Eiko Eurya Kuramae

1,9-decanediol, a rice-derived biological nitrification inhibitor (BNI) suppresses soil nitrification and nitrous-oxide emissions, but the mechanisms of action against ammonia-oxidizing bacteria remain unclear. Combining physiology and transcriptomics in Nitrosomonas europaea, we show that a dose-dependent and reversible inhibition of ammonia oxidation by 1,9-decanediol by up to 44.7%, while maintaining high cell viability. Transcriptomics reveal that inhibition of ammonia monooxygenase (AMO) triggered an energy crisis, downregulating the respiratory complexes (nuo, coxA/B, atp). We propose that the RegB-RegA two-component system senses the redox imbalance and contributes to a biosynthesis-to-defense transition, marked by an 8.9-fold induction of amoC3 and suppression of ribosomal and amino-acid synthesis. Activation of RND-efflux pumps and chemotaxis enable active counteraction and escape from the stressor. This study provides crude-enzyme-based evidence for AMO as a primary target of a reversible BNI and integrates it with genome-wide transcriptomics, offering molecular insight into designing nature-based nitrification inhibitors and BNI-enhanced crops.

Domestication of crops, such as rice, has resulted in the loss of beneficial root-associated microbiota central to plant nitrogen-use efficiency. Whether these microbes can be inherited through hybridization of wild and cultivated plants and the host genes involved is unclear. Here we used two recombinant inbred line populations, derived from cultivated rice ( Oryza sativa ) and its wild relative Oryza rufipogon to map host quantitative trait loci associated with core bacterial taxa. Integrating microbiome profiling, quantitative trait loci mapping, population genomics and transgenic validation, we identified 113 candidate plant genes. The receptor-like kinase-encoding gene OsRLK , found predominantly in wild rice, was significantly associated with Acinetobacter , which enhances plant nitrogen uptake. Knockout and overexpression of OsRLK , inoculated with an Acinetobacter synthetic community, validated their role in nitrogen-use efficiency. In field trials, the overexpression line significantly increased yield-related traits. These findings establish the genetic basis of microbiome re-domestication and provide a framework for microbiome-guided breeding of nutrient-efficient crops.

Soil properties critically shape sugarcane growth and its microbiome, yet their influence on gene expression remains unclear. We investigated the combined effects of soil type (clayey and sandy loam) and sugarcane genotype (IACSP‐5503 and IACSP‐6007) on microbiome composition and plant transcriptional profiles. Bacterial communities from soils and stalk tissues, as well as transcriptomes of 48‐h sprouted buds grown for 10 months, were analysed. Results showed that IACSP‐5503 (adapted to low‐fertility soils) and IACSP‐6007 (less adapted) recruited endophytic microbiota in a soil–genotype‐dependent manner. In sandy loam, IACSP‐5503 promoted diverse plant growth‐promoting bacteria (PGPB) (including Burkholderia , Leifsonia and Mycobacterium ), associated with nitrogen fixation, hormone production and stress tolerance, while IACSP‐6007 displayed reduced PGPB diversity and transcriptomic signatures of nutrient deficiencies. Conversely, in clayey soil, IACSP‐6007 recruited more PGPBs (such as Pseudomonas , Bacillus and Klebsiella ) linked to nutrient acquisition and defence responses. Both genotypes exhibited enhanced expression of defence‐ and antioxidant‐related genes in clayey soil, suggesting priming effects. Overall, our findings reveal soil‐dependent, genotype‐specific microbial recruitment strategies, particularly in IACSP‐5503, reflecting adaptive responses to nutrient‐poor conditions. The combined 16S metataxonomic and transcriptome data offered insights into how soil and genotype shape microbial recruitment and transcriptional plasticity in sugarcane.

Rhizosphere metabolites regulate organic pollutant dissipation through microbiome modulation, yet dynamic interrelationships among metabolite shifts, microbial assembly, and pollutant removal remain unclear. Using multiomics (16S rRNA sequencing, metabolomics, and metagenomics), this study deciphered the temporal dynamics of rhizosphere metabolites and microbiome during the dissipation of fomesafen in soybean pots. Fomesafen dissipation exhibited biphasic kinetics during soybean growth, with an initial rapid phase followed by prolonged stabilization, which was synchronized with time-dependent microbiome perturbations of initial enrichment and subsequent attenuation. Metabolomics revealed fomesafen-induced shifts in rhizosphere metabolites, with 2-naphthalenesulfonic acid (↓20.84%) and 2-hydroxyoctadecanoic acid (↑13.30%) exhibiting opposing effects on microbial assembly, which ultimately affect fomesafen dissipation, as outlined in our conceptual model. Microcosm experiments further demonstrated 2-naphthalenesulfonic acid enhanced while 2-hydroxyoctadecanoic acid inhibited fomesafen dissipation. Our findings highlight the significance of rhizosphere metabolite-mediated interactions between core microbes and potential fomesafen-degraders in governing fomesafen dissipation.

Recent evidence shows that plants can recruit beneficial microbiomes that contribute substantially to disease resistance. However, it remains unclear whether resistant varieties can generate soil microbial legacies that persist beyond a single growing cycle and influence subsequent plant health. We tested this hypothesis using two banana varieties differing in resistance to Fusarium wilt to condition soils. These conditioned soils were then used to grow the two banana varieties to assess whether prior soil conditioning affected disease outcomes. We further analysed the microbial communities in the conditioned soils to identify key taxa associated with disease suppression. Cultivation‐based approaches were also used to explore the pathogen inhibition potential of microbial populations that were enriched by the resistant banana variety. The soil legacy from the highly resistant variety positively influenced plant health, whereas the susceptible variety's soil led to pathogen enrichment. Microbial community analyses identified bacterial communities as being more responsive to feedback effects, while varietal differences more strongly influenced fungal communities. Beneficial microbes such as Dyella , Rhizobium and Sphingobium were enriched in the highly resistant variety's soil legacy, contributing to enhanced plant health. Synthesis and applications . Our findings highlight a nature‐based strategy for improving plant health through the intentional use of resistant crop varieties to engineer beneficial soil microbiomes. This approach could enhance the sustainability and disease resilience of modified agricultural systems. By informing the design of crop rotation and soil management practices, our results demonstrate how ecological processes can be actively managed to promote long‐term agroecosystem health.

Striga hermonthica (Striga) is a parasitic weed that severely affects sorghum yields in sub-Saharan Africa. Recent studies highlighted the soil microbiome’s potential to suppress Striga through interference with specific stages in its life cycle. In this study, meta-analysis of 48 Ethiopian field soils revealed that microbial communities and their interactions with soil physico-chemical properties correlated with Striga field occurrence. Striga infestation of sorghum and soil seedbank levels were negatively correlated with clay content and the nutrients potassium, sulfur, calcium, and carbon. Microbiome analyses indicated that fungal communities were more responsive than bacteria to changes in Striga infestation and seedbank levels, with distinct microbial compositions even in soils where Striga was not detected. Specific fungal and bacterial genera showed both positive and negative correlations with Striga measures, but patterns rarely held across taxonomic levels, highlighting the complexity of microbiome–Striga interactions. To begin to validate these correlations, we tested an isolate from the fungal genus Neocosmospora , which negatively correlated with the Striga seedbank, and showed that this isolate promotes Striga seed germination in vitro , suggesting potential for biological control of Striga. The data and analysis methods are integrated and shared in a public Shiny App for broader analysis and continued research on soil-Striga interactions.

Soil properties critically shape sugarcane growth and its microbiome, yet their influence on gene expression remains unclear. We investigated the combined effects of soil type (clayey and sandy loam) and sugarcane genotype (IACSP-5503 and IACSP-6007) on microbiome composition and plant transcriptional profiles. Bacterial communities from soils and stalk tissues, as well as transcriptomes of 48-hour sprouted buds grown for 10 months, were analyzed. Results showed that IACSP-5503 (adapted to low-fertility soils) and IACSP-6007 (less adapted) recruited endophytic microbiota in a soil-genotype-dependent manner. In sandy loam, IACSP-5503 promoted diverse plant growth-promoting bacteria (PGPB) (including Burkholderia , Leifsonia , and Mycobacterium ), associated with nitrogen fixation, hormone production, and stress tolerance, while IACSP-6007 displayed reduced PGPB diversity and transcriptomic signatures of nutrient deficiencies. Conversely, in clayey soil, IACSP-6007 recruited more PGPBs (such as Pseudomonas , Bacillus and Klebsiella ) linked to nutrient acquisition and defense responses. Both genotypes exhibited enhanced expression of defense- and antioxidant-related genes in clayey soil, suggesting priming effects. Overall, our findings reveal soil-dependent, genotype-specific microbial recruitment strategies, including a potential “cry for help” mechanism in IACSP-5503, reflecting adaptation under nutrient-poor conditions. The combined 16S metataxonomic and transcriptome data offered insights into how soil and genotype shape microbial recruitment and transcriptional plasticity in sugarcane.