Talat Ilyas, Mohammad Shahid, Nida Fatima, Alvina Farooqui, Shareen Niyazi, Mohammad Altaf
Aluminum (Al) is a major environmental pollutant that disrupts plant metabolism, inhibits growth, and reduces crop productivity. Beneficial metal-tolerant rhizobacteria can help plants mitigate Al stress. This study evaluated the potential of metal-tolerant rhizobacteria to enhance Al tolerance in maize (Zea mays L.). Pseudomonas azotoformans PSZ-1 (Accession no. PV605389.1) and Achromobacter sp. PSZ-5 (Accession no. PV639388.1) tolerated 120 and 100 μM Al, respectively, produced PGP substances, and effectively biosorbed Al3+ ions. Aluminum, particularly at 80 μM, had phytotoxic effects on maize, reducing growth and photosynthetic traits while elevating ROS, oxidative stress, and metal uptake. Inoculation with PSZ-1 and PSZ-5 alleviated Al-induced toxicity, enhancing maize performance under metal stress. Both strains significantly (p ≤ 0.05) improved root biomass (30.7%, 35.7%), carotenoids (23.4%, 29.8%), chlorophyll fluorescence (27.2%, 29.4%), photosynthetic rate (24.8%, 33%), and stomatal conductance (29.7%, 35.4%) in 20 μM Al3+-stressed maize over uninoculated controls. ROS (H2O2, superoxide) and oxidative stress markers (EL, MDA) were significantly reduced (p ≤ 0.001) in bacterial-primed maize. Bacterial inoculation reduced Al accumulation in roots and shoot tissues of maize. At 40 μM Al, PSZ-5 significantly upregulated the activities of APX, CT, and POD by 30.1%, 26.8%, and 22.6%, while PSZ-1 maximally enhanced SOD and GR by 37.8% and 25.6% in roots, respectively. Multivariate analyses confirmed the strong parameter associations among treatments. Overall, applied PGPR strains showed promise for bioremediation of Al-contaminated soils and improving maize growth and tolerance. Future work should validate their performance under field conditions and explore molecular mechanisms and microbial consortia development.
{"title":"Metal-Tolerant Rhizobacteria Alleviate Aluminum Toxicity in Maize Via Biosorption, Antioxidant Activation, and ROS Reduction.","authors":"Talat Ilyas, Mohammad Shahid, Nida Fatima, Alvina Farooqui, Shareen Niyazi, Mohammad Altaf","doi":"10.1111/ppl.70749","DOIUrl":"https://doi.org/10.1111/ppl.70749","url":null,"abstract":"<p><p>Aluminum (Al) is a major environmental pollutant that disrupts plant metabolism, inhibits growth, and reduces crop productivity. Beneficial metal-tolerant rhizobacteria can help plants mitigate Al stress. This study evaluated the potential of metal-tolerant rhizobacteria to enhance Al tolerance in maize (Zea mays L.). Pseudomonas azotoformans PSZ-1 (Accession no. PV605389.1) and Achromobacter sp. PSZ-5 (Accession no. PV639388.1) tolerated 120 and 100 μM Al, respectively, produced PGP substances, and effectively biosorbed Al<sup>3+</sup> ions. Aluminum, particularly at 80 μM, had phytotoxic effects on maize, reducing growth and photosynthetic traits while elevating ROS, oxidative stress, and metal uptake. Inoculation with PSZ-1 and PSZ-5 alleviated Al-induced toxicity, enhancing maize performance under metal stress. Both strains significantly (p ≤ 0.05) improved root biomass (30.7%, 35.7%), carotenoids (23.4%, 29.8%), chlorophyll fluorescence (27.2%, 29.4%), photosynthetic rate (24.8%, 33%), and stomatal conductance (29.7%, 35.4%) in 20 μM Al<sup>3+</sup>-stressed maize over uninoculated controls. ROS (H<sub>2</sub>O<sub>2</sub>, superoxide) and oxidative stress markers (EL, MDA) were significantly reduced (p ≤ 0.001) in bacterial-primed maize. Bacterial inoculation reduced Al accumulation in roots and shoot tissues of maize. At 40 μM Al, PSZ-5 significantly upregulated the activities of APX, CT, and POD by 30.1%, 26.8%, and 22.6%, while PSZ-1 maximally enhanced SOD and GR by 37.8% and 25.6% in roots, respectively. Multivariate analyses confirmed the strong parameter associations among treatments. Overall, applied PGPR strains showed promise for bioremediation of Al-contaminated soils and improving maize growth and tolerance. Future work should validate their performance under field conditions and explore molecular mechanisms and microbial consortia development.</p>","PeriodicalId":20164,"journal":{"name":"Physiologia plantarum","volume":"178 1","pages":"e70749"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146093789","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}
The fall armyworm [Spodoptera frugiperda (J. E. Smith)] is an invasive pest of maize, posing significant threats to crop productivity. While herbivore-induced plant volatiles (HIPVs) play a central role in indirect plant defenses, the contribution of hydrocarbon-based volatile organic compounds to S. frugiperda resistance remains underexplored. This study investigated the VOC profiles of maize seedlings infested by S. frugiperda compared to uninfested controls, and evaluated the bioactivity of selected synthetic VOCs on larval feeding performance. GC-MS analysis revealed qualitative and quantitative shifts in the maize volatilome following herbivory, with 11 VOCs-including mesitylene, cyclohexane, hexadecane, and eicosane-uniquely induced in infested plants. Hydrocarbon compounds dominated the altered profiles, suggesting their potential defensive function. To validate their bioactivity, nine synthetic hydrocarbons were applied to semi-synthetic diets, and their effects on larval development, feeding, and nutritional indices were assessed. Among them, eicosane and cyclohexane exhibited the strongest suppressive effects, significantly reducing larval weight gain, food intake, frass production, relative growth rate (RGR), relative consumption rate (RCR), and approximate digestibility (AD). Octane and pentatriacontane showed moderate inhibitory effects, while tetracosane and henicosane were largely ineffective. The results demonstrate that specific hydrocarbon-based VOCs not only correlate with herbivore attack but also directly impair pest growth and digestion. This study underscores the functional importance of herbivory-induced hydrocarbons in maize defense and identifies promising VOCs for development as biocompatible agents in sustainable pest management strategies.
秋粘虫[Spodoptera frugiperda (J. E. Smith)]是一种入侵性玉米害虫,对玉米产量构成严重威胁。虽然草食诱导的植物挥发物(HIPVs)在植物的间接防御中起着核心作用,但烃类挥发物对frugiperda抗性的贡献仍未得到充分研究。本研究研究了被frugiperda侵染的玉米幼苗与未侵染的玉米幼苗的挥发性有机化合物(VOC)分布,并评价了几种合成挥发性有机化合物对幼虫取食性能的生物活性。GC-MS分析揭示了草食后玉米挥发物的定性和定量变化,其中11种挥发性有机化合物(包括三甲苯、环己烷、十六烷和二十烷)在侵染植株中被独特诱导。蚀变剖面以烃类化合物为主,具有潜在的防御作用。为了验证9种合成烃在半合成饲料中的生物活性,研究了它们对幼虫发育、摄食和营养指标的影响。其中,二十烷和环己烷的抑制作用最强,显著降低了幼虫增重、采食量、粗草产量、相对生长率(RGR)、相对消耗率(RCR)和近似消化率(AD)。辛烷和五正康烷表现出中等的抑制作用,而四糖烷和苯二糖烷则基本无效。结果表明,特定烃类挥发性有机化合物不仅与食草动物的攻击有关,而且直接影响害虫的生长和消化。本研究强调了草食诱导的碳氢化合物在玉米防御中的功能重要性,并确定了有前途的挥发性有机化合物,作为可持续害虫管理策略的生物相容性剂。
{"title":"Herbivore-Induced Maize Volatiles Override Feeding Behavior and Elicit Antifeedant Responses in Spodoptera frugiperda.","authors":"Ramasamy Kanagaraj Murali-Baskaran, Yogesh Yele, Kailash Chander Sharma, Pankaj Sharma","doi":"10.1111/ppl.70751","DOIUrl":"https://doi.org/10.1111/ppl.70751","url":null,"abstract":"<p><p>The fall armyworm [Spodoptera frugiperda (J. E. Smith)] is an invasive pest of maize, posing significant threats to crop productivity. While herbivore-induced plant volatiles (HIPVs) play a central role in indirect plant defenses, the contribution of hydrocarbon-based volatile organic compounds to S. frugiperda resistance remains underexplored. This study investigated the VOC profiles of maize seedlings infested by S. frugiperda compared to uninfested controls, and evaluated the bioactivity of selected synthetic VOCs on larval feeding performance. GC-MS analysis revealed qualitative and quantitative shifts in the maize volatilome following herbivory, with 11 VOCs-including mesitylene, cyclohexane, hexadecane, and eicosane-uniquely induced in infested plants. Hydrocarbon compounds dominated the altered profiles, suggesting their potential defensive function. To validate their bioactivity, nine synthetic hydrocarbons were applied to semi-synthetic diets, and their effects on larval development, feeding, and nutritional indices were assessed. Among them, eicosane and cyclohexane exhibited the strongest suppressive effects, significantly reducing larval weight gain, food intake, frass production, relative growth rate (RGR), relative consumption rate (RCR), and approximate digestibility (AD). Octane and pentatriacontane showed moderate inhibitory effects, while tetracosane and henicosane were largely ineffective. The results demonstrate that specific hydrocarbon-based VOCs not only correlate with herbivore attack but also directly impair pest growth and digestion. This study underscores the functional importance of herbivory-induced hydrocarbons in maize defense and identifies promising VOCs for development as biocompatible agents in sustainable pest management strategies.</p>","PeriodicalId":20164,"journal":{"name":"Physiologia plantarum","volume":"178 1","pages":"e70751"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146053529","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}
Maria Pertesi, Zafiria Stefa, Katerina Thanasi, Anna Piperidou, Nikos Tostsidis, Andreas Benekos, Athanasios Koulopoulos, Christos Vasileiou, Elias Stathatos, George Zervoudakis
{"title":"Improving Plant Growth Under a Luminescent Solar Concentrator Emitting Red Light.","authors":"Maria Pertesi, Zafiria Stefa, Katerina Thanasi, Anna Piperidou, Nikos Tostsidis, Andreas Benekos, Athanasios Koulopoulos, Christos Vasileiou, Elias Stathatos, George Zervoudakis","doi":"10.1111/ppl.70750","DOIUrl":"10.1111/ppl.70750","url":null,"abstract":"","PeriodicalId":20164,"journal":{"name":"Physiologia plantarum","volume":"178 1","pages":"e70750"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12831100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146041273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ana R Circuncisão, Mateus Pereira, Maria Celeste Dias, Paulo R Oliveira-Pinto, Conceição Santos, Artur M S Silva, Manuel A Coimbra, Susana M Cardoso, Sónia Silva
Water deficit negatively affects crop yield and quality. Biostimulants, such as brown seaweed extracts, offer a sustainable solution to mitigate these effects. This study evaluated the impact of Laminaria digitata-aqueous extract (LE) on tomato performance and its potential to alleviate drought stress by examining morphological, physiological, and metabolic responses. Two-week-old tomato plants were foliar-sprayed with LE (0.0, 0.1, and 1.0 g L-1) and split into well-watered (WW) and water-limited (WL) groups. WW plants received regular irrigation, while WL faced a one-week drought. Then, half of the WL plants were rewatered and allowed to recover for 24 h (REC group). In general, LE effects were influenced by irrigation conditions, mainly impacting physiological and metabolomic parameters. Under WW conditions, LE decreased chlorophyll content, improved energy conversion by regulating photosystem antenna size, enhanced photochemical efficiency (ΦPSII) and gas exchange parameters (gs, Ci, PN), and promoted photosynthesis through stomatal modulation and RuBisCO activity. Conversely, under WL conditions, LE (especially 0.1 g L-1) decreased gas exchange parameters, but increased water use efficiency by inducing stomatal closure without impairing CO₂ assimilation. LE-treated plants exhibited ROS detoxification and phytohormone downregulation, which in turn negatively affected the content of certain secondary metabolites (e.g., catechin). Phytohormone modulation may result from reduced ROS levels or crosstalking with LE compounds, including mannitol, alginates, laminarans, minerals, and phlorotannins, which likely act synergistically to improve physiological regulation. Overall, LE application improved drought tolerance by enhancing photosystem regulation, phytohormone modulation, and antioxidant capacity in tomato plants, highlighting its potential use as a biostimulant for sustainable agriculture.
水分亏缺对作物产量和品质有不利影响。生物刺激剂,如褐藻提取物,提供了一个可持续的解决方案,以减轻这些影响。本研究通过形态、生理和代谢反应来评估海带水提取物(LE)对番茄生产性能的影响及其缓解干旱胁迫的潜力。2周龄番茄叶片喷施LE(0.0、0.1和1.0 g L-1),分为丰水(WW)组和限水(WL)组。WW的植物得到了定期灌溉,而WL则面临为期一周的干旱。然后,将一半的WL植株重新浇水,并让其恢复24 h (REC组)。总的来说,LE效应受灌溉条件的影响,主要影响生理和代谢组学参数。在WW条件下,LE降低叶绿素含量,通过调节光系统天线尺寸改善能量转换,提高光化学效率(ΦPSII)和气体交换参数(gs、Ci、PN),并通过气孔调节和RuBisCO活性促进光合作用。相反,在WL条件下,LE(尤其是0.1 g L-1)降低了气体交换参数,但在不影响CO 2同化的情况下,通过诱导气孔关闭提高了水分利用效率。le处理的植物表现出ROS解毒和植物激素下调,这反过来对某些次级代谢物(如儿茶素)的含量产生负面影响。植物激素调节可能是由于ROS水平降低或与LE化合物(包括甘露醇、海藻酸盐、层藻酸盐、矿物质和植绿单宁)的交叉作用,这些化合物可能协同作用以改善生理调节。总的来说,LE通过增强番茄的光系统调节、植物激素调节和抗氧化能力,提高了番茄的抗旱性,突出了其作为可持续农业生物刺激素的潜在用途。
{"title":"Exploiting Laminaria digitata L. Aqueous Extract for Tomato Biostimulation: A Physiological and Metabolomic Approach.","authors":"Ana R Circuncisão, Mateus Pereira, Maria Celeste Dias, Paulo R Oliveira-Pinto, Conceição Santos, Artur M S Silva, Manuel A Coimbra, Susana M Cardoso, Sónia Silva","doi":"10.1111/ppl.70762","DOIUrl":"10.1111/ppl.70762","url":null,"abstract":"<p><p>Water deficit negatively affects crop yield and quality. Biostimulants, such as brown seaweed extracts, offer a sustainable solution to mitigate these effects. This study evaluated the impact of Laminaria digitata-aqueous extract (LE) on tomato performance and its potential to alleviate drought stress by examining morphological, physiological, and metabolic responses. Two-week-old tomato plants were foliar-sprayed with LE (0.0, 0.1, and 1.0 g L<sup>-1</sup>) and split into well-watered (WW) and water-limited (WL) groups. WW plants received regular irrigation, while WL faced a one-week drought. Then, half of the WL plants were rewatered and allowed to recover for 24 h (REC group). In general, LE effects were influenced by irrigation conditions, mainly impacting physiological and metabolomic parameters. Under WW conditions, LE decreased chlorophyll content, improved energy conversion by regulating photosystem antenna size, enhanced photochemical efficiency (ΦPSII) and gas exchange parameters (g<sub>s</sub>, C<sub>i</sub>, P<sub>N</sub>), and promoted photosynthesis through stomatal modulation and RuBisCO activity. Conversely, under WL conditions, LE (especially 0.1 g L<sup>-1</sup>) decreased gas exchange parameters, but increased water use efficiency by inducing stomatal closure without impairing CO₂ assimilation. LE-treated plants exhibited ROS detoxification and phytohormone downregulation, which in turn negatively affected the content of certain secondary metabolites (e.g., catechin). Phytohormone modulation may result from reduced ROS levels or crosstalking with LE compounds, including mannitol, alginates, laminarans, minerals, and phlorotannins, which likely act synergistically to improve physiological regulation. Overall, LE application improved drought tolerance by enhancing photosystem regulation, phytohormone modulation, and antioxidant capacity in tomato plants, highlighting its potential use as a biostimulant for sustainable agriculture.</p>","PeriodicalId":20164,"journal":{"name":"Physiologia plantarum","volume":"178 1","pages":"e70762"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12848962/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146066011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Camellia oleifera Abel. is an important woody oil tree species in China, and increasing the content of polyunsaturated fatty acids (PUFAs), particularly α-linolenic acid (ALA), is critical for improving the quality of its oil. Fatty acid desaturase 7 (FAD7) is a key enzyme in ALA biosynthesis in plants. However, the allelic variation, functional role, and regulatory mechanisms underlying FAD7-mediated ALA accumulation in C. oleifera remain poorly understood. In the study, we cloned three homologous CoFAD7 genes: CoFAD7-1, CoFAD7-2, and CoFAD7-3 from C. oleifera 'Huashuo'. All three genes contained eight exons and seven introns, encoding 452 amino acids. Expression analysis revealed that CoFAD7 was highly expressed during the fruit maturation stage (258-333 DAP), correlating positively with seed ALA accumulation. Haplotypes analysis and transgenic experiments identified CoFAD7-G as a superior genotype associated with higher ALA content. Biochemical assays further showed that the transcription factor CoAP2-3 binds to the CoFAD7 promoter and activates its expression. These findings suggest that CoFAD7-G is a key determinant of ALA content, providing a theoretical basis for the early identification of high-ALA C. oleifera germplasm.
{"title":"Allelic Variants, Genetic Effects, and Transcriptional Regulation of CoFAD7 in Camellia oleifera.","authors":"Xiaoling Ma, Deyi Yuan, Yuting Zi, Jiaxin Chen, Jiaxi Zhang, Xinyue Tan, Yanxiu Zhang, Xiang Ouyang","doi":"10.1111/ppl.70780","DOIUrl":"https://doi.org/10.1111/ppl.70780","url":null,"abstract":"<p><p>Camellia oleifera Abel. is an important woody oil tree species in China, and increasing the content of polyunsaturated fatty acids (PUFAs), particularly α-linolenic acid (ALA), is critical for improving the quality of its oil. Fatty acid desaturase 7 (FAD7) is a key enzyme in ALA biosynthesis in plants. However, the allelic variation, functional role, and regulatory mechanisms underlying FAD7-mediated ALA accumulation in C. oleifera remain poorly understood. In the study, we cloned three homologous CoFAD7 genes: CoFAD7-1, CoFAD7-2, and CoFAD7-3 from C. oleifera 'Huashuo'. All three genes contained eight exons and seven introns, encoding 452 amino acids. Expression analysis revealed that CoFAD7 was highly expressed during the fruit maturation stage (258-333 DAP), correlating positively with seed ALA accumulation. Haplotypes analysis and transgenic experiments identified CoFAD7-G as a superior genotype associated with higher ALA content. Biochemical assays further showed that the transcription factor CoAP2-3 binds to the CoFAD7 promoter and activates its expression. These findings suggest that CoFAD7-G is a key determinant of ALA content, providing a theoretical basis for the early identification of high-ALA C. oleifera germplasm.</p>","PeriodicalId":20164,"journal":{"name":"Physiologia plantarum","volume":"178 1","pages":"e70780"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146143295","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}
Waterlogging stress typically causes submergence or partial submergence stress in plants, which negatively impacts agricultural production, from seed germination to vegetative and reproductive growth. Uniconazole (S3307) was recently used to minimize the damage caused by waterlogging. Here, we investigate the effects of S3307 on the growth, development, and yield of soybean under waterlogging stress. Morphological and physiological indexes, as well as the transcriptome and metabolome of soybean were analyzed in control condition and waterlogged condition with (WS) or without (W) spraying S3307. The results showed that waterlogging stress led to growth inhibition and reduced activity of antioxidant enzymes in soybean plants, resulting in a large accumulation of MDA content and ultimately causing yield reduction. Foliar spraying of S3307 increased stem diameter, reduced plant height, increased dry matter accumulation, increased antioxidant enzyme activities, inhibited MDA accumulation, and alleviated the yield reduction. The combined transcriptomics and metabolomics investigation demonstrated that, compared to Control, both W and WS treatments generated similar directional changes in triterpenoid metabolism and stress response pathways, suggesting that waterlogging stress activated these defense-related pathways. Notably, the strength of these reactions was considerably greater in the WS treatment than in the W treatment. Under waterlogging stress, foliar application of S3307 increased the expression of genes involved in flavonoid production and increased the accumulation of unsaturated fatty acids-substances known to help in cell membrane stability-when compared to the W treatment. In summary, our findings show that S3307 does not alter the direction of waterlogging-induced reactions but rather greatly increases their strength, thereby positively regulating soybean waterlogging tolerance. This establishes a biochemical mechanism and theoretical foundation for using plant growth regulators to reduce stress.
{"title":"Transcriptome and Metabolome Analyses Reveal the Mechanism by Which Uniconazole Affects Waterlogging Stress in Soybean.","authors":"Shiya Wang, Yang Liu, Hongtao Xiang, Chao Fang, Naijie Feng, Dianfeng Zheng","doi":"10.1111/ppl.70790","DOIUrl":"https://doi.org/10.1111/ppl.70790","url":null,"abstract":"<p><p>Waterlogging stress typically causes submergence or partial submergence stress in plants, which negatively impacts agricultural production, from seed germination to vegetative and reproductive growth. Uniconazole (S3307) was recently used to minimize the damage caused by waterlogging. Here, we investigate the effects of S3307 on the growth, development, and yield of soybean under waterlogging stress. Morphological and physiological indexes, as well as the transcriptome and metabolome of soybean were analyzed in control condition and waterlogged condition with (WS) or without (W) spraying S3307. The results showed that waterlogging stress led to growth inhibition and reduced activity of antioxidant enzymes in soybean plants, resulting in a large accumulation of MDA content and ultimately causing yield reduction. Foliar spraying of S3307 increased stem diameter, reduced plant height, increased dry matter accumulation, increased antioxidant enzyme activities, inhibited MDA accumulation, and alleviated the yield reduction. The combined transcriptomics and metabolomics investigation demonstrated that, compared to Control, both W and WS treatments generated similar directional changes in triterpenoid metabolism and stress response pathways, suggesting that waterlogging stress activated these defense-related pathways. Notably, the strength of these reactions was considerably greater in the WS treatment than in the W treatment. Under waterlogging stress, foliar application of S3307 increased the expression of genes involved in flavonoid production and increased the accumulation of unsaturated fatty acids-substances known to help in cell membrane stability-when compared to the W treatment. In summary, our findings show that S3307 does not alter the direction of waterlogging-induced reactions but rather greatly increases their strength, thereby positively regulating soybean waterlogging tolerance. This establishes a biochemical mechanism and theoretical foundation for using plant growth regulators to reduce stress.</p>","PeriodicalId":20164,"journal":{"name":"Physiologia plantarum","volume":"178 1","pages":"e70790"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146166326","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}
Alexis Brun, Marti Quevedo, Luis A Sterling, Dick H W Dekkers, Jeroen Demmers, Elton Paul Hudson, Åsa Strand
We have established a method for chromatin immunoprecipitation coupled to mass spectrometry (ChIP-MS) in Arabidopsis thaliana. We demonstrate its utility by investigating proteins associated with histone H3 lysine 27 acetylation (H3K27ac), a key epigenetic mark regulating photosynthesis-associated nuclear genes (PhANGs) during chloroplast development and establishment of photosynthesis. Purification of chromatin-associated proteins from light-grown Arabidopsis cell cultures identified 66 proteins associated with H3K27ac that met the selection criteria in the two replicate experiments: (i) 2-fold change in relation to IgG, (ii) at least two unique peptides, and (iii) relevant biological annotations. The identified proteins included chromatin remodelers, chromatin regulators and transcription factors with potential roles in H3K27ac deposition. To evaluate the physiological role of the candidates associated with the H3K27ac mark, we developed a rapid and reproducible phenotyping method based on controlled light scanning to determine chlorophyll accumulation in mutant seedlings. We complemented with pigment quantification and analysis of photosynthesis-associated nuclear genes (PhANGs) expression. Several mutants displayed altered greening, pigment accumulation, or affected photosynthetic gene expression consistent with a role during chloroplast development. Notably, chr11, chr17, and atpds5a mutants showed impaired pigment accumulation and reduced expression of PhANGs, whereas hmgb4 and mbd10 mutants exhibited increased greening and induction of PhANGs. Together, these findings establish ChIP-MS as a robust approach to identify histone mark-associated proteins in plants and provide a first set of candidate regulators of H3K27ac during chloroplast biogenesis. This technical advance opens new possibilities to discover chromatin-based regulation of plant development and environmental responses.
{"title":"ChIP-MS in Plant Systems: Mapping the H3K27ac Proteome During the Greening Process.","authors":"Alexis Brun, Marti Quevedo, Luis A Sterling, Dick H W Dekkers, Jeroen Demmers, Elton Paul Hudson, Åsa Strand","doi":"10.1111/ppl.70797","DOIUrl":"https://doi.org/10.1111/ppl.70797","url":null,"abstract":"<p><p>We have established a method for chromatin immunoprecipitation coupled to mass spectrometry (ChIP-MS) in Arabidopsis thaliana. We demonstrate its utility by investigating proteins associated with histone H3 lysine 27 acetylation (H3K27ac), a key epigenetic mark regulating photosynthesis-associated nuclear genes (PhANGs) during chloroplast development and establishment of photosynthesis. Purification of chromatin-associated proteins from light-grown Arabidopsis cell cultures identified 66 proteins associated with H3K27ac that met the selection criteria in the two replicate experiments: (i) 2-fold change in relation to IgG, (ii) at least two unique peptides, and (iii) relevant biological annotations. The identified proteins included chromatin remodelers, chromatin regulators and transcription factors with potential roles in H3K27ac deposition. To evaluate the physiological role of the candidates associated with the H3K27ac mark, we developed a rapid and reproducible phenotyping method based on controlled light scanning to determine chlorophyll accumulation in mutant seedlings. We complemented with pigment quantification and analysis of photosynthesis-associated nuclear genes (PhANGs) expression. Several mutants displayed altered greening, pigment accumulation, or affected photosynthetic gene expression consistent with a role during chloroplast development. Notably, chr11, chr17, and atpds5a mutants showed impaired pigment accumulation and reduced expression of PhANGs, whereas hmgb4 and mbd10 mutants exhibited increased greening and induction of PhANGs. Together, these findings establish ChIP-MS as a robust approach to identify histone mark-associated proteins in plants and provide a first set of candidate regulators of H3K27ac during chloroplast biogenesis. This technical advance opens new possibilities to discover chromatin-based regulation of plant development and environmental responses.</p>","PeriodicalId":20164,"journal":{"name":"Physiologia plantarum","volume":"178 1","pages":"e70797"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146220693","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}
Roberta Pace, Maurilia M Monti, Salvatore Cuomo, Antonio Affinito, Michelina Ruocco
Understanding soil microbiota dynamics is essential for enhancing bio-sustainability in agriculture, yet the complexity of microbial communities hampers the prediction of their functional roles. Artificial intelligence (AI) and machine learning (ML) offer powerful tools to analyse high-dimensional microbiome data generated by high-throughput sequencing. Here, we apply unsupervised AI-based algorithms to uncover microbial patterns that are not immediately recognisable but are crucial for characterising the biological status of agricultural soils. Soil samples were collected from a site in Northern Italy managed under four strategies: conventional farming without organic matter (C), with organic matter (C + O), with beneficial microorganisms but without organic matter (M), and with both beneficial microorganisms and organic matter (M + O). Metagenomic amplicon sequencing of the 16S ribosomal RNA (rRNA) gene and the internal transcribed spacer (ITS) region was used to profile bacterial and fungal communities. Principal component analysis (PCA), k-means clustering, and t-distributed stochastic neighbour embedding (t-SNE) revealed coherent temporal trajectories in both datasets, with sampling time and crop presence emerging as dominant drivers of community assembly and only subtle compositional shifts attributable to treatments. Fungal communities exhibited higher plasticity and a stronger response to management than bacterial communities, which converged towards a stable oligotrophic core. Our findings highlight the complementary roles of fungal and bacterial guilds and show that unsupervised ML-based workflows provide an effective framework to disentangle temporal and treatment effects in complex microbiome datasets. This exploratory study lays the groundwork for future predictive models aimed at identifying microbial indicators of soil biological status and supporting bio-sustainable agronomic decisions.
{"title":"Machine Learning Approaches to Assess Soil Microbiome Dynamics and Bio-Sustainability.","authors":"Roberta Pace, Maurilia M Monti, Salvatore Cuomo, Antonio Affinito, Michelina Ruocco","doi":"10.1111/ppl.70719","DOIUrl":"10.1111/ppl.70719","url":null,"abstract":"<p><p>Understanding soil microbiota dynamics is essential for enhancing bio-sustainability in agriculture, yet the complexity of microbial communities hampers the prediction of their functional roles. Artificial intelligence (AI) and machine learning (ML) offer powerful tools to analyse high-dimensional microbiome data generated by high-throughput sequencing. Here, we apply unsupervised AI-based algorithms to uncover microbial patterns that are not immediately recognisable but are crucial for characterising the biological status of agricultural soils. Soil samples were collected from a site in Northern Italy managed under four strategies: conventional farming without organic matter (C), with organic matter (C + O), with beneficial microorganisms but without organic matter (M), and with both beneficial microorganisms and organic matter (M + O). Metagenomic amplicon sequencing of the 16S ribosomal RNA (rRNA) gene and the internal transcribed spacer (ITS) region was used to profile bacterial and fungal communities. Principal component analysis (PCA), k-means clustering, and t-distributed stochastic neighbour embedding (t-SNE) revealed coherent temporal trajectories in both datasets, with sampling time and crop presence emerging as dominant drivers of community assembly and only subtle compositional shifts attributable to treatments. Fungal communities exhibited higher plasticity and a stronger response to management than bacterial communities, which converged towards a stable oligotrophic core. Our findings highlight the complementary roles of fungal and bacterial guilds and show that unsupervised ML-based workflows provide an effective framework to disentangle temporal and treatment effects in complex microbiome datasets. This exploratory study lays the groundwork for future predictive models aimed at identifying microbial indicators of soil biological status and supporting bio-sustainable agronomic decisions.</p>","PeriodicalId":20164,"journal":{"name":"Physiologia plantarum","volume":"178 1","pages":"e70719"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12766673/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145900883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Proteomics is defined as the identification, quantification, and characterization of the complete set of proteins expressed in a cell or tissue under specific conditions. The last two decades have witnessed rapid advancements in proteomics technologies, including the development of the Data-Independent Acquisition (DIA) mode, which has significantly improved the sensitivity, reproducibility, and depth of proteome coverage. These advancements, together with the development of cutting-edge data analysis tools, have undoubtedly facilitated the identification of stress-responsive proteins and potential biomarkers in different organisms. However, the identification of such stress-responsive proteins, particularly in plants, remains relatively challenging because of the presence of various high-abundance proteins such as RuBisCO, which hinders the identification and subsequent characterization of these stress-responsive proteins due to their low abundance. More recently, a four-dimensional (4D) proteomics approach has been introduced, which includes "ion mobility" as the fourth dimension to classical quantitative proteomics. This 4D-proteomics method utilizes trapped ion mobility spectrometry (TIMS) combined with parallel accumulation-serial fragmentation (PASEF), which significantly enhances the sensitivity and coverage of proteomics experiments, thus allowing the detection of low-abundance proteins. This review highlights the evolution of proteomic technologies, the development of the 4D proteomics workflow, and their potential application in unraveling the molecular mechanisms underlying plant responses to environmental stress conditions. In essence, this review article provides a comprehensive overview of the state-of-the-art in proteomics, emphasizing its transformative impact on plant science research and its potential to understand crop stress resilience.
{"title":"Introduction of 4D-Proteomics: A Breakthrough in Analyzing the Plant Proteomes During Stress Conditions.","authors":"Ravi Gupta","doi":"10.1111/ppl.70735","DOIUrl":"https://doi.org/10.1111/ppl.70735","url":null,"abstract":"<p><p>Proteomics is defined as the identification, quantification, and characterization of the complete set of proteins expressed in a cell or tissue under specific conditions. The last two decades have witnessed rapid advancements in proteomics technologies, including the development of the Data-Independent Acquisition (DIA) mode, which has significantly improved the sensitivity, reproducibility, and depth of proteome coverage. These advancements, together with the development of cutting-edge data analysis tools, have undoubtedly facilitated the identification of stress-responsive proteins and potential biomarkers in different organisms. However, the identification of such stress-responsive proteins, particularly in plants, remains relatively challenging because of the presence of various high-abundance proteins such as RuBisCO, which hinders the identification and subsequent characterization of these stress-responsive proteins due to their low abundance. More recently, a four-dimensional (4D) proteomics approach has been introduced, which includes \"ion mobility\" as the fourth dimension to classical quantitative proteomics. This 4D-proteomics method utilizes trapped ion mobility spectrometry (TIMS) combined with parallel accumulation-serial fragmentation (PASEF), which significantly enhances the sensitivity and coverage of proteomics experiments, thus allowing the detection of low-abundance proteins. This review highlights the evolution of proteomic technologies, the development of the 4D proteomics workflow, and their potential application in unraveling the molecular mechanisms underlying plant responses to environmental stress conditions. In essence, this review article provides a comprehensive overview of the state-of-the-art in proteomics, emphasizing its transformative impact on plant science research and its potential to understand crop stress resilience.</p>","PeriodicalId":20164,"journal":{"name":"Physiologia plantarum","volume":"178 1","pages":"e70735"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146047092","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}
Tao He, Huan-Zhan Zhou, Zhi-Min Xu, Kang Ma, Yi-Cai Zhang, Xi Zhang, Chu-Qin Feng, Ying-Ying Zhu, Si-Yi Wang, Wen-Xuan Hua, Qu-Sheng Li
To explore how plant growth-promoting rhizobacteria (PGPR) regulate stress-tolerant plant growth and enhance heavy metal remediation under combined cadmium (Cd) and salt stress, we conducted hydroponic experiments using Suaeda salsa inoculated with Escherichia coli-10,527. We investigated the changes in plant growth and stress tolerance, Cd translocation, cell ultrastructure, Cd subcellular distribution, and gene expression under hydroponic conditions. The results showed that inoculation improved plant biomass, stress tolerance, and Cd uptake, particularly under low Cd/salt concentrations. E. coli-10,527 colonized lateral root zones and secreted extracellular polymeric substances (EPS), which promoted flavonoid accumulation (by 12.68%-36.76%), thereby enhancing root growth and Cd accumulation. Compared with the uninoculated control, E. coli-10,527 inoculation altered the subcellular distribution of Cd in S. salsa; the proportion of Cd in the cytoplasm increased from 16.29% (29.06%) to 24.28% (45.57%) in roots (shoots). Transcriptomic analysis revealed the upregulation of genes (ZIPA, NRAMP3, and HMA4) potentially involved in enhanced Cd transport and vacuolar sequestration. Overall, inoculation with E. coli-10,527 can promote root development in S. salsa under Cd and salt stress, while facilitating simultaneous phytoremediation of Cd and salt. This study provides an effective microbial inoculation strategy for Cd remediation in saline soils affected by combined stresses.
{"title":"Integration of Cytological and Transcriptomics Analyses Reveals How Escherichia coli Inoculation Enhances Suaeda Salsa Root Growth and Alleviates Cadmium-Salt Stress.","authors":"Tao He, Huan-Zhan Zhou, Zhi-Min Xu, Kang Ma, Yi-Cai Zhang, Xi Zhang, Chu-Qin Feng, Ying-Ying Zhu, Si-Yi Wang, Wen-Xuan Hua, Qu-Sheng Li","doi":"10.1111/ppl.70763","DOIUrl":"https://doi.org/10.1111/ppl.70763","url":null,"abstract":"<p><p>To explore how plant growth-promoting rhizobacteria (PGPR) regulate stress-tolerant plant growth and enhance heavy metal remediation under combined cadmium (Cd) and salt stress, we conducted hydroponic experiments using Suaeda salsa inoculated with Escherichia coli-10,527. We investigated the changes in plant growth and stress tolerance, Cd translocation, cell ultrastructure, Cd subcellular distribution, and gene expression under hydroponic conditions. The results showed that inoculation improved plant biomass, stress tolerance, and Cd uptake, particularly under low Cd/salt concentrations. E. coli-10,527 colonized lateral root zones and secreted extracellular polymeric substances (EPS), which promoted flavonoid accumulation (by 12.68%-36.76%), thereby enhancing root growth and Cd accumulation. Compared with the uninoculated control, E. coli-10,527 inoculation altered the subcellular distribution of Cd in S. salsa; the proportion of Cd in the cytoplasm increased from 16.29% (29.06%) to 24.28% (45.57%) in roots (shoots). Transcriptomic analysis revealed the upregulation of genes (ZIPA, NRAMP3, and HMA4) potentially involved in enhanced Cd transport and vacuolar sequestration. Overall, inoculation with E. coli-10,527 can promote root development in S. salsa under Cd and salt stress, while facilitating simultaneous phytoremediation of Cd and salt. This study provides an effective microbial inoculation strategy for Cd remediation in saline soils affected by combined stresses.</p>","PeriodicalId":20164,"journal":{"name":"Physiologia plantarum","volume":"178 1","pages":"e70763"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146053496","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}