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Plants
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Decoding Plant Stress Responses: An Integration of Physiology and Biochemistry
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Decoding Plant Stress Responses: An Integration of Physiology and Biochemistry

A special issue of Plants (ISSN 2223-7747).

Deadline for manuscript submissions: 31 August 2026 | Viewed by 6188

Special Issue Editors

Dr. Yanqiang Gao

E-Mail Website
Guest Editor
College of Life Sciences, Northeast Forestry University, Harbin 150040, China
Interests: metabolic biology; stress biology; genetics
Prof. Dr. Lixin Li

E-Mail Website
Guest Editor
Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
Interests: the linkage between metabolic mechanisms and stress response; the mechanism of plant-growth-promoting bacteria enhancing plant stress adaptability
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Extreme weather events have become increasingly frequent, underscoring the critical need to deepen our understanding of plant adaptation and resilience to environmental fluctuations regarding climate change. Significant advancements have been made in understanding the regulatory networks at the molecular level, particularly in model organisms such as Arabidopsis thaliana. However, sudden and severe environmental stresses continue to present significant challenges. For instance, a late spring cold snap in 2024, characterized by a sudden temperature drop, adversely affected major grain crops, particularly winter wheat in the primary production regions of North China and the Huang-Huai-Hai area. There have been various reports on these events, which require further validation.

This Special Issue aims to advance our knowledge of plant stress responses and adaptive mechanisms by integrating physiological and biochemical approaches. Biochemicals such as soluble sugars, proline, flavonoids, and terpenoids play a positive role in modulating stress responses through various physiological processes. For instance, soluble sugars contribute to cold stress tolerance by modulating cellular osmotic pressure, while proline contributes by mitigating drought stress. Although flavonoids and terpenoids are broadly recognized for conferring resistance to both biotic and abiotic stresses, the specific metabolites involved and their underlying biochemical mechanisms require further investigation. A comprehensive understanding of stress-induced physiological and biochemical changes is essential, as they can provide valuable insights to inform modern breeding programs and drive other scientific advancements.

Manuscript Submission Information:

We invite researchers to contribute to this research topic and welcome original research articles, reviews, and perspectives that address the co-regulation of biotic and abiotic stressess in plants with a particular focus on the following topics:

  • Molecular mechanisms underlying biotic and abiotic stress response.
    • Interactions between transcription factors and other regulatory proteins, as well as downstream structural genes.
    • Impact of light, temperature, drought, salinity, pH, disease, and other environmental factors.
  • Use of omics technologies to unravel regulatory networks underlying specific stress conditions.
    • Role of physiology and biochemistry in plant stress responses.
    • Mechanism of metabolome change patterns in response to environmental stress. Plant bioactive components that are responsive to stress.
    • Advanced omics technologies, such as single-cell sequencing, spatial transcriptomics, and spatial metabolomics that are employed in studying plant stress responses.
  • The dynamic interplay of plants, microbes, and their environment.
  • Genetic manipulation of biotic and abiotic stress resistance for agricultural or industrial applications.

Dr. Yanqiang Gao
Prof. Dr. Lixin Li
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • stress response
  • omics
  • physiology and biochemistry
  • stress-related metabolites
  • microbial interactome

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Published Papers (8 papers)

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Research

17 pages, 5570 KB  
Article
Comprehensive Analysis of the Poplar DREB A4 Subfamily and the Role of PtrDREB4 in Response to Drought Stress
by Shuang Cheng, Zhihao Jia, Huolin Zhou, Limin Wang, Yanan Chen, Nan Sun, Dong Li, Bei Li, Hongxia Zhang, Yanfeng Liu and Lei Yang
Plants 2026, 15(5), 758; https://doi.org/10.3390/plants15050758 - 1 Mar 2026
Viewed by 472
Abstract
The dehydration response element binding protein (DREB) family of the AP2/ERF superfamily functions as a key regulatory component in plant adaptation to water-deficit conditions. However, studies on the DREB A4 subfamily in poplar (Populus trichocarpa) are insufficient. In this study, members [...] Read more.
The dehydration response element binding protein (DREB) family of the AP2/ERF superfamily functions as a key regulatory component in plant adaptation to water-deficit conditions. However, studies on the DREB A4 subfamily in poplar (Populus trichocarpa) are insufficient. In this study, members of the DREB A4 subgroup in poplar were identified and analyzed via bioinformatic analysis. A pCAMBIA-2300-PtrDREB4 expression vector was constructed and transformed into Arabidopsis, followed by phenotypic analysis of transgenic plant in response to drought stress. A total number of 29 DREB A4 members were identified in the poplar genome. Synteny analysis revealed that 19 gene pairs went through segmental duplication at least 12.84 million years ago. Their promoter regions were enriched with cis-elements related to stress resistance, hormone regulation, and growth and development. Upstream regulator analysis of poplar DREB A4 genes identified 425 transcription factor genes, which belonged to 39 families. Gene expression analysis demonstrated distinct expression patterns of DREB A4 genes in leaves, roots and stems with a notable response to drought stress. Ectopic expression of PtrDREB4 in yeast and Arabidopsis increased the drought tolerance of transformants, indicating the positive role of PtrDREB4 in response to drought stress. These findings collectively established a theoretical foundation for further functional exploration of DREB A4 genes in poplar. Full article
(This article belongs to the Special Issue Decoding Plant Stress Responses: An Integration of Physiology and Biochemistry)
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23 pages, 6224 KB  
Article
Overexpression of AmCML24 Improves Abiotic Stress Tolerance and Upregulates Stress-Responsive Genes in Arabidopsis
by Jing Niu, Jiexia Bai, Shijing Sun, Yuting Fan, Jiaxin Li, Yuhan Cao, Lin Li, Haoyuan Jin, Lili Zhang, Fanjuan Meng and Qiuxiang Luo
Plants 2026, 15(3), 420; https://doi.org/10.3390/plants15030420 - 30 Jan 2026
Viewed by 508
Abstract
With the intensification of global climate change, environmental issues such as soil salinization and drought have exerted an increasingly prominent impact on plants. Tibetan peach (Amygdalus mira), a rare native tree species of the genus Amygdalus in the Rosaceae family, possesses [...] Read more.
With the intensification of global climate change, environmental issues such as soil salinization and drought have exerted an increasingly prominent impact on plants. Tibetan peach (Amygdalus mira), a rare native tree species of the genus Amygdalus in the Rosaceae family, possesses extremely strong tolerance to cold, drought, and disease stress. In the previous study, we found that the protein abundance of a calcium-binding protein, AmCML24, was significantly upregulated in Tibetan peach under drought stress, leading us to hypothesize that it plays an important role in the molecular mechanisms underlying plant responses to abiotic stresses. Therefore, this study focuses on AmCML24, aiming to preliminarily characterize the stress-tolerant function of AmCML24 and explore its biological role in plant tolerance to saline–alkali and drought stresses. Results demonstrated that AmCML24 responds to multiple abiotic stresses. Yeast and Arabidopsis thaliana lines overexpressing AmCML24 exhibited enhanced tolerance to NaCl, NaHCO3, and mannitol stresses, with a significant upregulation in the expression of stress-responsive genes. This study lays a solid foundation for deciphering the stress regulatory network of Tibetan peach and elucidating the biological function of AmCML24, while also providing a scientific basis for the genetic improvement, exploitation, and utilization of Tibetan peach germplasm resources. Full article
(This article belongs to the Special Issue Decoding Plant Stress Responses: An Integration of Physiology and Biochemistry)
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18 pages, 6807 KB  
Article
Determining the Critical Period of Continuous Waterlogging in Maize: An Analysis of Physiological, Biochemical, and Transcriptomic Traits
by Denglong Chen, Cong Peng, Zhiming Liu, Wanrong Gu, Fanyun Yao, Lichun Wang, Yujun Cao and Yongjun Wang
Plants 2026, 15(2), 330; https://doi.org/10.3390/plants15020330 - 21 Jan 2026
Cited by 1 | Viewed by 464
Abstract
Waterlogging stress severely limits crop photosynthesis and energy supplies, resulting in significant yield reductions. However, the critical duration of waterlogging stress during the maize jointing stage remains unclear, and the physiological and molecular mechanisms underlying its effects on photosynthetic efficiency and energy synthesis [...] Read more.
Waterlogging stress severely limits crop photosynthesis and energy supplies, resulting in significant yield reductions. However, the critical duration of waterlogging stress during the maize jointing stage remains unclear, and the physiological and molecular mechanisms underlying its effects on photosynthetic efficiency and energy synthesis in maize require further investigation. In this study, we systematically analyzed the responses of physiological traits, transcriptomic profiles, and the yield formation in maize (Zea mays L.) to varying waterlogging durations imposed during the jointing stage, including 0 days (CK), 2 days (F2), 4 days (F4), 6 days (F6), 8 days (F8), and 10 days (F10). Our results indicate that the (1) grain weight (GW) showed no significant difference between F2 and CK. However, the GW in F4, F6, F8, and F10 decreased significantly by 17.49%, 26.45%, 60.24%, and 100.00%, respectively, compared to the CK. (2) Compared with the CK, the malondialdehyde content progressively increased from F4 to F10, while antioxidant enzyme activity gradually decreased. The chlorophyll content declined by 29.93% to 57.38%, and net photosynthetic efficiency decreased by 13.82% to 38.93%. Although the leaf sucrose content in from F4 to F10 gradually decreased, the leaf starch content remained stable in F4 and F6. In contrast, the starch content in F8 and F10 leaves was significantly reduced by 37.55% and 47.60%, respectively, compared with CK. (3) A transcriptomic analysis revealed that during from F2 to F4, genes encoding photosystem I subunit protein, such as PSAD, and the cytochrome b6f complex proteingene PETC were downregulated. At F6, these key genes encoding photosynthetic proteins were upregulated. However, at F8 and F10, their expression was significantly downregulated. Concurrently, genes related to ATP synthesis (e.g., ATPD) as well as starch and sucrose metabolism (e.g., SPP2, SS1) were also downregulated. In summary, when waterlogging stress persists for no longer than 6 days, plants can maintain their starch content to supply energy for growth, thereby ensuring basic developmental needs. When waterlogging persists for more than 6 days, energy synthesis is impaired, and the nutrient transport to the grains is significantly inhibited, ultimately resulting in a substantial reduction in yield. Therefore, 6 days of waterlogging can be considered the critical threshold for significant yield loss in maize during the jointing stage. Full article
(This article belongs to the Special Issue Decoding Plant Stress Responses: An Integration of Physiology and Biochemistry)
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20 pages, 10620 KB  
Article
LcSHMT4 from Sheepgrass Improves Tolerance to Cadmium and Manganese and Enhances Cd and Mn Accumulation in Grains
by Jianli Wang, Guili Di, Yuanyuan Lin, Linlin Mu, Xu Zhuang, Dongmei Zhang, Weibo Han, Tuanyao Chai, Aimin Zhou and Kun Qiao
Plants 2026, 15(1), 91; https://doi.org/10.3390/plants15010091 - 27 Dec 2025
Cited by 1 | Viewed by 630
Abstract
Heavy metal contamination is a serious environmental problem worldwide, with substantial negative ecological and economic effects. Serine hydroxymethyltransferase (SHMT) is a key metabolic and photorespiratory enzyme in plant cells, and it is also involved in stress responses. In this study, LcSHMT4 was isolated [...] Read more.
Heavy metal contamination is a serious environmental problem worldwide, with substantial negative ecological and economic effects. Serine hydroxymethyltransferase (SHMT) is a key metabolic and photorespiratory enzyme in plant cells, and it is also involved in stress responses. In this study, LcSHMT4 was isolated from sheepgrass (Leymus chinensis (Trin.) Tzvel) after transcriptome sequence analysis. The transcript levels of LcSHMT4 in sheepgrass seedlings increased under Cd and Mn stresses, and subcellular localization analysis in tobacco leaves revealed that its encoded protein localizes at the mitochondria. Transgenic yeast and rice lines overexpressing LcSHMT4 showed increased tolerance to Cd and Mn, compared with that of their controls. In addition, compared with the control, transgenic rice overexpressing LcSHMT4 accumulated more Cd and Mn in brown rice grains. The transcript levels of genes encoding Cd or Mn transporters were increased in the LcSHMT4-overexpressing transgenic rice lines. We speculate that LcSHMT4 may enhance Cd and Mn tolerance by increasing the activities of antioxidant enzymes and the glutathione content and increase heavy metal accumulation by inducing the expression of genes encoding transporters. These results highlight useful genetic resources and provide a theoretical basis for further research on heavy metal tolerance and the phytoremediation of heavy-metal-contaminated soil. Full article
(This article belongs to the Special Issue Decoding Plant Stress Responses: An Integration of Physiology and Biochemistry)
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19 pages, 11088 KB  
Article
Unraveling the Saline–Alkali–Tolerance Mystery of Leymus chinensis Nongjing–4: Insights from Integrated Transcriptome and Metabolome Analysis
by Jianli Wang, Mingyu Wang, Zijian Zhang, Jinxia Li, Qiuping Shen, Yuanhao Zhang, Dongmei Zhang, Linlin Mou, Xu Zhuang, Wenhui Wang, Zhaohui Li, Long Han, Zhongbao Shen and Lixin Li
Plants 2025, 14(24), 3852; https://doi.org/10.3390/plants14243852 - 17 Dec 2025
Cited by 2 | Viewed by 948
Abstract
Soil salinization–alkalization is a critical abiotic constraint on global agriculture, threatening agroecosystem sustainability. Leymus chinensis, a high–quality perennial forage with strong stress resilience, is an ideal model for studying saline–alkali tolerance in graminaceous crops. We integrated physiological, transcriptomic, and metabolomic profiling to [...] Read more.
Soil salinization–alkalization is a critical abiotic constraint on global agriculture, threatening agroecosystem sustainability. Leymus chinensis, a high–quality perennial forage with strong stress resilience, is an ideal model for studying saline–alkali tolerance in graminaceous crops. We integrated physiological, transcriptomic, and metabolomic profiling to dissect its responses under moderate vs. severe carbonate stress, mimicking natural saline–alkali soils rather than single salt stress treatments. Multi–omics analysis revealed drastic reprogramming of energy metabolism, carbohydrate homeostasis, water transport, and secondary metabolism. Our novel finding reveals that L. chinensis uses stress–severity–dependent mechanisms, with flavonoid biosynthesis as a central “regulatory hub”: moderate saline–alkali stress acts as a stimulus for “Adaptive Activation” (energy + antioxidants), promoting growth, while severe stress exceeds tolerance thresholds, causing “systemic imbalance” (oxidative damage + metabolic disruption) and growth retardation. Via WGCNA and metabolome–transcriptome modeling, 22 transcription factors linked to key flavonoid metabolites were identified, functioning as molecular switches for stress tolerance. Our integrated approach provides novel insights into L. chinensis’ tolerance networks, and the flavonoid biosynthesis pathways and regulatory genes offer targets for precision molecular breeding to enhance forage stress resistance and mitigate yield losses from salinization–alkalization. Full article
(This article belongs to the Special Issue Decoding Plant Stress Responses: An Integration of Physiology and Biochemistry)
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24 pages, 35618 KB  
Article
Saline–Alkaline Stress-Driven Rhizobacterial Community Restructuring and Alleviation of Stress by Indigenous PGPR in Alfalfa
by Min Wang, Ting Han, Fenghua Huang, Xiaochen Li, Jiayao Shan, Dongmei Zhang, Zhongbao Shen, Jianli Wang and Kun Qiao
Plants 2025, 14(24), 3844; https://doi.org/10.3390/plants14243844 - 17 Dec 2025
Cited by 1 | Viewed by 1015
Abstract
Background: The Songnen Plain in China contains soda saline–alkaline soil, wherein salinity and alkalinity severely constrain crop productivity. Alfalfa (Medicago sativa L.) is a forage legume that has adapted to moderate saline–alkaline conditions, but how its rhizosphere microbial community facilitated this adaptation [...] Read more.
Background: The Songnen Plain in China contains soda saline–alkaline soil, wherein salinity and alkalinity severely constrain crop productivity. Alfalfa (Medicago sativa L.) is a forage legume that has adapted to moderate saline–alkaline conditions, but how its rhizosphere microbial community facilitated this adaptation remains unclear. Methods: Using 16S rRNA gene sequencing, we compared alfalfa rhizosphere bacteria in saline–alkaline soil (AS) and control soil. Bacteria isolated from AS were screened for plant growth-promoting traits, with the most effective strains validated in pot experiments involving 50 mM NaHCO3. Results: Compared with the control soil bacterial community, the AS bacterial community was significantly enriched with Methylomirabilota and unclassified bacteria (phylum level), with the genus RB41 identified as the most discriminative biomarker. Gene functions predicted using PICRUSt2 reflected the responsiveness of this community to environmental stressors. Inoculations with Pseudomonas laurentiana strain M73 and Stenotrophomonas maltophilia strain M81, which were isolated from AS, significantly improved alfalfa growth and health under NaHCO3 stress. Conclusions: Saline–alkaline conditions in the Songnen Plain reshape the alfalfa rhizosphere bacterial community, enriching for specific taxa and potentially enhancing microbial functions associated with stress resistance. Strains M73 and M81 can effectively promote stress tolerance, making them useful microbial resources for improving soil conditions. Full article
(This article belongs to the Special Issue Decoding Plant Stress Responses: An Integration of Physiology and Biochemistry)
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20 pages, 7575 KB  
Article
The Defense Response of Honeyberry to Root Rot Pathogens: Evidence Based on Pathogen Identification and Host Mechanism
by Siyu Qiao, Dianwen Wei, Hui Chen, Jinghua Yu, Shufang Gong, Zhiyong Niu, Aimin Zhou, Kun Qiao and Jingang Wang
Plants 2025, 14(24), 3820; https://doi.org/10.3390/plants14243820 - 15 Dec 2025
Viewed by 748
Abstract
Honeyberry plants (Lonicera caerulea L., family Caprifoliaceae), which produce small, highly nutritious berries, have recently been subject to an outbreak of root rot, resulting in a drastic decrease in fruit yield. In this study, we isolated the fungal community from the roots [...] Read more.
Honeyberry plants (Lonicera caerulea L., family Caprifoliaceae), which produce small, highly nutritious berries, have recently been subject to an outbreak of root rot, resulting in a drastic decrease in fruit yield. In this study, we isolated the fungal community from the roots of diseased plants and analyzed the mechanisms of interaction between key fungi and honeyberry plants. Nine fungal morphotypes were identified via observation of cultures and internal transcribed spacer gene sequence analysis. Pathogenicity assays showed that infection with isolates from the genus Fusarium reproduced the typical root rot symptoms, and Fusarium foetens caused the most severe inhibition of root growth. Transcriptomic analysis of infected plants and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the biosynthesis of secondary metabolites was enriched in roots of honeyberry plants infected with F. foetens. This study elucidates that when honeyberry is affected by root rot disease, it produces secondary metabolites to defend against pathogenic invasion, providing a theoretical basis and molecular targets for the green management of this disease. Full article
(This article belongs to the Special Issue Decoding Plant Stress Responses: An Integration of Physiology and Biochemistry)
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17 pages, 5915 KB  
Article
A NaHCO3-Tolerant Endophyte Bacillus amyloliquefaciens ZmBA DSM7 Enhances Growth and Mitigates NaHCO3-Induced Alkaline Stress in Maize Through Multiple Mechanism
by Guoliang Li, Wenhao Wan, Miaoxin Shi, Huitao Cui, Fengshan Yang, Wei Yang and Shumei Jin
Plants 2025, 14(24), 3742; https://doi.org/10.3390/plants14243742 - 8 Dec 2025
Viewed by 824
Abstract
Background Soil alkalization inhibits plant growth and yield, the endophytic plant growth-promoting bacteria (PGPB) can alleviate salt stresses for plant. Methods: Isolate a NaHCO3-tolerant Bacillus amyloliquefaciens strain (ZmBA DSM7), characterize its PGP traits, elucidate the physiological and biochemical mechanisms [...] Read more.
Background Soil alkalization inhibits plant growth and yield, the endophytic plant growth-promoting bacteria (PGPB) can alleviate salt stresses for plant. Methods: Isolate a NaHCO3-tolerant Bacillus amyloliquefaciens strain (ZmBA DSM7), characterize its PGP traits, elucidate the physiological and biochemical mechanisms by which it enhances maize growth. Results: A ZmBA DSM7 strain was isolated from the root of maize growing in a mildly alkaline soil (pH 8.8). The strain exhibited high tolerance to 500 mM NaHCO3 and maintained its PGP traits, ZmBA DSM7 had a positive effect on maize seed germination and alkaline stress tolerance by enhancing seed vigor under normal or alkaline growth conditions. The maize seedlings inoculation with ZmBA DSM7 markedly improved chlorophyll content and reduced oxidative damage by lowering malondialdehyde (MDA) content and enhancing the antioxidant enzymes activities in the pots. In the field, ZmBA DSM7-inoculated plants showed a increase in yield (such as the ear length, the number of kernels row number, average spike weight, the 100-grain weight, and so on). Conclusion: The ZmBA DSM7 promotes maize growth and mitigates NaHCO3-induced alkaline stress in maize by a multifaceted mechanism involving enhanced nutrient acquisition (N, P and K) and antioxidant status and improved soil quality. Full article
(This article belongs to the Special Issue Decoding Plant Stress Responses: An Integration of Physiology and Biochemistry)
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