Understanding the spatiotemporal dynamics of microbial communities is essential for predicting their ecological roles and interactions with host plants. In a recent study, Wei and colleagues (Microbiol Spectr 13:e02097-24, 2024) investigated fungal diversity across multiple plant and soil compartments in rubber trees over two seasons and two geographically distinct regions in China. Their findings revealed that alpha diversity was primarily influenced by seasonal changes and physicochemical factors, while beta diversity exhibited a strong geographical pattern, shaped by leaf phosphorus and soil available potassium. These results highlight the role of environmental drivers in shaping within-community diversity, while other factors contribute to the differences between fungal communities across the soil-plant continuum. By distinguishing the effects of temporal and spatial factors, this study provides detailed insights into plant-associated microbiomes and emphasizes the need for further research on the functional implications of microbial diversity in the context of changing environmental and agricultural conditions.

With global warming, the frequency and intensity of drought episodes are projected to increase worldwide, especially in the boreal forest. This represents a serious threat to the boreal forest ecosystem's productivity and environmental services. It is thus crucial to better understand how drought or water limitation could affect boreal forest ecosystems functioning, and to be prepared to overcome damage caused by drought events. Studies suggest that microbes may mitigate the negative effects of drought or water shortage on plants. However, most of these studies focused on soil microbes and on agricultural ecosystems. Here, we used a rainout shelters and soil irrigation experimental design to study the response to rain exclusion and soil water content of epiphytic phyllosphere bacterial communities associated with four boreal conifer tree species. Our results showed only a weak response of phyllosphere bacterial communities to variation in soil water content. On the other hand, host tree species identity and rain exclusion were the main drivers of epiphytic phyllosphere bacterial communities' structure and diversity. This suggests that fewer rain events, in the context of climate change, would impact boreal trees phyllosphere microbiome composition.

China has significant mineral resources, but prolonged extraction has caused considerable environmental degradation. Interactions among rhizosphere, phyllosphere, and soil microorganisms, along with host plants, are essential for supporting plant growth and increasing stress tolerance. This study employed high-throughput sequencing to assess microbial diversity and community structure related to four common tree species in the mountainous areas of Shanxi Province, with samples collected from three regions over two seasons and three locations. The dominant fungal and bacterial phyla identified were Ascomycota, Basidiomycota, Mortierellomycota, Pseudomonadota, Actinobacteriota, Gemmatimonadota, Acidobacteria, Myxococcota, and Firmicutes. Alpha-diversity analysis revealed that Taiyue Mountain exhibited the highest fungal diversity among the plots, while Liushenyu displayed the highest bacterial diversity. Alpha-diversity was greater in spring than in summer across the seasons. Significant differences in Alpha-diversity were observed among different tree species, with Betula platyphylla showing the lowest diversity. In comparison to phyllosphere microorganisms, rhizosphere and soil microorganisms exhibited higher diversity, richness, and evenness. Beta-diversity analysis indicated significant differences in fungal and bacterial community composition between spring and summer samples, as well as among samples from leaves, roots, and soil. The assessment of soil physicochemical properties and redundancy analysis demonstrated that soil moisture content and organic matter were key factors influencing the composition of fungal and bacterial communities. These findings provide valuable insights into the structural changes in plant microbial communities in mining areas and the restoration of damaged ecosystems.

Microbial communities are essential for plant health, but using these relationships to enhance growth and pest protection is challenging. Leveraging the natural mechanisms plants employ to manage relationships with microbes is one promising means to selectively engineer whole microbial communities with beneficial properties. This approach, known as host-guided selection, has been successful in some model species targeting performance traits (e.g., biomass). However, few studies use crop plants or focus on defensive traits (e.g., pest resistance). Our goal was to naturally engineer tomato root-associated microbiomes that increase resistance to insect pests. First, we used an iterative soil microbial inoculation process to engineer insect-suppressive rhizosphere soil microbiomes that reduce damage from aphid feeding (Macrosiphum euphorbiae) or caterpillar defoliation (Manduca sexta, Spodoptera exigua). We then characterized the bacterial and fungal microbial communities of soils associated with differences in insect performance using metabarcoding approaches. Overall, soil microbiome selection produced transient differences in aphid performance, but caterpillar growth was unaffected. In four of nine generations, the aphid population growth rate was significantly lower on plants with rhizospheres selected for low insect performance, where abundance was reduced by up to 20%. Correspondingly minor shifts in fungal and bacterial relative abundance occurred in insect-suppressive communities. However, network analysis indicated that aphid feeding disrupted rhizosphere microbiome assembly, resulting in lower community complexity and connectivity and fewer structurally important taxa compared with uninfested controls. Overall, our results highlight critical factors for successful engineering of beneficial microbiomes, particularly insect feeding guild and microbial community stability.