Biochemical responses of rice roots to cold stress

CALMODULIN-LIKE16 and PIN-LIKES7a cooperatively regulate rice seedling primary root elongation under chilling

Low-temperature sensitivity at the germination stage is a challenge for direct seeding of rice in Asian countries. How Ca2+ and auxin (IAA) signaling regulate primary root growth under chilling remains unexplored. Here, we showed that OsCML16 interacted specifically with OsPILS7a to improve primary root elongation of early rice seedlings under chilling. OsCML16, a subgroup 6c member of the OsCML family, interacted with multiple cytosolic loop regions of OsPILS7a in a Ca2+-dependent manner. OsPILS7a localized to the endoplasmic reticulum membranes and functioned as an auxin efflux carrier in a yeast growth assay. Transgenics showed that presence of OsCML16 enhanced primary root elongation under chilling, whereas the ospils7a knockout mutant lines showed the opposite phenotype. Moreover, under chilling conditions, OsCML16 and OsPILS7a-mediated Ca2+ and IAA signaling and regulated the transcription of IAA signaling-associated genes (OsIAA11, OsIAA23, and OsARF16) and cell division marker genes (OsRAN1, OsRAN2, and OsLTG1) in primary roots. These results show that OsCML16 and OsPILS7a cooperatively regulate primary root elongation of early rice seedlings under chilling. These findings enhance our understanding of the crosstalk between Ca2+ and IAA signaling and reveal insights into the mechanisms underlying cold-stress response during rice germination.

MicroRNA Profiling Revealed the Mechanism of Enhanced Cold Resistance by Grafting in Melon (Cucumis melo L.)

Grafting is widely used to improve the resistance to abiotic stresses in cucurbit plants, but the effect and molecular mechanism of grafting on cold stress are still unknown in melon. In this study, phenotypic characteristics, physiological indexes, small-RNA sequencing and expression analyses were performed on grafted plants with pumpkin rootstock (PG) and self-grafted plants (SG) to explore the mechanism of changed cold tolerance by grafting in melon. Compared with SG plants, the cold tolerance was obviously enhanced, the malondialdehyde (MDA) content was significantly decreased and the activities of antioxidant enzymes (superoxide dismutase, SOD; catalase, CAT; peroxidase, POD) were significantly increased in PG plants. Depend on differentially expressed miRNA (DEM) identification and expression pattern analyses, cme-miR156b, cme-miR156f and chr07_30026 were thought to play a key role in enhancing low-temperature resistance resulting from grafting. Subsequently, 24, 37 and 17 target genes of cme-miR156b, cme-miR156f and chr07_30026 were respectively predicted, and 21 target genes were co-regulated by cme-miR156b and cme-miR156f. Among these 57 unique target genes, the putative promoter of 13 target genes contained the low-temperature responsive (LTR) cis-acting element. The results of qRT-PCR indicated that six target genes (MELO3C002370, MELO3C009217, MELO3C018972, MELO3C016713, MELO3C012858 and MELO3C000732) displayed the opposite expression pattern to their corresponding miRNAs. Furthermore, MELO3C002370, MELO3C016713 and MELO3C012858 were significantly downregulated in cold-resistant cultivars and upregulated in cold-sensitive varieties after cold stimulus, and they acted as the key negative regulators of low-temperature response in melon. This study revealed three key miRNAs and three putative target genes involved in the cold tolerance of melon and provided a molecular basis underlying how grafting improved the low-temperature resistance of melon plants.

Harnessing microbial interactions with rice: Strategies for abiotic stress alleviation in the face of environmental challenges and climate change

Rice, which feeds more than half of the world's population, confronts significant challenges due to environmental and climatic changes. Abiotic stressors such as extreme temperatures, drought, heavy metals, organic pollutants, and salinity disrupt its cellular balance, impair photosynthetic efficiency, and degrade grain quality. Beneficial microorganisms from rice and soil microbiomes have emerged as crucial in enhancing rice's tolerance to these stresses. This review delves into the multifaceted impacts of these abiotic stressors on rice growth, exploring the origins of the interacting microorganisms and the intricate dynamics between rice-associated and soil microbiomes. We highlight their synergistic roles in mitigating rice's abiotic stresses and outline rice's strategies for recruiting these microorganisms under various environmental conditions, including the development of techniques to maximize their benefits. Through an in-depth analysis, we shed light on the multifarious mechanisms through which microorganisms fortify rice resilience, such as modulation of antioxidant enzymes, enhanced nutrient uptake, plant hormone adjustments, exopolysaccharide secretion, and strategic gene expression regulation, emphasizing the objective of leveraging microorganisms to boost rice's stress tolerance. The review also recognizes the growing prominence of microbial inoculants in modern rice cultivation for their eco-friendliness and sustainability. We discuss ongoing efforts to optimize these inoculants, providing insights into the rigorous processes involved in their formulation and strategic deployment. In conclusion, this review emphasizes the importance of microbial interventions in bolstering rice agriculture and ensuring its resilience in the face of rising environmental challenges.

ROS scavenging enzyme-encoding genes play important roles in the desert moss Syntrichia caninervis response to extreme cold and desiccation stresses

Abiotic stress is one of the major environmental constraints limiting plant growth. Syntrichia caninervis is one of the unique plant models that can cope with harsh environments. Reactive oxygen species (ROS) are a vital signaling molecule for protecting plants from oxidative stress, but research on ROS in S. caninervis is limited. Here, we identified 112 ROS genes in S. caninervis, including 40 GSTs, 51 PODs, 9 SODs, 6 CATs, 3 GPXs and 3 APXs families. GO and KEGG analyses showed that ROS genes are involved in responses to various stimuli and phenylpropanoid biosynthesis. ROS genes contain many stress-responsive and hormonal cis-elements in their promoter regions. More ROS genes were induced by cold stress than desiccation stress, and both conditions changed the transcript abundances of several ROS genes. CAT and POD, H2O2, MDA, and GSH were also induced under biotic stress, specifically CAT activity. The results indicated that the ScCAT genes and their activities could be strongly associated with the regulation of ROS production. This is the first systematic identification of ROS genes in S. caninervis and our findings contribute to further research into the roles of ScROS adjustment under abiotic stress while also providing excellent genetic resources for plant breeding.

Chilling stress drives organ-specific transcriptional cascades and dampens diurnal oscillation in tomato

Improving chilling tolerance in cold-sensitive crops, e.g. tomato, requires knowledge of the early molecular response to low temperature in these under-studied species. To elucidate early responding processes and regulators, we captured the transcriptional response at 30 minutes and 3 hours in the shoots and at 3 hours in the roots of tomato post-chilling from 24°C to 4°C. We used a pre-treatment control and a concurrent ambient temperature control to reveal that majority of the differential expression between cold and ambient conditions is due to severely compressed oscillation of a large set of diurnally regulated genes in both the shoots and roots. This compression happens within 30 minutes of chilling, lasts for the duration of cold treatment, and is relieved within 3 hours of return to ambient temperatures. Our study also shows that the canonical ICE1/CAMTA-to-CBF cold response pathway is active in the shoots, but not in the roots. Chilling stress induces synthesis of known cryoprotectants (trehalose and polyamines), in a CBF-independent manner, and induction of multiple genes encoding proteins of photosystems I and II. This study provides nuanced insights into the organ-specific response in a chilling sensitive plant, as well as the genes influenced by an interaction of chilling response and the circadian clock.

Recent Molecular Aspects and Integrated Omics Strategies for Understanding the Abiotic Stress Tolerance of Rice

Rice is an important staple food crop for over half of the world's population. However, abiotic stresses seriously threaten rice yield improvement and sustainable production. Breeding and planting rice varieties with high environmental stress tolerance are the most cost-effective, safe, healthy, and environmentally friendly strategies. In-depth research on the molecular mechanism of rice plants in response to different stresses can provide an important theoretical basis for breeding rice varieties with higher stress resistance. This review presents the molecular mechanisms and the effects of various abiotic stresses on rice growth and development and explains the signal perception mode and transduction pathways. Meanwhile, the regulatory mechanisms of critical transcription factors in regulating gene expression and important downstream factors in coordinating stress tolerance are outlined. Finally, the utilization of omics approaches to retrieve hub genes and an outlook on future research are prospected, focusing on the regulatory mechanisms of multi-signaling network modules and sustainable rice production.

Auxin-cytokinin interplay shapes root functionality under low-temperature stress

Low-temperature stress alters root system architecture. In particular, changes in the levels and response to auxin and cytokinin determine the fate of root architecture and function under stress because of their vital roles in regulating root cell division, differentiation, and elongation. An intricate nexus of genes encoding components of auxin and cytokinin biosynthesis, signaling, and transport components operate to counteract stress and facilitate optimum development. We review the role of auxin transport and signaling and its regulation by cytokinin during root development and stem cell maintenance under low-temperature stress. We highlight intricate mechanisms operating in root stem cells to minimize DNA damage by altering phytohormone levels, and discuss a working model for cytokinin in low-temperatures stress response.

OsLPXC negatively regulates tolerance to cold stress via modulating oxidative stress, antioxidant defense and JA accumulation in rice

Exposure of crops to low temperature (LT) during emerging and reproductive stages influences their growth and development. In this study, we have isolated a cold induced, nucleus-localized lipid A gene from rice named OsLPXC, which encodes a protein of 321 amino acids. Knockout of OsLPXC resulted in enhance sensitivity to LT stress in rice, with increased accumulation of reactive oxygen species (ROS), malondialdehyde and electrolyte leakage, while expression and activities of antioxidant enzymes were significantly suppressed. The accumulation of chlorophyll content and net photosynthetic rate of knockout plants were also decreased compared with WT under LT stress. The functional analysis of differentially expressed genes (DEGs), showed that numerous genes associated with antioxidant defense, photosynthesis, cold signaling were solely expressed and downregulated in oslpxc plants compared with WT under LT. The accumulation of methyl jasmonate (MeJA) in leave and several DEGs related to the jasmonate biosynthesis pathway were significantly downregulated in OsLPXC knockout plants, which showed differential levels of MeJA regulation in WT and knockout plants in response to cold stress. These results indicated that OsLPXC positively regulates cold tolerance in rice via stabilizing the expression and activities of ROS scavenging enzymes, photosynthetic apparatus, cold signaling genes, and jasmonate biosynthesis.

Effects of Low Temperature Stress on Source-Sink Organs in Wheat and Phosphorus Mitigation Strategies

The 21st century presents many challenges to mankind, including climate change, fast growing human population, and serious concerns over food security. Wheat is a leading cereal crop that largely fulfills the global food needs. Low temperature stress accompanied by nutrient-starved soils is badly disrupting the source-sink relationship of wheat, thus causing an acute decline in final yield and deteriorating the grain quality. This review paper aimed to understand how low temperature stress affects wheat source-sink organs (i.e., leaves, roots, and spikes) and how phosphorus application reliefs in alleviating its harmful consequences. Also, we discussed mitigation strategies to enhance wheat capacity to adapt to varying temperature extremes and made rational recommendations based on modern agronomic and breeding approaches. Therefore, this study is likely to establish a solid foundation for improving the tolerance to low temperature stress and to improve its phosphorus utilization efficiency in wheat.

Psychrophilic Bacterial Phosphate-Biofertilizers: A Novel Extremophile for Sustainable Crop Production under Cold Environment

Abiotic stresses, including low-temperature environments, adversely affect the structure, composition, and physiological activities of soil microbiomes. Also, low temperatures disturb physiological and metabolic processes, leading to major crop losses worldwide. Extreme cold temperature habitats are, however, an interesting source of psychrophilic and psychrotolerant phosphate solubilizing bacteria (PSB) that can ameliorate the low-temperature conditions while maintaining their physiological activities. The production of antifreeze proteins and expression of stress-induced genes at low temperatures favors the survival of such organisms during cold stress. The ability to facilitate plant growth by supplying a major plant nutrient, phosphorus, in P-deficient soil is one of the novel functional properties of cold-tolerant PSB. By contrast, plants growing under stress conditions require cold-tolerant rhizosphere bacteria to enhance their performance. To this end, the use of psychrophilic PSB formulations has been found effective in yield optimization under temperature-stressed conditions. Most of the research has been done on microbial P biofertilizers impacting plant growth under normal cultivation practices but little attention has been paid to the plant growth-promoting activities of cold-tolerant PSB on crops growing in low-temperature environments. This scientific gap formed the basis of the present manuscript and explains the rationale for the introduction of cold-tolerant PSB in competitive agronomic practices, including the mechanism of solubilization/mineralization, release of biosensor active biomolecules, molecular engineering of PSB for increasing both P solubilizing/mineralizing efficiency, and host range. The impact of extreme cold on the physiological activities of plants and how plants overcome such stresses is discussed briefly. It is time to enlarge the prospects of psychrophilic/psychrotolerant phosphate biofertilizers and take advantage of their precious, fundamental, and economical but enormous plant growth augmenting potential to ameliorate stress and facilitate crop production to satisfy the food demands of frighteningly growing human populations. The production and application of cold-tolerant P-biofertilizers will recuperate sustainable agriculture in cold adaptive agrosystems.

Phosphoproteomics of cold stress-responsive mechanisms in Rhododendron chrysanthum

BACKGROUND

As an alpine plant, Rhododendron chrysanthum (R. chrysanthum) has evolved cold resistance mechanisms and become a valuable plant resource with the responsive mechanism of cold stress.

METHODS AND RESULTS

We adopt the phosphoproteomic and proteomic analysis combining with physiological measurement to illustrate the responsive mechanism of R. chrysanthum seedling under cold (4 °C) stress. After chilling for 12 h, 350 significantly changed proteins and 274 significantly changed phosphoproteins were detected. Clusters of Orthologous Groups (COG) analysis showed that significantly changed phosphoproteins and proteins indicated cold changed energy production and conversion and signal transduction.

CONCLUSIONS

The results indicated photosynthesis was inhibited under cold stress, but cold induced calcium-mediated signaling, reactive oxygen species (ROS) homeostasis and other transcription regulation factors could protect plants from the destruction caused by cold stress. These data provide the insight to the cold stress response and defense mechanisms of R. chrysanthum leaves at the phosphoproteome level.

Cold response and tolerance in cereal roots

Cold stress adversely affects plant growth and is a limiting factor in crop productivity. Temperature volatility as a consequence of climate change will increase the effects of cold stress on crop cultivation. Low temperatures frequently occur early after planting in temperate climates and severely affect root development in cereals. In this review we address the question how cereal root systems respond to cold on different scales. First, we summarize the morphological, physiological and cellular responses of cereal roots to cold stress and how these processes are regulated by phytohormones. Subsequently, we highlight the status of the genetic and molecular dissection of cold tolerance with emphasis on the role of cold-responsive genes in improving cold tolerance in cereal roots. Finally, we discuss the role of beneficial microorganisms and mineral nutrients in ameliorating the effects of cold stress in cereal roots. A comprehensive knowledge of the molecular mechanisms underlying cold tolerance will ensure yield stability by enabling the generation of cold-tolerant crop genotypes.

Interrelations of nutrient and water transporters in plants under abiotic stress

Environmental changes cause abiotic stress in plants, primarily through alterations in the uptake of the nutrients and water they require for their metabolism and growth and to maintain their cellular homeostasis. The plasma membranes of cells contain transporter proteins, encoded by their specific genes, responsible for the uptake of nutrients and water (aquaporins). However, their interregulation has rarely been taken into account. Therefore, in this review we identify how the plant genome responds to abiotic stresses such as nutrient deficiency, drought, salinity and low temperature, in relation to both nutrient transporters and aquaporins. Some general responses or regulation mechanisms can be observed under each abiotic stress such as the induction of plasma membrane transporter expression during macronutrient deficiency, the induction of tonoplast transporters and reduction of aquaporins during micronutrients deficiency. However, drought, salinity and low temperatures generally cause an increase in expression of nutrient transporters and aquaporins in tolerant plants. We propose that both types of transporters (nutrients and water) should be considered jointly in order to better understand plant tolerance of stresses.

Enhanced glutathione content improves lateral root development and grain yield in rice plants

Enhanced glutathione content improves lateral root development by positively regulating the transcripts of root development genes responsive to glutathione treatment, thereby increasing the overall productivity of rice plants. Glutathione is primarily known as a cellular antioxidant molecule, but its role in lateral root development in rice plants has not been elucidated. Here, we have investigated its role in lateral root development of rice Oryza sativa L. Exogenous glutathione (GSH) promoted both the number and length of lateral roots in rice, and the GSH biosynthesis inhibitor buthionine sulfoximine (BSO) significantly reduced these parameters, compared to untreated plants. The inhibition by BSO was reversed with exogenous GSH. Transcript profiling by RNA-seq revealed that expression of the transcription factor genes DREB and ERF and the hormone-related genes AOS, LOX, JAZ, and SAUR were significantly downregulated in the BSO-treated plants and, in contrast, upregulated in plants treated with GSH and with GSH and BSO together. We generated OsGS-overexpressing transgenic plants in which the transgene is controlled by the abiotic-stress-inducible OsRab21 promoter to study the effect of endogenously increased GSH levels. In cold stress, transgenic rice plants enhanced stress tolerance and lateral root development by maintaining redox homeostasis and improving upregulating the expression of transcription factors and hormone-related genes involved in lateral root development. We observed improved root growth of OsGS-overexpressing plants in paddy fields compared to the wild-type controls. These traits may have alleviated transplanting stress during early growth in the field and accounted for the increased productivity. These results provide information and perspectives on the role of GSH in gene expression, lateral root development, and grain yield in rice.

Root responses of contrasting rice genotypes to low temperature stress

Rice (Oryza sativa L.) ssp. indica is the most cultivated species in the South of Brazil. However, these plants face low temperature stress from September to November, which is the period of early sowing, affecting plant development during the initial stages of growth, and reducing rice productivity. This study aimed to characterize the root response to low temperature stress during the early vegetative stage of two rice genotypes contrasting in their cold tolerance (CT, cold-tolerant; and CS, cold-sensitive). Root dry weight and length, as well as the number of root hairs, were higher in CT than CS when exposed to cold treatment. Histochemical analyses indicated that roots of CS genotype present higher levels of lipid peroxidation and H₂O₂ accumulation, along with lower levels of plasma membrane integrity than CT under low temperature stress. RNAseq analyses revealed that the contrasting genotypes present completely different molecular responses to cold stress. The number of over-represented functional categories was lower in CT than CS under cold condition, suggesting that CS genotype is more impacted by low temperature stress than CT. Several genes might contribute to rice cold tolerance, including the ones related with cell wall remodeling, cytoskeleton and growth, signaling, antioxidant system, lipid metabolism, and stress response. On the other hand, high expression of the genes SRC2 (defense), root architecture associated 1 (growth), ACC oxidase, ethylene-responsive transcription factor, and cytokinin-O-glucosyltransferase 2 (hormone-related) seems to be related with cold sensibility. Since these two genotypes have a similar genetic background (sister lines), the differentially expressed genes found here can be considered candidate genes for cold tolerance and could be used in future biotechnological approaches aiming to increase rice tolerance to low temperature.

Regulation of ROS Metabolism in Plants under Environmental Stress: A Review of Recent Experimental Evidence

Various environmental stresses singly or in combination generate excess amounts of reactive oxygen species (ROS), leading to oxidative stress and impaired redox homeostasis. Generation of ROS is the obvious outcome of abiotic stresses and is gaining importance not only for their ubiquitous generation and subsequent damaging effects in plants but also for their diversified roles in signaling cascade, affecting other biomolecules, hormones concerning growth, development, or regulation of stress tolerance. Therefore, a good balance between ROS generation and the antioxidant defense system protects photosynthetic machinery, maintains membrane integrity, and prevents damage to nucleic acids and proteins. Notably, the antioxidant defense system not only scavenges ROS but also regulates the ROS titer for signaling. A glut of studies have been executed over the last few decades to discover the pattern of ROS generation and ROS scavenging. Reports suggested a sharp threshold level of ROS for being beneficial or toxic, depending on the plant species, their growth stages, types of abiotic stresses, stress intensity, and duration. Approaches towards enhancing the antioxidant defense in plants is one of the vital areas of research for plant biologists. Therefore, in this review, we accumulated and discussed the physicochemical basis of ROS production, cellular compartment-specific ROS generation pathways, and their possible distressing effects. Moreover, the function of the antioxidant defense system for detoxification and homeostasis of ROS for maximizing defense is also discussed in light of the latest research endeavors and experimental evidence.