The rhizosheath, or the layer of soil closely adhering to roots, can help plants to tolerate drought under moderate soil drying conditions. Rhizosheath formation is the result of poorly understood interactions between root exudates, microbes, and soil conditions. Here, we study the roles played by the soil microbiota in rhizosheath formation in barley (a dry crop). We show that barley rhizosheath formation is greater in acid soil than in alkaline soil, and inoculation with microbiota from acid soil enhances rhizosheath formation in alkaline soil. The rhizosheath-promoting activity is associated with the presence of Flavobacteriaceae and Paenibacillaceae bacteria that express genes for biosynthesis of indole-3-acetic acid (IAA, a common auxin), as determined by metagenomics and metatranscriptomics. Two bacterial strains isolated from rhizosheath (Chryseobacterium culicis and Paenibacillus polymyxa) produce IAA and enhance barley rhizosheath formation, while their IAA-defective mutants are unable to promote rhizosheath formation. Co-inoculation with the IAA-producing strains enhances barley grain yield in field experiments through an increase in spike number. Our findings contribute to our understanding of barley rhizosheath formation, and suggest potential strategies for crop improvement.

Auxin regulates a progressive cell cycle during adult maize lateral root formation.

Microbiomes inhabiting plants are crucial for plant productivity and well-being. A plethora of interactions between roots, microbiomes, and soil shapes the self-organization of the microbial community associated with the root system. The rhizosphere (i.e., the soil close to the root surface) and endosphere (i.e., all inner root tissues) are critical interfaces for the exchange of resources between roots and the soil environment. In recent years, next-generation sequencing technologies have enabled systemic studies of root-associated microbiomes in the endosphere and interactions between roots and microbes at the root-soil interfaces. Genetic factors such as species and genotype of host plants are the driving force of microbial community differentiation and composition. In this mini-review, we will survey the role of these factors on plant–microbe interactions by highlighting the results of next-generation genomic and transcriptomic studies in the rhizosphere and endosphere of land plants. Moreover, environmental factors such as geography and soil type shape the microbiome. Relationships between the root-associated microbiome, architectural variations and functional switches within the root system determine the health and fitness of the whole plant system. A detailed understanding of plant–microbe interactions is of fundamental agricultural importance and significance for crop improvement by plant breeding.

Background: Beneficial associations between plants and soil microorganisms are critical for crop fitness and resilience. However, it remains obscure how microorganisms are assembled across different root compartments and to what extent such recruited microbiomes determine crop performance. Here, we surveyed the root transcriptome and the root and rhizosphere microbiome via RNA sequencing and full-length (V1–V9) 16S rRNA gene sequencing from genetically distinct monogenic root mutants of maize (Zea mays L.) under different nutrient-limiting conditions. Results: Overall transcriptome and microbiome display a clear assembly pattern across the compartments, i.e., from the soil through the rhizosphere to the root tissues. Co-variation analysis identified that genotype dominated the effect on the microbial community and gene expression over the nutrient stress conditions. Integrated transcriptomic and microbial analyses demonstrated that mutations affecting lateral root development had the largest effect on host gene expression and microbiome assembly, as compared to mutations affecting other root types. Cooccurrence and trans-kingdom network association analysis demonstrated that the keystone bacterial taxon Massilia (Oxalobacteraceae) is associated with root functional genes involved in flowering time and overall plant biomass. We further observed that the developmental stage drives the differentiation of the rhizosphere microbial assembly, especially the associations of the keystone bacteria Massilia with functional genes in reproduction. Taking advantage of microbial inoculation experiments using a maize early flowering mutant, we confirmed that Massilia-driven maize growth promotion indeed depends on flowering time. Conclusion: We conclude that specific microbiota supporting lateral root formation could enhance crop performance by mediating functional gene expression underlying plant flowering time in maize.

Heterosis describes the superior performance of hybrid plants compared with their genetically distinct parents and is a pillar of global food security. Here we review the current status of the molecular dissection of heterosis. We discuss how extensive intraspecific structural genomic variation between parental genotypes leads to heterosis by genetic complementation in hybrids. Moreover, we survey how global gene expression complementation contributes to heterosis by hundreds of additionally active genes in hybrids and how overdominant single genes mediate heterosis in several species. Furthermore, we highlight the prominent role of the microbiome in improving the performance of hybrids. Taken together, the molecular understanding of heterosis will pave the way to accelerate hybrid productivity and a more sustainable agriculture.