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Purpose: The root-associated microbiota is essential to plant health, fitness and productivity, but the effect of plant domestication on the ecological process of microbial community assembly is unclear. Methods: High-throughput sequencing of the 16S rRNA genes was employed to investigated the the diversity, ecological assembly process and cooccurrence relationship of the bacterial communities of multiple root compartment niches (root zone, rhizosphere, and root endosphere) between wild and landrace accessions grown in three soil types. Results: Our results showed that the domestication effect on bacterial community increased from the root zone to the rhizosphere and endosphere, while the soil type effect decreased. Compared with wild soybean, the root endosphere bacterial community of the landraces was more sensitive to soil environmental change. The deterministic process dominated the assembly of the bacterial community in the rhizosphere and root endosphere, and its relative contribution was higher in the landraces than in wild soybeans. In the two root compartments, the increased root system selection pressure in the landraces was indicated by a greater loss of bacteria at the same taxon level and lower bacterial diversity. Furthermore, the family Oxalobacteraceae and the class Actinobacteria were identified as important root-associated biomarker taxa for wild soybeans, while Enterobacteriaceae was such for the landraces. Conclusions: Our findings provide crucial empirical evidence for the host selection and enrichment process of the microbial community under local domestication and are of great significance in understanding the coevolution of hosts and microbiota, which will aid in manipulating microbiota for future crop breeding. [ABSTRACT FROM AUTHOR]

Background: Leguminous crops could fix atmospheric nitrogen through their symbiotic and non-symbiotic associations with different microbes to survive and maintain nutrient in soils that are deficient in nitrogen. Only limited number of lateral roots of the legume prefers to formulate nodules. So far, it is unclear whether microbial communities in lateral roots with/without nodules are different, and whether the selection of microbiome among different types of lateral roots of a plant is a random process or is strictly controlled by the host plant. Methods: We investigated the diversity and community structure of prokaryotic and eukaryotic microorganisms inhabiting in lateral roots with and without nodules of soybean via high-throughput 16S rDNA and 18S rDNA amplicon sequencing. In addition, quantitative microbial element cycling method was applied to estimate the functional genes that are related to carbon, nitrogen, phosphorus, sulfur cycling and methane metabolism. Results: Microbiome in rhizosphere of lateral roots with nodules had significantly lower α-diversity and higher co-occurrence network complexity, compared to those of lateral roots without nodules. The neutral model analysis demonstrated that microbial community of lateral roots with nodules in rhizosphere soil were less affected by neutral process than that of lateral roots without nodules. In addition, we identified a keystone ecological cluster (Module #1) of the rhizosphere cross-kingdom network that positively correlated with multiple functional gene copies, suggesting that the microbial taxa in Module #1 could play important roles in nutrient cycling of rhizosphere microenvironment. Conclusions: Overall, our study revealed the differences in microbial communities in the lateral roots with/without the nodule of root systems and identified a keystone ecological cluster positively linking with multiple functional cycling. [ABSTRACT FROM AUTHOR]

Aims: Licorice (Glycyrrhiza uralensis Fisch.) is a crucial medicinal herb as it accumulates glycyrrhizin and liquiritin in roots. Licorice root-associated bacterial communities shaped by soil characteristics are supposed to regulate the accumulation of root secondary metabolites. Methods: The soil characteristics, root secondary metabolites, and root-associated bacterial communities were analyzed in licorice plants of different ages to explore their temporal dynamics and interaction mechanisms. Results: Temporal variation in soil characteristics and root secondary metabolites was distinct. The alpha-diversity of root-associated bacterial communities decreased with root proximity, and the community composition was clustered in the rhizosphere. Different taxa that were core-enriched from the dominant taxa in the bulk soil, rhizosphere soil, and root endosphere displayed varied time–decay relationships. Soil total potassium (TK) as a key factor regulated the temporal variation in some individual taxa in the bulk and rhizosphere soils; these taxa were associated with the adjustment of root secondary metabolites across different TK levels. Conclusions: Licorice specifically selects root-associated core bacteria over the course of plant development, and TK is correlated with root secondary metabolites and individual core-enriched taxa in the bulk and rhizosphere soils, which may have implications for practical licorice cultivation. [ABSTRACT FROM AUTHOR]