Effect of strigolactones on recruitment of the rice root-associated microbiome

Strigolactones are endogenous plant hormones regulating plant development and are exuded into the rhizosphere when plants experience nutrient deficiency. There, they promote the mutualistic association of plants with arbuscular mycorrhizal fungi that help the plant with the uptake of nutrients from the soil. This shows that plants actively establish - through the exudation of strigolactones - mutualistic interactions with microbes to overcome inadequate nutrition. The signaling function of strigolactones could possibly extend to other microbial partners, but the effect of strigolactones on the global root and rhizosphere microbiome remains poorly understood. Therefore, we analyzed the bacterial and fungal microbial communities of 16 rice genotypes differing in their root strigolactone exudation. Using multivariate analyses, distinctive differences in the microbiome composition were uncovered depending on strigolactone exudation. Moreover, the results of regression modeling showed that structural differences in the exuded strigolactones affected different sets of microbes. In particular, orobanchol was linked to the relative abundance of Burkholderia-Caballeronia-Paraburkholderia and Acidobacteria that potentially solubilize phosphate, while 4-deoxyorobanchol was associated with the genera Dyella and Umbelopsis. With this research, we provide new insight into the role of strigolactones in the interplay between plants and microbes in the rhizosphere

Northern Ireland’s 1968 at 50: agonism and protestant perspectives on civil rights

2018 marked the fiftieth anniversary of the seminal events of Northern Ireland’s 1968: a milestone offering up an opportunity to reassess a pivotal moment in the province’s recent past. This article will argue that the civil rights period has fitted into a common model of the past being used to perpetuate the divisions at the heart of Northern Irish society. It will go on to demonstrate how an innovative methodological and theoretical approach, based on oral history, education and – most crucially – agonism, has facilitated the unearthing and integration of complex and hitherto marginalised Ulster Protestant perspectives

Engaging audiences with difficult pasts: the Voices of ’68 Project at the Ulster Museum, Belfast

Can history museums influence the relationship between divided communities? This paper explores why an initially modest collaboration between the authors and the Ulster Museum on the non‐violent Northern Ireland Civil Rights Movement of 1968/69, eventually had substantial impact beyond the museum’s walls. Having placed the Northern Ireland Civil Rights Movement within the context of both the international protests of 1968 and the specific environment of Northern Ireland, particularly the virtual civil war known as the Troubles, the paper turns to the role of museums in responding to the legacy of this past, and the evolving practice of the Ulster Museum, as background to the project. The latter began as a limited intervention within an existing display, based on oral histories and underpinned by the theory of ‘agonism’, proposing that divided communities must learn to live with difference. It eventually included exhibitions, workshops, school study days, curricular materials and online provision. It has directly influenced the Northern Ireland GCSE History Curriculum and been held up as an example of good practice within the province’s peace process. The paper discusses why the project succeeded – location within a national museum; credibility with protagonists, academics, communities and audiences; starting small; a willingness to take risks and share control; multiple perspectives; and an acceptance that not everyone will be satisfied. With a version of the Voices of 68 exhibition now installed in the Museum’s permanent gallery, the next challenges are longitudinal studies on its impact and assessing the approach’s relevance to other museums working in post‐conflict societies

Integration of omics data to unravel root microbiome recruitment

The plant microbiome plays an essential role in supporting plant growth and health, but plant molecular mechanisms underlying its recruitment are still unclear. Multi-omics data integration methods can be used to unravel new signalling relationships. Here, we review the effects of plant genetics and root exudates on root microbiome recruitment, and discuss methodological advances in data integration approaches that can help us to better understand and optimise the crop–microbiome interaction for a more sustainable agriculture

Medicago truncatula genotype drives the plant nutritional strategy and its associated rhizosphere bacterial communities

International audienceWith the growing concern of developing a more sustainable agriculture, decreasing the use of inputs, and promoting biological diversity, harnessing plant microbiome through plant genetics is gaining of interest to improve plant growth, nutrition, and health. While genome-wide association studies have been conducted to identify plant genes driving the plant microbiome, more multidisciplinary studies are required to assess the relationships among plant the genetic effects, the plant microbiome and plant fitness. Using a metabarcoding approach, we characterized the rhizosphere bacterial communities of a core collection of 155 Medicago truncatula genotypes together with the plant phenotype, using an ecophysiological framework, and investigate the plant genetic effects through genome-wide association studies. The different genotypes within the M. truncatula core collection showed contrasted growth and carbon and nitrogen nutritional strategies but few loci were associated to these ecophysiological traits. To go further, we described its associated rhizosphere bacterial communities, dominated by Proteobacteria, Actinobacteria and Bacteroidetes, and defined acore rhizosphere bacterial community. Next, occurrence of bacterial candidates predicting plant ecophysiological traits of interest were identified using random forest analyzes. Some of them were heritable and plant loci were identified, pinpointing genes related to response to hormone stimulus, systemic acquired resistance, response to stress, nutrient starvation ortransport, and root development.Together, these results suggest that plant genetic can affect the plant growth and nutritional strategies harnessing keystones bacteria in a well-connected network community

Effect of strigolactones on recruitment of the rice root-associated microbiome

Strigolactones are endogenous plant hormones regulating plant development and are exuded into the rhizosphere when plants experience nutrient deficiency. There, they promote the mutualistic association of plants with arbuscular mycorrhizal fungi that help the plant with the uptake of nutrients from the soil. This shows that plants actively establish-through the exudation of strigolactones-mutualistic interactions with microbes to overcome inadequate nutrition. The signaling function of strigolactones could possibly extend to other microbial partners, but the effect of strigolactones on the global root and rhizosphere microbiome remains poorly understood. Therefore, we analyzed the bacterial and fungal microbial communities of 16 rice genotypes differing in their root strigolactone exudation. Using multivariate analyses, distinctive differences in the microbiome composition were uncovered depending on strigolactone exudation. Moreover, the results of regression modeling showed that structural differences in the exuded strigolactones affected different sets of microbes. In particular, orobanchol was linked to the relative abundance of Burkholderia-Caballeronia-Paraburkholderia and Acidobacteria that potentially solubilize phosphate, while 4-deoxyorobanchol was associated with the genera Dyella and Umbelopsis. With this research, we provide new insight into the role of strigolactones in the interplay between plants and microbes in the rhizosphere

A strategy for differential abundance analysis of sparse microbiome data with group-wise structured zeros

Comparing the abundance of microbial communities between different groups or obtained under different experimental conditions using count sequence data is a challenging task due to various issues such as inflated zero counts, overdispersion, and non-normality. Several methods and procedures based on counts, their transformation and compositionality have been proposed in the literature to detect differentially abundant species in datasets containing hundreds to thousands of microbial species. Despite efforts to address the large numbers of zeros present in microbiome datasets, even after careful data preprocessing, the performance of existing methods is impaired by the presence of inflated zero counts and group-wise structured zeros (i.e. all zero counts in a group). We propose and validate using extensive simulations an approach combining two differential abundance testing methods, namely DESeq2-ZINBWaVE and DESeq2, to address the issues of zero-inflation and group-wise structured zeros, respectively. This combined approach was subsequently successfully applied to two plant microbiome datasets that revealed a number of taxa as interesting candidates for further experimental validation