A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics

Plants, as sessile organisms, deploy transcriptional dynamics for adapting to extreme growth conditions such as cold stress. Emerging evidence suggests that chromatin architecture contributes to transcriptional regulation. However, the relationship between chromatin architectural dynamics and transcriptional reprogramming in response to cold stress remains unclear. Here, we apply a chemical-crosslinking assisted proximity capture (CAP-C) method to elucidate the fine-scale chromatin landscape, revealing chromatin interactions within gene bodies closely associated with RNA polymerase II (Pol II) densities across initiation, pausing, and termination sites. We observe dynamic changes in chromatin interactions alongside Pol II activity alterations during cold stress, suggesting local chromatin dynamics may regulate Pol II activity. Notably, cold stress does not affect large-scale chromatin conformations. We further identify a comprehensive promoter-promoter interaction (PPI) network across the genome, potentially facilitating co-regulation of gene expression in response to cold stress. Our study deepens the understanding of chromatin conformation-associated gene regulation in plant response to cold.

Mapping the race between crop phenology and climate risks for wheat in France under climate change

Climate change threatens food security by affecting the productivity of major cereal crops. To date, agroclimatic risk projections through indicators have focused on expected hazards exposure during the crop's current vulnerable seasons, without considering the non-stationarity of their phenology under evolving climatic conditions. We propose a new method for spatially classifying agroclimatic risks for wheat, combining high-resolution climatic data with a wheat's phenological model. The method is implemented for French wheat involving three GCM-RCM model pairs and two emission scenarios. We found that the precocity of phenological stages allows wheat to avoid periods of water deficit in the near future. Nevertheless, in the coming decades the emergence of heat stress and increasing water deficit will deteriorate wheat cultivation over the French territory. Projections show the appearance of combined risks of heat and water deficit up to 4 years per decade under the RCP 8.5 scenario. The proposed method provides a deep level of information that enables regional adaptation strategies: the nature of the risk, its temporal and spatial occurrence, and its potential combination with other risks. It's a first step towards identifying potential sites for breeding crop varieties to increase the resilience of agricultural systems.

A transposon insertion in the promoter of OsUBC12 enhances cold tolerance during japonica rice germination

Low-temperature germination (LTG) is an important agronomic trait for rice (Oryza sativa). Japonica rice generally has greater capacity for germination at low temperatures than the indica subpopulation. However, the genetic basis and molecular mechanisms underlying this complex trait are poorly understood. Here, we report that OsUBC12, encoding an E2 ubiquitin-conjugating enzyme, increases low-temperature germinability in japonica, owing to a transposon insertion in its promoter enhancing its expression. Natural variation analysis reveals that transposon insertion in the OsUBC12 promoter mainly occurs in the japonica lineage. The variation detected in eight representative two-line male sterile lines suggests the existence of this allele introgression by indica-japonica hybridization breeding, and varieties carrying the japonica OsUBC12 locus (transposon insertion) have higher low-temperature germinability than varieties without the locus. Further molecular analysis shows that OsUBC12 negatively regulate ABA signaling. OsUBC12-regulated seed germination and ABA signaling mainly depend on a conserved active site required for ubiquitin-conjugating enzyme activity. Furthermore, OsUBC12 directly associates with rice SUCROSE NON-FERMENTING 1-RELATED PROTEIN KINASE 1.1 (OsSnRK1.1), promoting its degradation. OsSnRK1.1 inhibits LTG by enhancing ABA signaling and acts downstream of OsUBC12. These findings shed light on the underlying mechanisms of UBC12 regulating LTG and provide genetic reference points for improving LTG in indica rice.

Silicon and iron nanoparticles protect rice against lead (Pb) stress by improving oxidative tolerance and minimizing Pb uptake

Lead (Pb) is toxic to the development and growth of rice plants. Nanoparticles (NPs) have been considered one of the efficient remediation techniques to mitigate Pb stress in plants. Therefore, a study was carried out to examine the underlying mechanism of iron (Fe) and silicon (Si) nanoparticle-induced Pb toxicity alleviation in rice seedlings. Si-NPs (2.5 mM) and Fe-NPs (25 mg L-1) were applied alone and in combination to rice plants grown without (control; no Pb stress) and with (100 µM) Pb concentration. Our results revealed that Pb toxicity severely affected all rice growth-related traits, such as inhibited root fresh weight (42%), shoot length (24%), and chlorophyll b contents (26%). Moreover, a substantial amount of Pb was translocated to the above-ground parts of plants, which caused a disturbance in the antioxidative enzyme activities. However, the synergetic use of Fe- and Si-NPs reduced the Pb contents in the upper part of plants by 27%. It reduced the lethal impact of Pb on roots and shoots growth parameters by increasing shoot length (40%), shoot fresh weight (48%), and roots fresh weight (31%). Both Si and Fe-NPs synergistic application significantly elevated superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and glutathione (GSH) concentrations by 114%, 186%, 135%, and 151%, respectively, compared to plants subjected to Pb stress alone. The toxicity of Pb resulted in several cellular abnormalities and altered the expression levels of metal transporters and antioxidant genes. We conclude that the synergistic application of Si and Fe-NPs can be deemed favorable, environmentally promising, and cost-effective for reducing Pb deadliness in rice crops and reclaiming Pb-polluted soils.

Greater ecophysiological stress tolerance in the core environment than in extreme environments of wild chickpea (Cicer reticulatum)

Global climate change and land use change underlie a need to develop new crop breeding strategies, and crop wild relatives (CWR) have become an important potential source of new genetic material to improve breeding efforts. Many recent approaches assume adaptive trait variation increases towards the relative environmental extremes of a species range, potentially missing valuable trait variation in more moderate or typical climates. Here, we leveraged distinct genotypes of wild chickpea (Cicer reticulatum) that differ in their relative climates from moderate to more extreme and perform targeted assessments of drought and heat tolerance. We found significance variation in ecophysiological function and stress tolerance between genotypes but contrary to expectations and current paradigms, it was individuals from more moderate climates that exhibited greater capacity for stress tolerance than individuals from warmer and drier climates. These results indicate that wild germplasm collection efforts to identify adaptive variation should include the full range of environmental conditions and habitats instead of only environmental extremes, and that doing so may significantly enhance the success of breeding programs broadly.

The long noncoding RNA LAL contributes to salinity tolerance by modulating LHCB1s' expression in Medicago truncatula

Long non-coding RNAs (lncRNAs) are abundant in plants, however, their regulatory roles remain unclear in most biological processes, such as response in salinity stress which is harm to plant production. Here we show a lncRNA in Medicago truncatula identified from salt-treated Medicago truncatula is important for salinity tolerance. We name the lncRNA LAL, LncRNA ANTISENSE to M. truncatula LIGHT-HARVESTING CHLOROPHYLL A/B BINDING (MtLHCB) genes. LAL is an antisense to four consecutive MtLHCB genes on chromosome 6. In salt-treated M. truncatula, LAL is suppressed in an early stage but induced later; this pattern is opposite to that of the four MtLHCBs. The lal mutants show enhanced salinity tolerance, while overexpressing LAL disrupts this superior tolerance in the lal background, which indicates its regulatory role in salinity response. The regulatory role of LAL on MtLHCB1.4 is further verified by transient co-expression of LAL and MtLHCB1.4-GFP in tobacco leaves, in which the cleavage of MtLHCB1.4 and production of secondary interfering RNA is identified. This work demonstrates a lncRNA, LAL, functioning as a regulator that fine-tunes salinity tolerance via regulating MtLHCB1s' expression in M. truncatula.

Exogenous glutathione protected wheat seedling from high temperature and water deficit damages

High temperatures (HT) and drought are two major factors restricting wheat growth in the early growth stages. This study investigated the role of glutathione (GSH) amendment (0.0, 0.5, 1.0, and 2.0 mM) to soil in mitigating the adverse effect of HT (33 °C, with 25 °C as a control), water regimes (60% of field capacity and control), and their combinations. HT decreased the length, project area, surface area, volume, and forks of the root, while drought had the reverse effect. Shoot length, leaf area, leaf relative water content, and shoot and root dry matter were significantly decreased by HT and drought, and their combined impact was more noticeable. GSH significantly promoted the root system, shoot growth, and leaf relative water content. The combined treatment reduced chlorophyll a, chlorophyll b, and total chlorophyll. However, 0.5 mM GSH raised chlorophyll a, chlorophyll b, and total chlorophyll by 28.6%, 41.4%, and 32.5%, respectively, relative to 0.0 mM GSH. At combined treatment, 0.5 mM GSH decreased malondialdehyde (MDA) by 29.5% and increased soluble protein content by 24.1%. GSH meaningfully enhanced the activity of superoxide dismutase, catalase, and ascorbate peroxide in different treatments. This study suggested that GSH could protect wheat seedlings from the adverse effects of HT and/or drought stresses.

Anatomy of a mega-radiation: Biogeography and niche evolution in Astragalus

PREMISE

Astragalus (Fabaceae), with more than 3000 species, represents a globally successful radiation of morphologically highly similar species predominant across the northern hemisphere. It has attracted attention from systematists and biogeographers, who have asked what factors might be behind the extraordinary diversity of this important arid-adapted clade and what sets it apart from close relatives with far less species richness.

METHODS

Here, for the first time using extensive phylogenetic sampling, we asked whether (1) Astragalus is uniquely characterized by bursts of radiation or whether diversification instead is uniform and no different from closely related taxa. Then we tested whether the species diversity of Astragalus is attributable specifically to its predilection for (2) cold and arid habitats, (3) particular soils, or to (4) chromosome evolution. Finally, we tested (5) whether Astragalus originated in central Asia as proposed and (6) whether niche evolutionary shifts were subsequently associated with the colonization of other continents.

RESULTS

Our results point to the importance of heterogeneity in the diversification of Astragalus, with upshifts associated with the earliest divergences but not strongly tied to any abiotic factor or biogeographic regionalization tested here. The only potential correlate with diversification we identified was chromosome number. Biogeographic shifts have a strong association with the abiotic environment and highlight the importance of central Asia as a biogeographic gateway.

CONCLUSIONS

Our investigation shows the importance of phylogenetic and evolutionary studies of logistically challenging "mega-radiations." Our findings reject any simple key innovation behind high diversity and underline the often nuanced, multifactorial processes leading to species-rich clades.

Zeocin-induced DNA damage response in barley and its dependence on ATR

DNA damage response (DDR) is an essential mechanism by which living organisms maintain their genomic stability. In plants, DDR is important also for normal growth and yield. Here, we explored the DDR of a temperate model crop barley (Hordeum vulgare) at the phenotypic, physiological, and transcriptomic levels. By a series of in vitro DNA damage assays using the DNA strand break (DNA-SB) inducing agent zeocin, we showed reduced root growth and expansion of the differentiated zone to the root tip. Genome-wide transcriptional profiling of barley wild-type and plants mutated in DDR signaling kinase ATAXIA TELANGIECTASIA MUTATED AND RAD3-RELATED (hvatr.g) revealed zeocin-dependent, ATR-dependent, and zeocin-dependent/ATR-independent transcriptional responses. Transcriptional changes were scored also using the newly developed catalog of 421 barley DDR genes with the phylogenetically-resolved relationships of barley SUPRESSOR OF GAMMA 1 (SOG1) and SOG1-LIKE (SGL) genes. Zeocin caused up-regulation of specific DDR factors and down-regulation of cell cycle and histone genes, mostly in an ATR-independent manner. The ATR dependency was obvious for some factors associated with DDR during DNA replication and for many genes without an obvious connection to DDR. This provided molecular insight into the response to DNA-SB induction in the large and complex barley genome.

Variovorax sp. strain P1R9 applied individually or as part of bacterial consortia enhances wheat germination under salt stress conditions

Endophytes isolated from extremophile plants are interesting microbes for improving the stress tolerance of agricultural plants. Here, we isolated and characterized endophytic bacteria showing plant growth-promoting (PGP) traits from plants in two extreme Chilean biomes (Atacama Desert and Chilean Patagonia). Forty-two isolates were characterized as both halotolerant auxin producers (2-51 mg L-1) and 1-aminocyclopropane-1-carboxylate (ACC)-degrading bacteria (15-28 µmol αKB mg protein-1 h-1). The most efficient isolates were tested as single strains, in dual and triple consortia, or in combination with previously reported PGP rhizobacteria (Klebsiella sp. 27IJA and 8LJA) for their impact on the germination of salt-exposed (0.15 M and 0.25 M NaCl) wheat seeds. Interestingly, strain P1R9, identified as Variovorax sp., enhanced wheat germination under salt stress conditions when applied individually or as part of bacterial consortia. Under salt stress, plants inoculated with dual consortia containing the strain Variovorax sp. P1R9 showed higher biomass (41%) and reduced lipid peroxidation (33-56%) than uninoculated plants. Although the underlying mechanisms remain elusive, our data suggest that the application of Variovorax sp. P1R9, alone or as a member of PGP consortia, may improve the salt stress tolerance of wheat plants.

Potassium humate and cobalt enhance peanut tolerance to water stress through regulation of proline, antioxidants, and maintenance of nutrient homeostasis

Water stress is an important factor that substantially impacts crop production. As a result, there is a need for various strategies that can mitigate these negative effects. One such strategy is the application of potassium humate (Kh) and cobalt (Co), which have been reported to enhance the resistance of crop plants. Therefore, the present experiment was designed to investigate whether the application of Kh and Co could positively affect proline, chlorophyll and mineral elements contents, and antioxidant defense systems which in turn will mitigate the negative impact of water stress under different irrigation strategies. In 2021 and 2022, an open-field experiments were conducted by using a split-plot design. The main plots were divided to represent different irrigation strategies (ST), with additional control of full irrigation requirements (ST1). Four STs were implemented, with ST1, followed by the application of 75%, 50%, and 25% irrigation strategies in ST2, ST3, and ST4 respectively, in the next irrigation, followed by the full requirements, and so on. In the subplots, peanut plants were treated with tap water (Control), Kh at 2 g l-1 and 3 g l-1, Co, Co + Kh 2 g l-1 and Co + Kh 3 g l-1. The yield was negatively affected by the implementation of ST4, despite the increase in proline contents. Furthermore, there was a decrease in relative water content, chlorophyll content, antioxidant enzymes, protein, and mineral nutrient elements. However, the application of Kh or Co showed better improvements in most of the studied parameters. It is worth noting that there was an antagonistic relationship between Co and iron/manganese, and the intensity of this relationship was found to depend on the STs implemented. The highest mineral nutrient accumulation, chlorophyll content, relative water content, protein content, oil content, seed yield, and water productivity were observed when peanut plants were treated with Kh 3 g l-1 + Co under the ST2 water strategy.

Ferric reduction by a CYBDOM protein counteracts increased iron availability in root meristems induced by phosphorus deficiency

To mobilize sparingly available phosphorus (P) in the rhizosphere, many plant species secrete malate to release P sorbed onto (hydr)oxides of aluminum and iron (Fe). In the presence of Fe, malate can provoke Fe over-accumulation in the root apoplast, triggering a series of events that inhibit root growth. Here, we identified HYPERSENSITIVE TO LOW P1 (HYP1), a CYBDOM protein constituted of a DOMON and a cytochrome b561 domain, as critical to maintain cell elongation and meristem integrity under low P. We demonstrate that HYP1 mediates ascorbate-dependent trans-plasma membrane electron transport and can reduce ferric and cupric substrates in Xenopus laevis oocytes and in planta. HYP1 expression is up-regulated in response to P deficiency in the proximal zone of the root apical meristem. Disruption of HYP1 leads to increased Fe and callose accumulation in the root meristem and causes significant transcriptional changes in roots. We further demonstrate that HYP1 activity overcomes malate-induced Fe accumulation, thereby preventing Fe-dependent root growth arrest in response to low P. Collectively, our results uncover an ascorbate-dependent metalloreductase that is critical to protect root meristems of P-deficient plants from increased Fe availability and provide insights into the physiological function of the yet poorly characterized but ubiquitous CYBDOM proteins.

A CYBDOM protein impacts iron homeostasis and primary root growth under phosphate deficiency in Arabidopsis

Arabidopsis primary root growth response to phosphate (Pi) deficiency is mainly controlled by changes in apoplastic iron (Fe). Upon Pi deficiency, apoplastic Fe deposition in the root apical meristem activates pathways leading to the arrest of meristem maintenance and inhibition of cell elongation. Here, we report that a member of the uncharacterized cytochrome b561 and DOMON domain (CYBDOM) protein family, named CRR, promotes iron reduction in an ascorbate-dependent manner and controls apoplastic iron deposition. Under low Pi, the crr mutant shows an enhanced reduction of primary root growth associated with increased apoplastic Fe in the root meristem and a reduction in meristematic cell division. Conversely, CRR overexpression abolishes apoplastic Fe deposition rendering primary root growth insensitive to low Pi. The crr single mutant and crr hyp1 double mutant, harboring a null allele in another member of the CYDOM family, shows increased tolerance to high-Fe stress upon germination and seedling growth. Conversely, CRR overexpression is associated with increased uptake and translocation of Fe to the shoot and results in plants highly sensitive to Fe excess. Our results identify a ferric reductase implicated in Fe homeostasis and developmental responses to abiotic stress, and reveal a biological role for CYBDOM proteins in plants.

Proximity to Photosystem II is necessary for activation of Plastid Terminal Oxidase (PTOX) for photoprotection

The Plastid Terminal Oxidase (PTOX) is a chloroplast localized plastoquinone oxygen oxidoreductase suggested to have the potential to act as a photoprotective safety valve for photosynthesis. However, PTOX overexpression in plants has been unsuccessful at inducing photoprotection, and the factors that control its activity remain elusive. Here, we show that significant PTOX activity is induced in response to high light in the model species Eutrema salsugineum and Arabidopsis thaliana. This activation correlates with structural reorganization of the thylakoid membrane. Over-expression of PTOX in mutants of Arabidopsis thaliana perturbed in thylakoid stacking also results in such activity, in contrast to wild type plants with normal granal structure. Further, PTOX activation protects against photoinhibition of Photosystem II and reduces reactive oxygen production under stress conditions. We conclude that structural re-arrangements of the thylakoid membranes, bringing Photosystem II and PTOX into proximity, are both required and sufficient for PTOX to act as a Photosystem II sink and play a role in photoprotection.

Polystyrene nanoparticles induce concerted response of plant defense mechanisms in plant cells

Recent advances in knowledge suggest that micro- and nanoplastics pose a threat to plant health, however, the responses of plants to this stressor are not well-known. Here we examined the response of plant cell defence mechanisms to nanoparticles of commonly used plastic, polystyrene. We used plant cell cultures of widely cultivated plants, the monocots wheat and barley (Triticum aestivum L., Hordeum vulgare L.) and the dicots carrot and tomato (Daucus carota L., Solanum lycopersicum L.). We measured the activities of enzymes involved in the scavenging of reactive oxygen species and nonenzymatic antioxidants and we estimated potential damages in plant cell structures and functioning via lipid peroxidation and DNA methylation levels. Our results demonstrate that the mode of action of polystyrene nanoparticles on plant cells involves oxidative stress. However, the changes in plant defence mechanisms are dependent on plant species, exposure time and nanoplastic concentrations. In general, both monocots showed similar responses to nanoplastics, but the carrot followed more the response of monocots than a second dicot, a tomato. Higher H2O2, lipid peroxidation and lower enzyme activities scavenging H2O2 suggest that tomato cells may be more susceptible to polystyrene-induced stress. In conclusion, polystyrene nanoplastics induce oxidative stress and the response of the plant defense mechanisms involving several chain reactions leading to oxidoreductive homeostasis.

Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa)

The APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) gene family plays vital roles in plants, serving as a key regulator in responses to abiotic stresses. Despite its significance, a comprehensive understanding of this family in lettuce remains incomplete. In this study, we performed a genome-wide search for the AP2/ERF family in lettuce and identified a total of 224 members. The duplication patterns provided evidence that both tandem and segmental duplications contributed to the expansion of this family. Ka/Ks ratio analysis demonstrated that, following duplication events, the genes have been subjected to purifying selection pressure, leading to selective constraints on their protein sequence. This selective pressure provides a dosage benefit against stresses in plants. Additionally, a transcriptome analysis indicated that some duplicated genes gained novel functions, emphasizing the contribution of both dosage effect and functional divergence to the family functionalities. Furthermore, an orthologous relationship study showed that 60% of genes descended from a common ancestor of Rosid and Asterid lineages, 28% from the Asterid ancestor, and 12% evolved in the lettuce lineage, suggesting lineage-specific roles in adaptive evolution. These results provide valuable insights into the evolutionary mechanisms of the AP2/ERF gene family in lettuce, with implications for enhancing abiotic stress tolerance, ultimately contributing to the genetic improvement of lettuce crop production.

Enhancing maize productivity by mitigating alkaline soil challenges through acidified biochar and wastewater irrigation

In alkaline soil conditions, the availability of essential nutrients for plant growth becomes limited, posing a significant challenge for achieving optimal maize growth and yield. Exploring the impact of biochar and waste irrigation on soil alkalinity and maize production in arid regions has received limited attention. This study aimed to evaluate the effects of three levels of acidified biochar (0, 5, and 10 Mg ha-1) in two growing seasons of maize-spring and autumn. The treatments were applied following a randomized complete block design with three replications. Biochar was applied only in the autumn season, and its residual effects were evaluated in the spring season. The study found that using acidifying biochar at a rate of 10 Mg ha-1 significantly increased maize yield by 35.8% compared to no application and by 16.4% compared to a rate of 5 Mg ha-1. In the autumn, applying acidified biochar at 10 Mg ha-1 reduced soil pH by 3.65% and 6.41% compared to 0 and 5 Mg ha-1. In the spring, the same application led to a decrease in soil pH by 5.84% and 7.37% compared to the lower rates. Additionally, using 10 Mg ha-1 of acidifying biochar increased soil phosphorus concentration by 87.6% and soil potassium concentration by 38.0% compared to not using biochar, and by 46.2% and 35.0% compared to the 5 Mg ha-1 application. These findings suggest that the reduction of soil pH by applying biochar at a rate of 10 Mg ha-1 facilitated an increase in nutrient availability in the soil, consequently leading to higher maize yield. Notably, no significant differences were observed in maize productivity and soil properties between the spring and autumn seasons. Therefore, this study paves the way for further exploration into the long-term effects of acidifying biochar on maize productivity and soil properties in similar agroecological contexts.

Symbiodiniaceae photophysiology and stress resilience is enhanced by microbial associations

Symbiodiniaceae form associations with extra- and intracellular bacterial symbionts, both in culture and in symbiosis with corals. Bacterial associates can regulate Symbiodiniaceae fitness in terms of growth, calcification and photophysiology. However, the influence of these bacteria on interactive stressors, such as temperature and light, which are known to influence Symbiodiniaceae physiology, remains unclear. Here, we examined the photophysiological response of two Symbiodiniaceae species (Symbiodinium microadriaticum and Breviolum minutum) cultured under acute temperature and light stress with specific bacterial partners from their microbiome (Labrenzia (Roseibium) alexandrii, Marinobacter adhaerens or Muricauda aquimarina). Overall, bacterial presence positively impacted Symbiodiniaceae core photosynthetic health (photosystem II [PSII] quantum yield) and photoprotective capacity (non-photochemical quenching; NPQ) compared to cultures with all extracellular bacteria removed, although specific benefits were variable across Symbiodiniaceae genera and growth phase. Symbiodiniaceae co-cultured with M. aquimarina displayed an inverse NPQ response under high temperatures and light, and those with L. alexandrii demonstrated a lowered threshold for induction of NPQ, potentially through the provision of antioxidant compounds such as zeaxanthin (produced by Muricauda spp.) and dimethylsulfoniopropionate (DMSP; produced by this strain of L. alexandrii). Our co-culture approach empirically demonstrates the benefits bacteria can deliver to Symbiodiniaceae photochemical performance, providing evidence that bacterial associates can play important functional roles for Symbiodiniaceae.

Adaptive traits of cysts of the snow alga Sanguina nivaloides unveiled by 3D subcellular imaging

Sanguina nivaloides is the main alga forming red snowfields in high mountains and Polar Regions. It is non-cultivable. Analysis of environmental samples by X-ray tomography, focused-ion-beam scanning-electron-microscopy, physicochemical and physiological characterization reveal adaptive traits accounting for algal capacity to reside in snow. Cysts populate liquid water at the periphery of ice, are photosynthetically active, can survive for months, and are sensitive to freezing. They harbor a wrinkled plasma membrane expanding the interface with environment. Ionomic analysis supports a cell efflux of K+, and assimilation of phosphorus. Glycerolipidomic analysis confirms a phosphate limitation. The chloroplast contains thylakoids oriented in all directions, fixes carbon in a central pyrenoid and produces starch in peripheral protuberances. Analysis of cells kept in the dark shows that starch is a short-term carbon storage. The biogenesis of cytosolic droplets shows that they are loaded with triacylglycerol and carotenoids for long-term carbon storage and protection against oxidative stress.

Application of bio-organic amendments improves soil quality and yield of fennel (Foeniculum vulgare Mill.) plants in saline calcareous soil

The impact of bio-organic amendments on crop production is poorly understood in saline calcareous soils. The aim in the present study was to determine the effects of the application of organic manure along with lactic acid bacteria (LAB) on soil quality, and morpho-physio-biochemical responses, seed yield (SY) and essential oil yield (EOY) of fennel plants (Foeniculum vulgare Mill.) grown in saline calcareous soils. Eight treatments of farmyard manure (FM) or poultry manure (PM) individually or combined with Lactobacillus plantarum (Lp) and/or Lactococcus lactis (Ll) were applied to saline calcareous soil in two growing seasons. Either FM or PM combined with LAB had beneficial effects on lowering ECe, pH and bulk density and increasing total porosity, organic matter, and water and nutrient retention capacities in addition to total bacterial population in the soil. Growth, nutrient uptake, SY and EOY of plants were also enhanced when fennel seeds were inoculated with Lp and/or Ll and the soil was amended with any of the organic manures under unfavorable conditions. Compared to control (no bio-organic amendments), FM + Lp + Lt or PM + Lp + Lt treatment signficantlly (P ≤ 0.05) increased plant height by 86.2 or 65.0%, total chlorophyll by 73 or 50%, proline by 35 or 45%, glutathione by 100 or 138%, SY by 625 or 463% and EOY by 300 or 335%, respectively, in fennel plants. Co-application of the naturally occurring microorganisms (i.e., LAB) and organically-derived, nutrient-rich fertilizer (i.e., FM or PM) is recommended to improve yield of fennel plants in saline calcareous soils.

Advancements and prospects of CRISPR/Cas9 technologies for abiotic and biotic stresses in sugar beet

Sugar beet is a crop with high sucrose content, known for sugar production and recently being considered as an emerging raw material for bioethanol production. This crop is also utilized as cattle feed, mainly when animal green fodder is scarce. Bioethanol and hydrogen gas production from this crop is an essential source of clean energy. Environmental stresses (abiotic/biotic) severely affect the productivity of this crop. Over the past few decades, the molecular mechanisms of biotic and abiotic stress responses in sugar beet have been investigated using next-generation sequencing, gene editing/silencing, and over-expression approaches. This information can be efficiently utilized through CRISPR/Cas 9 technology to mitigate the effects of abiotic and biotic stresses in sugar beet cultivation. This review highlights the potential use of CRISPR/Cas 9 technology for abiotic and biotic stress management in sugar beet. Beet genes known to be involved in response to alkaline, cold, and heavy metal stresses can be precisely modified via CRISPR/Cas 9 technology for enhancing sugar beet's resilience to abiotic stresses with minimal off-target effects. Similarly, CRISPR/Cas 9 technology can help generate insect-resistant sugar beet varieties by targeting susceptibility-related genes, whereas incorporating Cry1Ab and Cry1C genes may provide defense against lepidopteron insects. Overall, CRISPR/Cas 9 technology may help enhance sugar beet's adaptability to challenging environments, ensuring sustainable, high-yield production.

Transcriptome-based strategies for identifying aluminum tolerance genes in popcorn (Zea mays L. var. everta)

Aluminum (Al) toxicity limits crop production worldwide. Although studies have identified genes associated with Al tolerance in crops, a large amount of data remains unexplored using other strategies. Here, we searched for single substitutions and InDels across differentially expressed genes (DEGs), linked DEGs to Al-tolerance QTLs reported in the literature for common maize, and investigated the alternative splicing regulated by Al3+ toxicity. We found 929 substitutions between DEGs in Al-tolerant and 464 in Al-sensitive inbred lines, of which 165 and 80 were non-synonymous, respectively. Only 12 NS variants had deleterious predicted effect on protein function in Al-tolerant and 13 in Al-sensitive. Moreover, 378 DEGs were mapped in Al-QTL regions for the Al-tolerant and 213 for the Al-sensitive. Furthermore, Al stress is primarily regulated at the transcriptional level in popcorn. Important genes identified, such as HDT1, SWEET4a, GSTs, SAD9, PIP2-2, CASP-like 5, and AGP, may benefit molecular assisted popcorn breeding or be useful in biotechnological approaches. These findings offer insights into the mechanisms of Al tolerance in popcorn and provide a 'hypothesis-free' strategy for identifying and prioritizing candidate genes that could be used to develop molecular markers or cultivars resilient to acidic soils.

Alleviation of cadmium and drought stress in wheat by improving growth and chlorophyll contents amended with GA3 enriched deashed biochar

Drought and cadmium (Cd) stress are both major issues that significantly affect the growth and development of wheat plants. Both drought stress and Cd toxicity disrupt physiological processes i.e., nutrient uptake, cell expansion, and enzymatic reactions resulting in poor crop growth. To overcome these issues, the use of activated carbon and gibberellic acid (GA3) are considered valuable amendments. However, the current study aimed to add value using GA3-enriched biochar (GA3-BC). That's why, a lab experiment was conducted on wheat to assess the effectiveness of GA3-BC against Cd and drought stress. For GA3 enrichment in biochar, 10 µg GA3/g biochar was mixed. There were 3 levels of GA3-BC i.e., 0, 0.6 (GA3-BC1), and 0.9% (GA3-BC). All levels were applied in 3 replicates under no stress (0Cd + no drought), drought stress (DS), and 6 mg Cd/ kg soil (6Cd). Results showed that GA3-BC2 caused a significant improvement in shoot length (44.99%), root length (99.73%), seedling length (60.13%) and shoot fresh weight (63.59%) over control at 6Cd + drought stress. A significant improvement in chlorophyll a, chlorophyll b, and total chlorophyll while a decrease in electrolyte leakage and regulation of antioxidants i.e., lipid peroxidation, SOD, CAT, APx, GR, GPx, GST, and DPHH also signified the effectiveness of GA3-BC2 compared to control at 6Cd + drought stress. In conclusion, GA3-BC2 is an efficacious amendment for simultaneously alleviating drought and Cd stress in wheat. More investigations are recommended at the field level on different cereal crops cultivated in different soil textures to declare GA3-BC2 as the best treatment for mitigation of drought stress and Cd toxicity.

A mitochondrial pentatricopeptide repeat protein enhances cold tolerance by modulating mitochondrial superoxide in rice

Cold stress affects rice growth and productivity. Defects in the plastid-localized pseudouridine synthase OsPUS1 affect chloroplast ribosome biogenesis, leading to low-temperature albino seedlings and accumulation of reactive oxygen species (ROS). Here, we report an ospus1-1 suppressor, sop10. SOP10 encodes a mitochondria-localized pentatricopeptide repeat protein. Mutations in SOP10 impair intron splicing of the nad4 and nad5 transcripts and decrease RNA editing efficiency of the nad2, nad6, and rps4 transcripts, resulting in deficiencies in mitochondrial complex I, thus decrease ROS generation and rescuing the albino phenotype. Overexpression of different compartment-localized superoxide dismutases (SOD) genes in ospus1-1 reverses the ROS over-accumulation and albino phenotypes to various degrees, with Mn-SOD reversing the best. Mutation of SOP10 in indica rice varieties enhances cold tolerance with lower ROS levels. We find that the mitochondrial superoxide plays a key role in rice cold responses, and identify a mitochondrial superoxide modulating factor, informing efforts to improve rice cold tolerance.

A silicon transporter gene required for healthy growth of rice on land

Silicon (Si) is the most abundant mineral element in the earth's crust. Some plants actively accumulate Si as amorphous silica (phytoliths), which can protect plants from stresses. Here, we report a gene (SIET4) that is required for the proper accumulation and cell-specific deposition of Si in rice and show that it is essential for normal growth. SIET4 is constitutively expressed in leaves and encodes a Si transporter. SlET4 polarly localizes at the distal side of epidermal cells and cells surrounding the bulliform cells (motor cells) of the leaf blade, where Si is deposited. Knockout of SIET4 leads to the death of rice in the presence but not absence of Si. Further analysis shows that SIET4 knockout induces abnormal Si deposition in mesophyll cells and the induction of hundreds of genes related to various stress responses. These results indicate that SIET4 is required for the proper export of Si from leaf cells to the leaf surface and for the healthy growth of rice on land.

Bioinoculants as a means of increasing crop tolerance to drought and phosphorus deficiency in legume-cereal intercropping systems

Ensuring plant resilience to drought and phosphorus (P) stresses is crucial to support global food security. The phytobiome, shaped by selective pressures, harbors stress-adapted microorganisms that confer host benefits like enhanced growth and stress tolerance. Intercropping systems also offer benefits through facilitative interactions, improving plant growth in water- and P-deficient soils. Application of microbial consortia can boost the benefits of intercropping, although questions remain about the establishment, persistence, and legacy effects within resident soil microbiomes. Understanding microbe- and plant-microbe dynamics in drought-prone soils is key. This review highlights the beneficial effects of rhizobacterial consortia-based inoculants in legume-cereal intercropping systems, discusses challenges, proposes a roadmap for development of P-solubilizing drought-adapted consortia, and identifies research gaps in crop-microbe interactions.

In vivo spectroscopy and machine learning for the early detection and classification of different stresses in apple trees

The use of in vivo spectroscopy to detect plant stress in its early stages has the potential to enhance food safety and reduce the need for plant protection products. However, differentiating between various stress types before symptoms appear remains poorly studied. In this study, we investigated the potential of Vis-NIR spectroscopy to differentiate between stress types in apple trees (Malus x domestica Borkh.) exposed to apple scab, waterlogging, and herbicides in a greenhouse. Using a spectroradiometer, we collected spectral signatures of leaves still attached to the tree and utilized machine learning techniques to develop predictive models for detecting stress presence and classifying stress type as early as 1-5 days after exposure. Our findings suggest that changes in spectral reflectance at multiple regions accurately differentiate various types of plant stress on apple trees. Our models were highly accurate (accuracies between 0.94 and 1) when detecting the general presence of stress at an early stage. The wavelengths important for classification relate to photosynthesis via pigment functioning (684 nm) and leaf water (~ 1800-1900 nm), which may be associated with altered gas exchange as a short-term stress response. Overall, our study demonstrates the potential of spectral technology and machine learning for early diagnosis of plant stress, which could lead to reduced environmental burden through optimizing resource utilization in agriculture.

The CBL1/9-CIPK1 calcium sensor negatively regulates drought stress by phosphorylating the PYLs ABA receptor

The stress hormone, Abscisic acid (ABA), is crucial for plants to respond to changes in their environment. It triggers changes in cytoplasmic Ca2+ levels, which activate plant responses to external stresses. However, how Ca2+ sensing and signaling feeds back into ABA signaling is not well understood. Here we reveal a calcium sensing module that negatively regulates drought stress via modulating ABA receptor PYLs. Mutants cbl1/9 and cipk1 exhibit hypersensitivity to ABA and drought resilience. Furthermore, CIPK1 is shown to interact with and phosphorylate 7 of 14 ABA receptors at the evolutionarily conserved site corresponding to PYL4 Ser129, thereby suppressing their activities and promoting PP2C activities under normal conditions. Under drought stress, ABA impedes PYLs phosphorylation by CIPK1 to respond to ABA signaling and survive in unfavorable environment. These findings provide insights into a previously unknown negative regulatory mechanism of the ABA signaling pathway, which is mediated by CBL1/9-CIPK1-PYLs, resulting in plants that are more sensitive to drought stress. This discovery expands our knowledge about the interplay between Ca2+ signaling and ABA signaling.

Rice straw-derived smoke water promotes rice root growth under phosphorus deficiency by modulating oxidative stress and photosynthetic gene expression

Plant-derived smoke has been shown to promote plant growth and seed germination, but its roles and mechanisms in response to nutrient deficiency stress remain unclear. Plants respond to phosphorus (P) deficiency by undergoing morphological, physiological, and transcriptional changes in order to improve nutrient uptake efficiency. Here, we showed that rice straw-derived smoke water could promote root growth in rice (Oryza sativa cv. Nipponbare) grown under P-sufficient and P-deficient conditions. Transcriptome analysis of the root tissues identified 1309 genes up-regulated and 1311 genes down-regulated by smoke water under P-deficient conditions. The GO terms 'glutathione transferase activity' and 'photosynthesis-light reaction' were found to be significantly enriched among the genes that were up- and down-regulated by smoke water, respectively. Biochemical analysis showed that smoke water reduced P-deficient-induced accumulation of H2O2 and malondialdehyde (MDA), a lipid peroxidation marker, reduced sucrose contents, but increased Fe accumulation. Furthermore, smoke water suppressed the expression of strigolactone biosynthesis genes, which were strongly induced by P deficiency as an adaptive strategy to improve root P uptake. These results revealed a potential mechanism by which smoke water promotes root growth and interacts with P deficiency-induced transcriptional regulation to mitigate P deficiency stress in rice.

Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone

Subnival glasshouse plants provide a text-book example of high-altitude adaptation with reproductive organs enclosed in specialized semi-translucent bracts, monocarpic reproduction and continuous survival under stress. Here, we present genomic, transcriptomic and metabolomic analyses for one such plant, the Noble rhubarb (Rheum nobile). Comparative genomic analyses show that an expanded number of genes and retained genes from two recent whole-genome duplication events are both relevant to subnival adaptation of this species. Most photosynthesis genes are downregulated within bracts compared to within leaves, and indeed bracts exhibit a sharp reduction in photosynthetic pigments, indicating that the bracts no longer perform photosynthesis. Contrastingly, genes related to flavonol synthesis are upregulated, providing enhanced defense against UV irradiation damage. Additionally, anatomically abnormal mesophyll combined with the downregulation of genes related to mesophyll differentiation in bracts illustrates the innovation and specification of the glass-like bracts. We further detect substantial accumulation of antifreeze proteins (e.g. AFPs, LEAs) and various metabolites (e.g. Proline, Protective sugars, procyanidins) in over-wintering roots. These findings provide new insights into subnival adaptation and the evolution of glasshouse alpine plants.

microRNA165 and 166 modulate response of the Arabidopsis root apical meristem to salt stress

In plants, developmental plasticity allows for the modulation of organ growth in response to environmental cues. Being in contact with soil, roots are the first organ that responds to various types of soil abiotic stress such as high salt concentration. In the root, developmental plasticity relies on changes in the activity of the apical meristem, the region at the tip of the root where a set of self-renewing undifferentiated stem cells sustain growth. Here, we show that salt stress promotes differentiation of root meristem cells via reducing the dosage of the microRNAs miR165 and 166. By means of genetic, molecular and computational analysis, we show that the levels of miR165 and 166 respond to high salt concentration, and that miR165 and 166-dependent PHABULOSA (PHB) modulation is central to the response of root growth to this stress. Specifically, we show that salt-dependent reduction of miR165 and 166 causes a rapid increase in PHB expression and, hence, production of the root meristem pro-differentiation hormone cytokinin. Our data provide direct evidence for how the miRNA-dependent modulation of transcription factor dosage mediates plastic development in plants.

The OsSGS3-tasiRNA-OsARF3 module orchestrates abiotic-biotic stress response trade-off in rice

Recurrent heat stress and pathogen invasion seriously threaten crop production, and abiotic stress often antagonizes biotic stress response against pathogens. However, the molecular mechanisms of trade-offs between thermotolerance and defense remain obscure. Here, we identify a rice thermo-sensitive mutant that displays a defect in floret development under high temperature with a mutation in SUPPRESSOR OF GENE SILENCING 3a (OsSGS3a). OsSGS3a interacts with its homolog OsSGS3b and modulates the biogenesis of trans-acting small interfering RNA (tasiRNA) targeting AUXIN RESPONSE FACTORS (ARFs). We find that OsSGS3a/b positively, while OsARF3a/b and OsARF3la/lb negatively modulate thermotolerance. Moreover, OsSGS3a negatively, while OsARF3a/b and OsARF3la/lb positively regulate disease resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo) and the fungal pathogen Magnaporthe oryzae (M. oryzae). Taken together, our study uncovers a previously unknown trade-off mechanism that regulates distinct immunity and thermotolerance through the OsSGS3-tasiRNA-OsARF3 module, highlighting the regulation of abiotic-biotic stress response trade-off in plants.

Nanosilica modulates C:N:P stoichiometry attenuating phosphorus toxicity more than deficiency in Megathyrsus maximus cultivated in an Oxisol and Entisol

Silicon (Si) nanoparticles can attenuate nutritional disorders caused by phosphorus in forages through nutritional homeostasis. This paper aims to evaluate the effects of P deficiency and toxicity in Megathyrsus maximus cultivated in two types of soils and to verify whether Si application via fertigation can mitigate these imbalances. The following two experiments were carried out: cultivation of forage plants in pots with Entisol and Oxisol, in a 3 × 2 factorial design, with three nutritional levels of phosphorus (deficient, adequate, and excessive) and two Si concentrations in the irrigation water (0 and 1.5 mmol L-1). Height, number of tillers, rate of leaf senescence, dry matter production, C:N, C:Si, C:P, and N:P ratios; and C, P, and N use efficiencies were evaluated in two growth cycles. P imbalances hampered carbon assimilation, C:N:P homeostasis, and dry matter production. Nanosilica fertigation promoted silicon uptake, improving C:N:P homeostasis and nutritional efficiency in plants under P deficiency and toxicity. Leaf senescence was reduced with addition of Si in plants grown in Oxisol in the three nutritional states of P. Silicon attenuated the stress caused by P toxicity in Entisol and Oxisol, improving production in plants without nutritional stress in Oxisol. The supply of Si nanoparticles in the cultivation of M. maximus can contribute to a more efficient and sustainable use of phosphorus in pastures.

A phylotranscriptomic dataset of angiosperm species under cold stress

Angiosperms are one of the most diverse and abundant plant groups that are widely distributed on Earth, from tropical to temperate and polar zones. The wide distribution of angiosperms may be attributed to the evolution of sophisticated mechanisms of environmental adaptability, including cold tolerance. Since the development of high-throughput sequencing, transcriptome has been widely utilized to gain insights into the molecular mechanisms of plants in response to cold stress. However, previous studies generally focused on single or two species, and comparative transcriptome analyses for multispecies responding to cold stress were limited. In this study, we selected 11 representative angiosperm species, performed phylotranscriptome experiments at four time points before and after cold stress, and presented a profile of cold-induced transcriptome changes in angiosperms. Our multispecies cold-responsive RNA-seq datasets provide valuable references for exploring conserved and evolutionary mechanisms of angiosperms in adaptation to cold stress.

Rootstock-scion interaction affects Malus transcriptome profiles in response to cadmium

Apple production is threatened by cadmium contamination in orchards. Cd accumulation and tolerance in grafted Malus plants is affected by rootstock, scion, and their interaction. This dataset is part of an experiment investigating the molecular mechanism of Cd bioaccumulation and tolerance in different apple rootstock-scion combinations. We exposed four rootstock-scion combinations to Cd treatment consisting of Hanfu and Fuji apple (Malus domestica) scions grafted onto apple rootstocks of M. baccata or M. micromalus "qingzhoulinqin". RNA sequencing was conducted in roots and leaves of grafting combinations under 0 or 50 μM CdCl2 conditions. A comprehensive transcriptional dataset of affected rootstock, scion, and their interaction among different graft combinations was obtained. This dataset provides new insights in the transcriptional control of Cd bioaccumulation and tolerance in grafting plants regulated by rootstock and scion. Herein, we discuss the molecular mechanism underlying Cd absorption and bioaccumulation.

Hydroxyl Radical Transformations of Perfluoroalkyl Acid (PFAA) Precursors in Aqueous Film Forming Foams (AFFFs)

Historical releases of aqueous film forming foam (AFFF) are significant sources of poly- and perfluoroalkyl substances (PFASs), including perfluoroalkyl acids (PFAAs) and their precursors, to the environment. While several studies have focused on microbial biotransformation of polyfluorinated precursors to PFAAs, the role of abiotic transformations at AFFF-impacted sites is less clear. Herein, we use photochemically generated hydroxyl radical to demonstrate that environmentally relevant concentrations of hydroxyl radical (^•OH) can play a significant role in these transformations. High-resolution mass spectrometry (HRMS) was used to perform targeted analysis, suspect screening, and nontargeted analyses, which were used to identify the major products of AFFF-derived PFASs as perfluorocarboxylic acids, though several potentially semi-stable intermediates were also observed. Using competition kinetics in a UV/H₂O₂ system, hydroxyl radical rate constants (k_OH) for 24 AFFF-derived polyfluoroalkyl precursors were measured to be 0.28 to 3.4 × 10⁹ M^-1 s^-1. Differences in k_OH were observed for compounds with differing headgroups and perfluoroalkyl chain lengths. Also, differences in k_OH measured for the only relevant precursor standard available, n-[3-propyl]tridecafluorohexanesulphonamide (AmPr-FHxSA), as compared to AmPr-FHxSA present in AFFF suggest that intermolecular associations in the AFFF matrix may affect k_OH. Considering environmentally relevant [^•OH]_ss, polyfluoroalkyl precursors are expected to exhibit half-lives of ∼8 days in sunlit surface waters and possibly as short as ∼2 h during oxygenation of Fe(II)-rich subsurface systems.

Low-temperature and circadian signals are integrated by the sigma factor SIG5

Chloroplasts are a common feature of plant cells and aspects of their metabolism, including photosynthesis, are influenced by low-temperature conditions. Chloroplasts contain a small circular genome that encodes essential components of the photosynthetic apparatus and chloroplast transcription/translation machinery. Here, we show that in Arabidopsis, a nuclear-encoded sigma factor that controls chloroplast transcription (SIGMA FACTOR5) contributes to adaptation to low-temperature conditions. This process involves the regulation of SIGMA FACTOR5 expression in response to cold by the bZIP transcription factors ELONGATED HYPOCOTYL5 and ELONGATED HYPOCOTYL5 HOMOLOG. The response of this pathway to cold is gated by the circadian clock, and it enhances photosynthetic efficiency during long-term cold and freezing exposure. We identify a process that integrates low-temperature and circadian signals, and modulates the response of chloroplasts to low-temperature conditions.

Metal-tolerant and siderophore producing Pseudomonas fluorescence and Trichoderma spp. improved the growth, biochemical features and yield attributes of chickpea by lowering Cd uptake

Industrialization and human urbanization have led to an increase in heavy metal (HM) pollution which often cause negative/toxic effect on agricultural crops. The soil-HMs cannot be degraded biologically however, microbe-mediated detoxification of toxic HMs into lesser toxic forms are reported. Considering the potentiality of HMs-tolerant soil microbes in metal detoxification, Pseudomonas fluorescence PGPR-7 and Trichoderma sp. T-4 were recovered from HM-affected areas. Under both normal and cadmium stress, the ability of both microorganisms to produce different plant hormones and biologically active enzymes was examined. Strains PGPR-7 and T-4 tolerated cadmium (Cd) an up-to 1800 and 2000 µg mL^-1, respectively, and produced various plant growth regulating substances (IAA, siderophore, ACC deaminase ammonia and HCN) in Cd-stressed condition. The growth promoting and metal detoxifying ability of both strains were evaluated (either singly/combined) by applying them in chickpea (Cicer arietinum L.) plants endogenously contaminated with different Cd levels (0-400 µg kg^-1 soils). The higher Cd concentration (400 µg kg^-1 soils) negatively influenced the plant parameters which, however, improved following single/combined inoculation of P. fluorescence PGPR-7 and Trichoderma sp. T-4. Both microbial strains increased the growth of Cd-treated chickpeas however, their combined inoculation (PGPR-7 + T-4) caused the most positive effect. For instance, 25 µg Cd Kg^-1 + PGPR-7 + T4 treatment caused maximum increase in germination percentage (10%), root dry biomass (71.4%) and vigour index (33%), chl-a (38%), chl-b (41%) and carotenoid content (52%). Furthermore, combined inoculation of P. fluorescence PGPR-7 and Trichoderma sp. T-4 maximally decreased the proline, MDA content, POD and CAT activities by 50%, 43% and 62%, respectively following their application in 25 µg Cd kg^-1 soils-treated chickpea. Additionally, microbial strains lowered the plant uptake of Cd. For example, Cd-uptake in root tissues was decreased by 42 and 34% when 25 µg Cd Kg^-1- treated chickpea plants were inoculated with P. fluorescence PGPR-7, Trichoderma sp. T-4 and co-inoculation (PGPR-7 + T4) of both strains, respectively. Therefore, from the current observation, it is suggested that dual inoculation of metal tolerant P. fluorescence and Trichoderma sp. may potentially be used in detoxification and reclamation of metal-contaminated soils.

Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses

Abiotic stresses negatively impact ecosystems and the yield of crops, and climate change will increase their frequency and intensity. Despite progress in understanding how plants respond to individual stresses, our knowledge of plant acclimatization to combined stresses typically occurring in nature is still lacking. Here, we used a plant with minimal regulatory network redundancy, Marchantia polymorpha, to study how seven abiotic stresses, alone and in 19 pairwise combinations, affect the phenotype, gene expression, and activity of cellular pathways. While the transcriptomic responses show a conserved differential gene expression between Arabidopsis and Marchantia, we also observe a strong functional and transcriptional divergence between the two species. The reconstructed high-confidence gene regulatory network demonstrates that the response to specific stresses dominates those of others by relying on a large ensemble of transcription factors. We also show that a regression model could accurately predict the gene expression under combined stresses, indicating that Marchantia performs arithmetic multiplication to respond to multiple stresses. Lastly, two online resources ( https://conekt.plant.tools and http://bar.utoronto.ca/efp_marchantia/cgi-bin/efpWeb.cgi ) are provided to facilitate the study of gene expression in Marchantia exposed to abiotic stresses.

Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics

Peatlands are crucial sinks for atmospheric carbon but are critically threatened due to warming climates. Sphagnum (peat moss) species are keystone members of peatland communities where they actively engineer hyperacidic conditions, which improves their competitive advantage and accelerates ecosystem-level carbon sequestration. To dissect the molecular and physiological sources of this unique biology, we generated chromosome-scale genomes of two Sphagnum species: S. divinum and S. angustifolium. Sphagnum genomes show no gene colinearity with any other reference genome to date, demonstrating that Sphagnum represents an unsampled lineage of land plant evolution. The genomes also revealed an average recombination rate an order of magnitude higher than vascular land plants and short putative U/V sex chromosomes. These newly described sex chromosomes interact with autosomal loci that significantly impact growth across diverse pH conditions. This discovery demonstrates that the ability of Sphagnum to sequester carbon in acidic peat bogs is mediated by interactions between sex, autosomes and environment.

The importance of a holistic approach to the factors determining population abundances

Research Highlight: Ogilvie, J. E., & CaraDonna, P. J. (2022). The shifting importance of abiotic and biotic factors across the life cycles of wild pollinators. Journal of Animal Ecology, 91, 2412-2423. https://doi.org/10.1111/1365-2656.13825. As global change and its multiple impacts continue to unfold across most of the planet, understanding how populations of wild species respond to changing conditions has become a major focus of ecological studies. Ogilvie and CaraDonna (Ogilvie & CaraDonna, 2022) focus on understanding how biotic and abiotic conditions affect bumblebee abundances. A major advance in their work is that, rather than focusing on a single measure of abundance at a particular life stage for each of the seven bumblebee species they survey (e.g. adult abundance), they focus on understanding the drivers of population abundance across the different stages of the species' life cycles. The authors specifically assess how three factors in particular, climate conditions, floral resource availability and previous life-stage abundances impact these abundances. A main finding in their study is that each of these three factors directly impacted a different life stage, showing that just focusing on a single life-stage would have resulted on a biased and incomplete picture of how abiotic and biotic factors affect bumblebee population dynamics. Studies like this one emphasize the need to focus on understanding the demographic mechanisms that determine population abundances.

TLD 6B under abiotic stress

Chlorella sp. TLD 6B, a microalgae growing in the Taklamakan Desert, Xinjiang of China, is a good model material for studying the physiological and environmental adaptation mechanisms of plants in their arid habitats, as its adaptation to the harsh desert environment has led to its strong resistance. However, when using real-time quantitative polymerase chain reaction (RT-qPCR) to analyze the gene expression of this algae under abiotic stress, it is essential to find the suitable endogenous reference genes so to obtain reliable results. This study assessed the expression stability of 9 endogenous reference genes of Chlorella sp. TLD 6B under four abiotic stresses (drought, salt, cold and heat). These genes were selected based on the analysis results calculated by the three algorithmic procedures of geNorm, NormFinder, and BestKeeper, which were ranked by refinder. Our research showed that 18S and GTP under drought stress, 18S and IDH under salt stress, CYP and 18S under cold stress, GTP and IDH under heat stress were the most stable endogenous reference genes. Moreover, UBC and 18S were the most suitable endogenous reference gene combinations for all samples. In contrast, GAPDH and α-TUB were the two least stable endogenous reference genes in all experimental samples. Additionally, the selected genes have been verified to be durable and reliable by detecting POD and PXG3 genes using above endogenous reference genes. The identification of reliable endogenous reference genes guarantees more accurate RT-qPCR quantification for Chlorella sp. TLD 6B, facilitating functional genomics studies of deserts Chlorella as well as the mining of resistance genes.

Resilience of soybean cultivars to drought stress during flowering and early-seed setting stages

Drought stress during the reproductive stage and declining soybean yield potential raise concerns about yield loss and economic return. In this study, ten cultivars were characterized for 20 traits to identify reproductive stage (R1-R6) drought-tolerant soybean. Drought stress resulted in a marked reduction (17%) in pollen germination. The reduced stomatal conductance coupled with high canopy temperature resulted in reduced seed number (45%) and seed weight (35%). Drought stress followed by rehydration increased the hundred seed weight at the compensation of seed number. Further, soybean oil decreased, protein increased, and cultivars responded differently under drought compared to control. In general, cultivars with high tolerance scores for yield displayed lower tolerance scores for quality content and vice versa. Among ten cultivars, LS5009XS and G4620RX showed maximum stress tolerance scores for seed number and seed weight. The observed variability in leaf reflectance properties and their relationship with physiological or yield components suggested that leaf-level sensing information can be used for differentiating drought-sensitive soybean cultivars from tolerant ones. The study led to the identification of drought-resilient cultivars/promising traits which can be exploited in breeding to develop multi-stress tolerant cultivars.

Potassium nutrient status drives posttranslational regulation of a low-K response network in Arabidopsis

Under low-potassium (K+) stress, a Ca2+ signaling network consisting of calcineurin B-like proteins (CBLs) and CBL-interacting kinases (CIPKs) play essential roles. Specifically, the plasma membrane CBL1/9-CIPK pathway and the tonoplast CBL2/3-CIPK pathway promotes K+ uptake and remobilization, respectively, by activating a series of K+ channels. While the dual CBL-CIPK pathways enable plants to cope with low-K+ stress, little is known about the early events that link external K+ levels to the CBL-CIPK proteins. Here we show that K+ status regulates the protein abundance and phosphorylation of the CBL-CIPK-channel modules. Further analysis revealed low K+-induced activation of VM-CBL2/3 happened earlier and was required for full activation of PM-CBL1/9 pathway. Moreover, we identified CIPK9/23 kinases to be responsible for phosphorylation of CBL1/9/2/3 in plant response to low-K+ stress and the HAB1/ABI1/ABI2/PP2CA phosphatases to be responsible for CBL2/3-CIPK9 dephosphorylation upon K+-repletion. Further genetic analysis showed that HAB1/ABI1/ABI2/PP2CA phosphatases are negative regulators for plant growth under low-K+, countering the CBL-CIPK network in plant response and adaptation to low-K+ stress.

Discovery of endogenous nitroxyl as a new redox player in Arabidopsis thaliana

Nitroxyl (HNO) is the one-electron reduced and protonated congener of nitric oxide (•NO), owning a distinct chemical profile. Based on real-time detection, we demonstrate that HNO is endogenously formed in Arabidopsis. Senescence and hypoxia induce shifts in the redox balance, triggering HNO decay or formation mediated by non-enzymatic •NO/HNO interconversion with cellular reductants. The stimuli-dependent HNO generation supports or competes with •NO signalling, depending on the local redox environment.