Pub Date : 2026-02-05DOI: 10.1038/s41477-026-02224-9
Pengfei Lu, Jintong Liu, Haijia Yu, Jiejie Li
Stomatal immunity is a critical first barrier in plant defence, yet the organelle-level mechanisms underpinning this process remain poorly understood. Here we show that the outer mitochondrial membrane protein MIRO1 is essential for flg22-triggered stomatal closure in Arabidopsis. Upon immune activation, MIRO1 promotes mitochondrial fusion in guard cells. This mitochondrial remodelling is necessary to maintain mitochondrial function, including membrane potential, ATP synthesis, mitochondrial reactive oxygen species production and the activation of organic acid metabolism. In miro1 mutants, these mitochondrial functions are compromised, which is associated with defective stomatal closure and increased bacterial entry. We further show that flg22 triggers MPK3/6-dependent phosphorylation of MIRO1 at Ser14. Phosphorylated MIRO1 displays enhanced oligomerization at mitochondrial contact sites to facilitate fusion. Mutations disrupting MIRO1 phosphorylation or oligomerization abolish its immune function. Collectively, our findings establish MIRO1 as a key molecular link between immune signalling and mitochondrial dynamics during stomatal defence regulation.
{"title":"MIRO1-mediated mitochondrial fusion is required for stomatal immunity in Arabidopsis.","authors":"Pengfei Lu, Jintong Liu, Haijia Yu, Jiejie Li","doi":"10.1038/s41477-026-02224-9","DOIUrl":"https://doi.org/10.1038/s41477-026-02224-9","url":null,"abstract":"<p><p>Stomatal immunity is a critical first barrier in plant defence, yet the organelle-level mechanisms underpinning this process remain poorly understood. Here we show that the outer mitochondrial membrane protein MIRO1 is essential for flg22-triggered stomatal closure in Arabidopsis. Upon immune activation, MIRO1 promotes mitochondrial fusion in guard cells. This mitochondrial remodelling is necessary to maintain mitochondrial function, including membrane potential, ATP synthesis, mitochondrial reactive oxygen species production and the activation of organic acid metabolism. In miro1 mutants, these mitochondrial functions are compromised, which is associated with defective stomatal closure and increased bacterial entry. We further show that flg22 triggers MPK3/6-dependent phosphorylation of MIRO1 at Ser14. Phosphorylated MIRO1 displays enhanced oligomerization at mitochondrial contact sites to facilitate fusion. Mutations disrupting MIRO1 phosphorylation or oligomerization abolish its immune function. Collectively, our findings establish MIRO1 as a key molecular link between immune signalling and mitochondrial dynamics during stomatal defence regulation.</p>","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146125885","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-04DOI: 10.1038/s41477-026-02228-5
Jingkun Zhang, Hong Yu
{"title":"Novel crop rotation via de novo pennycress domestication","authors":"Jingkun Zhang, Hong Yu","doi":"10.1038/s41477-026-02228-5","DOIUrl":"https://doi.org/10.1038/s41477-026-02228-5","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"91 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2026-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146115657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-03DOI: 10.1038/s41477-025-02213-4
{"title":"Fast-growing alien trees surge as slow native species decline worldwide.","authors":"","doi":"10.1038/s41477-025-02213-4","DOIUrl":"https://doi.org/10.1038/s41477-025-02213-4","url":null,"abstract":"","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146113641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-03DOI: 10.1038/s41477-025-02210-7
Nannan Li, Guoliang Li, Xiaofang Huang, Lige Ma, Danning Wang, Yu Luo, Xulv Cao, Yantao Zhu, Jianxin Mu, Ran An, Jianhua Zhao, Yongfeng Wang, Cuiling Yang, Hao Chen, Ying Xu, Lixi Jiang, Meng Luo, Xiaodan Li, Yachen Dong, Xinping Chen, Frank Hochholdinger, Yong Jiang, Jochen C. Reif, Daojie Wang, Yanfeng Zhang, Yang Bai, Peng Yu
The rhizosphere microbiome plays a crucial role in determining plant performance and fitness. Nevertheless, regulatory mechanisms linking host genetic variation, root gene regulation and microbiome assembly—and their collective influence on plant nutritional traits—remain poorly understood. Here we generated and integrated 1,341 paired datasets, including root transcriptomes, rhizosphere bacterial 16S rRNA profiles and root ionomes, across 175 resequenced Brassica napus ecotypes grown at two contrasting field sites. We identified 203 highly heritable bacterial amplicon sequence variants (ASVs), many of which were significantly associated with root nitrogen (N) levels. Host transcriptome-wide gene expression and these microbial features together explained up to 45% of natural variation in N uptake while genome-wide association analyses revealed host loci regulating ASV abundance, many of which were under the control of eQTL hotspots linked to carbon and N metabolism. Isolate-level inoculation, whole-genome sequencing, metabolite profiling and confocal imaging demonstrated that the dominant, genetically regulated bacterial genus Sphingopyxis modulates auxin biosynthesis and promotes lateral root development to enhance N acquisition under stress. This study therefore identifies Sphingopyxis as a functionally relevant taxon with potential for microbiome-assisted breeding of nutrient-efficient crops.
{"title":"Large-scale multi-omics unveils host–microbiome interactions driving root development and nitrogen acquisition","authors":"Nannan Li, Guoliang Li, Xiaofang Huang, Lige Ma, Danning Wang, Yu Luo, Xulv Cao, Yantao Zhu, Jianxin Mu, Ran An, Jianhua Zhao, Yongfeng Wang, Cuiling Yang, Hao Chen, Ying Xu, Lixi Jiang, Meng Luo, Xiaodan Li, Yachen Dong, Xinping Chen, Frank Hochholdinger, Yong Jiang, Jochen C. Reif, Daojie Wang, Yanfeng Zhang, Yang Bai, Peng Yu","doi":"10.1038/s41477-025-02210-7","DOIUrl":"https://doi.org/10.1038/s41477-025-02210-7","url":null,"abstract":"The rhizosphere microbiome plays a crucial role in determining plant performance and fitness. Nevertheless, regulatory mechanisms linking host genetic variation, root gene regulation and microbiome assembly—and their collective influence on plant nutritional traits—remain poorly understood. Here we generated and integrated 1,341 paired datasets, including root transcriptomes, rhizosphere bacterial 16S rRNA profiles and root ionomes, across 175 resequenced Brassica napus ecotypes grown at two contrasting field sites. We identified 203 highly heritable bacterial amplicon sequence variants (ASVs), many of which were significantly associated with root nitrogen (N) levels. Host transcriptome-wide gene expression and these microbial features together explained up to 45% of natural variation in N uptake while genome-wide association analyses revealed host loci regulating ASV abundance, many of which were under the control of eQTL hotspots linked to carbon and N metabolism. Isolate-level inoculation, whole-genome sequencing, metabolite profiling and confocal imaging demonstrated that the dominant, genetically regulated bacterial genus Sphingopyxis modulates auxin biosynthesis and promotes lateral root development to enhance N acquisition under stress. This study therefore identifies Sphingopyxis as a functionally relevant taxon with potential for microbiome-assisted breeding of nutrient-efficient crops.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"29 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146102111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-02DOI: 10.1038/s41477-026-02221-y
Hao Liu, Jinquan Li, Jihua Wu, Bo Li, Ming Nie
Wetlands, among Earth’s most carbon-dense ecosystems, are vital for climate change mitigation. While plant diversity has been widely shown to increase soil carbon storage in terrestrial ecosystems, its influence in natural wetlands remains unclear. Here, using data from 1,268 natural wetlands surveyed in the US National Wetland Condition Assessment (NWCA), we examined how trait-based plant diversity (functional diversity) and composition (functional identity) affect soil carbon storage. We show that functional diversity had a minimal effect on carbon stocks, and its influence was weakened by elevated soil nutrient availability and non-native plant stress. In contrast, soil carbon storage was generally greater in wetlands dominated by larger, slow-growing and highly hydrophytic plants. Moreover, the benefits of functional identity were contingent on higher water levels and lower human disturbance. These findings suggest that the conservation and restoration of wetlands dominated by large, conservative and hydrophytic species under hydric conditions could help achieve climate change mitigation goals.
{"title":"Large slow-growing hydrophytes increase wetland carbon storage","authors":"Hao Liu, Jinquan Li, Jihua Wu, Bo Li, Ming Nie","doi":"10.1038/s41477-026-02221-y","DOIUrl":"https://doi.org/10.1038/s41477-026-02221-y","url":null,"abstract":"Wetlands, among Earth’s most carbon-dense ecosystems, are vital for climate change mitigation. While plant diversity has been widely shown to increase soil carbon storage in terrestrial ecosystems, its influence in natural wetlands remains unclear. Here, using data from 1,268 natural wetlands surveyed in the US National Wetland Condition Assessment (NWCA), we examined how trait-based plant diversity (functional diversity) and composition (functional identity) affect soil carbon storage. We show that functional diversity had a minimal effect on carbon stocks, and its influence was weakened by elevated soil nutrient availability and non-native plant stress. In contrast, soil carbon storage was generally greater in wetlands dominated by larger, slow-growing and highly hydrophytic plants. Moreover, the benefits of functional identity were contingent on higher water levels and lower human disturbance. These findings suggest that the conservation and restoration of wetlands dominated by large, conservative and hydrophytic species under hydric conditions could help achieve climate change mitigation goals.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"31 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146102112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Amino acids are plant-available organic nitrogen (N) that can be directly absorbed, but their availability relies on microbial decomposition of organic matter in the soil. Natural variation in Lysine-Histidine-Type Transporter-1 (OsLHT1) (NCBI Gene ID: 3974662 ) is associated with higher amino acid uptake in japonica rice than in indica. However, how this genetic variation influences rhizosphere microbiome assembly and its subsequent impact on amino acid acquisition remains unclear. In this study, we demonstrate that the OsLHT1a allele in japonica is prevalent in rice grown in high-organic-N soils, where it recruits a distinct rhizosphere microbiome to enhance amino acid acquisition. A synthetic microbiota composed of bacteria enriched by the OsLHT1a allele in japonica enhanced amino acid production in soil through organic matter decomposition and increased root amino acid uptake by upregulating OsLHT1 gene expression. The rhizosphere colonization of the synthetic microbiota was specifically driven by the function of OsLHT1. Notably, organic fertilization facilitated this colonization, thereby improving organic N use efficiency and rice yield. This root-rhizosphere microbiome functional synergy under organic fertilization presents a promising strategy to increase organic fertilizer use efficiency and demonstrates the potential for harnessing plant-gene-associated rhizosphere microbiomes for sustainable agriculture.
{"title":"Amino-acid-transporter-mediated assembly of rhizosphere microbiota enhances soil organic nitrogen acquisition in rice.","authors":"Aiyuan Ma,Weibing Xun,Shunan Zhang,Shuxin Liang,Wei Wei,Han Huang,Qirong Shen,Guohua Xu,Ruifu Zhang","doi":"10.1038/s41477-025-02217-0","DOIUrl":"https://doi.org/10.1038/s41477-025-02217-0","url":null,"abstract":"Amino acids are plant-available organic nitrogen (N) that can be directly absorbed, but their availability relies on microbial decomposition of organic matter in the soil. Natural variation in Lysine-Histidine-Type Transporter-1 (OsLHT1) (NCBI Gene ID: 3974662 ) is associated with higher amino acid uptake in japonica rice than in indica. However, how this genetic variation influences rhizosphere microbiome assembly and its subsequent impact on amino acid acquisition remains unclear. In this study, we demonstrate that the OsLHT1a allele in japonica is prevalent in rice grown in high-organic-N soils, where it recruits a distinct rhizosphere microbiome to enhance amino acid acquisition. A synthetic microbiota composed of bacteria enriched by the OsLHT1a allele in japonica enhanced amino acid production in soil through organic matter decomposition and increased root amino acid uptake by upregulating OsLHT1 gene expression. The rhizosphere colonization of the synthetic microbiota was specifically driven by the function of OsLHT1. Notably, organic fertilization facilitated this colonization, thereby improving organic N use efficiency and rice yield. This root-rhizosphere microbiome functional synergy under organic fertilization presents a promising strategy to increase organic fertilizer use efficiency and demonstrates the potential for harnessing plant-gene-associated rhizosphere microbiomes for sustainable agriculture.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"4 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2026-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146088943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
How somatic cells acquire totipotency and subsequently develop into a whole plant (plantlet) remains a mystery in plant biology. Here we used three Kalanchoe species to address this fundamental question. By assembling high-quality chromosome-level reference genomes and conducting comparative genomic analyses, we reveal hidden signatures of gene expansion, contraction and loss during the evolution of Kalanchoe species and elucidate conserved temporal gene expression signatures and epigenetic states during plantlet formation. Remarkably, we uncover three innovations contributing to the plantlet formation in Kalanchoe. Specifically, our results suggest that the loss of the F-box gene LCR is a prerequisite for plantlet formation. Both gene duplication and increased chromatin accessibility of pluripotency-associated genes further create conditions that enhance the potential of plantlet formation. The previously uncharacterized gene KdLBD19 could be leveraged to improve crop transformation efficiency. Overall, this study reveals the genetic basis underlying the acquisition of totipotency and plantlet formation in Kalanchoe.
{"title":"Unravelling the predominant genetic paths for asexual reproduction in Kalanchoe.","authors":"Xiang-Ru Meng,Qian-Qian Wang,Shang-Li Zhu,Jia-Li Wang,Chen-Ze Qi,Jiao Yu,Yu Zhang,Zhou-Geng Xu,Yan-Xia Mai,Zhong-Yuan Chang,Ying-Juan Cheng,Jia-Yu Xue,Ye Liu,Tian-Qi Zhang","doi":"10.1038/s41477-025-02214-3","DOIUrl":"https://doi.org/10.1038/s41477-025-02214-3","url":null,"abstract":"How somatic cells acquire totipotency and subsequently develop into a whole plant (plantlet) remains a mystery in plant biology. Here we used three Kalanchoe species to address this fundamental question. By assembling high-quality chromosome-level reference genomes and conducting comparative genomic analyses, we reveal hidden signatures of gene expansion, contraction and loss during the evolution of Kalanchoe species and elucidate conserved temporal gene expression signatures and epigenetic states during plantlet formation. Remarkably, we uncover three innovations contributing to the plantlet formation in Kalanchoe. Specifically, our results suggest that the loss of the F-box gene LCR is a prerequisite for plantlet formation. Both gene duplication and increased chromatin accessibility of pluripotency-associated genes further create conditions that enhance the potential of plantlet formation. The previously uncharacterized gene KdLBD19 could be leveraged to improve crop transformation efficiency. Overall, this study reveals the genetic basis underlying the acquisition of totipotency and plantlet formation in Kalanchoe.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":"5 1","pages":""},"PeriodicalIF":18.0,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146073016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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