Environmental and Experimental Botany最新文献

{"title":"Influence of ploidy on radiation resilience in extremophilic alga Galdieria sulphuraria under extreme ionizing conditions","authors":"Grzegorz Wałpuski ,&nbsp;Andrzej Rafalski ,&nbsp;Marta Galas ,&nbsp;Zygmunt Szefliński ,&nbsp;Maksymilian Zienkiewicz","doi":"10.1016/j.envexpbot.2025.106231","DOIUrl":"10.1016/j.envexpbot.2025.106231","url":null,"abstract":"<div><div>Ionizing radiation is one of the key physicochemical factors affecting living organisms, but its impact on unicellular algae remains poorly understood. <em>Cyanidiophyceae</em> are a class of extremophilic microalgae capable of thriving under the highly inhospitable conditions of volcanic hot springs. Among them, <em>Galdieria sulphuraria</em> is a unique species capable of mixotrophy, sexual reproduction, and exists in both haploid and diploid stages depending on environmental conditions. This study investigates, for the first time, the effects of ionizing radiation (2–6 kGy) on a representative extremophilic <em>Cyanidiophyceae,</em> focusing on radiation-induced damage and recovery in relation to ploidy. Our findings reveal that <em>Galdieria sulphuraria</em> in the diploid state exhibits extraordinary radiation resistance, surviving exposure to enormous doses as high as 6 kGy, making it one of the most radiation-tolerant photoautotrophic organisms known. Furthermore, diploids exhibit significantly higher tolerance than haploids, as evidenced by their superior survival, shorter duration of radiation sickness, enhanced synthesis of protective carotenoids, reduced oxidative damage, and high photosynthetic efficiency during recovery. These results provide novel insights into the role of ploidy in radiation resistance in algae and contribute to a broader understanding of extremophile adaptations. Given the relevance of ionizing radiation in astrobiology and space exploration, <em>Galdieria sulphuraria</em> emerges as a promising model for studying eukaryotic survival in extraterrestrial environments.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":"240 ","pages":"Article 106231"},"PeriodicalIF":4.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145476005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Barley nuclear cap-binding complex subunits, HvCBP20 and HvCBP80, play distinct roles in drought adaptation at reproductive phase of development","authors":"Hubert Matkowski,&nbsp;Anna Collin,&nbsp;Ewa Sybilska,&nbsp;Izabela Potocka,&nbsp;Agata Daszkowska-Golec","doi":"10.1016/j.envexpbot.2025.106266","DOIUrl":"10.1016/j.envexpbot.2025.106266","url":null,"abstract":"<div><div>Drought remains a major constraint to crop productivity. The nuclear cap-binding complex (CBC), composed of CBP20 and CBP80, regulates pre-mRNA splicing and has been increasingly associated with abscisic acid (ABA) signaling, as suggested by recent studies. Here, we investigated the transcriptomic and physiological impacts of mutations in genes encoding barley nuclear CBC (<em>hvcbp20.ab, hvcbp80</em>.<em>b</em>, and <em>hvcbp20.ab/hvcbp80.b</em>) under drought applied at the booting stage. The mutants exhibited both shared- and mutation-specific adaptations to drought. Transcriptomic profiling revealed that mutation in <em>HvCBP80</em> significantly reduced transcriptional and splicing activities while inducing the expression of photosynthesis-related genes, resulting in enhanced photosynthetic efficiency under both optimal and drought conditions. Conversely, mutation in <em>HvCBP20</em> intensified ABA-responsive gene expression and prolonged stress signaling. Physiologically, the <em>hvcbp20.ab</em> mutants displayed increased stomatal conductance despite reduced stomatal density, whereas the <em>hvcbp80.b</em> mutants exhibited decreased conductance under optimal conditions. Despite improved photosynthesis and dehydration avoidance traits, none of the mutations enhanced yield-related parameters under either optimal or drought conditions. Our findings establish that nuclear CBC is a pivotal regulator of drought stress responses and rewatering, capable of reprogramming the transcriptomic landscape to promote enhanced barley resilience.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":"240 ","pages":"Article 106266"},"PeriodicalIF":4.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145476006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-enabled phosphorus acquisition strategy drives the rapid reproduction of water hyacinth (Pontederia crassipes) leading to global invasion","authors":"Fangyu Liu ,&nbsp;Linhe Sun ,&nbsp;Yunhan Li ,&nbsp;Yangyang Deng ,&nbsp;Jixiang Liu ,&nbsp;Wei Wang ,&nbsp;Jinfeng Li ,&nbsp;Zhengnan Zhang ,&nbsp;Yingchun Xu ,&nbsp;Yajun Chang ,&nbsp;Yaoyao Wu ,&nbsp;Jian Cui ,&nbsp;Dongrui Yao","doi":"10.1016/j.envexpbot.2025.106278","DOIUrl":"10.1016/j.envexpbot.2025.106278","url":null,"abstract":"<div><div>The global expansion of water hyacinth (<em>Pontederia crassipes</em>) endangers water ecological security and high-quality economic development; moreover, its invasion mechanism at the genomic and molecular levels remains unclear. Here, a high-quality, chromosome-level genome of water hyacinth (1.25 Gb; N50 = 80.91 Mb) was assembled for the first time. Of the 59,361 genes, 64,988 transcripts were annotated using transcriptome data from five distinct water hyacinth tissues. Compared to the allied species <em>Pontederia cordata</em>, one more whole-genome duplication event occurred approximately 4 Mya. Gene families related to P metabolic pathways have significantly expanded during evolution. Nine of the twenty-two differentially expressed genes between stolons and other tissues were involved in P metabolism, including four genes that encode purple acid phosphatases (PAPs). Under 2.0 P, water hyacinth ramets exhibited a 1.4-fold increase compared to those under 1.0 P during the 40-day culture. Acid phosphatase content in roots significantly increased from 219.42 ± 78.10 U/g under P deficiency stress to 44.89 ± 15.23 U/g under P-sufficient water (p &lt; 0.05). Organic P can restore water hyacinth growth under P deficiency. Subcellular localisation showed that PcPAP19 and PcPAP53 were located in the cell membrane. Thus, PcPAPs play a key role in P regulation during water hyacinth growth. These findings demonstrate how the assembled genome advances understanding of the molecular mechanism underlying P-use efficiency and proliferation in plants.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":"240 ","pages":"Article 106278"},"PeriodicalIF":4.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145620849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abscisic acid plays a pivotal role in stomatal defense at the early infection of Verticillium dahliae in Gossypium hirsutum","authors":"Shujuan Xue ,&nbsp;Kun Li ,&nbsp;Heng Zhang ,&nbsp;Shican Xu ,&nbsp;Yunfeng Dou ,&nbsp;Luyao Li ,&nbsp;Yuxin Ning ,&nbsp;Xiao Wang ,&nbsp;Kunpeng Jia ,&nbsp;Jose R. Botella ,&nbsp;Yuchen Miao","doi":"10.1016/j.envexpbot.2025.106282","DOIUrl":"10.1016/j.envexpbot.2025.106282","url":null,"abstract":"<div><div>Plant leaf stomata serve as primary conduits for gas exchange while simultaneously mediating immune responses against phyllosphere pathogen infection and colonization. However, the contribution of stomatal responses to interactions between plants and the rhizosphere pathogen <em>Verticillium dahliae</em> (<em>V. dahliae</em>) remains poorly understood. Our results show that inoculation of cotton roots with <em>V. dahliae</em> induces rapid stomatal closure preceding pathogen colonization of leaves, which is associated with elevated levels of second messengers including hydrogen peroxide (H₂O₂), cytosolic calcium (Ca²⁺), and nitric oxide (NO). Transcriptomic analyses reveal that hormone signaling pathways predominantly govern stomatal-mediated immunity. Specifically, accumulation of endogenous salicylic acid (SA) promotes stomatal closure in an abscisic acid (ABA)-dependent manner in response to <em>V. dahliae</em> infection. Live imaging indicates that during early infection stages, stomatal opening facilitates increased <em>V. dahliae</em> colonization and disease progression, highlighting the important function of stomatal dynamics and hydraulic regulation in <em>V. dahliae</em>-cotton interactions. Our findings establish a link between stomata and <em>V. dahliae</em> infection, providing a new understanding of stomatal biology in the context of plant-rhizosphere pathogen interactions. Further understanding of the stomatal response to <em>V. dahliae</em> infection may provide new strategies to enhance <em>Verticillium</em> wilt resistance in cotton.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":"240 ","pages":"Article 106282"},"PeriodicalIF":4.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145620851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regulation of polyadenylation site choice in plant nuclear mRNA","authors":"Wei Zeng ,&nbsp;Xiutao Wang ,&nbsp;Qiying Zhou ,&nbsp;Shengli Jing","doi":"10.1016/j.envexpbot.2025.106274","DOIUrl":"10.1016/j.envexpbot.2025.106274","url":null,"abstract":"<div><div>The polyadenylation machinery plays a critical role in the processing of pre-mRNA into mature mRNA. This process involves a large multiprotein complex that recognizes polyadenylation signals and determines the polyadenylation sites (PASs). The presence of multiple polyadenylation signals within many genes suggests that alternative polyadenylation (APA) mechanism contributes to transcriptome diversity through the production of distinct mRNA isoforms. APA plays a crucial role in plant growth and development, regulates multiple signaling pathways, and modulates responses to various abiotic and biotic stresses. The selection of PASs is regulated by multiple factors, including dysfunction of core polyadenylation machinery components, various stress stimuli, epigenetic modifications, intron splicing, and so on. However, the molecular mechanisms that determine PAS choice in plants are still not fully elucidated. In this review, the classification of PAS switches, biological functions, and regulatory elements of the alterations between two PASs were summarized to explore the underlying mechanisms.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":"240 ","pages":"Article 106274"},"PeriodicalIF":4.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145577328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional identification of sly-miR1919c in tomato resistance to Phytophthora infestans","authors":"Yuanyuan Guan ,&nbsp;Kaige Wang ,&nbsp;Yali Wang ,&nbsp;Haiyan Hu ,&nbsp;Chengwei Li","doi":"10.1016/j.envexpbot.2025.106272","DOIUrl":"10.1016/j.envexpbot.2025.106272","url":null,"abstract":"<div><div>MicroRNAs (miRNAs) play crucial regulatory roles in plant defense against pathogens. Our previous work identified sly-miR1919c as a potential participant in tomato resistance to late blight. In this study, qRT-PCR analysis revealed that the expression of mature sly-miR1919c was significantly suppressed in tomato leaves following inoculation with <em>Phytophthora infestans</em> or treatment with salicylic acid, whereas jasmonic acid treatment markedly induced its expression. Bioinformatic analysis showed that the miR1919 family has a limited phylogenetic distribution, being present in only three plant species, with high sequence conservation among mature members. <em>Solyc08g067580</em> (<em>UNP</em>) was confirmed as the target gene of sly-miR1919c through 5′ RLM-RACE validation. qRT-PCR confirmed that <em>UNP</em> expression was upregulated in <em>P. infestans</em>-infected tomato leaves. The transgenic lines overexpressing sly-miR1919c (OE-miR1919c) exhibited increased susceptibility to late blight, which was associated with reduced <em>UNP</em> expression. Furthermore, silencing <em>UNP</em> via dsRNA-based SIGS demonstrated its function as a positive regulator of tomato resistance to late blight. Moreover, OE-miR1919c plants developed more severe disease symptoms characterized by enlarged necrotic lesions, increased cell death, and elevated accumulation of reactive oxygen species (ROS). These plants also exhibited leaf chlorosis and increased lateral branching. The osmotin-like protein (OLP) was identified as the UNP-interacting protein through yeast two-hybrid screening(Y2H) and Luciferase complementation imaging (LCI) assays. RNA-seq analysis revealed that overexpression of sly-miR1919c significantly altered the expression of genes associated with hormone signal transduction, MAPK signaling pathways, phenylpropanoid biosynthesis, and photosynthesis. During <em>P. infestans</em> infection, genes involved in hormone signal transduction and photosynthesis pathways were significantly downregulated in OE-miR1919c plants, and these genes were predominantly enriched in the GO term “response to stimulus”. Taken together, this study provides novel insights into the molecular mechanism underlying sly-miR1919c-mediated tomato resistance and highlights its potential as a genetic resource for tomato disease-resistant breeding.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":"240 ","pages":"Article 106272"},"PeriodicalIF":4.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145527125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling the impact of phosphorus availability on growth, root morphological and physiological traits of different phosphorus-tolerant alfalfa (Medicago sativa L.) in acidic soils in the karst region of southwest China","authors":"Yunfei Hao ,&nbsp;Xiaowen Wang ,&nbsp;Jin He ,&nbsp;Rama Dhanushkodi ,&nbsp;Yinglong Chen ,&nbsp;Zhou Li ,&nbsp;Xuechun Zhao ,&nbsp;Jihui Chen ,&nbsp;Xinyao Gu ,&nbsp;Chao Chen ,&nbsp;Rui Dong","doi":"10.1016/j.envexpbot.2025.106271","DOIUrl":"10.1016/j.envexpbot.2025.106271","url":null,"abstract":"<div><div>The cultivation of alfalfa (<em>Medicago sativa</em> L.) in acidic soils in southern China poses significant challenges, primarily due to two key factors present in soils at low pH: phosphorus (P) deficiency and aluminum (Al) toxicity. This study aimed to assess the morphological and physiological responses of alfalfa roots under conditions of P limitation and low pH. A pot experiment compared the growth and root characteristics of an Al-sensitive cultivar (Longzhong) and anAl -tolerant cultivar (Trifecta) of alfalfa in acidic soil. This was achieved by supplying six P levels (0, 10, 20, 40, 80, and 120 mg P kg⁻¹ soil) and utilizing two soil types (limestone soil pH 6.01 and yellow soil pH 5.46). Phosphorus application alleviated acid-aluminum stress and enhanced alfalfa growth, but aboveground growth did not further increase when the P supply exceeded 40 mg P kg⁻¹ soil. Trifecta exhibited higher P uptake and P utilization efficiency, along with increased total root length, compared to Longzhong. In both soil types, the two alfalfa cultivars allocated more biomass to the roots to maximize P extraction from the soil. The superior root morphological traits observed in Al-tolerant alfalfa enhanced P uptake and biomass production in acidic soil conditions. The secretion of more oxalate in yellow loam soil is an effective strategy for alfalfa to improve P acquisition. Under the P application of 20 P kg-1, the oxalate secretion of the tolerant and sensitive genotypes was 1.6 times and 2.5 times that of the control. However, excessive application of acidic P fertilizers, such as calcium dihydrogen phosphate, can markedly decrease soil pH, increase the concentration of exchangeable aluminum, and ultimately inhibit plant growth. This suggests that tailoring phosphorus fertilizer application strategies to specific soil acidity can improve fertilizer use efficiency and enhance alfalfa yield and tolerance, not only providing breeding strategies for acid-Al -tolerant alfalfa development but also offering fertilization guidance for alfalfa cultivation in this region.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":"240 ","pages":"Article 106271"},"PeriodicalIF":4.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145527126","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Helium-enriched solution enhances rapeseed salinity tolerance via reestablishing ion homeostasis and decreasing methylglyoxal accumulation","authors":"Genmei Chen ,&nbsp;Ke Jiang ,&nbsp;Chenxu Cai ,&nbsp;Rongzhan Guan ,&nbsp;Wenbiao Shen","doi":"10.1016/j.envexpbot.2025.106277","DOIUrl":"10.1016/j.envexpbot.2025.106277","url":null,"abstract":"<div><div>Helium was previously regarded as a biologically inert gas. However, whether or how this by-product of natural gas influences crop physiology remains largely unknown. Here, our hydroponic experiments showed that helium-enriched solution increases NaCl tolerance in rapeseed, as seedling root growth was less inhibited than saline solution alone. Helium addition decreased Na⁺ to K⁺ ratio in roots, caused by the enhanced accumulation of K⁺ (impaired K⁺ efflux) and reduced accumulation of Na⁺ (increased Na⁺ efflux), further confirmed by up-regulating sodium and potassium transporters genes. Consistently, reactive oxygen species (ROS)-mediated lipid peroxidation in roots was remarkably abolished, supported by the stimulation of ascorbate-glutathione cycle and other antioxidant enzymes. Importantly, helium could decrease methylglyoxal accumulation by stimulating glyoxalase enzyme activity. Thus, helium reestablished ion and redox homeostasis to combat NaCl stress, which opens a new window for helium-based biology.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":"240 ","pages":"Article 106277"},"PeriodicalIF":4.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145620848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hydration-driven metabolic activity enhances the resilience of Xanthoria parietina (L.) Th. Fr. to nitrate stress","authors":"Jakub Styburski ,&nbsp;Kaja Skubała","doi":"10.1016/j.envexpbot.2025.106276","DOIUrl":"10.1016/j.envexpbot.2025.106276","url":null,"abstract":"<div><div>Lichens can utilise nitrogen in molecular, reduced, and oxidized forms, but they preferentially use ammonium due to low energetic cost of its assimilation. The effects of ammonium on lichen physiology have been extensively studied, whereas much less is known about lichen responses to nitrate. Lichens depend on external water sources to hydrate the thallus, which triggers metabolic activity essential for dealing with environmental stress. We aimed to determine the effect of exposure to nitrate under different humidity conditions on the physiological response, as well as ammonium and nitrate accumulation in <em>Xanthoria parietina</em>. Lichen samples were exposed to nitrate for 30 days under two humidity conditions, with physiological traits measured before and after the experiment. Our study demonstrated that air humidity and the related time of thallus hydration strongly influenced the physiological response of <em>X. parietina</em>. Lichens exposed to high air humidity maintained hydration for longer, which extended the period of potential metabolic activity. This contributed to low oxidative stress and high water-soluble protein concentrations. Conversely, nitrate exposure under low-humidity conditions triggered oxidative stress due to the accumulation of toxic ammonia in cells. Lichens were able to take up nitrate ions; however, their ability to assimilate these ions remains unclear. The revealed pattern suggests that the duration of metabolic activity may be a critical factor in determining lichen resilience to nitrate stress. Our results have important implications in the context of climate change, in which water availability is becoming increasingly unpredictable, suggesting that metabolic activity sustained under favourable moisture conditions may be critical for maintaining lichen physiological performance.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":"240 ","pages":"Article 106276"},"PeriodicalIF":4.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145620850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A multi-omics comparative analysis reveals differential responses of epiphytic and terrestrial orchids in Cymbidium to waterlogging","authors":"Tian-Yang Gao ,&nbsp;Ning-Yu Liu ,&nbsp;Bei-Bei Zhou ,&nbsp;Shi-Bao Zhang","doi":"10.1016/j.envexpbot.2025.106268","DOIUrl":"10.1016/j.envexpbot.2025.106268","url":null,"abstract":"<div><div>Waterlogging stress is a major abiotic constraint that impedes plant growth and development by inducing root hypoxia, metabolic imbalances, and oxidative damage. Orchids, valued as important ornamental and medicinal plants, are highly susceptible to waterlogging, which frequently leads to severe root rot, as observed in field investigations and cultivation practices. Orchids include both epiphytic and terrestrial species that occupy habitats with pronounced differences in water availability. While the drought adaptation mechanisms of these two orchid life-forms have been extensively studied, the strategies underlying their adaptation to waterlogging remain poorly understood. Here, we investigated the responses of terrestrial <em>Cymbidium sinense</em> and epiphytic <em>C. tracyanum</em> to waterlogging stress using integrated physiological, metabolomic, and transcriptomic analyses. Under waterlogging stress, <em>C. tracyanum</em> suffered more severe morphological and ultrastructural damage compared to <em>C. sinense</em>, as well as greater rhizosphere hypoxia, reduced root activity, depletion of soluble sugars, and higher oxidative stress. Metabolomic and transcriptomic analyses revealed fundamentally divergent strategies between the species. <em>C. sinense</em> preferentially accumulated primary metabolites, particularly lipids, and specifically up-regulated genes related to triacylglycerol biosynthesis and UDP-glycosyltransferases. Integrated multi-omics analysis confirmed its reliance on enhanced primary metabolic pathways, such as alanine, aspartate, and glutamate metabolism, as well as linoleic acid metabolism, supporting waterlogging resilience. In contrast, <em>C. tracyanum</em> accumulated a diverse array of secondary metabolites and relied extensively on pathways such as phenylpropanoid and tyrosine metabolism. This high-investment strategy may have underlain its heightened sensitivity to waterlogging stress. Collectively, our findings provide mechanistic insights into the differential waterlogging responses between terrestrial and epiphytic <em>Cymbidium</em> species, thus offering perspectives on their adaptation and evolution while informing improved cultivation strategies.</div></div>","PeriodicalId":11758,"journal":{"name":"Environmental and Experimental Botany","volume":"240 ","pages":"Article 106268"},"PeriodicalIF":4.7,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145577330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}