Abstract. Plants accommodate diverse microbial communities, termed the microbiome, which can change dynamically during plant adaptation to varying environm

Read the full paper: Genomic signatures in Variovorax enabling colonization of the Populus endosphere

From ecological principles to precision engineering of plant microbiomes for sustainable agriculture. The plant holobiont integrates diverse microbial niches (including rhizosphere, endosphere, phyll...

Most soil microbes are dormant, so they must exit dormancy to have the potential to carry out plant-beneficial functions. It is unclear if dormant microbes revive in proximity to plant-produced resources and if overcoming dormancy in the soil is important ...

From ecological principles to precision engineering of plant microbiomes for sustainable agriculture. The plant holobiont integrates diverse microbial niches (including rhizosphere, endosphere, phyll....

BackgroundWhether domestication, post-domestication spread, and breeding affected the maize leaf endosphere microbiota is poorly understood despite the well-...

Background and aims While intensive fertilization has wide-ranging impact on microbial communities, its effects on microbial recolonization of soil niches and associated enzyme activities as well as hotspots distribution remain underexplored. Methods Using soil zymography and high-throughput sequencing, we investigated the hotspots and activities of C-, N- and P-acquiring hydrolases, as well as bacterial community dynamics across hotspots, coldspots, and root endosphere within rice rhizosphere in sterilized and non-sterilized soils following NPK fertilization. Results Bacterial community reassembly after sterilization was primarily governed by compartment niches rather than by fertilization, although fertilization accelerated bacterial recovery by increasing diversity and network complexity. Specifically, the dominant taxa and major contributor of genes encoding hydrolases in the rhizosphere of non-sterilized soil shifted from Actinomycetota (K-strategists) to Pseudomonadota and Bacillota (r-strategists). In contrast, root endosphere communities had greater resilience during recolonization and likely supported rice growth by expanding enzyme hotspots area. Higher enzyme activities in hotspots, compared to coldspots, correlated strongly with increased bacterial network complexity, and less with differences in diversity and overall community composition. Fertilization triggered a trade-off between enzyme activities and hotspots area, with increased activities for β-glucosidase and leucine aminopeptidase but reduced hotspots area, whereas acid phosphatase had the opposite trend. Conclusion The trade-offs between enzyme activities and hotspots area highlight the micro-scale spatial heterogeneity in nutrient mobilization in paddy soils, suggesting adaptive strategies that plants and microorganisms use to regulate nutrient investment. These findings provide valuable insights for optimizing fertilization management to accelerate microbial processes and enzyme-mediated nutrient cycling. Graphical Abstract

Abstract. The intensification of agriculture has led to environmental degradation, including the loss of biodiversity. This has prompted interest in perenn

•Rhizobacteria have shown great promise in enabling sustainable crop agriculture. •Low rhizosphere competence of rhizobacteria have hindered their widespread adoption. •Root exudate engineering can theoretically improve rhizosphere competence. •Root exudates can be enriched for beneficial metabolites, but there are pitfalls. •Temporal regulation of metabolite release may be a useful approach to rhizosphere engineering.

Drought stress impacts plant–microbe interactions, reshaping microbial community composition and biogeochemical cycling, thereby reducing crop productivity and threatening food security. However, the specific microbial responses and roles of plant-derived metabolites remain underexplored. Here we reveal that drought stress shifts the composition of wheat-associated microbiota across the phyllosphere, rhizosphere and root endosphere by favouring Actinobacteria and Ascomycota while depleting Proteobacteria and Basidiomycota. Targeted single-cell sorting and sequencing identified 21 active drought-tolerant bacteria (DTB) enriched in genes related to plant fitness and nutrient cycling. These DTB showed significant positive correlations with drought-enriched plant phytochemicals such as jasmonic acid and pipecolic acid. Moreover, the inoculation of synthetic community including four identified drought-tolerant taxa significantly stimulates the wheat growth under drought stress. A global exploration confirmed the widespread distribution of DTB, underscoring their promising potential to enhance crop resilience. This study provides new insights into drought-induced microbiome shifts and highlights microbial candidates for improving crop resilience in a changing climate.

From ecological principles to precision engineering of plant microbiomes for sustainable agriculture. The plant holobiont integrates diverse microbial niches (including rhizosphere, endosphere, phyll...