key features for the introduction of annual legumes to low input cropping systems and for enlarging cultivated area. Adaptation to intercropping requires adapted genotypes. Improved health and nutritional value for humans are key objectives for developing new markets. Modifying product composition often requires the development of specific cultivars and sometimes the need to break negative genetic correlations with yield. A holistic approach in legume breeding is important for defining objectives with farmers, processors and consumers. The cultivar structures are likely to be more complex, combining genotypes, plant species and associated symbionts. New tools to build and evaluate them are important if legumes are to deliver their exciting potential in terms of agricultural productivity and sustainability as well as for feed and food.

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

Cited by 15 publications

References 191 publications

Bacterial Community of the Rice Floodwater Using Cultivation-Independent Approaches

Bacterial Community of the Rice Floodwater Using Cultivation-Independent Approaches

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

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

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