The non-canonically organized members of MIR395 gene family in Brassica juncea are associated with developmentally regulated, sulfate-stress responsive bidirectional promoters that exhibit orientation-dependent differential transcriptional activity

Several MICRORNA genes belonging to same family or different families are often found in homologous or non-homologous clusters. Among the various classes, head-to-head arranged genes form one of the largest categories of non-canonically organized genes. Such head-to-head arranged, non-canonically organized genes possibly share cis-regulatory region with the intergenic sequence having the potential to function as bi-directional promoter (BDP). The transcriptional regulation of head-to-head arranged genes, especially with bidirectional promoters, remains an enigma. In the past, bidirectional promoters have been characterized for a small set of protein-coding gene pairs in plants; however, to the best of our knowledge, no such study has been carried so far for MICRORNA genes. The present study thus functionally characterizes bidirectional promoters associated with members of MIR395 family, which is evolutionary conserved and is most frequently occurring cluster across plant kingdom. In Arabidopsis thaliana, the MIR395 gene family contains six members with two head-to-head arranged gene pairs- MIR395A-B and MIR395E-F. This organization was found to be conserved at seven loci for MIR395A-B, and eleven loci for MIR395E-F in five Brassica sps. Sequence analysis of the putative bidirectional promoters revealed variation in length, GC content and distribution of strict TATA-box. Comparatively higher level of conservation at both the ends of the bidirectional promoters, corresponding to ca. 250 bp upstream of 5'end of the respective MIRNA precursor, was observed. These conserved regions harbour several abiotic stress (nutrient, salt, drought) and hormone (ABA, ethylene) responsive cis-motifs. Functional characterization of putative bidirectional promoters associated with MIR395A-B and MIR395E-F from Arabidopsis and their respective orthologs from Brassica juncea (Bj_A08 MIR395A-B, Bj_B03 MIR395A-B, Bj_A07.1 MIR395E-F and Bj_A07.2 MIR395E-F) was carried out using a dual-reporter vector with β-glucuronidase (GUS) and Green Fluorescent Protein (GFP). Analysis of transcriptional regulation of the two reporter genes - GUS and GFP during developmental stages confirmed their bidirectional nature. Orientation-dependent differential reporter activity indicated asymmetric nature of the promoters. Comparison of the reporter activity amongst orthologs, paralogs and homeologs revealed regulatory diversification, an outcome expected in polyploid genomes. Interestingly, reporter gene activities driven by selected bidirectional promoters were also observed in anther and siliques apart vegetative tissues indicating role of miR395 in anther and fruit development. Finally, we evaluated the activity of reporter genes driven under transcriptional regulation of bidirectional promoters under normal and sulfate-deprived conditions which revealed asymmetric inducibility under sulfate-starvation, in agreement with the known role of miR395 in sulfate homeostasis.

Rice seed storability: From molecular mechanisms to agricultural practices

The storability of rice seeds is crucial for ensuring flexible planting options, agricultural seed security, and global food safety. With the intensification of global climate change and the constant fluctuations in agricultural production conditions, enhancing the storability of rice seeds has become particularly important. Seed storability is a complex quantitative trait regulated by both genetic and environmental factors. This article reviews the main regulatory mechanisms of rice seed storability, including the accumulation of seed storage proteins, late embryogenesis abundant (LEA) proteins, heat shock proteins, sugar signaling, hormonal regulation by gibberellins and abscisic acid, and the role of the ubiquitination pathway. Additionally, this article explores the improvement of storability using wild rice genes, molecular marker-assisted selection, and gene editing techniques such as CRISPR/Cas9 in rice breeding. By providing a comprehensive scientific foundation and practical guidance, this review aims to promote the development of rice varieties with enhanced storability to meet evolving agricultural demands.

Effects of combined ultrasound and calcium ion pretreatments on polyphenols during mung bean germination: Exploring underlying mechanisms

Mung beans were pretreated with a combination of ultrasonic and calcium ion to enhance the polyphenol content and antioxidant capacity during germination. Changes in polyphenol content and antioxidant capacity during germination, along with underlying mechanisms, were investigated. Both single ultrasound and combined ultrasound-Ca2+ pretreatments significantly increased the polyphenol content and enhanced the antioxidant capacity (p < 0.05) of mung beans depending on germination period. Among 74 polyphenolic metabolites identified in germinated mung beans, 50 were differential. Notably, 23 of these metabolites showed a significant positive correlation with antioxidant activity. Ultrasound pretreatment promoted flavonoid biosynthesis, whereas ultrasound-Ca2+ pretreatment favored the tyrosine synthesis pathway. Polyphenol composition and accumulation changes were mainly influenced by metabolic pathways like flavonoid, isoflavonoid, anthocyanin, and flavone/flavonol biosynthesis. The results suggest that ultrasound alone or combined with calcium ion pretreatments effectively enhance mung bean polyphenol content and antioxidant capacity during germination.

Three enzymes governed the rise of O2 on Earth

Current views of O2 accumulation in Earth history depict three phases: The onset of O2 production by ∼2.4 billion years ago; 2 billion years of stasis at ∼1 % of modern atmospheric levels; and a rising phase, starting about 500 million years ago, in which oxygen eventually reached modern values. Purely geochemical mechanisms have been proposed to account for this tripartite time course of Earth oxygenation. In particular the second phase, the long period of stasis between the advent of O2 and the late rise to modern levels, has posed a puzzle. Proposed solutions involve Earth processes (geochemical, ecosystem, day length). Here we suggest that Earth oxygenation was not determined by geochemical processes. Rather it resulted from emergent biological innovations associated with photosynthesis and the activity of only three enzymes: 1) The oxygen evolving complex of cyanobacteria that makes O2; 2) Nitrogenase, with its inhibition by O2 causing two billion years of oxygen level stasis; 3) Cellulose synthase of land plants, which caused mass deposition and burial of carbon, thus removing an oxygen sink and therefore increasing atmospheric O2. These three enzymes are endogenously produced by, and contained within, cells that have the capacity for exponential growth. The catalytic properties of these three enzymes paved the path of Earth's atmospheric oxygenation, requiring no help from Earth other than the provision of water, CO2, salts, colonizable habitats, and sunlight.

Arg24 and 26 of the D2 protein are important for photosystem II assembly and plastoquinol exchange in Synechocystis sp. PCC 6803

Photosystem II (PS II) assembly is a stepwise process involving preassembly complexes or modules focused around four core PS II proteins. The current model of PS II assembly in cyanobacteria is derived from studies involving the deletion of one or more of these core subunits. Such deletions may destabilize other PS II assembly intermediates, making constructing a clear picture of the intermediate events difficult. Information on plastoquinone exchange pathways operating within PS II is also unclear and relies heavily on computer-aided simulations. Deletion of PsbX in [S. Biswas, J.J. Eaton-Rye, Biochim. Biophys. Acta - Bioenerg. 1863 (2022) 148519] suggested modified QB binding in PS II lacking this subunit. This study has indicated the phenotype of the ∆PsbX mutant arose by disrupting a conserved hydrogen bond between PsbX and the D2 (PsbD) protein. We mutated two conserved arginine residues (D2:Arg24 and D2:Arg26) to further understand the observations made with the ∆PsbX mutant. Mutating Arg24 disrupted the interaction between PsbX and D2, replicating the high-light sensitivity and altered fluorescence decay kinetics observed in the ∆PsbX strain. The Arg26 residue, on the other hand, was more important for either PS II assembly or for stabilizing the fully assembled complex. The effects of mutating both arginine residues to alanine or aspartate were severe enough to render the corresponding double mutants non-photoautotrophic. Our study furthers our knowledge of the amino-acid interactions stabilizing plastoquinone-exchange pathways while providing a platform to study PS II assembly and repair without the actual deletion of any proteins.

Copper stress in rice: Perception, signaling, bioremediation and future prospects

Copper (Cu) is an indispensable micronutrient for plants, animals, and microorganisms and plays a vital role in different physiological processes. However, excessive Cu accumulation in agricultural soil, often through anthropogenic action, poses a potential risk to plant health and crop productivity. This review article provided a comprehensive overview of the available information regarding Cu dynamics in agricultural soils, major sources of Cu contamination, factors influencing its mobility and bioavailability, and mechanisms of Cu uptake and translocation in rice plants. This review examined the impact of Cu toxicity on the germination, growth, and photosynthesis of rice plants. It also highlighted molecular mechanisms underlying Cu stress signaling and the plant defense strategy, involving chelation, compartmentalization, and antioxidant responses. This review also identified significant areas that need further research, such as Cu uptake mechanism in rice, Cu signaling process, and the assessment of Cu-polluted paddy soil and rice toxicity under diverse environmental conditions. The development of rice varieties with reduced Cu accumulation through comprehensive breeding programs is also necessary. Regulatory measures, fungicide management, plant selection, soil and environmental investigation are recommended to prevent Cu buildup in agricultural lands to achieve sustainable agricultural goals.

Comprehensive evaluation of phosphate deficiency tolerance in common vetch germplasms and the adaption mechanism to phosphate deficiency

Common vetch (Vicia sativa L.) is widely planted as forage, green manure and food. Phosphate (Pi) deficiency is an important constraint for legume crop production. In this study, P-deficiency tolerance in 40 common vetch collections was evaluated under hydroponic condition. The collections were clustered into three groups based on the tolerance level. Physiological responses to P-deficiency in two tolerant collections (418 and 426) in comparison with one sensitive collection (415) were investigated. Greater growth inhibition was observed in sensitive collection compared with two tolerant collections, although the inorganic phosphorus (P) content in sensitive collection was higher than those in tolerant collections. The internal and external purple acid phosphatase activity in plants showed no significant difference between 418 and 415 under low phosphate condition. Transcriptomic analysis in the tolerant collection 426 in response to Pi starvation showed that many common adaptive strategies were applied and PHOSPHATE STARVATION RESPONSE (PHR)-related Pi signaling and transporter genes were altered. VsPHT1.2 had the highest expression level in root among all VsPHT1s, and it was remarkably upregulated after short time of P-deficiency treatment in tolerant collections compared with sensitive collection. In conclusion, common vetch response to P starvation by altering the expressions of core genes involved in Pi transport and signaling, and the elevated expression of VsPHT1.2 gene might contribute to higher Pi acquisition efficiency in P-deficiency tolerant collections.

Nano-Fe3O4: Enhancing the tolerance of Elymus nutans to Cd stress through regulating programmed cell death

Cadmium (Cd) poses a significant threat to plant growth and the environment. Nano-Fe3O4 is effective in alleviating Cd stress in plants. Elymus nutans Griseb. is an important fodder crop on the Qinghai-Tibetan Plateau (QTP). However, the potential mechanism by which nano-Fe3O4 alleviates Cd stress in E. nutans is not well understood. E. nutans were subjected to single Cd, single nano-Fe3O4, and co-treatment with nano-Fe3O4 and Cd, and the effects on morphology, Cd uptake, antioxidant enzyme activity, reactive oxygen species (ROS) levels and programmed cell death (PCD) were studied to clarify the regulatory mechanism of nano-Fe3O4. The results showed that Cd stress significantly decreased the germination percentage and biomass of E. nutans. The photosynthetic pigment content decreased significantly under Cd stress. Cd stress also caused oxidative stress and lipid peroxidation, accumulation of excessive ROS, resulting in PCD, but the effect of nano-Fe3O4 was different. Seed germination, seedling growth, and physiological processes were analyzed to elucidate the regulatory role of nano-Fe3O4 nanoparticles in promoting photosynthesis, reducing Cd accumulation, scavenging ROS, and regulating PCD, to promote seed germination and seedling growth in E. nutans. This report provides a scientific basis for improving the tolerance of Elymus to Cd stress by using nano-Fe3O4.

The structure of Mn(II)-bound Rubisco from Spinacia oleracea

The rate of photosynthesis and, thus, CO2 fixation, is limited by the rate of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Not only does Rubisco have a relatively low catalytic rate, but it also is promiscuous regarding the metal identity in the active site of the large subunit. In Nature, Rubisco binds either Mg(II) or Mn(II), depending on the chloroplastic ratio of these metal ions; most studies performed with Rubisco have focused on Mg-bound Rubisco. Herein, we report the first crystal structure of a Mn-bound Rubisco, and we compare its structural properties to those of its Mg-bound analogues.

Challenges to rhizobial adaptability in a changing climate: Genetic engineering solutions for stress tolerance

Rhizobia interact with leguminous plants in the soil to form nitrogen fixing nodules in which rhizobia and plant cells coexist. Although there are emerging studies on rhizobium-associated nitrogen fixation in cereals, the legume-rhizobium interaction is more well-studied and usually serves as the model to study rhizobium-mediated nitrogen fixation in plants. Rhizobia play a crucial role in the nitrogen cycle in many ecosystems. However, rhizobia are highly sensitive to variations in soil conditions and physicochemical properties (i.e. moisture, temperature, salinity, pH, and oxygen availability). Such variations directly caused by global climate change are challenging the adaptive capabilities of rhizobia in both natural and agricultural environments. Although a few studies have identified rhizobial genes that confer adaptation to different environmental conditions, the genetic basis of rhizobial stress tolerance remains poorly understood. In this review, we highlight the importance of improving the survival of rhizobia in soil to enhance their symbiosis with plants, which can increase crop yields and facilitate the establishment of sustainable agricultural systems. To achieve this goal, we summarize the key challenges imposed by global climate change on rhizobium-plant symbiosis and collate current knowledge of stress tolerance-related genes and pathways in rhizobia. And finally, we present the latest genetic engineering approaches, such as synthetic biology, implemented to improve the adaptability of rhizobia to changing environmental conditions.

Structure and properties of the exopolysaccharide isolated from Flavobacterium sp. Root935

Flavobacterium strains exert a substantial influence on roots and leaves of plants. However, there is still limited understanding of how the specific interactions between Flavobacterium and their plant hosts are and how these bacteria thrive in this competitive environment. A crucial step in understanding Flavobacterium - plant interactions is to unravel the structure of bacterial envelope components and the molecular features that facilitate initial contact with the host environment. Here, we have revealed structure and properties of the exopolysaccharides (EPS) produced by Flavobacterium sp. Root935. Chemical analyses revealed a complex and interesting branched heptasaccharidic repeating unit, containing a variety of sugar moieties, including Rha, Fuc, GlcN, Fuc4N, Gal, Man and QuiN and an important and extended substitution pattern, including acetyl and lactyl groups. Additionally, conformational analysis using molecular dynamics simulation showed an extended hydrophobic interface and a distinctly elongated, left-handed helicoidal arrangement. Furthermore, properties of the saccharide chain, and likely the huge substitution pattern prevented interaction and recognition by host lectins and possessed a low immunogenic potential, highlighting a potential role of Flavobacterium sp. Root935 in plant-microbial crosstalk.

Sublethal pesticide exposure in non-target terrestrial ecosystems: From known effects on individuals to potential consequences on trophic interactions and network functioning

Over the last decades, the intensification of agriculture has resulted in an increasing use of pesticides, which has led to widespread contamination of non-target ecosystems in agricultural landscapes. Plants and arthropods inhabiting these systems are therefore chronically exposed to, at least, low levels of pesticides through direct pesticide drift, but also through the contamination of their nutrient sources (e.g. soil water or host/prey tissues). Pesticides (herbicides, acaricides/insecticides and fungicides) are chemical substances used to control pests, such as weeds, phytophagous arthropods and pathogenic microorganisms. These molecules are designed to disturb specific physiological mechanisms and induce mortality in targeted organisms. However, under sublethal exposure, pesticides also affect biological processes including metabolism, development, reproduction or inter-specific interactions even in organisms that do not possess the molecular target of the pesticide. Despite the broad current knowledge on sublethal effects of pesticides on organisms, their adverse effects on trophic interactions are less investigated, especially within terrestrial trophic networks. In this review, we provide an overview of the effects, both target and non-target, of sublethal exposures to pesticides on traits involved in trophic interactions between plants, phytophagous insects and their natural enemies. We also discuss how these effects may impact ecosystem functioning by analyzing studies investigating the responses of Plant-Phytophage-Natural enemy trophic networks to pesticides. Finally, we highlight the current challenges and research prospects in the understanding of the effects of pesticides on trophic interactions and networks in non-target terrestrial ecosystems.

Advancing plant cell wall modelling: Atomistic insights into cellulose, disordered cellulose, and hemicelluloses - A review

The complexity of plant cell walls on different hierarchical levels still impedes the detailed understanding of biosynthetic pathways, interferes with processing in industry and finally limits applicability of cellulose materials. While there exist many challenges to readily accessing these hierarchies at (sub-) angström resolution, the development of advanced computational methods has the potential to unravel important questions in this field. Here, we summarize the contributions of molecular dynamics simulations in advancing the understanding of the physico-chemical properties of natural fibres. We aim to present a comprehensive view of the advancements and insights gained from molecular dynamics simulations in the field of carbohydrate polymers research. The review holds immense value as a vital reference for researchers seeking to undertake atomistic simulations of plant cell wall constituents. Its significance extends beyond the realm of molecular modeling and chemistry, as it offers a pathway to develop a more profound comprehension of plant cell wall chemistry, interactions, and behavior. By delving into these fundamental aspects, the review provides invaluable insights into future perspectives for exploration. Researchers within the molecular modeling and carbohydrates community can greatly benefit from this resource, enabling them to make significant strides in unraveling the intricacies of plant cell wall dynamics.

Structural characterization and immunomodulating assessment of ultra-purified water extracted fucoidans from Saccharina latissima, Alaria esculenta and Laminaria hyperborea

Fucoidans, a group of high molecular weight polysaccharides derived mainly from brown algae, are characterized by their high fucose content, degree of sulfation (DS), and intra- and interspecific structural variation. Fucoidans are increasingly recognized due to various reported bioactivities, potentially beneficial for human health. To unlock their potential use within biomedical applications, a better understanding of their structure-functional relationship is needed. To achieve this, systematic bioactivity studies based on well-defined, pure fucoidans, and the establishment of standardized, satisfactory purification protocols are required. We performed a comprehensive compositional and structural characterization of crude and ultra-purified fucoidans from three kelps: Saccharina latissima (SL), Alaria esculenta (AE) and Laminaria hyperborea (LH). Further, the complement-inhibiting activity of the purified fucoidans was assessed in a human whole blood model. The purification process led to fucoidans with higher DS and fucose and lower concentrations of other monosaccharides. Fucoidans from SL and LH resembles homofucans, while AE is a heterofucan rich in galactose with comparably lower DS. Fucoidans from SL and LH showed complement-inhibiting activity in blood and blood plasma, while no inhibition was observed for AE under the same conditions. The results emphasize the importance of high DS and possibly fucose content for fucoidans' bioactive properties.

The yellow-cotyledon gene (ATYCO) is a crucial factor for thylakoid formation and photosynthesis regulation in Arabidopsis

Chloroplast development underpins plant growth, by facilitating not only photosynthesis but also other essential biochemical processes. Nonetheless, the regulatory mechanisms and functional components of chloroplast development remain largely uncharacterized due to their complexity. In our study, we identified a plastid-targeted gene, ATYCO/RP8/CDB1, as a critical factor in early chloroplast development in Arabidopsis thaliana. YCO knock-out mutant (yco) exhibited a seedling-lethal, albino phenotype, resulting from dysfunctional chloroplasts lacking thylakoid membranes. Conversely, YCO knock-down mutants produced a chlorophyll-deficient cotyledon and normal leaves when supplemented with sucrose. Transcription analysis also revealed that YCO deficiency could be partially compensated by sucrose supplementation, and that YCO played different roles in the cotyledons and the true leaves. In YCO knock-down mutants, the transcript levels of plastid-encoded RNA polymerase (PEP)-dependent genes and nuclear-encoded photosynthetic genes, as well as the accumulation of photosynthetic proteins, were significantly reduced in the cotyledons. Moreover, the chlorophyll-deficient phenotype in YCO knock-down line can be effectively suppressed by inhibition of PSI cyclic electron transport activity, implying an interaction between YCO and PSI cyclic electron transport. Taken together, our findings de underscore the vital role of YCO in early chloroplast development and photosynthesis.

Comparative transcriptome analysis of Cyperus esculentus and C. rotundus with contrasting oil contents in tubers defines genes and regulatory networks involved in oil accumulation

Plant vegetative organs present great potential for lipid storage, with tubers of Cyperus esculentus as a unique example. To investigate the genome and transcriptomic features of C. esculentus and related species, we sequenced and assembled the C. esculentus genome at the contig level. Through a comparative study of high-quality transcriptomes across 36 tissues from high-oil and intermediate-oil C. esculentus and low-oil Cyperus rotundus, we identified potential genes and regulatory networks related to tuber oil accumulation. First, we identified tuber-specific genes in two C. esculentus cultivars. Second, genes involved in fatty acid (FA) biosynthesis, triacylglycerol synthesis, and TAG packaging presented increased activity in the later stages of tuber development. Notably, tubers with high oil contents presented higher levels of these genes than those with intermediate oil contents did, whereas tubers with low oil contents presented minimal gene expression. Notably, a large fragment of the FA biosynthesis rate-limiting enzyme-encoding gene BCCP1 was missing from the C. rotundus transcript, which might be responsible for blocking FA biosynthesis in its tubers. WGCNA pinpointed a gene module linked to tuber oil accumulation, with a coexpression network involving the transcription factors WRI1, MYB4, and bHLH68. The ethylene-related genes in this module suggest a role for ethylene signaling in oil accumulation, which is supported by the finding that ethylene (ETH) treatment increases the oil content in C. esculentus tubers. This study identified potential genes and networks associated with tuber oil accumulation in C. esculentus, highlighting the role of specific genes, transcription factors, and ethylene signaling in this process.

Jasmonic acid mediates Ca2+ dependent signal transduction and plant immunity

Pathogen attacks can cause significant damage to plants, posing a threaten to global food production. Plants have developed exquisite methods to rapidly store a key defensive hormone jasmonate (JA), which stimulates their entire evolutionary adaptive response to pathogen attack. However, understanding how plants initiate JA biosynthesis in response to pathogen attacks has remained elusive. In this review, we discuss the newly discovered JAV1-JAZ8-WRKY51 (JJW) complex, which plays a crucial role in regulating JA production to deter insect attacks. The JJW complex inhibits JA production in plants, maintaining a low baseline level of JA that promotes optimal plant development. However, when plants are attacked by insects, a rapid influx of calcium stimulates the JAV1 calcium-dependent protein phosphate, leading to the breakdown of the JJW complex and the activation of JA production. This surge in JA levels, initiates plant defense mechanisms against the invading insects. These findings shed light on the intricate defense system that plants have evolved to combat diseases.

Assembly of root-associated bacterial community and soil health in cadmium-contaminated soil affected by nano/bulk-biochar compost associations

Biochar (BC) has been proven effective in promoting the production of safety food in cadmium (Cd)-polluted soil and the impact can be further enhanced through interaction with compost (CM). However, there existed unclear impacts of biochar with varying particle sizes in conjunction with compost on microbiome composition, rhizosphere functions, and soil health. Hence, in this study, two bulk-biochar derived from wood chips and pig manure were fabricated into nano-biochar using a ball-milling method. Subsequently, in a field experiment, the root-associated bacterial community and microbial functions of lettuce were evaluated in respond to Cd-contaminated soil remediated with nano/bulk-BCCM. The results showed that compared to bulk-BCCM, nano-BCCM significantly reduced the Cd concentration in the edible part of lettuce and the available Cd in the soil. Both nano-BCCM and bulk-BCCM strongly influenced the composition of bacterial communities in the four root-associated niches, and enhanced rhizosphere functions involved in nitrogen, phosphorus, and carbon cycling, as well as the relative abundance and biodiversity of keystone modules in rhizosphere soil. Furthermore, soil quality index analysis indicated that nano-BCCM exhibited greater potential than bulk-BCCM in maintaining soil health. The data revealed that nano-BCCM could regulate the Cd concentration in lettuce shoot by promoting microbial biodiversity of keystone modules in soil-root continuum and rhizosphere bacterial functions. These findings suggest that nano-biochar compost associations can be a superior strategy for enhancing microbial functions, maintaining soil health, and ensuring crop production safety in the Cd-contaminated soil compared to the mix of bulk-biochar and compost.

Outward-rectifying potassium channels GORK and SKOR function in regulation of root growth under salt stress in Arabidopsis thaliana

Plants often face high salinity as a significant environmental challenge with roots being the first responders to this stress. Maintaining K+/Na+ ratio within plant cells is crucial for survival, as the intracellular K+ level decreases and the intracellular Na+ level increases under saline conditions. However, knowledge about the molecular regulatory mechanisms of K+ loss in response to salt stress through outward-rectifying K+ channels in plants is largely unknown. In this study, we found that the Arabidopsis double mutant gorkskor, in which the GORK and SKOR genes are disrupted, showed an improved primary root growth under salt stress compared to wild-type (WT) and the gork and skor single-mutant plants. No significant differences in the sensitivity to mannitol stress between the WT and gorkskor mutant were observed. Accumulation of ROS induced by salt stress was reduced in the gorkskor roots. The gorkskor mutant seedlings had significantly higher K+ content, lower Na+ content, and a greater resultant K+/Na+ ratio than the WT under salt stress. Moreover, salt-stress-induced elevation of cytosolic free Ca2+ concentration was reduced in the gorkskor roots. Taken together, these results suggest that Arabidopsis Shaker-type outward-rectifying K+ channels GORK and SKOR may redundantly function in regulation of primary root growth under salt stress and are involved in not only the late-stage response (e.g. K+ leakage) but also the early response including ROS production and [Ca2+]cyt elevation.

Combined metabolomics and bioactivity assays kernelby-productsof two native Chinese cherry species: The sources of bioactive nutraceutical compounds

Cherry kernels are a by-product of cherries that are usually discarded, leading to waste and pollution. In this study, the chemical composition of 21 batches of cherry kernels from two different cherry species was analyzed using untargeted metabolomics. The in vitro antioxidant activity, cellular antioxidant activity, and antiproliferative activity of these kernel extracts were also determined, and a correlation analysis was conducted between differential compounds and biological activity. A total of 49 differential compounds were screened. The kernels of Prunus tomentosa were found to have significantly higher total phenol, total flavonoid content, and biological activity than those of Prunus pseudocerasus (P < 0.05). Correlation analysis showed that flavonoids had the greatest contribution to biological activity. The study suggests that both species of cherry kernel, particularly Prunus tomentosa, could be a potential source of bioactive compounds that could be used in the pharmaceutical, cosmetic, and food industries.

Preparation, bioactivities, and food industry applications of tuber and tuberous roots peptides: A review

Tuber and tuberous roots proteins are important sources for producing bioactive peptides. The objective of this review is to present the current research status of tubers and tuberous roots bioactive peptides (TTRBP), including its preparation methods, purification techniques, structure identification approaches, biological functions, and applications in the food industry. Moreover, the current challenges and future development trends of TTRBP are elucidated. Currently, TTRBP are mainly produced by enzymatic hydrolysis and fermentation. Pretreatment like high static pressure, ultrasound and microwave can assist enzymatic hydrolysis and facilitate TTRBP production. In addition, TTRBP are structurally diverse, which is related to the molecular weight, amino acids composition, and linkage mode. Accordingly, they have various biological activities (such as antioxidant, antihypertensive, hypoglycemic) and have been utilized in the food industry as functional ingredients and food additives. This review will provide valuable insights for the optimal utilization of tuber and tuberous roots.

Unveiling novel insights into Bacillus velezensis 16B pectin lyase for improved fruit juice processing

Microbial pectinolytic enzymes are important in various industries, particularly food processing. This study focuses on uncovering insights into a novel pectin lyase, BvPelB, from Bacillus velezensis 16B, with the aim of enhancing fruit juice processing. The study examines the structural and functional characteristics of pectinolytic enzyme, underscoring the critical nature of substrate specificity and enzymatic reaction mechanisms. BvPelB was successfully expressed and purified, exhibiting robust activity under alkaline conditions and thermal stability. Structural analysis revealed similarities with other pectin lyases, despite limited sequence identity. Biochemical characterization showed BvPelB's preference for highly methylated pectins and its endo-acting mode of cleavage. Treatment with BvPelB significantly increased juice yield and clarity without generating excessive methanol, making it a promising candidate for fruit juice processing. Overall, this study provides valuable insights into the enzymatic properties of BvPelB and its potential industrial applications in improving fruit juice processing efficiency and quality.

Transcriptome analysis reveals the key network of axillary bud outgrowth modulated by topping in citrus

Topping, an important tree shaping and pruning technique, can promote the outgrowth of citrus axillary buds. However, the underlying molecular mechanism is still unclear. In this study, spring shoots of Citrus reticulata 'Huagan No.2' were topped and transcriptome was compared between axillary buds of topped and untopped shoots at 6 and 11 days after topping (DAT). 1944 and 2394 differentially expressed genes (DEGs) were found at 6 and 11 DAT, respectively. KEGG analysis revealed that many DEGs were related to starch and sucrose metabolism, signal transduction of auxin, cytokinin and abscisic acid. Specially, transcript levels of auxin synthesis, transport, and signaling-related genes (SAURs and ARF5), cytokinin signal transduction related genes (CRE1, AHP and Type-A ARRs), ABA signal responsive genes (PYL and ABF) were up-regulated by topping; while transcript levels of auxin receptor TIR1, auxin responsive genes AUX/IAAs, ABA signal transduction related gene PP2Cs and synthesis related genes NCED3 were down-regulated. On the other hand, the contents of sucrose and fructose in axillary buds of topped shoots were significantly higher than those in untopped shoots; transcript levels of 16 genes related to sucrose synthase, hexokinase, sucrose phosphate synthase, endoglucanase and glucosidase, were up-regulated in axillary buds after topping. In addition, transcript levels of genes related to trehalose 6-phosphate metabolism and glycolysis/tricarboxylic acid (TCA) cycle, as well to some transcription factors including Pkinase, Pkinase_Tyr, Kinesin, AP2/ERF, P450, MYB, NAC and Cyclin_c, significantly responded to topping. Taken together, the present results suggested that topping promoted citrus axillary bud outgrowth through comprehensively regulating plant hormone and carbohydrate metabolism, as well as signal transduction. These results deepened our understanding of citrus axillary bud outgrowth by topping and laid a foundation for further research on the molecular mechanisms of citrus axillary bud outgrowth.

Optimization of saponin extraction from the leaves of Panax notoginseng and Panax quinquefolium and evaluation of their antioxidant, antihypertensive, hypoglycemic and anti-inflammatory activities

Panax notoginseng and Panax quinquefolium are important economic plants that utilize dried roots for medicinal and food dual purposes; there is still insufficient research of their stems and leaves, which also contain triterpenoid saponins. The extraction process was developed with a total saponin content of 12.30 ± 0.34% and 12.19 ± 0.64% for P. notoginseng leaves (PNL) and P. quinquefolium leaves (PQL) extracts, respectively. PNL and PQL saponin extracts showed good antioxidant, antihypertensive, hypoglycemic, and anti-inflammatory properties in vitro and RAW264.7 cells. A total of 699 metabolites were identified in PNL and PQL saponin extracts, with the majority being triterpenoid saponins, flavonoids and amino acids. Fourteen ginsenosides, 18 flavonoids or alkaloids, and 16 amino acids were enriched in both saponin extracts. Overall, the utilization of saponins from medicinal plants PNL and PQL has been developed to facilitate systematic research in the functional food and natural product industries.

Metabolic profiling and spatial metabolite distribution in wild soybean (G. soja) and cultivated soybean (G. max) seeds

Wild soybeans retain many substances significantly reduced or lost in cultivars during domestication. This study utilized LC-MS to analyze metabolites in the seed coats and embryos of wild and cultivated soybeans. 866 and 815 metabolites were identified in the seed extracts of both soybean types, with 35 and 10 significantly differing metabolites in the seed coat and embryos, respectively. The upregulated metabolites in wild soybeans are linked to plant defense, stress responses, and nitrogen cycling. MALDI-MSI results further elucidated the distribution of these differential metabolites in the cotyledons, hypocotyls, and radicles. In addition to their role in physiological processes like growth and response to environmental stimuli, the prevalent terpenoids, lipids, and flavonoids present in wild soybeans exhibit beneficial bioactivities, including anti-inflammatory, antibacterial, anticancer, and cardiovascular disease prevention properties. These findings underscore the potential of wild soybeans as a valuable resource for enhancing the nutritional and ecological adaptability of cultivated soybeans.

A tonoplast-localized TPK-type K+ transporter (TPKa) regulates potassium accumulation in tobacco

Potassium ion (K+) is one of the most essential nutrients for the growth and development of tobacco (Nicotiana tabacum L.), however, the molecular regulation of K+ concentration in tobacco remains unclear. In this study, a two-pore K (TPK) channel gene NtTPKa was cloned from tobacco, and NtTPKa protein contains the unique K+ selection motif GYGD and its transmembrane region primarily locates in the tonoplast membrane. The expression of NtTPKa gene was significantly increased under low-potassium stress conditions. The concentrations of K+ in tobacco were significantly increased in the NtTPKa RNA interference lines and CRISPR/Cas9 knockout mutants. In addition, the transport of K+ by NtTPKa was validated using patch clamp technique, and the results showed that NtTPKa channel protein exclusively transported K+ in a concentration-dependent manner. Together, our results strongly suggested that NtTPKa is a key gene in maintaining K+ homeostasis in tobacco, and it could provide a new genetic resource for increasing the concentration of K+ in tobacco.

Preparation, pungency and bioactivity transduction of piperine from black pepper (Piper nigrum L.): A comprehensive review

Piperine, derived from black pepper (Piper nigrum L.), is responsible for the pungent sensation. The diverse bioactivities of piperine underscores its promising potential as a functional food ingredient. This review presents a comprehensive overview of the research progress in extraction, synthesis, pungency transduction mechanism and bioactivities of piperine. Piperine can be extracted through various methods, such as traditional, modern, and innovative extraction techniques. Its synthesis mainly included both chemical and biosynthetic approaches. It exhibits a diverse range of bioactivities, including anticancer, anticonvulsant, antidepressant, anti-inflammatory, antioxidant, immunomodulatory, anti-obesity, neuroprotective, antidiabetic, hepatoprotective, and cardiovascular protective activities. Piperine can bind to TRPV1 receptor to elicit pungent sensation. Overall, the present review can provide a theoretical reference for advancing the potential application of piperine in the field of food science.

Sugarcane (Saccharum officinarum L.) induces psychostimulant, anxiolytic-like effects and improvement of motor performance in rats

ETHNOPHARMACOLOGICAL RELEVANCE

Sugarcane (Saccharum officinarum L.) is reported by traditional medicine as tonic, stimulating and beneficial in increasing resistance to fatigue. Previous preclinical studies in rats using aqueous extract of sugarcane leaves (AE) revealed pharmacological effects on the central nervous and cardiovascular systems involving the participation of dopaminergic pathways. This neurotransmission system is also related to motor, emotional and cognitive activities, which could, in part, justify the ethnopharmacological information.

AIM OF STUDY

The present study aimed to investigate the motor, emotional and cognitive activities of rats submitted to AE treatment using behavioral tests in order to correlate the pharmacological effects with the therapeutic benefits postulated by traditional medicine. Additionally, the chemical profile of AE was evaluated by HPLC-UV/Vis, and the presence of shikimic acid, vitexin, and ferulic acid, as possible chemical markers, was investigated through comparisons of chemical parameters with the authentic patterns, and a UV-Vis scan of known spectra.

MATERIAL AND METHODS

Rats received water (1.5 mL/kg, p.o.) and AE (0.5, 10 and 500 mg/kg, p.o.) in the absence and presence of haloperidol (0.5 mg/kg, i.p.), 90 min before open field; rotarod; elevated plus maze and inhibitory avoidance tests for investigation of motor; emotional and cognitive responses. As a positive control was used apomorphine (0.25 mg/kg, s.c.). The chemical profile of AE was evaluated by HPLC-UV/Vis and the presence of shikimic acid, vitexin and ferulic acid, as possible chemical markers, was investigated through comparisons with the retention times, an increase of the integral of the peak area determined by co-injection of AE with the authentic patterns, and a UV-Vis scan of known spectra.

RESULTS

In open field, it revealed that AE increased locomotion; reduced rearing but did not change freezing and grooming. Besides, AE increased motor performance in rotarod and reduced anxiety in elevated plus maze. A relation dose-response was observed in these tests where the lowest dose of AE was more effective in developing pharmacological responses. Previous administration of haloperidol inhibited the responses of AE. Inhibitory avoidance test revealed that AE did not modify fast-learning and associative memory.

CONCLUSIONS

Sugarcane induced psychostimulant, anxiolytic-like effects, and improvement of motor performance in rats, with the involvement of dopaminergic pathways. The present study points to AE as a potential adaptogen but, in addition to behavioral assessments, metabolic and molecular aspects, that involve the participation of a variety of regulatory systems, will be investigated in futures studies. Phytochemical analyses showed that AE is a complex matrix and revealed shikimic acid, vitexin, and ferulic acid as potential chemical markers.

Responses of fine particulate matter (PM2.5) air quality to future climate, land use, and emission changes: Insights from modeling across shared socioeconomic pathways

Air pollution induced by fine particulate matter with diameter ≤ 2.5 μm (PM2.5) poses a significant challenge for global air quality management. Understanding how factors such as climate change, land use and land cover change (LULCC), and changing emissions interact to impact PM2.5 remains limited. To address this gap, we employed the Community Earth System Model and examined both the individual and combined effects of these factors on global surface PM2.5 in 2010 and projected scenarios for 2050 under different Shared Socioeconomic Pathways (SSPs). Our results reveal biomass-burning and anthropogenic emissions as the primary drivers of surface PM2.5 across all SSPs. Less polluted regions like the US and Europe are expected to experience substantial PM2.5 reduction in all future scenarios, reaching up to ~5 μg m-3 (70 %) in SSP1. However, heavily polluted regions like India and China may experience varied outcomes, with a potential decrease in SSP1 and increase under SSP3. Eastern China witness ~20 % rise in PM2.5 under SSP3, while northern India may experience ~70 % increase under same scenario. Depending on the region, climate change alone is expected to change PM2.5 up to ±5 μg m-3, while the influence of LULCC appears even weaker. The modest changes in PM2.5 attributable to LULCC and climate change are associated with aerosol chemistry and meteorological effects, including biogenic volatile organic compound emissions, SO2 oxidation, and NH4NO3 formation. Despite their comparatively minor role, LULCC and climate change can still significantly shape future air quality in specific regions, potentially counteracting the benefits of emission control initiatives. This study underscores the pivotal role of changes in anthropogenic emissions in shaping future PM2.5 across all SSP scenarios. Thus, addressing all contributing factors, with a primary focus on reducing anthropogenic emissions, is crucial for achieving sustainable reduction in surface PM2.5 levels and meeting sustainable pollution mitigation goals.

Interactions between U and V sex chromosomes during the life cycle of Ectocarpus

In many animals and flowering plants, sex determination occurs in the diploid phase of the life cycle with XX/XY or ZW/ZZ sex chromosomes. However, in early diverging plants and most macroalgae, sex is determined by female (U) or male (V) sex chromosomes in a haploid phase called the gametophyte. Once the U and V chromosomes unite at fertilization to produce a diploid sporophyte, sex determination no longer occurs, raising key questions about the fate of the U and V sex chromosomes in the sporophyte phase. Here, we investigate genetic and molecular interactions of the UV sex chromosomes in both the haploid and diploid phases of the brown alga Ectocarpus. We reveal extensive developmental regulation of sex chromosome genes across its life cycle and implicate the TALE-HD transcription factor OUROBOROS in suppressing sex determination in the diploid phase. Small RNAs may also play a role in the repression of a female sex-linked gene, and transition to the diploid sporophyte coincides with major reconfiguration of histone H3K79me2, suggesting a more intricate role for this histone mark in Ectocarpus development than previously appreciated.

Arabinoxylo-oligosaccharides production from unexploited agro-industrial sesame (Sesamum indicum L.) hulls waste

This work demonstrates that sesame (Sesamum indicum L.) hull, an unexploited food industrial waste, can be used as an efficient source for the extraction of hemicellulose and/or pectin polysaccharides to further obtain functional oligosaccharides. Different polysaccharides extraction methods were surveyed including alkaline and several enzymatic treatments. Based on the enzymatic release of xylose, arabinose, glucose, and galacturonic acid from sesame hull by using different enzymes, Celluclast®1.5 L, Pectinex®Ultra SP-L, and a combination of them were selected for the enzymatic extraction of polysaccharides at 50 °C, pH 5 up to 24 h. Once the polysaccharides were extracted, Ultraflo®L was selected to produce arabinoxylo-oligosaccharides (AXOS) at 40 °C up to 24 h. Apart from oligosaccharides production from extracted polysaccharides, alternative approaches for obtaining oligosaccharides were also explored. These were based on the analysis of the supernatants resulting from the polysaccharide extraction, alongside a sequential hydrolysis performed with Celluclast®1.5 L and Ultraflo®L of the starting raw sesame hull. The different fractions obtained were comprehensively characterized by determining low molecular weight carbohydrates and monomeric compositions, average Mw and dispersity, and oligosaccharide structure by MALDI-TOF-MS. The results indicated that sesame hull can be a useful source for polysaccharides extraction (pectin and hemicellulose) and derived oligosaccharides, especially AXOS.

Sustainable soil management under drought stress through biochar application: Immobilizing arsenic, ameliorating soil quality, and augmenting plant growth

Rise in climate change-induced drought occurrences have amplified pollution of metal(loid)s, deteriorated soil quality, and deterred growth of crops. Rice straw-derived biochars (RSB) and cow manure-enriched biochars (CEB) were used in the investigation (at doses of 0%, 2.5%, 5%, and 7.5%) to ameliorate the negative impacts of drought, improve soil fertility, minimize arsenic pollution, replace agro-chemical application, and maximize crop yields. Even in soils exposed to severe droughts, 3 months of RSB and CEB amendment (at 7.5% dose) revealed decreased bulk density (13.7% and 8.9%), and increased cation exchange capacity (6.0% and 6.3%), anion exchange capacity (56.3% and 28.0%), porosity (12.3% and 7.9%), water holding capacity (37.5% and 12.5%), soil respiration (17.8% and 21.8%), and nutrient contents (especially N and P). Additionally, RSB and CEB decreased mobile (30.3% and 35.7%), bio-available (54.7% and 45.3%), and leachable (55.0% and 56.5%) fractions of arsenic. Further, pot experiments with Bengal gram and coriander plants showed enhanced growth (62-188% biomass and 90-277% length) and reduced arsenic accumulation (49-54%) in above ground parts of the plants. Therefore, biochar application was found to improve physico-chemical properties of soil, minimize arsenic contamination, and augment crop growth even in drought-stressed soils. The investigation suggests utilisation of cow manure for eco-friendly fabrication of nutrient-rich CEB, which could eventually promote sustainable agriculture and circular economy. With the increasing need for sustainable agricultural practices, the use of biochar could provide a long-term solution to enhance soil quality, mitigate the effects of climate change, and ensure food security for future generations. Future research should focus on optimizing biochar application across various soil types and climatic conditions, as well as assessing its long-term effectiveness.

Multiscale chromatin dynamics and high entropy in plant iPSC ancestors

Plant protoplasts provide starting material for of inducing pluripotent cell masses that are competent for tissue regeneration in vitro, analogous to animal induced pluripotent stem cells (iPSCs). Dedifferentiation is associated with large-scale chromatin reorganisation and massive transcriptome reprogramming, characterised by stochastic gene expression. How this cellular variability reflects on chromatin organisation in individual cells and what factors influence chromatin transitions during culturing are largely unknown. Here, we used high-throughput imaging and a custom supervised image analysis protocol extracting over 100 chromatin features of cultured protoplasts. The analysis revealed rapid, multiscale dynamics of chromatin patterns with a trajectory that strongly depended on nutrient availability. Decreased abundance in H1 (linker histones) is hallmark of chromatin transitions. We measured a high heterogeneity of chromatin patterns indicating intrinsic entropy as a hallmark of the initial cultures. We further measured an entropy decline over time, and an antagonistic influence by external and intrinsic factors, such as phytohormones and epigenetic modifiers, respectively. Collectively, our study benchmarks an approach to understand the variability and evolution of chromatin patterns underlying plant cell reprogramming in vitro.

Characterization of a novel AA16 lytic polysaccharide monooxygenase from Thermothelomyces thermophilus and comparison of biochemical properties with an LPMO from AA9 family

Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes which are categorized in the CAZy database under auxiliary activities families AA9-11, 13, 14-17. Secreted by various microorganisms, they play a crucial role in carbon recycling, particularly in fungal saprotrophs. LPMOs oxidize polysaccharides through monooxygenase/peroxygenase activities and exhibit peroxidase and oxidase activities, with variations among different families. AA16, a newly identified LPMO family, is noteworthy due to limited studies on its members, thus rendering the characterization of AA16 enzymes vital for addressing controversies around their functions. This study focused on heterologous expression and biochemical study of an AA16 LPMO from Thermothelomyces thermophilus (formerly known as Myceliophthora thermophila), namely MtLPMO16A. Substrate specificity evaluation of MtLPMO16A showed oxidative cleavage of hemicellulosic substrates and no activity on cellulose, accompanied by a strong oxidase activity. A comparative analysis with an LPMO from AA9 family explored correlations between these families, while MtLPMO16A was shown to boost the activity of some AA9 family LPMOs. The results offer new insights into the AA16 family's action mode and microbial hemicellulose decomposition mechanisms in nature.

The roles of nitric oxide in improving postharvest fruits quality: Crosstalk with phytohormones

Nowadays, improving the quality of postharvest fruits has become a hot research topic. Nitric oxide (NO) is often regarded as a signaling molecule that delays the postharvest senescence of fruits. Moreover, phytohormones affect the postharvest senescence of fruits. This review mainly describes how NO improves the postharvest quality of fruits by delaying postharvest fruit senescence, mitigating fruit cold damage and controlling postharvest diseases. Furthermore, the crosstalk of NO and multiple plant hormones effectively delays the postharvest senescence of fruits, and the major crosstalk mechanisms include (1) mediating phytohormone signaling. (2) inhibiting ETH production. (3) stimulating antioxidant enzyme activity. (4) decreasing membrane lipid peroxidation. (5) maintaining membrane integrity. (6) inhibiting respiration rate. (7) regulating gene expression related to fruit senescence. This review concluded the roles and mechanisms of NO in delaying postharvest fruit senescence. In addition, the crosstalk mechanisms between NO and various phytohormones on the regulation of postharvest fruit quality are also highlighted, which provides new ideas for the subsequent research.

Clivia biosensor: Soil moisture identification based on electrophysiology signals with deep learning

Research has shown that plants have the ability to detect environmental changes and generate electrical signals in response. These electrical signals can regulate the physiological state of plants and produce corresponding feedback. This suggests that plants have the potential to be used as biosensors for monitoring environmental information. However, there are current challenges in linking environmental information with plant electrical signals, especially in collecting and classifying the corresponding electrical signals under soil moisture gradients. This study documented the electrical signals of clivia under different soil moisture gradients and created a dataset for classifying electrical signals. Subsequently, we proposed a lightweight convolutional neural network (CNN) model (PlantNet) for classifying the electrical signal dataset. Compared to traditional CNN models, our model achieved optimal classification performance with the lowest computational resource consumption. The model achieved an accuracy of 99.26%, precision of 99.31%, recall of 92.26%, F1-score of 99.21%, with 0.17M parameters, a size of 7.17MB, and 14.66M FLOPs. Therefore, this research provides scientific evidence for the future development of plants as biosensors for detecting soil moisture, and offers insight into developing plants as biosensors for detecting signals such as ozone, PM2.5, Volatile Organic Compounds(VOCs), and more. These studies are expected to drive the development of environmental monitoring technology and provide new pathways for better understanding the interaction between plants and the environment.

Organic acids released by submerged macrophytes with damaged leaves alter the denitrification microbial community in rhizosphere

Submerged macrophytes have important impacts on the denitrification and anaerobic ammonia-oxidizing (anammox) processes. Leaf damage in these plants probably changes the rhizosphere environment, affecting organic acid release and denitrifying bacteria. However, there is a lack of comprehensive understanding of the specific changes. This study investigated these changes in the rhizosphere of Potamogeton crispus with four degrees of leaf excision. When 0 %, 30 %, 50 % and 70 % of leaves were excised, the concentrations of total organic acid were 31.45, 32.67, 38.26, and 35.16 mg/L, respectively. The abundances of nirS-type denitrifying bacteria were 2.10 × 1010, 1.59 × 1010, 2.54 × 1010, and 4.67 × 1010 copies/g dry sediment, respectively. The abundances of anammox bacteria were 7.58 × 109, 4.59 × 109, 3.81 × 109, and 3.90 × 109 copies/g dry sediment, respectively. The concentration of total organic acids and the abundance of two denitrification microorganisms in the rhizosphere zone were higher than those in the root zone and non-rhizosphere zone. With increasing leaf damage, the number of OTUs in the Pseudomonas genus of nirS-type denitrifying bacteria first increased and then decreased, while that of the Thauera genus was relatively stable. The overall increase in the OTU number of anammox bacteria indicated that leaf damage promotes root exudates release, thereby leading to an increase in their diversity. The co-occurrence network revealed that the two denitrification microorganisms had about 60.52 % positive connections in rhizosphere while 64.73 % negative connections in non-rhizosphere. The abundance and community composition of both denitrification microorganisms were positively correlated with the concentrations of various substances such as oxalic acid, succinic acid, total organic acids and NO2--N. These findings demonstrate that submerged plant damage has significantly impacts on the structure of denitrification microbial community in the rhizosphere, which may alter the nitrogen cycling process in the deposit sediment. SYNOPSIS: This study reveals leaf damage of macrophyte changed the rhizosphere denitrification microbial community, which is helpful to further understand the process of nitrogen cycle in water.

Selective shifts in the rhizosphere microbiome during the drought season could explain the success of the invader Nicotiana glauca in semiarid ecosystems

The rhizosphere microbiome plays a crucial role in the ability of plants to colonize and thrive in stressful conditions such as drought, which could be decisive for the success of exotic plant invasion in the context of global climate change. The aim of this investigation was to examine differences in the composition, structure, and functional traits of the microbial community of the invader Nicotiana glauca R.C. Graham and native species growing at seven different Mediterranean semiarid locations under two distinct levels of water availability, corresponding to the wet and dry seasons. The results show that the phylum Actinobacteriota was an indicator phylum of the dry season as well as for the community of N. glauca. The dominant indicator bacterial families of the dry season were 67-14 (unclassified family), Pseudonocardiaceae, and Sphingomonadaceae, being relatively more abundant in the invasive rhizosphere. The relative abundances of the indicator fungal families Aspergillaceae (particularly the indicator genus Aspergillus), Glomeraceae, and Claroideoglomeraceae were higher in the invasive rhizosphere. The relative abundance of mycorrhizal fungi was higher in the invasive rhizosphere in the dry season (by about 40 % in comparison to that of native plants), without significant differences between invasive and native plants in the wet season. Bacterial potential functional traits related to energy and precursor metabolites production and also biosynthesis of cell wall, cofactors, vitamins, and amino acids as well as catabolic enzymes involved in the P cycle prevailed in the invasive rhizosphere under drought conditions. This study shows that the pronounced and beneficial shifts in the microbiome assembly and functions in the rhizosphere of N. glauca under conditions of low soil water availability can represent a clear advantage for its establishment.

Cenococcum geophilum impedes cadmium toxicity in Pinus massoniana by modulating nitrogen metabolism

Nitrogen (N) is of great significance to the absorption, distribution and detoxification of cadmium (Cd). Ectomycorrhizal fungi (EMF) are able to affect the key processes of plant N uptake to resist Cd stress, while the mechanism is still unclear. Therefore, we explored potential strategies of Cenococcum geophilum (C. geophilum) symbiosis to alleviate Cd stress in Pinus massoniana (P. massoniana) from the perspective of plant N metabolism and soil N transformation. The results showed that inoculation of C. geophilum significantly increased the activities of NR, NiR and GS in the shoots and roots of P. massoniana, thereby promoting the assimilation of NO3- and NH4+ into amino acids. Moreover, C. geophilum promoted soil urease and protease activities, but decreased soil NH4+ content, indicating that C. geophilum might increase plant uptake of soil inorganic N. qRT-PCR results showed that C3 symbiosis significantly up-regulated the expression of genes encoding functions involved in NH4+ uptake (AMT3;1), NO3- uptake (NRT2.1, NRT2.4, NRT2.9), as well as Cd resistance (ABCC1 and ABCC2), meanwhile down-regulated the expression of NRT7.3, Cd transporter genes (HMA2 and NRAMP3) in the roots of P. massoniana seedlings. These results demonstrated that C. geophilum was able to alleviate Cd stress by increasing the absorption and assimilation of inorganic N in plants and inhibiting the transport of Cd from roots to shoots, which provided new insights into how EMF improved host resistance to abiotic stress.

Plant metabolic responses to soil herbicide residues differ under herbivory in two woodland strawberry genotypes

The use of glyphosate-based herbicides (GBHs) to control weeds has increased exponentially in recent decades, and their residues and degradation products have been found in soils across the globe. GBH residues in soil have been shown to affect plant physiology and specialised metabolite biosynthesis, which, in turn, may impact plant resistance to biotic stressors. In a greenhouse study, we investigated the interactive effects between soil GBH residues and herbivory on the performance, phytohormone concentrations, phenolic compound concentrations and volatile organic compound (VOC) emissions of two woodland strawberry (Fragaria vesca) genotypes, which were classified as herbivore resistant and herbivore susceptible. Plants were subjected to herbivory by strawberry leaf beetle (Galerucella tenella) larvae, and to GBH residues by growing in soil collected from a field site with GBH treatments twice a year over the past eight years. Soil GBH residues reduced the belowground biomass of the susceptible genotype and the aboveground biomass of both woodland strawberry genotypes. Herbivory increased the belowground biomass of the resistant genotype and the root-shoot ratio of both genotypes. At the metabolite level, herbivory induced the emission of several VOCs. Jasmonic acid, abscisic acid and auxin concentrations were induced by herbivory, in contrast to salicylic acid, which was only induced by herbivory in combination with soil GBH residues in the resistant genotype. The concentrations of phenolic compounds were higher in the resistant genotype compared to the susceptible genotype and were induced by soil GBH residues in the resistant genotype. Our results indicate that soil GBH residues can differentially affect plant performance, phytohormone concentrations and phenolic compound concentrations under herbivore attack, in a genotype-dependent manner. Soil GBH altered plant responses to herbivory, which may impact plant resistance traits and species interactions. With ongoing agrochemical pollution, we need to consider plant cultivars with better resistance to polluted soils while maintaining plant resilience under challenging environmental conditions.

Topsoil dilution by subsoil admixture had less impact on soil organic carbon stock development than fertilizer form and erosion state

Enhancing the agroecosystems carbon (C) sink function for climate mitigation faced challenges, particularly with traditional measures with limited suitability for increasing soil organic carbon (SOC) stocks. Inducing a SOC undersaturation in the topsoil by abrupt subsoil admixture is a way to create an additional C sink. However, the deep tillage traditionally used for this topsoil dilution was not always successful. It was due to a lack of knowledge and suitable approaches to record the effect of all relevant factors in SOC recovery, including soil conditions and fertilizer forms. We addressed these problems by establishing a three-factorial experiment: I) "moderate topsoil dilution," II) "N fertilization form," and III) "soil erosion state," representing three soil types in the hummocky ground moraine landscape of NE Germany. SOC dynamics were determined over a year of winter rye cropping using a novel robotic chamber system capable of measuring CO2 exchange on 36 experimental plots with a reduced methodological bias than previous measuring systems. The averaged net ecosystem carbon balance, a proxy for SOC stock change, indicated that topsoil dilution only reduced further SOC losses. The N fertilizer form had a significantly stronger and more differentiated effect. While the mineral N fertilization consistently produced only C sources, the organic fertilization, in combination with the diluted topsoil, led to a C sink. This C-sink function was, however, more pronounced in the eroded soil than in the non-eroded soil. Overall, the results have made clear that the impact of topsoil dilution on the further development of the SOC stock is only possible if the effect of other relevant factors, such as N fertilizer form and erosion state, are taken into account.

Effects of polystyrene microplastic composite with florfenicol on photosynthetic carbon assimilation of rice (Oryza sativa L.) seedlings: Light reactions, carbon reactions, and molecular metabolism

The effects of co-exposure to antibiotics and microplastics in agricultural systems are still unclear. This study investigated the effects of florfenicol (FF) and polystyrene microplastics (PS-MPs) on photosynthetic carbon assimilation in rice seedlings. Both FF and PS-MPs inhibited photosynthesis, while PS-MPs can alleviate the toxicity of FF. Chlorophyll synthesis genes (HEMA, HEMG, CHLD, CHLG, CHLM, and CAO) were down-regulated, whereas electron transport chain genes (PGR5, PGRL1A, PGRL1B, petH, and ndhH) were up-regulated. FF inhibited linear electron transfer (LET) and activated cyclic electron transfer (CET), which was consistent with the results of the chlorophyll fluorescence parameters. The photosynthetic carbon assimilation pathway was altered, the C3 pathway enzyme Ribulose1,5-bisphosphatecarboxylase/oxygenase (RuBisCO) was affected, C4 enzyme ((phosphoenolpyruvate carboxykinase (PEPCK), pyruvate orthophosphate dikinase (PPDK), malate dehydrogenase (MDH), and phosphoenolpyruvate carboxylase (PEPC))) and related genes were significantly up-regulated, suggesting that the C3 pathway is converted to C4 pathway for self-protection. The key enzymes involved in photorespiration, glycolate oxidase (GO) and catalase (CAT), responded positively, photosynthetic phosphorylation was inhibited, and ATP content and H+-ATPase activity were suppressed, nutrient content (K, P, N, Ca, Mg, Fe, Cu, Zn, Mn, and Ni) significantly affected. Transcriptomic analysis showed that FF and PS-MPs severely affected the photosynthetic capacity of rice seedlings, including photosystem I, photosystem II, non-photochemical quenching coefficients, and photosynthetic electron transport.

A newly identified algicidal bacterium of Pseudomonas fragi YB2: Algicidal compounds and effects

Harmful algal bloom (HAB) is an unresolved existing problem worldwide. Here, we reported a novel algicidal bacterium, Pseudomonas fragi YB2, capable of lysing multiple algal species. To Chlorella vulgaris, YB2 exhibited a maximum algicidal rate of 95.02 % at 120 h. The uniqueness of YB2 lies in its ability to self-produce three algicidal compounds: 2-methyl-1, 3-cyclohexanedione (2-MECHD), N-phenyl-2-naphthylamine, and cyclo (Pro-Leu). The algicidal properties of 2-MECHD have not been previously reported. YB2 significantly affected the chloroplast and mitochondrion, thus decreasing in chlorophyll a by 4.74 times for 120 h and succinate dehydrogenase activity by 103 times for 36 h. These physiological damages disrupted reactive oxygen species and Ca2+ homeostasis at the cellular level, increasing cytosolic superoxide dismutase (23 %), catalase (35 %), and Ca2+ influx. Additionally, the disruption of Ca2+ homeostasis rarely reported in algicidal bacteria-algae interaction was observed using the non-invasive micro-test technology. We proposed a putative algicidal mechanism based on the algicidal outcomes and physiological algicidal effects and explored the potential of YB2 through an algicidal simulation test. Overall, this study is the first to report the algicidal bacterium P. fragi and identify a novel algicidal compound, 2-MECHD, providing new insights and a potent microbial resource for the biocontrol of HAB.

Transcriptomic analysis of Chaetoceros muelleri in response to different nitrogen concentrations reveals the activation of pathways to enable efficient nitrogen uptake

Nitrogen is the principal nutrient deficiency that increases lipids and carbohydrate content in diatoms but negatively affects biomass production. Marine diatom Chaetoceros muelleri is characterized by lipid and carbohydrate accumulation under low nitrogen concentration without affecting biomass. To elucidate the molecular effects of nitrogen concentrations, we performed an RNA-seq analysis of C. muelleri grown under four nitrogen concentrations (3.53 mM, 1.76 mM, 0.44 mM, and 0.18 mM of NaNO3). This research revealed that changes in global transcription in C. muelleri are differentially expressed by nitrogen concentration. "Energetic metabolism", "Carbohydrate metabolism" and "Lipid metabolism" pathways were identified as the most upregulated by N deficiency. Due to N limitation, alternative pathways to self-supply nitrogen employed by microalgal cells were identified. Additionally, nitrogen limitation decreased chlorophyll content and caused a greater response at the transcriptional level with a higher number of unigenes differentially expressed. By contrast, the highest N concentration (3.53 mM) recorded the lowest number of differentially expressed genes. Amt1, Nrt2, Fad2, Skn7, Wrky19, and Dgat2 genes were evaluated by RT-qPCR. In conclusion, C. muelleri modify their metabolic pathways to optimize nitrogen utilization and minimize nitrogen losses. On the other hand, the assembled transcriptome serves as the basis for metabolic engineering focused on improving the quantity and quality of the diatom for biotechnological applications. However, proteomic and metabolomic analysis is also required to compare gene expression, protein, and metabolite accumulation.

Selective lead capture using amide-containing COFs: A novel strategy for efficient soil remediation

A critical consideration in the application of phytoremediation to remediate sludge soil contaminated with heavy metals is the potential for leaching risks that prevail prior to the efficient uptake of these metals by plants. The most cost-effective method is to use heavy metal stabilizers with selective adsorption. A novel amide-based COF material (COF-TH) has been synthesized as a heavy metal stabilizer for Pb. COF-TH exhibits significant selectivity for Pb in five-metal-mixed solutions, with a distribution coefficient KD as high as 3279 mL·g-1, which was more than 7.3 times that of other heavy metals. The maximum adsorption capacity of COF-TH for Pb was 189 mg·g-1. The adsorption fitted Langmuir model and intra-particle diffusion model, and satisfied pseudo-second-order kinetic model. The excellent selectivity and adsorption performance originate from the complexation between abundant amide groups and Pb ions. Pot experiments and leaching assays confirm that COF-TH decreased Pb leachate concentrations by 77.8 % without significantly decreasing total phytoextracted amounts of other heavy metals, due to the high selectivity of COF-TH to Pb. Additionally, its positive impact on plant growth and microbial diversity makes it a promising soil remediation agent. This investigation offers a novel approach to mitigate the leaching risk of a specific heavy metal Pb during sludge land application by integrating soil phytoremediation with stabilization techniques.

Regulation of eukaryotic transcription initiation in response to cellular stress

Transcription initiation is a vital step in the regulation of eukaryotic gene expression. It can be dysregulated in response to various cellular stressors which is associated with numerous human diseases including cancer. Transcription initiation is facilitated via many gene-specific trans-regulatory elements such as transcription factors, activators, and coactivators through their interactions with transcription pre-initiation complex (PIC). These trans-regulatory elements can uniquely facilitate PIC formation (hence, transcription initiation) in response to cellular nutrient stress. Cellular nutrient stress also regulates the activity of other pathways such as target of rapamycin (TOR) pathway. TOR pathway exhibits distinct regulatory mechanisms of transcriptional activation in response to stress. Like TOR pathway, the cell cycle regulatory pathway is also found to be linked to transcriptional regulation in response to cellular stress. Several transcription factors such as p53, C/EBP Homologous Protein (CHOP), activating transcription factor 6 (ATF6α), E2F, transforming growth factor (TGF)-β, Adenomatous polyposis coli (APC), SMAD, and MYC have been implicated in regulation of transcription of target genes involved in cell cycle progression, apoptosis, and DNA damage repair pathways. Additionally, cellular metabolic and oxidative stressors have been found to regulate the activity of long non-coding RNAs (lncRNA). LncRNA regulates transcription by upregulating or downregulating the transcription regulatory proteins involved in metabolic and cell signaling pathways. Numerous human diseases, triggered by chronic cellular stressors, are associated with abnormal regulation of transcription. Hence, understanding these mechanisms would help unravel the molecular regulatory insights with potential therapeutic interventions. Therefore, here we emphasize the recent advances of regulation of eukaryotic transcription initiation in response to cellular stress.

LpNAC5 positively regulates drought, salt and alkalinity tolerance of Lilium pumilum

NACs (NAM、ATAF1/2、CUC1/2), as a large family of plant transcription factors, are widely involved in abiotic stress responses. This study aimed to isolate and clone a novel stress-responsive transcription factor LpNAC5 from Lilium pumilum bulbs. Drought, salt, alkali, and ABA stresses induced the expression of LpNAC5. Transgenic tobacco plants overexpressing LpNAC5 were generated using the Agrobacterium-mediated method to understand the role of this factor in stress response. These plants exhibited increased tolerance to drought, salt, and alkali stresses. The tobacco plants overexpressing LpNAC5 showed strong drought, salt, and alkaline tolerance. Under the three abiotic stresses, the activities of antioxidant enzymes were enhanced, the contents of proline and chlorophyll increased, and the contents of malondialdehyde decreased. The functional analysis revealed that LpNAC5 enabled plants to positively regulate drought and salt stresses. These findings not only provided valuable insights into stress tolerance mechanisms in L. pumilum but also offered a potential genetic resource for breedi.

Real-time monitoring abscisic acid release from single rice protoplast by amperometry at microelectrodes modified with abscisic acid receptor PYL2

It was previously reported that stress induces a cellular production of abscisic acid in plants, but no direct method shows the evidence. Here, an electrochemical microsensor involving an abscisic acid receptor PYL2 modified carbon fiber microelectrode was fabricated by self-assembly method, where the Cu2+ combined with the histidine tag of PYL2 on the surface of microelectrode was used as the detection probe, the mediated reaction between Cu+ and ferricyanide realized the amplification responses and provided the microsensor with a high sensitivity for detection of abscisic acid with a detection limit of 0.8 nM. With use of this microsensor, an increase of extracellular abscisic acid from single rice protoplast induced by sulfate, osmotic and salinity stress was real-time monitored. Direct measurement of free extracellular abscisic acid in single plant cells might offer important new insights into its role in plants challenged by abiotic stresses.

Small molecule, big impacts: Nano-nutrients for sustainable agriculture and food security

Human existence and the long-term viability of society depend on agriculture. Overuse of synthetic fertilizers results in increased contamination of the land, water, and atmosphere as well as financial constraints. In today's modern agriculture, environmentally friendly technology is becoming more and more significant as a substitute for conventional fertilizers and chemical pesticides. Using nanotechnology, agricultural output can be improved in terms of quality, biological support, financial stability, and environmental safety. There is a lot of promise for the sustainable application of nano-fertilizers in crop productivity and soil fertility, with little or no negative environmental effects. In this context, the present review provided an overview of the benefits of using nanofertilizers, its application and types. Mechanistic approach for increasing soil fertility and yield via nanofertilizers also described in detail. We concluded this article to compare the advantages of nanofertilizers over chemicals and nano-chemicals. Nonetheless, additional investigation is required to comprehend the effects and possible hazards of nanomaterials in the food production chain.