Genome sequences provide fundamental information for both basic and applied life sciences. Whole-genome sequencing is now requested for describing novel prokaryotic species and designating their type strains, which serve as representative and well-characterized strains of the species. Indeed, the number of sequenced prokaryotic genomes has been rapidly increasing. However, a considerable number of isolated strains, particularly technically demanding strains such as strict anaerobes and slow growers, remain without genome sequence information. Here we report the whole-genome sequencing of 290 bacterial and 61 archaeal strains, including technically demanding type strains, obtained from the Japan Collection of Microorganisms (JCM) using a combination of short- and long-read sequencing technologies. The data set includes 284 type-strain genomes and 235 complete genomes. Notably, in the data set, genomes of more than 200 strains, including more than 150 type strains, have not been made publicly available. Comparative genomic analysis suggests that some strains need to be assigned to novel taxa or reclassified. Functional gene survey indicates that some strains possess previously unrecognized potential for carbon fixation or bioactive secondary metabolite production. Our data set will contribute to more accurate taxonomic classification, fill gaps in the phylogeny of prokaryotes, and provide insights into their physiology and ecology.

Plasma membrane-localized pattern-recognition receptors (PRRs) play a crucial role in detecting pathogen-associated molecular patterns (PAMPs). Among them, leucine-rich repeat (LRR) receptor-like kinases (RLKs) are particularly important in plants. However, their structural complexity and membrane association pose significant challenges for biochemical analysis. Many LRR-RLKs exhibit low expression levels in planta, and their hydrophobic surfaces contribute to instability, often requiring detergent-based extraction. These properties complicate co-immunoprecipitation (Co-IP), hindering the identification of interacting proteins and post-translational modifications. Recent advancements in immunoprecipitation technologies have improved the isolation of membrane proteins, enabling the analysis of protein-protein interactions and phosphorylation dynamics. Here, we describe an optimized immunoprecipitation protocol for studying plant plasma membrane receptor-like kinases, facilitating robust characterization of their interactomes and regulatory modifications.

Redox-related molecules, such as quinones and reactive oxygen species (ROS), are important signaling molecules for all living organisms. A plant-specific leucine-rich repeat receptor-like kinase (LRR-RLK) CANNOT RESPOND TO DMBQ 1 (CARD1), also known as HYDROGEN-PEROXIDE-INDUCED Ca2+ INCREASES (HPCA1), perceives both quinones and ROS, but the mechanism by which it distinguishes between these two types of signals remains unclear. Here, we determine the structure of the CARD1 ectodomain and uncover its unique features. Structural studies, coupled with genetics and biochemical analysis, demonstrate that previously identified unique cysteine residues are not essential for signal perception in CARD1. Interestingly, CARD1 harbors a copper ion on the surface of the ectodomain via histidine-coordination that is crucial for hydrogen peroxide signaling. Our work reports a unique copper-dependent redox perception in plants and provides insight into interactions between receptors and non-peptide stimuli during perception.

Plants face constant environmental changes and must integrate external and internal cues to coordinate growth, development, reproduction, and stress responses. A major strategy is perception at the cell surface via a large, diverse network of receptors. Here, we outline how these receptors recognise extracellular signals and assemble active complexes with appropriate co-receptors. Diverse ectodomain structures enable the recognition of peptides and proteins, glycans, lipids, phytohormones, and other small molecules, as well as changes in cell wall status. We then summarise the downstream pathways, highlighting how cytosolic kinase domains couple to receptor-like cytoplasmic kinases, MAPK modules and other signalling components, and how timing, partner choice, and cellular context confer specificity to produce distinct physiological outputs across diverse processes. Finally, we discuss the origin and evolution of cell surface receptors. Receptor-like kinases share a single origin and significantly diversified around the emergence of land plants to support new functions. Together, this perception system repeatedly adapted to new roles and point to opportunities to reprogramme cell surface receptors for resilience and crop improvement.

Bradyrhizobium, the largest rhizobial genus, is characterized by a variety of exopolysaccharide (EPS) components, such as penta- and tetrasaccharides, depending on the species. However, several genes involved in EPS synthesis remain unknown. In this study, we investigated whether 186 Bradyrhizobium strains possess homologous genes in the EPS cluster I, which is responsible for the synthesis of a pentasaccharide EPS by B. diazoefficiens USDA110. The absence of homologous genes in the B. elkanii and Photosynthetic Bradyrhizobium supergroups, in contrast to the B. japonicum supergroup, suggests that these lineages may utilize distinct and uncharacterized genes involved in tetrasaccharide EPS biosynthesis.

Many plant pathogenic fungi penetrate host surfaces mechanically, using turgor pressure generated by specialized infection cells called appressoria. These appressoria develop semipermeable cell walls and accumulate osmolytes internally to create turgor by osmosis. Although melanin is known to be important for turgor generation, the mechanism underlying wall semipermeability remains unclear. By using reverse genetics, we identified that the enzymes PKS2 and PBG13 are required for forming the semipermeable barrier in fungi causing anthracnose and rice blast diseases. These enzymes synthesize 3,5-dihydroxyhexanoic acid polymers that are essential for pathogenicity. These polymers reduce cell wall permeability and generate turgor, independently of melanization. Our findings uncover a mechanism of fungal turgor generation, linking enzyme function to pathogen penetration and disease potential, presenting new targets for disease control.

Plant roots are hotspots for interactions with soil microbes, where a characteristic bacterial community structure is formed. Plant specialized metabolites often play pivotal roles in this assembly process. However, the molecular basis underlying root microbiota responses to these bioactive compounds, and how such metabolic interactions shape the assembly of host-specific root microbiota, remain largely unknown. Nicotine is a toxic alkaloid predominantly produced by the genus Nicotiana, and the genus Arthrobacter is known as one of the nicotine-degrading bacteria in the tobacco root microbiota. In this study, we used the tobacco–Arthrobacter interaction system as a model and integrated comparative genomics and experimental genetic manipulation assays to uncover the role of bacterial catabolism capacity for host specialized metabolites in shaping host-specific root microbiota. Nicotine catabolism genes are uniquely found in the Arthrobacter strains derived from nicotine-containing environments, and this restricted gene distribution is driven by a plasmid-mediated horizontal gene transfer. To assess the ecological consequences of this genomic adaptation in Arthrobacter fitness in tobacco roots, we characterized the nicotine utilization ability of Arthrobacter and conducted adaptation assays under in planta conditions using genetically manipulated Arthrobacter strains and tobacco mutants impaired in nicotine catabolism and biosynthesis, respectively. Nicotine improves Arthrobacter colonization of tobacco roots through a catabolism-dependent mechanism. Bacterial community analysis using a synthetic community approach further demonstrated that this metabolic adaptation enhances Arthrobacter fitness within tobacco root microbiota. Our findings illustrated that bacterial catabolic capacity toward host-derived plant specialized metabolites is key for successful root colonization. This metabolic adaptation is driven by plasmid-mediated horizontal gene transfer and ultimately shapes the structure of the root microbiota community.

Regeneration involves large-scale transcriptional reprogramming to drive cell identity transitions. These transcriptional changes are tightly coupled with chromatin remodeling, but the molecular mechanisms that coordinate these changes remain unclear. Here, we show that WOUND INDUCED DEDIFFERENTIATION 1 (WIND1) transcription factor promotes somatic embryogenesis by repressing pre-existing cell fate and activating new cell identity programs. WIND1 interacts with histone deacetylase HISTONE DEACETYLASE 9 and histone acetyltransferase complex component HOMOLOG OF YEAST ADA1 2a via a conserved N-terminal domain. These interactions enable WIND1 to mediate both H3K27 deacetylation and acetylation at distinct target loci, leading to repression of organ-primordium/procambium development genes such as AINTEGUMENTA and activation of embryogenesis regulators, including LEAFY COTYLEDON 2. Our study identifies WIND1 as a bifunctional chromatin regulator that integrates opposing histone acetylation dynamics to coordinate transcriptional reprogramming, providing a molecular framework for how a transcription factor directs complex cell fate transitions during regeneration.

Defined microbial communities (DMCs; also known as SynComs) offer a promising strategy to enhance plant growth and stress tolerance by harnessing beneficial plant-associated microbes. However, the rational design and efficient exploration of complex DMC configurations remain challenging. Here, we present an interpretable model-guided framework that integrates plant phenotyping, microbial genomics, and machine learning to optimize DMC outcomes and identify microbial interactions relevant to plant performance. Using tomato as a model, we evaluated diverse DMC, temperature, and metabolite combinations in growth experiment and used a quality-controlled dataset comprising 301 plants representing 102 DMC compositions for predictive modeling. An Elastic Net regression model trained on plant biomass data and DMC composition features enabled prediction of unseen DMC outcomes, and incorporating genomic features substantially improved predictive performance, supporting the importance of functional potential in modeling community effects. We applied the model to prioritize and design improved DMCs, which were validated in laboratory assays and field trials. One model-guided DMC significantly enhanced plant growth in the field and improved heat stress tolerance under controlled conditions. Model interpretation and multi-omics analyses highlighted specific microbial interactions, including metabolite-associated relationships involving Sphingobium sp. and tomatine, that were linked to host stress-responsive gene expression. Together, our results demonstrate a scalable framework for predicting and prioritizing DMCs and identify candidate metabolite-associated microbial interactions that may contribute to plant growth promotion and abiotic stress tolerance.

Synthetic microbial communities (SynComs) represent a promising approach to enhance crop growth and stress resilience through microbiome engineering. However, the systematic design and field validation of SynComs remain limited. Here, we present a predictive framework for SynCom optimization, integrating plant phenotyping, microbial genomics, and machine learning. Using tomato as a model, we tested over 800 SynCom–temperature combinations consisting of root endophytic bacteria and rhizosphere metabolites. An Elastic Net regression model trained on plant biomass data accurately predicted the performance of unseen SynComs, with prediction accuracy plateauing at ∼5% (301/6144) of all possible SynCom–temperature combinations. Incorporating genomic features significantly improved model performance, whereas microbiome compositional data alone were not informative. We applied the model to design novel SynComs, which were tested in both laboratory and field conditions using a commercial tomato cultivar. The model-informed SynCom enhanced plant growth in field trials and improved heat stress tolerance under controlled laboratory conditions. Multi-omics analyses and feature importance metrics identified specific microbial taxa, including Sphingobium sp., whose enrichment was linked to host plant metabolite (e.g., tomatine) and stress-responsive gene expression. Our results demonstrate a scalable strategy for the predictive design of beneficial microbiomes to improve resilient crop performance under real-world conditions. ### Competing Interest Statement The authors have declared no competing interest. Japan Science and Technology Agency CREST, JPMJCR15O2, JPMJCR17O2 GteX Program Japan, JPMJGX23B2 RIKEN TRIP Initiative

Cell-surface receptors perceive environmental cues and trigger appropriate responses. In plants, these receptors comprise ectodomain, juxta-membrane, and cytosolic regions that define ligand specificity, modulate co-receptor associations, and fine-tune downstream signaling, respectively. Here we highlight the mechanistic principles underlying each module and discuss strategies to reprogram them. By integrating structural insights with illustrative examples, we provide a blueprint for designing cell-surface receptors with customized recognition specificity and programmable outputs, offering new opportunities to enhance plant resilience in the face of rapid climate change.

Soybeans fix atmospheric N2 through symbiosis with rhizobia. The relationship between rhizobia and soybeans, particularly those with high nitrous oxide (N2O)-reducing (N2OR) activities, can be leveraged to reduce N2O emissions from agricultural soils. However, inoculating soybeans with these rhizobia under field conditions often fails because of the competition from indigenous rhizobia that possess low or no N2OR activity. In this work, we utilize natural incompatibility systems between soybean and rhizobia to address this challenge. Specifically, Rj2 and GmNNL1 inhibit certain rhizobial infections in response to NopP, an effector protein. By combining a soybean line with a hybrid accumulation of the Rj2 and GmNNL1 genes and bradyrhizobia lacking the nopP gene, we develop a soybean-bradyrhizobial symbiosis system in which strains with high N2OR activity predominantly infect. Our optimize symbiotic system substantially reduces N2O emissions in field and laboratory tests, presenting a promising approach for sustainable agricultural practices.

Background: Plant roots are hotspots for interactions with soil microbes, where a characteristic bacterial community structure is formed. Plant specialized metabolites often play pivotal roles in this assembly process. However, the molecular basis underlying root microbiota responses to these bioactive compounds, and how such metabolic interactions shape the assembly of host-specific root microbiota, remain largely unknown. Nicotine is a toxic alkaloid predominantly produced by the genus Nicotiana, and the genus Arthrobacter is known as one of the nicotine-degrading bacteria in the tobacco root microbiota. In this study, we used the tobacco-Arthrobacter interaction system as a model and integrated comparative genomics and experimental genetic manipulation assays to uncover the role of bacterial catabolism capacity for host specialized metabolites in shaping host-specific root microbiota. Results: Nicotine catabolism genes are uniquely found in the Arthrobacter strains derived from nicotine-containing environments, and this restricted gene distribution is driven by a plasmid-mediated horizontal gene transfer. To assess the ecological consequences of this genomic adaptation in Arthrobacter fitness in tobacco roots, we conducted adaptation assays under both in vitro and in planta conditions using genetically manipulated Arthrobacter and tobacco mutants, which are impaired in nicotine catabolism and biosynthesis, respectively. Nicotine improves Arthrobacter colonization to the tobacco roots through both catabolism-dependent and catabolism-independent mechanisms. Bacterial community analysis using a synthetic community approach further demonstrated that these metabolic interactions, mediated by tobacco nicotine biosynthesis and its catabolism by Arthrobacter, jointly affect root microbiota composition. Conclusions: Our findings illustrated that bacterial catabolic capacity toward host-derived plant specialized metabolites is key for successful root colonization. This metabolic adaptation is driven by plasmid-mediated horizontal gene transfer and ultimately shapes the structure of the overall root microbiota community. ### Competing Interest Statement The authors have declared no competing interest. Japan Society for the Promotion of Science, Research Fellowship for Young Scientists PD, 22KJ3147 Japan Society for the Promotion of Science, KAKENHI grants, 22K21367 Mayekawa Houonkai Foundation, https://ror.org/05qkcsb49 Humanosphere Science Research of RISH RIKEN TRIP initiative

Plant-parasitic nematodes (PPNs) cause major agricultural losses worldwide, yet the molecular basis of plant immunity against these pathogens remains poorly understood. To investigate how plants recognize PPNs, we aimed to identify microbe-associated molecular patterns (MAMPs) from nematodes and the corresponding plant immune components. Due to the limited availability of material from obligate PPNs, we used Caenorhabditis elegans , a free-living nematode, as a MAMP source. C. elegans extracts activated MAMP-triggered immune responses in Arabidopsis Col-0. Through chromatography-based purification, we identified a secreted trehalase and pinpointed a conserved peptide region essential for its MAMP activity. A corresponding peptide from root-knot nematode trehalase enabled the identification of lectin receptor kinases LecRK-V.5 and LecRK-V.6 as key components in immune induction. Notably, this peptide region is conserved across insect and fungal pathogens, with LecRK-Vs required for immune responses to these peptides, highlighting the role of LecRK-V-mediated mechanism for broad-spectrum pathogen detection via trehalase-derived peptides. ### Competing Interest Statement The authors have declared no competing interest.

Parasitic plants will initiate rapid de novo organogenesis of a specialized feeding structure called a haustorium upon contact with their hosts. Currently, little is known about the internal signals regulating haustorium development. Here, we identify root meristem growth factor (RGF) peptides in Phtheirospermum japonicum as endogenous inducers of prehaustorium formation. Treatment with specific RGF peptides in the absence of hosts triggered prehaustoria and induced expression of PjYUC3, a gene required for auxin biosynthesis and prehaustorium formation. CRISPR-mediated knockouts showed that PjRGFR1 and PjRGFR3, receptors activated by the haustorium-specific RGF peptides PjRGF2 and PjRGF5, are essential for prehaustorium formation, revealing functional redundancy. Phylogenetic analyses indicate that PjRGF2 is broadly conserved among Orobanchaceae, whereas PjRGF5 appears to have recently evolved through segmental tandem multiplication. Our findings establish RGF peptides and their corresponding receptors as critical components of haustorium developmental signaling and provide insights into the evolutionary trajectories that shape plant parasitism.

Symbiosis between Bradyrhizobium strains isolated from Lao People's Democratic Republic (Lao PDR) and intercropped legumes (Arachis hypogaea, Vigna radiata, and V. mungo) was regulated by the type III secretion system (T3SS), which delivers effector proteins (T3Es) into host plant cells to modulate nodulation. To explore this mechanism, we sequenced and analyzed seven Bradyrhizobium genomes, identifying putative T3Es across five T3SS groups (G.1-G.5), which were classified based on the sequence of rhcN, a conserved ATPase gene essential for T3SS function. Phylogenetic analysis of rhcN more closely reflected the evolutionary relationships of nodulation genes than those based on 16S rRNA or whole-genome comparisons, underscoring its symbiotic relevance. Functional assays using rhcN mutants revealed group-specific effects on nodulation; G.1 strains showed neutral effects on A. hypogaea, negative effects on V. radiata, and positive effects on V. mungo. G.2 strains consistently promoted nodulation across all hosts and lacked effectors related to SUMO (small ubiquitin-like modifier) pathways, which have been implicated in host defense regulation. G.3 strains reduced nodulation in A. hypogaea but enhanced it in Vigna species. G.4 strains suppressed nodulation in A. hypogaea, and G.5 strains inhibited nodulation across all tested legumes. These findings highlight the diversity in T3SS organization, effector composition, and symbiotic responses among native Bradyrhizobium strains. The identification of known and uncharacterized effectors suggests roles in host compatibility and specificity. These strains, along with their effector profiles, provide a foundation for future functional studies to better understand T3SS-mediated interactions and support the development of targeted inoculants for legume hosts.IMPORTANCEThis study advances our understanding of legume-Bradyrhizobium symbiosis by examining the genetic organization and evolutionary patterns of T3SS genes. Our findings revealed that T3SS gene evolution does not always align with phylogenies based on 16S rRNA or whole-genome sequences, suggesting that horizontal gene transfer and functional adaptation may shape diversification. The observed variation in T3SS architecture and effector profiles among the five distinct Bradyrhizobium groups was correlated with host-specific nodulation outcomes in A. hypogaea, V. radiata, and V. mungo. We also identified novel candidate genes influencing symbiotic signaling and compatibility. These insights into the diversity and function of T3SS components contribute to a broader understanding of host-microbe communication and may support the development of more targeted and efficient rhizobial inoculants for sustainable legume cultivation and improved biological nitrogen fixation.

Plants recognize pathogen-associated molecular patterns via pattern recognition receptors, leading to the activation of pattern-triggered immunity in response to pathogen attack. Phytophthora infestans ceramide D (Pi-Cer D) is a sphingolipid from the oomycete pathogen P. infestans. Pi-Cer D is cleaved by the plant extracellular ceramidase NEUTRAL CERAMIDASE 2 (NCER2), and the resulting 9-methyl-branched sphingoid base is recognized by the plant receptor RESISTANT TO DFPM-INHIBITION OF ABSCISIC ACID SIGNALING 2 (RDA2) at the plasma membrane to transduce a defense signal. However, additional components are likely involved in sphingolipid recognition, which remain to be identified. Here, we employed a screen based on Lumi-Map technology to look for Arabidopsis (Arabidopsis thaliana) mutants with altered defense responses to Pi-Cer D. We identified three mutants showing diminished responses to Pi-Cer D and elf18, each carrying mutations in STAUROSPORIN AND TEMPERATURE SENSITIVE 3-LIKE A (STT3A), which encodes an oligosaccharyltransferase. The stt3a mutants exhibited higher susceptibility to the pathogen Colletotrichum higginsianum than the wild type. In stt3a mutants, the molecular mass of NCER2 and RDA2 proteins appeared smaller, indicating that STT3A is involved in posttranslational modification of the proteins. An enzymatic deglycosylation assay revealed that NCER2 and RDA2 are N-glycosylated. These findings suggest that STT3A contributes to plant immunity via posttranslational modification of proteins including NCER2 and RDA2. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Centromeres are essential for chromosome function, yet their role in shaping genome evolution in polyploid plants remains poorly understood. Allopolyploidy, where post-hybridization genome doubling merges parental genomes that may differ markedly in chromosomal architecture, has the potential to increase centromeric complexity and influence genomic plasticity. We explore this possibility in carnivorous Caryophyllales, a morphologically and chromosomally diverse plant lineage encompassing sundews, Venus flytraps, and Nepenthes pitcher plants. Focusing on sundews ( Drosera ), we generated chromosome-scale assemblies of holocentric D. regia and monocentric D. capensis , which share an allohexaploid origin but have diverged dramatically in genome structure. D. regia retains ancestral chromosomal fusions, dispersed centromeric repeats, and conserved synteny, whereas D. capensis exhibits extensive chromosomal reorganization and regionally localized centromeres after a lineage-specific genome duplication. Phylogenomic evidence traces D. regia to an ancient hybridization between sundew- and Venus flytrap-like ancestors, setting it apart within its infrageneric context. Genus-wide satellite DNA repeat profiling reveals rapid turnover and species-level variation in centromere organization. Together, these results establish sundews as a natural system for investigating how centromere dynamics interact with recurrent polyploidization and episodes of ecological innovation to shape genomic resilience. ### Competing Interest Statement The authors have declared no competing interest.

Parasitic plants rarely attack themselves, suggesting the existence of a kin-avoidance mechanism. In the root parasitic plant Phtheirospermum japonicum, prehaustorium formation is triggered by host-secreted haustorium-inducing factors (HIFs), but it is unresponsive to its own exudates. Here we report the identification of the spontaneous prehaustorium 1 (spoh1) mutant, which forms prehaustoria without external host signals. spoh1 harbors a point mutation in the gene encoding uridine diphosphate-glucosyltransferase UGT72B1, an enzyme that glucosylates and thereby inactivates phenolic HIFs. PjUGT72B1 has a different substrate specificity than its ortholog of the host Arabidopsis. Introduction of PjUGT72B1 into Arabidopsis reduced prehaustorium induction activity, indicating that UGT72B1 regulates haustorium induction by hosts. Our findings suggest that Orobanchaceae hemiparasitic plants have evolved kin-avoidance mechanisms through the glucosylation of endogenous HIFs.