(1) Background: Plant diversity has long been assumed to predict soil microbial diversity. The mutualistic symbiosis between forest trees and ectomycorrhizal (EM) fungi favors strong correlations of EM fungal diversity with host density in terrestrial ecosystems. Nevertheless, in contrast with host tree effects, neighboring plant effects are less well studied. (2) Methods: In the study presented herein, we examined the α-diversity, community composition, and co-occurrence patterns of EM fungi in Quercus acutissima across different forest types (pure forests, mixed forests with Pinus tabuliformis, and mixed forests with other broadleaved species) to ascertain how the EM fungi of focal trees are related to their neighboring plants and to identify the underlying mechanisms that contribute to this relationship. (3) Results: The EM fungal community exhibited an overall modest but positive correlation with neighboring plant richness, with the associations being more pronounced in mixed forests. This neighboring effect was mediated by altered abiotic (i.e., SOC, TN, LC, and LP) and biotic (i.e., bacterial community) factors in rhizosphere soil. Further analysis revealed that Tomentella_badia, Tomentella_galzinii, and Sebacina_incrustans exhibited the most significant correlations with plant and EM fungal diversity. These keystone taxa featured low relative abundance and clear habitat preferences and shared similar physiological traits that promote nutrient uptake through contact, short-distance and medium-distance smooth contact-based exploration types, thereby enhancing the potential correlations between EM fungi and the neighboring plant community. (4) Conclusions: Our findings contribute to the comprehension of the effect of neighboring plants on the EM fungal community of focal trees of different forest communities and the biodiversity sensitivity to environmental change.

Cupressus gigantea is an endangered species mainly distributed on beach land, down-slope, and middle-slope positions along the Yarlung Zangbo River on the Tibet Plateau of China, with an altitude ranging from 3000 to 3400 m. We investigated the rhizosphere and fine root microbiomes of C. gigantea at these three slope positions through metagenomic analysis. Slope positions had a greater influence on microbiome composition in the rhizosphere than that in the fine roots. Down- and middle-slope positions presented higher microbial richness indeces and community similarity, while a more complex co-occurrence network was observed in the beach land samples. Rhizosphere bacterial community assembly was determined via deterministic processes in the beach land and via stochastic processes in the down- and middle-slope positions. Archaeal and fungal community assemblies were both dominated by stochastic processes in the rhizosphere and fine roots at the three slope positions. Nitrogen (N) functional genes were more sensitive to changes in slope positions than phosphorus (N) functional genes. Soil properties explained more than 60% and 34% of the variations in the N and P functional genes and more than 30% and 10% of the variations in the microbiomes in the rhizosphere and fine roots, respectively. Variation in the microbiome was significantly driven by total nirtogen, total potassium, pH, and soil moisture in rhizosphere, and by pH and soil moisture in fine roots. Our observations suggest that the effect of slope position on the microbiomes of C. gigantea was greater for the rhizosphere than the fine roots, with down- and middle-slope positions presenting higher community similarity.

Breed selection alters the coevolution of plant–microbiome associations that have developed over long periods of natural evolution. We investigated the effects of breed selection on the rhizosphere microbiomes and metabolites of hybrid parents (I101 and 84K) and their offspring (Q1–Q5) using metagenomics and untargeted metabolomics. Rhizosphere archaeal, bacterial and fungal community β-diversity significantly differed among hybrid parents and offspring, but only the dominant bacterial phyla and bacterial community α-diversity revealed significant differences. Approximately 5.49%, 14.90% and 7.86% of the archaeal, bacterial and fungal species significantly differed among the poplar hybrid parents and offspring. Rhizosphere microbial functional genes and metabolites were both clustered into the following three groups: I101 and 84K; Q2 and Q4; and Q1, Q3 and Q5. Compared with the hybrid parents, 15 phytochemical compounds were enriched in the hybrid offspring and explained 7.15%, 18.24% and 6.68% of the total variation in the archaeal, bacterial and fungal community compositions, respectively. Rhizosphere metabolites significantly affected the bacterial community, rather than the archaeal and fungal communities. Our observations suggested that poplar breed selection imposed greater selection pressure on the rhizosphere bacterial community, which was mainly driven by metabolites.