Seed‐borne, endospheric and rhizospheric core microbiota as predictors of plant functional traits across rice cultivars are dominated by deterministic processes

Abstract

A host-plant and its associated microbiota depend on one another. However, the assembly process and the functioning of host-associated microbiota are poorly understood.Herein, rice was used as model plant to investigate the assemblage of bacterial microbiota, including those in the seed, root endosphere and rhizosphere. We also assessed the degree to which endosphere and rhizosphere communities were influenced by vertical transmission through seed and identified the core microbes that potentially associated with plant phenotypic properties.Plant microhabitat, rather than subspecies type, was the major driver shaping plant-associated bacterial microbiota. Deterministic processes were primarily responsible for community assembly in all microhabitats. The influence of vertical transmission from seed to root-associated bacterial communities appeared to be quite weak (endosphere) or even absent (rhizosphere). A core microbial community composed of 15 generalist species persisted across different microhabitats and represented key connectors in networks. Host-plant functional traits were linked to the relative abundance of these generalist core microbes and could be predicted from them using machine learning algorithms.Overall, bacterial microbiota is assembled by host-plant interactions in a deterministicbased manner. This study enhances our understanding of the driving mechanisms and associations of microbiota in various plant microhabitats and provides new perspectives to improve plant performance.

Prioritizing host phenotype to understand microbiome heritability in plants

“…1) (Zarraonaindia et al ., 2015). Sample type or ‘compartment’ consistently explains more microbiome variation than genotype or environment (Hamonts et al ., 2018; Singer et al ., 2019; Guo et al ., 2021). Because a given pair of host genotypes might exhibit more phenotypic variation in one compartment than another, patterns of microbiome heritability can differ among plant parts.…”

Comparative analysis of diversity and environmental niches of soil bacterial, archaeal, fungal and protist communities reveal niche divergences along environmental gradients in the Alps

“…Finally, we evaluated the relative importance of stochastic processes using the modi ed stochasticity ratio (MST) (Ning et al, 2019, Guo et al, 2021. This metric estimates ecological stochasticity according to a null-model-based framework.…”

Reconstitution and Transmission of Gut Microbiomes and Their Genes between Generations

“…It should be mentioned that several recent reviews have been published on different aspects of microbiome transmission. These reviews discuss plant microbiomes [12][13][14][15], animal microbiomes [4,[16][17][18][19][20], and human microbiomes [21][22][23][24][25]. This article is an updated opinion review that discusses plants and animals, including humans.…”