Na Wang, Meiyu Wang, Xuanzhu Zhao, Jie Xu, Ruijie Chen, Zhirui Ji, Junxiang Zhang
Data availability
All data are available in the main text or Dataset S1, Figs S1–S13, and Tables S1–S3).
数据可用性所有数据均可在正文或数据集S1、图S1 - s13和表S1 - s3中获得。
{"title":"A Colletotrichum gloeosporioides effector Vne1 targets the transcription factor MdAHL17 to subvert MdCNL1-mediated plant immunity in apple","authors":"Na Wang, Meiyu Wang, Xuanzhu Zhao, Jie Xu, Ruijie Chen, Zhirui Ji, Junxiang Zhang","doi":"10.1111/nph.70931","DOIUrl":"https://doi.org/10.1111/nph.70931","url":null,"abstract":"<h2>Data availability</h2>\u0000<p>All data are available in the main text or Dataset S1, Figs S1–S13, and Tables S1–S3).</p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"39 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146001548","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}
Axel Beringue, Lucie Castel, Cécile Monard, Fabrice Martin‐Laurent, Jérémie Béguet, Marion Devers‐Lamrani, Nathalie Le Bris, Frédérique Pallois, Valérie Gouesbet, Stéphanie Llopis, Cécile Sulmon, Cécile Le Lann
Summary Agriculture intensification, massively relying on pesticides, led to the widespread contamination of noncrop terrestrial ecosystems. Soil contamination with pesticide residues widely occurs but its cryptic effects on terrestrial biotic interactions remain unclear, especially at the metabolic scale. We studied the effects of an environmental dose of the herbicide isoproturon on an isoproturon‐degrading Sphingomonas soil bacteria – Lolium perenne (Poaceae) and Rhopalosiphum padi (Hemiptera: aphididae) system – in the laboratory. This system is typical of contaminated peri‐agricultural ecosystems, such as vegetated buffer strips. We found that isoproturon and its main degradation product transferred from the substrate to aphids, accumulating in plant shoots. No macroscopic effects of the herbicide were observed, but primary metabolites varied in both plants and herbivores. Inoculation of isoproturon‐degrading bacteria reduced isoproturon levels in the substrate and suppressed most metabolic variations. Moreover, inoculation of the non‐degrading bacterial strain impacted plant metabolism, potentially through mutualistic interaction, underlining the close link between soil microbiota and aboveground organisms. This study shows that isoproturon residues can transfer in a typical grassland trophic system, altering the metabolism of each biological level. It emphasizes the need to consider above‐ and belowground interactions when assessing seminatural ecosystems' responses to chronic contamination.
{"title":"Herbicide‐induced metabolic changes in a plant–aphid system: how soil bacteria drive the fate and impact of a residual dose of Isoproturon?","authors":"Axel Beringue, Lucie Castel, Cécile Monard, Fabrice Martin‐Laurent, Jérémie Béguet, Marion Devers‐Lamrani, Nathalie Le Bris, Frédérique Pallois, Valérie Gouesbet, Stéphanie Llopis, Cécile Sulmon, Cécile Le Lann","doi":"10.1111/nph.70891","DOIUrl":"https://doi.org/10.1111/nph.70891","url":null,"abstract":"Summary <jats:list list-type=\"bullet\"> <jats:list-item> Agriculture intensification, massively relying on pesticides, led to the widespread contamination of noncrop terrestrial ecosystems. Soil contamination with pesticide residues widely occurs but its cryptic effects on terrestrial biotic interactions remain unclear, especially at the metabolic scale. </jats:list-item> <jats:list-item> We studied the effects of an environmental dose of the herbicide isoproturon on an isoproturon‐degrading <jats:italic>Sphingomonas</jats:italic> soil bacteria – <jats:italic>Lolium perenne</jats:italic> (Poaceae) and <jats:italic>Rhopalosiphum padi</jats:italic> (Hemiptera: aphididae) system – in the laboratory. This system is typical of contaminated peri‐agricultural ecosystems, such as vegetated buffer strips. </jats:list-item> <jats:list-item> We found that isoproturon and its main degradation product transferred from the substrate to aphids, accumulating in plant shoots. No macroscopic effects of the herbicide were observed, but primary metabolites varied in both plants and herbivores. Inoculation of isoproturon‐degrading bacteria reduced isoproturon levels in the substrate and suppressed most metabolic variations. Moreover, inoculation of the non‐degrading bacterial strain impacted plant metabolism, potentially through mutualistic interaction, underlining the close link between soil microbiota and aboveground organisms. </jats:list-item> <jats:list-item> This study shows that isoproturon residues can transfer in a typical grassland trophic system, altering the metabolism of each biological level. It emphasizes the need to consider above‐ and belowground interactions when assessing seminatural ecosystems' responses to chronic contamination. </jats:list-item> </jats:list>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"30 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145986489","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}
Fabian Jörg Fischer, Jérôme Chave, Amy Zanne, Tommaso Jucker, Alex Fajardo, Adeline Fayolle, Renato Augusto Ferreira de Lima, Ghislain Vieilledent, Hans Beeckman, Wannes Hubau, Tom De Mil, Daniel Wallenus, Ana María Aldana, Esteban Alvarez‐Dávila, Luciana F. Alves, Deborah M. G. Apgaua, Fátima Arcanjo, Jean‐François Bastin, Andrii Bilous, Philippe Birnbaum, Volodymyr Blyshchyk, Joli Borah, Vanessa Boukili, J. Julio Camarero, Luisa Casas, Roberto Cazzolla Gatti, Jeffrey Q. Chambers, Ezequiel Chimbioputo Fabiano, Brendan Choat, Georgina Conti, Will Cornwell, Javid Ahmad Dar, Ashesh Kumar Das, Magnus Dobler, Dao Dougabka, David P. Edwards, Robert Evans, Daniel Falster, Philip Fearnside, Olivier Flores, Nikolaos Fyllas, Jean Gérard, Rosa C. Goodman, Daniel Guibal, L. Francisco Henao‐Diaz, Vincent Hervé, Peter Hietz, Jürgen Homeier, Thomas Ibanez, Jugo Ilic, Steven Jansen, Rinku Moni Kalita, Tanaka Kenzo, Liana Kindermann, Subashree Kothandaraman, Martyna Kotowska, Yasuhiro Kubota, Patrick Langbour, James Lawson, André Luiz Alves de Lima, Roman Mathias Link, Anja Linstädter, Rosana López, Cate Macinnis‐Ng, Luiz Fernando S. Magnago, Adam R. Martin, Ashley M. Matheny, James K. McCarthy, Regis B. Miller, Arun Jyoti Nath, Bruce Walker Nelson, Marco Njana, Euler Melo Nogueira, Alexandre Oliveira, Rafael Oliveira, Mark Olson, Yusuke Onoda, Keryn Paul, Daniel Piotto, Phil Radtke, Onja Razafindratsima, Tahiana Ramananantoandro, Jennifer Read, Sarah Richardson, Enrique G. de la Riva, Oris Rodríguez‐Reyes, Samir G. Rolim, Victor Rolo, Julieta A. Rosell, Roberto Salguero‐Gómez, Nadia S. Santini, Bernhard Schuldt, Luitgard Schwendenmann, Arne Sellin, Timothy Staples, Pablo R. Stevenson, Somaiah Sundarapandian, Masha T. van der Sande, Bernard Thibaut, David Yue Phin Tng, José Marcelo Domingues Torezan, Boris Villanueva, Aaron Weiskittel, Jessie Wells, S. Joseph Wright, Kasia Zieminska
Summary Wood density is central for estimating vegetation carbon storage and a plant functional trait of great ecological and evolutionary importance. However, the global extent of wood density variation is unclear, especially at the intraspecific level. We assembled the most comprehensive wood density collection to date, including 109 626 records from 16 829 plant species across woody life forms and biomes (GWDD v.2, available here: doi: 10.5281/zenodo.16919509 ). Using the GWDD v.2, we explored the sources of wood density variation within individuals, within species and across environmental gradients. Intraspecific variation accounted for c . 15% of overall wood density variation (SD = 0.068 g cm −3 ). Variance was 50% smaller in sapwood than heartwood, and 30% smaller in branchwood than trunkwood. Individuals in extreme environments (dry, hot and acidic soils) had higher wood density than conspecifics elsewhere (+0.02 g cm −3 , c . 4% of the mean). Intraspecific environmental effects strongly tracked interspecific patterns ( r = 0.83) but were 70–80% smaller and varied considerably among taxa. Individual plant wood density was difficult to predict (root mean square error > 0.08 g cm −3 ; single‐measurement R2 = 0.59). We recommend (1) systematic sampling of multiple individuals and tissues for local applications, and (2) expanded taxonomic coverage combined with integrative models for robust estimates across ecological scales.
木材密度是估算植被碳储量的核心，也是具有重要生态和进化意义的植物功能性状。然而，木材密度变化的全球程度尚不清楚，特别是在种内水平上。我们收集了迄今为止最全面的木材密度数据，包括来自16 829种木本生物形式和生物群落的植物物种的109 626条记录（GWDD v.2），可在这里获得：doi: 10.5281/zenodo。16919509)。使用GWDD v.2，我们探索了个体内、物种内和跨环境梯度的木材密度变化的来源。种内变异占c。木材总密度变化的15% （SD = 0.068 g cm−3）。边材的方差比心材小50%，枝材的方差比干材小30%。极端环境（干燥、炎热和酸性土壤）的个体木材密度高于其他地方的同种个体（+0.02 g cm - 3, c）。平均值的4%)。种内环境效应与种间模式密切相关（r = 0.83），但在不同分类群间差异较大，且较小。单株木材密度难以预测（均方根误差>； 0.08 g cm - 3；单次测量r2 = 0.59）。我们建议：(1)在局部应用中对多个个体和组织进行系统采样；(2)结合综合模型扩大分类学覆盖范围，以便在整个生态尺度上进行可靠的估计。
{"title":"Beyond species means – the intraspecific contribution to global wood density variation","authors":"Fabian Jörg Fischer, Jérôme Chave, Amy Zanne, Tommaso Jucker, Alex Fajardo, Adeline Fayolle, Renato Augusto Ferreira de Lima, Ghislain Vieilledent, Hans Beeckman, Wannes Hubau, Tom De Mil, Daniel Wallenus, Ana María Aldana, Esteban Alvarez‐Dávila, Luciana F. Alves, Deborah M. G. Apgaua, Fátima Arcanjo, Jean‐François Bastin, Andrii Bilous, Philippe Birnbaum, Volodymyr Blyshchyk, Joli Borah, Vanessa Boukili, J. Julio Camarero, Luisa Casas, Roberto Cazzolla Gatti, Jeffrey Q. Chambers, Ezequiel Chimbioputo Fabiano, Brendan Choat, Georgina Conti, Will Cornwell, Javid Ahmad Dar, Ashesh Kumar Das, Magnus Dobler, Dao Dougabka, David P. Edwards, Robert Evans, Daniel Falster, Philip Fearnside, Olivier Flores, Nikolaos Fyllas, Jean Gérard, Rosa C. Goodman, Daniel Guibal, L. Francisco Henao‐Diaz, Vincent Hervé, Peter Hietz, Jürgen Homeier, Thomas Ibanez, Jugo Ilic, Steven Jansen, Rinku Moni Kalita, Tanaka Kenzo, Liana Kindermann, Subashree Kothandaraman, Martyna Kotowska, Yasuhiro Kubota, Patrick Langbour, James Lawson, André Luiz Alves de Lima, Roman Mathias Link, Anja Linstädter, Rosana López, Cate Macinnis‐Ng, Luiz Fernando S. Magnago, Adam R. Martin, Ashley M. Matheny, James K. McCarthy, Regis B. Miller, Arun Jyoti Nath, Bruce Walker Nelson, Marco Njana, Euler Melo Nogueira, Alexandre Oliveira, Rafael Oliveira, Mark Olson, Yusuke Onoda, Keryn Paul, Daniel Piotto, Phil Radtke, Onja Razafindratsima, Tahiana Ramananantoandro, Jennifer Read, Sarah Richardson, Enrique G. de la Riva, Oris Rodríguez‐Reyes, Samir G. Rolim, Victor Rolo, Julieta A. Rosell, Roberto Salguero‐Gómez, Nadia S. Santini, Bernhard Schuldt, Luitgard Schwendenmann, Arne Sellin, Timothy Staples, Pablo R. Stevenson, Somaiah Sundarapandian, Masha T. van der Sande, Bernard Thibaut, David Yue Phin Tng, José Marcelo Domingues Torezan, Boris Villanueva, Aaron Weiskittel, Jessie Wells, S. Joseph Wright, Kasia Zieminska","doi":"10.1111/nph.70860","DOIUrl":"https://doi.org/10.1111/nph.70860","url":null,"abstract":"Summary Wood density is central for estimating vegetation carbon storage and a plant functional trait of great ecological and evolutionary importance. However, the global extent of wood density variation is unclear, especially at the intraspecific level. We assembled the most comprehensive wood density collection to date, including 109 626 records from 16 829 plant species across woody life forms and biomes (GWDD v.2, available here: doi: <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"https://doi.org/10.5281/zenodo.16919509\">10.5281/zenodo.16919509</jats:ext-link> ). Using the GWDD v.2, we explored the sources of wood density variation within individuals, within species and across environmental gradients. Intraspecific variation accounted for <jats:italic>c</jats:italic> . 15% of overall wood density variation (SD = 0.068 g cm <jats:sup>−3</jats:sup> ). Variance was 50% smaller in sapwood than heartwood, and 30% smaller in branchwood than trunkwood. Individuals in extreme environments (dry, hot and acidic soils) had higher wood density than conspecifics elsewhere (+0.02 g cm <jats:sup>−3</jats:sup> , <jats:italic>c</jats:italic> . 4% of the mean). Intraspecific environmental effects strongly tracked interspecific patterns ( <jats:italic>r</jats:italic> = 0.83) but were 70–80% smaller and varied considerably among taxa. Individual plant wood density was difficult to predict (root mean square error > 0.08 g cm <jats:sup>−3</jats:sup> ; single‐measurement <jats:italic>R</jats:italic> <jats:sup>2</jats:sup> = 0.59). We recommend (1) systematic sampling of multiple individuals and tissues for local applications, and (2) expanded taxonomic coverage combined with integrative models for robust estimates across ecological scales.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"20 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145986436","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}
Xiaobin Pan,Yann Hautier,Jan Lepš,Shaopeng Wang,Kathryn E Barry,Manuele Bazzichetto,Stefano Chelli,Jiří Doležal,Nico Eisenhauer,Franz Essl,Felícia M Fischer,Oscar Godoy,Daniel Gómez-García,Lars Götzenberger,Clara Gracia,Anaclara Guido,Lauren M Hallett,Susan Harrison,Miao He,Andrew Hector,Pubin Hong,Forest Isbell,George A Kowalchuk,Victor Lecegui,Xiaofei Li,Maowei Liang,Frédérique Louault,Maria Májeková,Rob Marrs,Neha Mohanbabu,Akira S Mori,Robin J Pakeman,Alain Paquette,Begoña Peco,Josep Peñuelas,Valério D Pillar,Marta Rueda,Wolfgang Schmidt,Jules Segrestin,Marta Gaia Sperandii,Enrique Valencia,Vigdis Vandvik,Shengnan Wang,David Ward,Susan Wiser,Ben A Woodcock,Chong Xu,Truman Young,Fei-Hai Yu,Liting Zheng,Zhiwei Zhong,Francesco de Bello
Maintaining ecological stability is essential for sustaining ecosystem functions and the benefits they provide to society. Ecological theory predicts that plant diversity destabilizes local populations, yet empirical studies report variable effects. We hypothesize that this discrepancy arises at least in part from differences captured by different diversity (average vs cumulative richness, i.e. the mean annual richness vs the cumulative richness across years) and stability metrics (abundance-unweighted vs weighted mean population stability). To test this, we analyzed data from > 8000 permanent vegetation plots across biomes on five continents. We found a negative (i.e. destabilizing) diversity-stability relationship when using abundance-weighted rather than unweighted measures of population stability, which are more influenced by dominant species. Similarly, cumulative richness - capturing total species occurrence over time and long-term turnover - reveals a stronger destabilizing effect compared to average annual richness. Our findings reveal that, when specific metrics of diversity and stability are considered, more species and potentially the associated increase in interspecific competition tend to destabilize populations across natural ecosystems world-wide - particularly those of dominant species.
{"title":"Reconciling links between diversity and population stability across global plant communities.","authors":"Xiaobin Pan,Yann Hautier,Jan Lepš,Shaopeng Wang,Kathryn E Barry,Manuele Bazzichetto,Stefano Chelli,Jiří Doležal,Nico Eisenhauer,Franz Essl,Felícia M Fischer,Oscar Godoy,Daniel Gómez-García,Lars Götzenberger,Clara Gracia,Anaclara Guido,Lauren M Hallett,Susan Harrison,Miao He,Andrew Hector,Pubin Hong,Forest Isbell,George A Kowalchuk,Victor Lecegui,Xiaofei Li,Maowei Liang,Frédérique Louault,Maria Májeková,Rob Marrs,Neha Mohanbabu,Akira S Mori,Robin J Pakeman,Alain Paquette,Begoña Peco,Josep Peñuelas,Valério D Pillar,Marta Rueda,Wolfgang Schmidt,Jules Segrestin,Marta Gaia Sperandii,Enrique Valencia,Vigdis Vandvik,Shengnan Wang,David Ward,Susan Wiser,Ben A Woodcock,Chong Xu,Truman Young,Fei-Hai Yu,Liting Zheng,Zhiwei Zhong,Francesco de Bello","doi":"10.1111/nph.70921","DOIUrl":"https://doi.org/10.1111/nph.70921","url":null,"abstract":"Maintaining ecological stability is essential for sustaining ecosystem functions and the benefits they provide to society. Ecological theory predicts that plant diversity destabilizes local populations, yet empirical studies report variable effects. We hypothesize that this discrepancy arises at least in part from differences captured by different diversity (average vs cumulative richness, i.e. the mean annual richness vs the cumulative richness across years) and stability metrics (abundance-unweighted vs weighted mean population stability). To test this, we analyzed data from > 8000 permanent vegetation plots across biomes on five continents. We found a negative (i.e. destabilizing) diversity-stability relationship when using abundance-weighted rather than unweighted measures of population stability, which are more influenced by dominant species. Similarly, cumulative richness - capturing total species occurrence over time and long-term turnover - reveals a stronger destabilizing effect compared to average annual richness. Our findings reveal that, when specific metrics of diversity and stability are considered, more species and potentially the associated increase in interspecific competition tend to destabilize populations across natural ecosystems world-wide - particularly those of dominant species.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"5 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145986355","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}
Isaac Ahanamungu Makelele, Kris Verheyen, Pascal Boeckx, Viktor Van de Velde, Landry Cizungu Ntaboba, Basile Mujinya Bazirake, Faustin Boyemba Bosela, Fabrice Kimbesa, Jonathan Bachiseze Magala, Joseph Lokana Mande, Dries Landuyt, Corneille Ewango, Marijn Bauters
Summary Carbon (C) uptake in regrowing secondary forests increasingly dominates landscape‐scale C dynamics in the tropics. Understanding the recovery trajectories of net primary productivity (NPP) and C allocation, along with the underlying demographic and functional drivers of biomass recovery, is therefore critical. Using a space‐for‐time setup spanning five successional stages, we showed that – for forests in the Yoko reserve, in central Africa – C fluxes related to recruitment and mortality decreased along succession, alongside a gradual transition from a forest with high stem density and acquisitive species to one with lower stem density and more conservative species. In the first decade of succession, NPP allocation shifted from being dominated by woody productivity to canopy productivity. Higher tree mortality in early succession counterbalanced the higher woody NPP, producing a relatively constant net woody C sink along succession. While being positive, this woody C sink was small, suggesting a slow but steady recovery to old‐growth aboveground C stocks ranging between 171 and 238 Mg C ha −1 . Overall, our findings demonstrate the potential of secondary forests in the Congo basin to mitigate climate change, but also emphasize the need to conserve old‐growth forest C stocks and expand long‐term observational data to better constrain regional C recovery dynamics.
热带地区再生次生林的碳(C)吸收日益主导着景观尺度的碳动态。因此，了解净初级生产力（NPP）和碳分配的恢复轨迹，以及生物量恢复的潜在人口和功能驱动因素至关重要。利用跨越5个演替阶段的时空设置，我们发现——对于非洲中部Yoko保护区的森林——与补充和死亡相关的碳通量随着演替而减少，同时从高茎密度和获取物种的森林逐渐过渡到低茎密度和更保守物种的森林。在演替的前10年，NPP的分配由以木本生产力为主转向以冠层生产力为主。演替早期较高的树木死亡率抵消了较高的木本NPP，在演替过程中产生相对稳定的净木本碳汇。虽然是正的，但这个木质碳汇很小，表明地表上的碳储量缓慢而稳定地恢复到171 - 238 Mg C ha - 1之间。总体而言，我们的研究结果证明了刚果盆地次生林在减缓气候变化方面的潜力，但也强调了保护原生林碳储量和扩大长期观测数据以更好地约束区域碳恢复动态的必要性。
{"title":"Net primary productivity and carbon allocation along secondary succession in a central African tropical forest","authors":"Isaac Ahanamungu Makelele, Kris Verheyen, Pascal Boeckx, Viktor Van de Velde, Landry Cizungu Ntaboba, Basile Mujinya Bazirake, Faustin Boyemba Bosela, Fabrice Kimbesa, Jonathan Bachiseze Magala, Joseph Lokana Mande, Dries Landuyt, Corneille Ewango, Marijn Bauters","doi":"10.1111/nph.70888","DOIUrl":"https://doi.org/10.1111/nph.70888","url":null,"abstract":"Summary <jats:list list-type=\"bullet\"> <jats:list-item> Carbon (C) uptake in regrowing secondary forests increasingly dominates landscape‐scale C dynamics in the tropics. Understanding the recovery trajectories of net primary productivity (NPP) and C allocation, along with the underlying demographic and functional drivers of biomass recovery, is therefore critical. </jats:list-item> <jats:list-item> Using a space‐for‐time setup spanning five successional stages, we showed that – for forests in the Yoko reserve, in central Africa – C fluxes related to recruitment and mortality decreased along succession, alongside a gradual transition from a forest with high stem density and acquisitive species to one with lower stem density and more conservative species. </jats:list-item> <jats:list-item> In the first decade of succession, NPP allocation shifted from being dominated by woody productivity to canopy productivity. Higher tree mortality in early succession counterbalanced the higher woody NPP, producing a relatively constant net woody C sink along succession. While being positive, this woody C sink was small, suggesting a slow but steady recovery to old‐growth aboveground C stocks ranging between 171 and 238 Mg C ha <jats:sup>−1</jats:sup> . </jats:list-item> <jats:list-item> Overall, our findings demonstrate the potential of secondary forests in the Congo basin to mitigate climate change, but also emphasize the need to conserve old‐growth forest C stocks and expand long‐term observational data to better constrain regional C recovery dynamics. </jats:list-item> </jats:list>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"101 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145972018","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}
Anaïs Delers, Anne Bennion, Ambre Guillory, Lisa Frances, Elizaveta Krol, Fanny Bonnafous, Laurena Medioni, Javier Serrania, Rémi Peyraud, Joëlle Fournier, Fernanda de Carvalho-Niebel, Anke Becker
<h2> Introduction</h2> <p>Symbiotic relationships with soil microorganisms can help plants access the nutrients they need for growth. Certain angiosperm species in the nitrogen-fixing clade evolved the ability to obtain nitrogen through symbiosis with bacteria, which they host intracellularly in specialized organs called root nodules (Huisman & Geurts, <span>2020</span>). These interactions have been well-studied in legume plants, notably in model species such as <i>Medicago truncatula</i>, which hosts the rhizobia symbiont <i>Sinorhizobium meliloti</i>. Establishing this interaction requires precise molecular exchanges between partners (Krönauer & Radutoiu, <span>2021</span>) before bacteria can colonize their host, which occurs in most cases via a tunnel-like apoplastic compartment called the infection thread (IT) (Gage, <span>2004</span>).</p> <p>ITs initiate in root hairs and proceed through well-defined stages (reviewed in de Carvalho-Niebel <i>et al</i>., <span>2024</span>). Root hairs curl around Nod factor-producing rhizobia (Esseling <i>et al</i>., <span>2003</span>) and enclose them in a radially expanding infection chamber where they proliferate until polarized secretion creates the tip-growing IT tubular structure (Fournier <i>et al</i>., <span>2015</span>). ITs are sequentially reinitiated in successive cell layers to guide rhizobia transcellularly from root hairs to the developing nodule primordium, where they are released, endocytosed, and differentiated into N-fixing bacteroids (Yang <i>et al</i>., <span>2022</span>).</p> <p>The successful formation and progression of ITs within plant cells depends on the plant's specific perception or controlled degradation of rhizobial Nod factors or exopolysaccharide signals (Kawaharada <i>et al</i>., <span>2017</span>; Malolepszy <i>et al</i>., <span>2018</span>). The plant host also triggers a series of cellular events (reviewed in de Carvalho-Niebel <i>et al</i>., <span>2024</span>) to create the optimal IT apoplastic environment for rhizobia colonization. Inside the IT space, rhizobia progress in a sparse, single-file arrangement, slightly behind the IT tip that extends in a cytoplasmic bridge connected with the migrating nucleus (Fournier <i>et al</i>., <span>2008</span>; Guillory <i>et al</i>., <span>2024</span>). It has been proposed that rhizobia progress in the IT environment by combining cell proliferation and collective movement, though the form of motility they actually use is unknown.</p> <p>Bacteria can adopt different types of movement to translocate. These can be categorized as swimming motility in aqueous solutions or surface-associated motility in solid environments. While swimming motility depends on flagellar rotation, surface motility relies on different mechanisms, with the most prominent modes being twitching, gliding, swarming, and sliding (reviewed by Wadhwa & Berg, <span>2022</span>). Twitching is mediated by type IV pili, which extend, adhere to a surface
与土壤微生物的共生关系可以帮助植物获得生长所需的养分。固氮进化分支中的某些被子植物物种进化出了通过与细菌共生获取氮的能力，它们将细菌寄主在称为根瘤的细胞内特殊器官中（Huisman & Geurts, 2020）。这些相互作用已经在豆科植物中得到了很好的研究，特别是在模式物种如紫花苜蓿（Medicago truncatula）中，它是根瘤菌共生体Sinorhizobium meliloti的宿主。建立这种相互作用需要伙伴之间精确的分子交换（Krönauer & Radutoiu, 2021），然后细菌才能定植宿主，这在大多数情况下是通过称为感染线（IT）的隧道状外胞体隔室发生的（Gage, 2004）。ITs起源于根毛，并经过明确的阶段（de Carvalho-Niebel et al., 2024）。根毛在产生Nod因子的根瘤菌周围卷曲（Esseling et al., 2003），并将其包围在放射状扩张的感染室中，在那里它们增殖，直到极化分泌形成尖端生长的IT管状结构（Fournier et al., 2015）。ITs在连续的细胞层中依次重新启动，引导根瘤菌从根毛到发育中的根瘤原基，在那里它们被释放、内噬并分化成固定n的类细菌（Yang et al., 2022）。ITs在植物细胞内的成功形成和进展取决于植物对根瘤菌Nod因子或胞外多糖信号的特定感知或受控降解（Kawaharada et al., 2017; Malolepszy et al., 2018）。植物寄主还会触发一系列细胞事件（de Carvalho-Niebel et al., 2024），为根瘤菌定植创造最佳的IT胞外环境。在IT空间内，根瘤菌以稀疏的单纵队排列前进，稍微落后于IT尖端，延伸成与迁移核连接的细胞质桥（Fournier et al., 2008; Guillory et al., 2024）。有人提出根瘤菌在It环境中通过结合细胞增殖和集体运动来进展，尽管它们实际使用的运动形式尚不清楚。细菌可以通过不同的运动方式进行迁移。这些可以分类为在水溶液中游泳运动或在固体环境中与表面相关的运动。游泳运动依赖于鞭毛旋转，而水面运动依赖于不同的机制，最突出的模式是抽搐、滑翔、群体和滑动（Wadhwa & Berg, 2022）。抽动是由IV型菌毛介导的，它们伸展、附着在表面并收缩以拉动细胞向前（Maier & Wong, 2015; Craig et al., 2019）。滑动涉及附着在表面的黏附复合物，并在细胞的长度上移动（McBride, 2001; Kearns, 2011）。蜂群是由鞭毛驱动的集体运动，通过渗透物或表面活性剂的分泌，在表面上的薄层液体中以高细胞密度发生（Kearns, 2011; Wadhwa & Berg, 2022）。滑动是一种独立于鞭毛、毛和粘附复合物的被动运动形式，它依赖于细胞增殖施加的压力，并通过释放表面活性剂来减少摩擦（Holscher & Kovacs, 2017）。Sinorhizobium meliloti能够游泳（Gotz & Schmitt, 1987），并通过群体和滑动在表面上移动（Soto等人，2002；Nogales等人，2012），但没有正式的证据表明s.m iloti具有滑翔或抽搐运动（Zatakia等人，2014;Wadhwa & Berg, 2022），因为滑翔或产生参与抽搐运动的IVa型菌毛所必需的基因不存在于其基因组中。S. meliloti个体的游动运动是通过周围鞭毛的旋转来实现的（Gotz & Schmitt, 1987），这也有助于S. meliloti在固体表面上的集体游动（Nogales et al., 2012）。然而，S. meliloti也可以在独立于鞭毛的表面传播，这被归因于滑动（Nogales et al., 2012）。在S. meliloti中，鞭毛功能部分的组装——细丝、带有推进细丝的马达的基体，以及连接这两个部分的钩——是由三个等级调控的基因控制的，这些基因聚集在一个连续的45kb染色体区域（Sourjik et al., 1999,2000）。S. meliloti的鞭毛生物合成也受到ExpR/Sin群体感应系统的调控，该系统可以在高种群密度下下调鞭毛生物合成基因的表达（Hoang et al., 2004）。该群体感应系统还调节胞外多糖的产生（Hoang et al., 2004），包括具有共生活性的EPS II（半乳糖葡聚糖），它促进了主要由熵力驱动的不寻常的表面运动。 渗透流和损耗吸引)称为冲浪（Dilanji et al., 2014）。经常被用于在M. truncatula中进行共生研究的Sinorhizobium meliloti菌株1021和2011在expR中被破坏（Pellock等，2002）。尽管这些菌株的EPS II生物合成减少，但仍观察到表面运动，尽管依赖于铁载体根瘤菌（Rhb） 1021的生物合成（Nogales et al., 2010, 2012）。因此，Rhb1021可能作为表面活性剂促进表面运动。铁载体是包括细菌在内的许多生物分泌的高亲和力铁螯合剂（Timofeeva et al., 2022）。Rhb1021由rhbABCDEF操纵子上编码的酶合成的修饰柠檬酸盐骨架组成（Lynch et al., 2001）。在清除铁之后，铁载体在被泵回细胞之前结合外膜受体（Timofeeva等，2022）。在S. meliloti中，Rhb1021的摄取依赖于rhtA编码的外膜受体和rhtX编码的渗透酶（Lynch等，2001；Cuív等，2004）。虽然在缺乏expr的s.m iloti菌株中，Rhb1021生物合成基因的突变会破坏表面运动，但当仅阻止rhta介导的铁载体摄取时，它不会受到影响，这表明Rhb1021的表面运动功能在细胞外（Nogales et al., 2010）。运动对根瘤菌与豆科寄主的共生相互作用也至关重要。鞭毛运动有助于趋化运动的根瘤菌宿主根(Caetano-Anolles et al ., 1988;心血来潮et al ., 1990;米勒et al ., 2007; Aroney et al ., 2021;康普顿,Scharf, 2021; Navarro-Gomez et al ., 2024),殖民,和对根表面(Fujishige et al ., 2006;郑et al ., 2015),以及增加竞争力结节入住率(艾姆斯,伯格曼,1981;Mellor et al ., 1987; Caetano-Anolles et al ., 1988;米勒et al ., 2007; Aroney et al ., 2021年,2024年)。此外，一项豆科根瘤菌的转座子插入测序基因研究发现，功能性鞭毛基因可提高根瘤发育后期细菌的存活和生长（Wheatley et al., 2020）。但是，到目前为止，非活动鞭毛突变体似乎没有显著影响结瘤或固氮，至少在苜蓿和三叶草中是这样（Ames & Bergm
{"title":"Rhizobial motility preference in root colonization of Medicago truncatula","authors":"Anaïs Delers, Anne Bennion, Ambre Guillory, Lisa Frances, Elizaveta Krol, Fanny Bonnafous, Laurena Medioni, Javier Serrania, Rémi Peyraud, Joëlle Fournier, Fernanda de Carvalho-Niebel, Anke Becker","doi":"10.1111/nph.70897","DOIUrl":"https://doi.org/10.1111/nph.70897","url":null,"abstract":"<h2> Introduction</h2>\u0000<p>Symbiotic relationships with soil microorganisms can help plants access the nutrients they need for growth. Certain angiosperm species in the nitrogen-fixing clade evolved the ability to obtain nitrogen through symbiosis with bacteria, which they host intracellularly in specialized organs called root nodules (Huisman & Geurts, <span>2020</span>). These interactions have been well-studied in legume plants, notably in model species such as <i>Medicago truncatula</i>, which hosts the rhizobia symbiont <i>Sinorhizobium meliloti</i>. Establishing this interaction requires precise molecular exchanges between partners (Krönauer & Radutoiu, <span>2021</span>) before bacteria can colonize their host, which occurs in most cases via a tunnel-like apoplastic compartment called the infection thread (IT) (Gage, <span>2004</span>).</p>\u0000<p>ITs initiate in root hairs and proceed through well-defined stages (reviewed in de Carvalho-Niebel <i>et al</i>., <span>2024</span>). Root hairs curl around Nod factor-producing rhizobia (Esseling <i>et al</i>., <span>2003</span>) and enclose them in a radially expanding infection chamber where they proliferate until polarized secretion creates the tip-growing IT tubular structure (Fournier <i>et al</i>., <span>2015</span>). ITs are sequentially reinitiated in successive cell layers to guide rhizobia transcellularly from root hairs to the developing nodule primordium, where they are released, endocytosed, and differentiated into N-fixing bacteroids (Yang <i>et al</i>., <span>2022</span>).</p>\u0000<p>The successful formation and progression of ITs within plant cells depends on the plant's specific perception or controlled degradation of rhizobial Nod factors or exopolysaccharide signals (Kawaharada <i>et al</i>., <span>2017</span>; Malolepszy <i>et al</i>., <span>2018</span>). The plant host also triggers a series of cellular events (reviewed in de Carvalho-Niebel <i>et al</i>., <span>2024</span>) to create the optimal IT apoplastic environment for rhizobia colonization. Inside the IT space, rhizobia progress in a sparse, single-file arrangement, slightly behind the IT tip that extends in a cytoplasmic bridge connected with the migrating nucleus (Fournier <i>et al</i>., <span>2008</span>; Guillory <i>et al</i>., <span>2024</span>). It has been proposed that rhizobia progress in the IT environment by combining cell proliferation and collective movement, though the form of motility they actually use is unknown.</p>\u0000<p>Bacteria can adopt different types of movement to translocate. These can be categorized as swimming motility in aqueous solutions or surface-associated motility in solid environments. While swimming motility depends on flagellar rotation, surface motility relies on different mechanisms, with the most prominent modes being twitching, gliding, swarming, and sliding (reviewed by Wadhwa & Berg, <span>2022</span>). Twitching is mediated by type IV pili, which extend, adhere to a surface ","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"58 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145972017","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}
Posy E. Busby, Austen Apigo, Dagmara Sirova, Eduardo Pérez-Pazos, Kyle A. Gervers, Abigail Neat, María-José Romero-Jiménez, Leander D. L. Anderegg, Gail Taylor
Elucidating the factors controlling plant microbiome assembly is a major research goal in plant biology given a growing awareness of microbial community contributions to host plant health and fitness. While stomata have long been recognized to influence pathogen colonization, less is known about whether or how stomatal traits regulate diverse communities of nonpathogenic microbes that make up the majority of the leaf microbiome. In this Viewpoint, we propose that stomata are a primary filter by which plants influence the assembly of leaf-associated microbial communities. We discuss three nonmutually exclusive hypotheses for how stomatal traits influence leaf microbes, including preliminary support for each based on published studies of foliar fungi and bacteria. The stomatal density hypothesis argues that a greater density of pores increases the rate of microbial entry into the leaf, while the stomatal function hypothesis posits that the duration and speed of stomatal opening and closing regulate microbial access into the leaf. The stomatal covariation hypothesis recognizes that many other leaf traits covary with stomatal traits and thus could contribute to observed relationships between stomatal traits and leaf microbiome structure. Finally, we propose research priorities to improve our understanding of stomatal control over leaf microbiome assembly.
{"title":"Do stomatal traits modulate leaf microbiome assembly?","authors":"Posy E. Busby, Austen Apigo, Dagmara Sirova, Eduardo Pérez-Pazos, Kyle A. Gervers, Abigail Neat, María-José Romero-Jiménez, Leander D. L. Anderegg, Gail Taylor","doi":"10.1111/nph.70914","DOIUrl":"https://doi.org/10.1111/nph.70914","url":null,"abstract":"Elucidating the factors controlling plant microbiome assembly is a major research goal in plant biology given a growing awareness of microbial community contributions to host plant health and fitness. While stomata have long been recognized to influence pathogen colonization, less is known about whether or how stomatal traits regulate diverse communities of nonpathogenic microbes that make up the majority of the leaf microbiome. In this Viewpoint, we propose that stomata are a primary filter by which plants influence the assembly of leaf-associated microbial communities. We discuss three nonmutually exclusive hypotheses for how stomatal traits influence leaf microbes, including preliminary support for each based on published studies of foliar fungi and bacteria. The stomatal density hypothesis argues that a greater density of pores increases the rate of microbial entry into the leaf, while the stomatal function hypothesis posits that the duration and speed of stomatal opening and closing regulate microbial access into the leaf. The stomatal covariation hypothesis recognizes that many other leaf traits covary with stomatal traits and thus could contribute to observed relationships between stomatal traits and leaf microbiome structure. Finally, we propose research priorities to improve our understanding of stomatal control over leaf microbiome assembly.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"39 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145972020","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}
Summary Osmotic stress threatens plant survival and agricultural safety. Despite the progress made to elucidate how plants sense and adapt to osmotic stress, the knowledge underlying plant osmosensing remains limited. Notably, recent discoveries uncovering protein phase separation as an osmosensing and stress‐adaptive mechanism have shed new light on this field. From a combined biological and physicochemical perspective, we dissect how osmotic stress affects a plant meristematic cell, propose macromolecular crowding and water content as previously overlooked osmosignals, discuss their perception by phase‐separable proteins, and summarize the features of osmotic stress adaptation mediated by biomolecular condensates. We hope this review provides fresh insights into understanding osmotic stress and plant osmosensing.
{"title":"Condense to sense: a new path for plant osmosensing","authors":"Zhenyu Wang, Hongwei Guo","doi":"10.1111/nph.70899","DOIUrl":"https://doi.org/10.1111/nph.70899","url":null,"abstract":"Summary Osmotic stress threatens plant survival and agricultural safety. Despite the progress made to elucidate how plants sense and adapt to osmotic stress, the knowledge underlying plant osmosensing remains limited. Notably, recent discoveries uncovering protein phase separation as an osmosensing and stress‐adaptive mechanism have shed new light on this field. From a combined biological and physicochemical perspective, we dissect how osmotic stress affects a plant meristematic cell, propose macromolecular crowding and water content as previously overlooked osmosignals, discuss their perception by phase‐separable proteins, and summarize the features of osmotic stress adaptation mediated by biomolecular condensates. We hope this review provides fresh insights into understanding osmotic stress and plant osmosensing.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"270 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145972016","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}
<p>Prime editing (PE), a new Clustered regularly interspaced short palindromic repeats (CRISPR)-based tool, enables a broad spectrum of genetic changes. PE combines a fusion protein of a Cas9 nickase (nCas9) and M-MLV reverse transcriptase with a PE guide (peg)RNA composed of a single guide (sg)RNA and a 3′ extension containing the reverse transcription (RT) template and primer-binding site (PBS). When initially developed, PE, PE2, which uses a single pegRNA and engineered PE harboring five mutations, and PE3, which uses the engineered PE coupled with single pegRNA and additional nicking sgRNA targeting the nonedited strand, were developed in a stepwise manner, establishing PE3 as a highly reproducible method in mammalian cells (Anzalone <i>et al</i>., <span>2019</span>). However, efficiency varied considerably among target sites and cell types (Anzalone <i>et al</i>., <span>2019</span>). Efficient PE systems have now been applied widely to programmable and precise genome editing in a variety of organisms, including several plant species (Chen & Liu, <span>2023</span>). Efforts to further optimize effective PE in mammalian (Anzalone <i>et al</i>., <span>2022</span>; Choi <i>et al</i>., <span>2022</span>) and plant (J. Li <i>et al</i>., <span>2022</span>; Jiang <i>et al</i>., <span>2022</span>) cells have encompassed several approaches, including transient inhibition of p53 (M. Li <i>et al</i>., <span>2022</span>) or mismatch repair-related protein (Chen <i>et al</i>., <span>2021</span>), separation of nCas9 and RT enzyme (B. Liu <i>et al</i>., <span>2022</span>), addition of T5 exonucleases to the RT enzyme (Liang <i>et al</i>., <span>2023</span>), engineering the RT enzyme (Zong <i>et al</i>., <span>2022</span>), treatment with Histone Deacetylase (HDAC) inhibitor (N. Liu <i>et al</i>., <span>2022</span>), and improving the pegRNA by using circular RNA (B. Liu <i>et al</i>., <span>2022</span>). Among these previous reports, major breakthroughs have been achieved using: (1) engineered pegRNA (epegRNA) with an RNA pseudoknot sequence at the 3′ end to enhance stability and prevent degradation (Nelson <i>et al</i>., <span>2022</span>); and (2) paired pegRNAs (Lin <i>et al</i>., <span>2021</span>) to edit different DNA strands simultaneously by RT of two templates.</p><p>The increased PE frequency highlights the concomitant introduction of undesired edits (roughly classified into two types) occurring in addition to desired mutations at target sites (Anzalone <i>et al</i>., <span>2019</span>; Nelson <i>et al</i>., <span>2022</span>; Zong <i>et al</i>., <span>2022</span>). One type of undesired mutation occurring via PE is the insertion/deletion (indel) mutations and/or tandem duplications induced by endogenous DNA repair pathways. Fusion of an nCas9 variant (H840A + N854A) with M-MLV RT enzyme led to the decreased introduction of unwanted indels and increased frequency of correct edits compared with nCas9 (H840A) in mammalian cells (Lee <i>et al</
引体编辑（PE）是一种新的基于聚类规则间隔短回文重复序列（CRISPR）的工具，可以实现广泛的遗传变化。PE将Cas9缺口酶（nCas9）和M-MLV逆转录酶的融合蛋白与PE向导（peg）RNA结合，该RNA由单个向导（sg）RNA和包含逆转录（RT）模板和引物结合位点（PBS）的3 '延伸组成。在最初开发时，PE、PE2（使用单个pegRNA和含有五个突变的工程PE）和PE3（使用工程PE与单个pegRNA和额外靶向非编辑链的切口sgRNA）以逐步方式开发，使PE3在哺乳动物细胞中成为一种高度可重复性的方法（Anzalone等人，2019）。然而，不同靶点和细胞类型的效率差异很大（Anzalone et al., 2019）。高效的PE系统现已广泛应用于多种生物，包括几种植物物种的可编程和精确基因组编辑（Chen & Liu, 2023）。进一步优化哺乳动物（Anzalone et al., 2022; Choi et al., 2022）和植物(J. Li et al., 2022；江et al ., 2022)细胞包含几种方法,包括瞬态抑制p53 (m .李et al ., 2022)或不匹配repair-related蛋白质(Chen et al ., 2021),分离nCas9和RT酶(b .刘et al ., 2022),增加T5核酸外切酶RT酶(梁et al ., 2023),工程RT酶(宗庆后et al ., 2022),治疗组蛋白脱乙酰酶(HDAC)抑制剂(n .刘et al ., 2022),和改善pegRNA利用环状RNA (b .刘et al ., 2022)。在这些先前的报道中，主要的突破已经实现了：(1)在3 '端具有RNA假结序列的工程pegRNA (epegRNA)，以增强稳定性和防止降解（Nelson等，2022）；(2)配对pegRNAs (Lin et al., 2021)，通过两个模板的RT同时编辑不同的DNA链。增加的PE频率突出表明，除了在目标位点发生所需突变外，还会同时引入不希望的编辑（大致分为两种类型）（Anzalone等人，2019；Nelson等人，2022；Zong等人，2022）。通过PE发生的一种不希望发生的突变是由内源性DNA修复途径诱导的插入/删除（indel）突变和/或串联复制。与哺乳动物细胞中的nCas9 （H840A + N854A）相比，将nCas9变体（H840A + N854A）与M-MLV RT酶融合可以减少不需要的indel引入，并增加正确编辑的频率（Lee等，2023）。第二种不希望发生的突变是由pegRNA的支架序列的逆转录产物并入基因组而产生的支架衍生副产物。Chen等人（2021）重新编码了pegRNA支架的3 '端，以避免与基因组靶标序列同源，并报道了支架衍生副产物的发生率降低；然而，这种方法虽然很有希望，但尚未得到充分的研究。最近，我们测定了基于nspcas9的pe - pegrna -靶DNA复合物的低温电镜结构，发现M-MLV-RT酶可以将逆转录延伸到RT模板末端以外的支架区域（Shuto et al., 2024）。此外，使用PE2进行的体外PE测定显示，RT产物始终比RT模板序列的长度长3个核苷酸（Shuto等，2024）。因此，我们通过修改支架序列，将pegRNA支架的最后3-nt （5 ' -UGC-3 '）替换为RT模板附近的目标序列的3-nt，从而开发出高保真的pegRNA (pegRNA- hf)，改变了茎环形成区域的匹配对（Shuto et al., 2024）。然而，在哺乳动物细胞中，不希望的支架衍生突变比容易出错的修复诱导的突变要少得多（Chen et al., 2021; Shuto et al., 2024）；因此，尚不清楚pegRNA-HF是否能抑制哺乳动物细胞中支架来源的突变（Shuto et al., 2024）。在这里，我们提出了一种高效的水稻PE系统，利用工程pegRNA （epegRNA）的组合开发，以提高稳定性和防止3 '延伸的降解，并配对pegRNA靶向不同的DNA链，同时通过RT每个模板合成编辑的DNA序列。使用这种方法，我们观察到，在再生水稻植株中，不希望的支架衍生突变比DNA双链断裂（DSB）修复引起的突变更频繁。为了提高精确编辑的保真度，我们接下来测试了使用配对epegRNA-HFs的PE系统（PE与配对epegRNA-HFs）。我们的研究结果表明，水稻PE与配对的epegRNA-HFs避免了将不需要的支架衍生副产物引入目标位点，从而在植物细胞中建立了高效准确的PE系统。 我们在8个或9个表达epegRNAs或epegRNA-HFs的独立愈伤组织再生的植株中分别检测到oor基因的杂合或纯合R115H突变，突变率为20%至100%。然而，我们在一小部分表达epegRNAs（4/8系，50%）或epegRNA-HFs（2/9系，22%）的再生植株中观察到不希望的副产物（表S3）。与表达epegRNA-HFs的植物相比，表达epegRNA-HFs的植物的不良副产物明显减少（表S3）。T1个子代来自自花授粉的T0个再生植株，这些植株携带oor基因的杂合R115H突变。对T1个子代的OsOr基因分型证实，通过PE引入的R115H突变稳定地从T0个植株遗传给T1个子代（图S2C）。与WT相比，由成熟种子的盾部衍生出的带有oor基因纯合子R115H突变（OsOrR115H）的愈伤组织颜色变得更黄（图2e）。与此观察结果一致的是，在OsOrR115H愈伤组织中检测到β-胡萝卜素，而在WT愈伤组织（图S3A）或WT和OsOrR115H的种子中检测不到β-胡萝卜素（图S3B）。我们进一步评估了PE与配对的epegRNAs和epegRNA-HFs在另外两个水稻靶点上的有效性和准确性。设计成对的epegrna和epegRNA-HFs分别将F140H和D20转化为OsHSL1和OsWaxy基因中的停止密码子（图3a，b）。将F140H突变引入OsHSL1基因有望赋予对4-羟基苯基丙酮酸双加氧酶（HPPD）除草剂的耐受性（Dong et al, 2024）。OsWaxy已被用作几种植物物种基因组编辑的模型基因，因为据报道，敲除这些基因会导致蜡质表型（Nishizawa-Yokoi et al., 2015）。在OsHSL1和OsWaxy基因上，epegRNAs和epegRNA-HFs在转基因愈伤组织中的PE频率没有显著差异（图3c）。用epegRNAs表达PE的转基因愈伤组织的T0个再生植株的序列分析显示，除了期望的突变外，在几个品系（OsHSL1中3/5的品系和OsWaxy中2/5的品系）中检测到支架衍生的不希望的突变（表S3；图S4A，B）。另一方面，在表达epegRNA-HFs的PE的T0再生植株中，这些靶基因（OsHSL1的0/5系和OsWaxy的0/5系）的不良突变发生率被完全抑制（表S3）。本研究通过将PE与配对的epegRNAs结合在水稻中，成功建立了一个更高效的PE系统（图S1E， S2B）。有报道称，利用复合聚合酶II Cestrum yellow
{"title":"Efficient and accurate prime editing system in plants","authors":"Ayako Nishizawa-Yokoi, Keiko Iida, Akiko Mori, Miho Takemura, Yutaro Shuto, Ryoya Nakagawa, Osamu Nureki, Seiichi Toki","doi":"10.1111/nph.70890","DOIUrl":"10.1111/nph.70890","url":null,"abstract":"<p>Prime editing (PE), a new Clustered regularly interspaced short palindromic repeats (CRISPR)-based tool, enables a broad spectrum of genetic changes. PE combines a fusion protein of a Cas9 nickase (nCas9) and M-MLV reverse transcriptase with a PE guide (peg)RNA composed of a single guide (sg)RNA and a 3′ extension containing the reverse transcription (RT) template and primer-binding site (PBS). When initially developed, PE, PE2, which uses a single pegRNA and engineered PE harboring five mutations, and PE3, which uses the engineered PE coupled with single pegRNA and additional nicking sgRNA targeting the nonedited strand, were developed in a stepwise manner, establishing PE3 as a highly reproducible method in mammalian cells (Anzalone <i>et al</i>., <span>2019</span>). However, efficiency varied considerably among target sites and cell types (Anzalone <i>et al</i>., <span>2019</span>). Efficient PE systems have now been applied widely to programmable and precise genome editing in a variety of organisms, including several plant species (Chen & Liu, <span>2023</span>). Efforts to further optimize effective PE in mammalian (Anzalone <i>et al</i>., <span>2022</span>; Choi <i>et al</i>., <span>2022</span>) and plant (J. Li <i>et al</i>., <span>2022</span>; Jiang <i>et al</i>., <span>2022</span>) cells have encompassed several approaches, including transient inhibition of p53 (M. Li <i>et al</i>., <span>2022</span>) or mismatch repair-related protein (Chen <i>et al</i>., <span>2021</span>), separation of nCas9 and RT enzyme (B. Liu <i>et al</i>., <span>2022</span>), addition of T5 exonucleases to the RT enzyme (Liang <i>et al</i>., <span>2023</span>), engineering the RT enzyme (Zong <i>et al</i>., <span>2022</span>), treatment with Histone Deacetylase (HDAC) inhibitor (N. Liu <i>et al</i>., <span>2022</span>), and improving the pegRNA by using circular RNA (B. Liu <i>et al</i>., <span>2022</span>). Among these previous reports, major breakthroughs have been achieved using: (1) engineered pegRNA (epegRNA) with an RNA pseudoknot sequence at the 3′ end to enhance stability and prevent degradation (Nelson <i>et al</i>., <span>2022</span>); and (2) paired pegRNAs (Lin <i>et al</i>., <span>2021</span>) to edit different DNA strands simultaneously by RT of two templates.</p><p>The increased PE frequency highlights the concomitant introduction of undesired edits (roughly classified into two types) occurring in addition to desired mutations at target sites (Anzalone <i>et al</i>., <span>2019</span>; Nelson <i>et al</i>., <span>2022</span>; Zong <i>et al</i>., <span>2022</span>). One type of undesired mutation occurring via PE is the insertion/deletion (indel) mutations and/or tandem duplications induced by endogenous DNA repair pathways. Fusion of an nCas9 variant (H840A + N854A) with M-MLV RT enzyme led to the decreased introduction of unwanted indels and increased frequency of correct edits compared with nCas9 (H840A) in mammalian cells (Lee <i>et al</","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"249 5","pages":"2163-2172"},"PeriodicalIF":8.1,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/nph.70890","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145961375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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