Transcriptional profiling of long noncoding RNAs associated with flower color formation in Ipomoea nil.

MAIN CONCLUSION: LncRNAs regulate flower color formation in Ipomoea nil via vacuolar pH, TCA cycle, and oxidative phosphorylation pathways. The significance of long noncoding RNA (lncRNA) in diverse biological processes is crucial in plant kingdoms. Although study on lncRNAs has been extensive in mammals and model plants, lncRNAs have not been identified in Ipomoea nil (I. nil). In this study, we employed whole transcriptome strand-specific RNA sequencing to identify 11,203 expressed lncRNA candidates, including 961 known lncRNA and 10,242 novel lncRNA in the I. nil genome. These lncRNAs in I. nil had fewer exons and were generally shorter in length compared to mRNA genes. Totally, 1141 different expression lncRNAs (DELs) were significantly identified between white and red flowers. The functional analysis indicated that lncRNA-targeted genes were enriched in the TCA cycle, photosynthesis, and oxidative phosphorylation-related pathway, which was also found in differentially expressed genes (DEGs) functional enrichments. LncRNAs can regulate transcriptional levels through cis- or trans-acting mechanisms. LncRNA cis-targeted genes were significantly enriched in potassium and lysosome. For trans-lncRNA, two energy metabolism pathways, TCA cycles and oxidative phosphorylation, were identified from positive association pairs of trans-lncRNA and mRNA. This research advances our understanding of lncRNAs and their role in flower color development, providing valuable insights for future selective breeding of I. nil.

State-of-the-art OMICS strategies against toxic effects of heavy metals in plants: A review.

Environmental pollution of heavy metals (HMs), mainly due to anthropogenic activities, has received growing attention in recent decades. HMs, especially the non-essential carcinogenic ones, including chromium (Cr), cadmium (Cd), mercury (Hg), aluminum (Al), lead (Pb), and arsenic (As), have appeared as the most significant air, water, and soil pollutants, which adversely affect the quantity, quality, and security of plant-based food all over the world. Plants exposed to HMs could experience significant decline in growth and yield. To avoid or tolerate the toxic effects of HMs, plants have developed complicated defense mechanisms, including absorption and accumulation of HMs in cell organelles, immobilization by forming complexes with organic chelates, extraction by using numerous transporters, ion channels, signalling cascades, and transcription elements, among others. OMICS strategies have developed significantly to understand the mechanisms of plant transcriptomics, genomics, proteomics, metabolomics, and ionomics to counter HM-mediated stress stimuli. These strategies have been considered to be reliable and feasible for investigating the roles of genomics (genomes), transcriptomic (coding), mRNA transcripts (non-coding), metabolomics (metabolites), and ionomics (metal ions) to enhance stress resistance or tolerance in plants. The recent developments in the mechanistic understandings of the HMs-plant interaction in terms of their absorption, translocation, and toxicity invasions at the molecular and cellular levels, as well as plants' response and adaptation strategies against these stressors, are summarized in the present review. Transcriptomics, genomics, metabolomics, proteomics, and ionomics for plants against HMs toxicities are reviewed, while challenges and future recommendations are also discussed.

Evaluation of heavy metal phytoremediation potential of six tree species of Faisalabad city of Pakistan during summer and winter seasons.

Environmental pollution induced by heavy metals has been identified as a leading threat in the modern era. Woody tree species may play a crucial role in the removal of heavy metals from soil and air, thus minimizing pollution potential. The present study was designed to evaluate the phytoremediation potential of six tree species; Azadirachta indica, Cassia fistula, Conocarpus erectus, Eucalyptus camaldulensis, Morus alba, and Populus deltoids, respectively, in the industrial and residential areas of Faisalabad based on the concentrations of lead (Pb), zinc (Zn), cadmium (Cd), and copper (Cu) in their leaves and barks in winter (2018) and summer (2019) seasons. The seasonal contents of heavy metals in both the leaves and barks of these trees decreased in the order of: Zn > Pb > Cu > Cd at both study sites. The highest heavy metal contents were recorded in the leaves and barks of trees grown in the industrial areas as compared to residential areas, with leaves and barks having higher contents of heavy metals in the summer than winter. The tree species exhibited significantly different capacity for heavy metal accumulation, with the accumulation of Cd decreased in the order of: E. camaldulensis > M. alba > C. erectus > A. indica > P. deltoids > C. fistula, and while the order varied for different heavy metals. Overall, M. alba, E. camaldulensis and A. indica performed well in accumulating the targeted heavy metals from the ambient environment. Among the six tree species grown commonly in Faisalabad city, M. alba, E. camaldulensis, and A. indica are recommended for the industrial and residential areas due to their phytoremediation capacity for heavy metals.

Effects of nitrogen application on winter wheat growth, water use, and yield under different shallow groundwater depths.

Shallow groundwater plays a vital role in physiology morphological attributes, water use, and yield production of winter wheat, but little is known of its interaction with nitrogen (N) application. We aimed to explore the effects of N fertilization rate and shallow groundwater table depth (WTD) on winter wheat growth attributes, yield, and water use. Experiments were carried out in micro-lysimeters at WTD of 0.6, 0.9, 1.2, and 1.5 m with 0, 150, 240, and 300 kg/ha N application levels for the winter wheat (Triticum aestivum L.). The results showed that there was an optimum groundwater table depth (Op-wtd), in which the growth attributes, groundwater consumption (GC), yield, and water use efficiency (WUE) under each N application rate were maximum, and the Op-wtd decreased with the increase in N application. The Op-wtd corresponding to the higher velocity of groundwater consumption (Gv) appeared at the late jointing stage, which was significantly higher than other WTD treatments under the same N fertilization. WTD significantly affected the Gv during the seeding to the regreening stage and maturity stage; the interaction of N application, WTD, and N application was significant from the jointing to the filling stage. The GC, leaf area index (LAI), and yield increased with an increase of N application at 0.6-0.9-m depth-for example, the yield and the WUE of the NF300 treatment with 0.6-m depth were significantly higher than those of the NF150-NF240 treatment at 20.51%, and 14.81%, respectively. At 1.2-1.5-m depth, the N application amount exceeding 150-240 kg/ha was not conducive to wheat growth, groundwater use, grain yield, and WUE. The yield and the WUE of 150-kg/ha treatment were 15.02% and 10.67% higher than those of 240-300-kg/ha treatment at 1.2-m depth significantly. The optimum N application rate corresponding to yield indicated a tendency to decrease with the WTD increase. Considering the winter wheat growth attributes, GC, yield, and WUE, application of 150-240 kg/ha N was recommended in our experiment.

Toxic effects of lead (Pb), cadmium (Cd) and tetracycline (TC) on the growth and development of Triticum aestivum: A meta-analysis.

The environmental issue of lead (Pb), cadmium (Cd), and tetracycline (TC) contamination in cereal crops has become a growing concern worldwide. An in-depth understanding of this issue would be of importance to promote effective management strategies for heavy metals and antibiotics worldwide. The present study was conducted to assess the toxic effects of heavy metals (Cd, Pb) and antibiotics (TC) on Triticum aestivum (T. aestivum, common wheat) based on studies conducted in the past 22 years. Data pertaining to the growth and development of T. aestivum were extracted and analyzed from 89 publications spanning from 2000 to 2022. Our results showed that Pb, Cd and TC significantly reduced growth and development by 11 %, 9 %, and 5 %, respectively. Additionally, significant accumulation of Cd (42 %) and Pb (17 %) was observed in T. aestivum samples, although there was little change in TC accumulation, which showed limited absorption, accumulation, and translocation of TC in wheat plants. Pb had the greatest impact on the yield of T. aestivum, followed by Cd, while TC had no apparent effect. Furthermore, exposure to Cd, Pb and TC reduced the photosynthetic rate due to chlorophyll reduction, with Cd having the most pronounced effect (58 %), followed by Pb (37 %) and TC (8 %). Cd exposure also significantly enhanced gaseous exchange (37 %) compared to TC and Pb, which reduced gaseous exchange by 4 % and 10 %, respectively. However, the treatments with TC (>50-100 mgL-1), Pb (>1000-2000 mg L-1) and Cd (>500-1000 mg L-1) increased the defense system of T. aestivum samples by 38 %, 15 %, and 11 %, respectively. The obtained findings have significant implications for risk assessment, pollution prevention, and remediation strategies to address soil contamination from Pb, Cd and TC in farmland.

Assessing the effects of limestone dust and lead pollution on the ecophysiology of some selected urban tree species.

Soil and air pollution caused by heavy metals and limestone dust are prevalent in urban environments and they are an alarming threat to the environment and humans. This study was designed to investigate the changes in morphological and physiological traits of three urban tree species seedlings (Bombax ceiba, Conocarpus lancifolius, and Eucalyptus camaldulensis) under the individual as well as synergetic effects of heavy metal lead (Pb) and limestone dust toxicities. The tree species were grown under controlled environmental conditions with nine treatments consisting of three levels of dust (0, 10, and 20 g) and three levels of Pb contaminated water irrigation (0, 5, and 10 mg L-1). The results depicted that the growth was maximum in T1 and minimum in T9 for all selected tree species. B. ceiba performed better under the same levels of Pb and limestone dust pollution as compared with the other two tree species. The B. ceiba tree species proved to be the most tolerant to Pb and limestone pollution by efficiently demolishing oxidative bursts by triggering SOD, POD, CAT, and proline contents under different levels of lead and dust pollution. The photosynthetic rate, stomatal conductance, evapotranspiration rate, and transpiration rate were negatively influenced in all three tree species in response to different levels of lead and dust applications. The photosynthetic rate was 1.7%, 3.1%, 7.0%, 11.03%, 16.2%, 23.8%, 24.8%, and 30.7%, and the stomatal conductance was 5%, 10.5%, 23.5%, 40%, 50.01%, 61.5%, 75%, and 90.9%, greater in T2, T3, T4, T5, T6, T7, T8, and T9 plants of B. ceiba, respectively, as compared to T1. Based on the findings, among these three tree species, B. ceiba is strongly recommended for planting in heavy metal and limestone dust-polluted areas followed by E. camaldulensis and C. lancifolius due to their better performance and efficient dust and heavy metal-scavenging capability.

Strategic analysis on development of simultaneous adsorption and catalytic biodegradation over advanced bio-carriers for zero-liquid discharge of industrial wastewater.

With rapid industrial development, millions of tons of industrial wastewater are produced that contain highly toxic, carcinogenic, mutagenic compounds. These compounds may consist of high concentration of refractory organics with plentiful carbon and nitrogen. To date, a substantial proportion of industrial wastewater is discharged directly to precious water bodies due to the high operational costs associated with selective treatment methods. For example, many existing treatment processes rely on activated sludge-based treatments that only target readily available carbon using conventional microbes, with limited capacity for nitrogen and other nutrient removal. Therefore, an additional set-up is often required in the treatment chain to address residual nitrogen, but even after treatment, refractory organics persist in the effluents due to their low biodegradability. With the advancements in nanotechnology and biotechnology, novel processes such as adsorption and biodegradation have been developed, and one promising approach is integration of adsorption and biodegradation over porous substrates (bio-carriers). Regardless of recent focus in a few applied researches, the process assessment and critical analysis of this approach is still missing, and it highlights the urgency and importance of this review. This review paper discussed the development of the simultaneous adsorption and catalytic biodegradation (SACB) over a bio-carrier for the sustainable treatment of refractory organics. It provides insights into the physico-chemical characteristics of the bio-carrier, the development mechanism of SACB, stabilization techniques, and process optimization strategies. Furthermore, the most efficient treatment chain is proposed, and its technical aspects are critically analysed based on updated research. It is anticipated that this review will contribute to the knowledge of academia and industrialist for sustainable upgradation of existing industrial wastewater treatment plants.

Toxic effects of cadmium on the physiological and biochemical attributes of plants, and phytoremediation strategies: A review.

Anthropogenic activities pose a more significant threat to the environment than natural phenomena by contaminating the environment with heavy metals. Cadmium (Cd), a highly poisonous heavy metal, has a protracted biological half-life and threatens food safety. Plant roots absorb Cd due to its high bioavailability through apoplastic and symplastic pathways and translocate it to shoots through the xylem with the help of transporters and then to the edible parts via the phloem. The uptake and accumulation of Cd in plants pose deleterious effects on plant physiological and biochemical processes, which alter the morphology of vegetative and reproductive parts. In vegetative parts, Cd stunts root and shoot growth, photosynthetic activities, stomatal conductance, and overall plant biomass. Plants' male reproductive parts are more prone to Cd toxicity than female reproductive parts, ultimately affecting their grain/fruit production and survival. To alleviate/avoid/tolerate Cd toxicity, plants activate several defense mechanisms, including enzymatic and non-enzymatic antioxidants, Cd-tolerant gene up-regulations, and phytohormonal secretion. Additionally, plants tolerate Cd through chelating and sequestering as part of the intracellular defensive mechanism with the help of phytochelatins and metallothionein proteins, which help mitigate the harmful effects of Cd. The knowledge on the impact of Cd on plant vegetative and reproductive parts and the plants' physiological and biochemical responses can help selection of the most effective Cd-mitigating/avoiding/tolerating strategy to manage Cd toxicity in plants.

Soil microbial and enzyme activities in different land use systems of the Northwestern Himalayas.

Soil microbial activity (SMA) is vital concerning carbon cycling, and its functioning is recognized as the primary factor in modifying soil carbon storage potential. The composition of the microbial community (MC) is significant in sustaining environmental services because the structure and activity of MC also influence nutrient turnover, distribution, and the breakdown rate of soil organic matter. SMA is an essential predictor of soil quality alterations, and microbiome responsiveness is imperative in addressing the escalating sustainability concerns in the Himalayan ecosystem. This study was conducted to evaluate the response of soil microbial and enzyme activities to land conversions in the Northwestern Himalayas (NWH), India. Soil samples were collected from five land use systems (LUSs), including forest, pasture, apple, saffron, and paddy-oilseed, up to a depth of 90 cm. The results revealed a significant difference (p < 0.05) in terms of dehydrogenase (9.97-11.83 TPF µg g-1 day-1), acid phosphatase (22.40-48.43 µg P-NP g-1 h-1), alkaline phosphatase (43.50-61.35 µg P-NP g-1 h-1), arylsulphatase (36.33-48.12 µg P-NP g-1 h-1), fluorescein diacetate hydrolase (12.18-21.59 µg g-1 h-1), bacterial count (67.67-123.33 CFU × 106 g-1), fungal count (19.33-67.00 CFU × 105 g-1), and actinomycetes count (12.00-42.33 CFU × 104 g-1), with the highest and lowest levels in forest soils and paddy-oilseed soils, respectively. Soil enzyme activities and microbial counts followed a pattern: forest > pasture > apple > saffron > paddy-oilseed at all three depths. Paddy-oilseed soils exhibited up to 35% lower enzyme activities than forest soils, implying that land conversion facilitates the depletion of microbiome diversity from surface soils. Additionally, reductions of 49.80% and 62.91% were observed in enzyme activity and microbial counts, respectively, with soil depth (from 0-30 to 60-90 cm). Moreover, the relationship analysis (principal component analysis and correlation) revealed a high and significant (p = 0.05) association between soil microbial and enzyme activities and physicochemical attributes. These results suggest that land conversions need to be restricted to prevent microbiome depletion, reduce the deterioration of natural resources, and ensure the sustainability of soil health.

A review of the influence of nanoparticles on the physiological and biochemical attributes of plants with a focus on the absorption and translocation of toxic trace elements.

Trace elements (TEs) from various natural and anthropogenic activities contaminate the agricultural water and soil environments. The use of nanoparticles (NPs) as nano-fertilizers or nano-pesticides is gaining popularity worldwide. The NPs-mediated fertilizers encourage the balanced availability of essential nutrients to plants compared to traditional fertilizers, especially in the presence of excessive amounts of TEs. Moreover, NPs could reduce and/or restrict the bioavailability of TEs to plants due to their high sorption ability. In this review, we summarize the potential influence of NPs on plant physiological attributes, mineral absorption, and TEs sorption, accumulation, and translocation. It also unveils the NPs-mediated TE scavenging-mechanisms at plant and soil interface. NPs immobilized TEs in soil solution effectively by altering the speciation of TEs and modifying the physiological, biochemical, and biological properties of soil. In plants, NPs inhibit the transfer of TEs from roots to shoots by inducing structural modifications, altering gene transcription, and strengthening antioxidant defense mechanisms. On the other hand, the mechanisms underpinning NPs-mediated TEs absorption and cytotoxicity mitigation differ depending on the NPs type, distribution strategy, duration of NP exposure, and plants (e.g., types, varieties, and growth rate). The review highlights that NPs may bring new possibilities for resolving the issue of TE cytotoxicity in crops, which may also assist in reducing the threats to the human dietary system. Although the potential ability of NPs in decontaminating soils is just beginning to be understood, further research is needed to uncover the sub-cellular-based mechanisms of NPs-induced TE scavenging in soils and absorption in plants.

Mercury fractionation, bioavailability, and the major factors predicting its transfer and accumulation in soil-wheat systems.

Soil mercury (Hg) and its bioaccumulation in food crops have attracted widespread concerns globally due to its harmful effects on biota. However, soil mercury fractionation, bioavailability, and the major factors predicting its transfer and accumulation in soil-wheat-systems have not been thoroughly explored. Twenty-one (21) soil samples collected throughout China with a wide spectrum of physico-chemical characteristics were contaminated with HgCl2 and winter wheat (Triticum aestivum L.) was grown on the soils in a greenhouse pot-culture experiment for 180 days. A four-step sequential extraction was used segregating soil Hg into water-soluble (F1, 0.21 %), exchangeable (F2, 0.07 %), organically bound (F3, 16.40 %), and residual fractions (F4, 83.32 %). Step-wise multiple linear regression (SMLR) and path analysis (PA) were used to develop a prediction model and identify the major controlling factors of soil-wheat Hg transference. The SMLR results revealed that wheat Hg in leaves, husk, and grain was positively correlated with soil total and available Hg, and crystalline manganese (Cryst-Mn), while negatively correlated with soil pH, amorphous manganese (Amor-Mn) and crystalline aluminium (Cryst-Al). Bioconcentration factor (BCF) values were significantly higher in acidic soils (highest 0.05), with phytotoxic effects in some soils, as compared to alkaline soils (lowest 0.006). Furthermore, wheat grain Hg was significantly correlated with total (R2 = 0.25), water-soluble (R2 = 0.54) and NH4Ac-extractable Hg (R2 = 0.43) while also had a good correlation with soil pH (R2 = -0.20). In conclusion, the soil total and available Hg (water-soluble + exchangeable fraction), pH, organic matter, and Amor-Mn are the most important soil variables that support Hg uptake in the wheat plants, which benefit managing Hg-enriched agricultural soils for safe wheat production.

Microbial-assisted soil chromium immobilization through zinc and iron-enriched rice husk biochar.

Soil chromium toxicity usually caused by the tannery effluent compromises the environment and causes serious health hazards. The microbial role in strengthening biochar for its soil chromium immobilization remains largely unknown. Hence, this study evaluated the effectiveness of zinc and iron-enriched rice husk biochar (ZnBC and FeBC) with microbial combinations to facilitate the chromium immobilization in sandy loam soil. We performed morphological and molecular characterization of fungal [Trichoderma harzianum (F1), Trichoderma viride (F2)] and bacterial [Pseudomonas fluorescence (B1), Bacillus subtilis (B2)] species before their application as soil ameliorants. There were twenty-five treatments having ZnBC and FeBC @ 1.5 and 3% inoculated with bacterial and fungal isolates parallel to wastewater in triplicates. The soil analyses were conducted in three intervals each after 20, 30, and 40 days. The combination of FeBC 3%+F2 reduced the soil DTPA-extractable chromium by 96.8% after 40 days of incubation (DAI) relative to wastewater. Similarly, 92.81% reduction in chromium concentration was achieved through ZnBC 3%+B1 after 40 DAI compared to wastewater. Under the respective treatments, soil Cr(VI) retention trend increased with time such as 40 > 30 > 20 DAI. Langmuir adsorption isotherm verified the highest chromium adsorption capacity (41.6 mg g-1) with FeBC 3% at 40 DAI. Likewise, principal component analysis (PCA) and heat map disclosed electrical conductivity-chromium positive, while cation exchange capacity-chromium and pH-organic matter negative correlations. PCA suggested the ZnBC-bacterial while FeBC-fungal combinations as effective Cr(VI) immobilizers with >70% data variance at 40 DAI. Overall, the study showed that microbes + ZnBC/FeBC resulted in low pH, high OM, and CEC, which ultimately played a role in maximum Cr(VI) adsorption from wastewater applied to the soil. The study also revealed the interrelation and alternations in soil dynamics with pollution control treatments. Based on primitive soil characteristics such as soil metal concentration, its acidity, and alkalinity, the selection criteria can be set for treatments application to regulate the soil properties. Additionally, FeBC with Trichoderma viride should be tested on the field scale to remediate the Cr(VI) toxicity.

Suitable nitrogen application mode and lateral spacing for drip-irrigated winter wheat in North China Plain.

To propose an appropriate nitrogen application mode and suitable drip irrigation lateral spacing, a field experiment was conducted during 2017-2018 and 2018-2019 growing seasons to quantify the different drip irrigation lateral spacings and nitrogen fertigation strategies effects on winter wheat growth, yield, and water use efficiency (WUE) in the North China Plain (NCP). The experiment consisted of three drip irrigation lateral spacing (LS) (40, 60, and 80 cm, referred to as D40, D60, and D80 respectively) and three percentage splits of nitrogen application modes (NAM) (basal and top dressing application ratio as 50:50 (N50:50), 25:75 (N25:75), and 0:100 (N0-100) respectively). The experimental findings depicted that yield and its components, and WUE were markedly affected by LS and NAM. Fertigation of winter wheat at N25:75 NAM notably (P<0.05) increased the grain yield by 4.88%, 1.83% and 8.03%, 4.61%, and WUE by 3.10%, 3.18% and 5.37%, 7.82%, compared with those at NAM N50:50 and N0:100 in 2017-2018 and 2018-2019 growing seasons, respectively. LS D40 appeared very fruitful in terms of soil moisture and nitrogen distribution, WUE, grain yield, and yield components than that of other LS levels. The maximum grain yield (8.73 and 9.40 t ha-1) and WUE (1.70 and 1.95 kg m-3) were obtained under D40N25:75 during both growing seasons, which mainly due to that all main yield components in D40N25:75 treatment, such as spikes per unit area, 1000-grain weight, and grains per spike were significantly higher as compared to other treatments. The outcomes of this research may provide a scientific basis of lateral spacing and nitrogen fertigation management for the production of drip-irrigated winter wheat in NCP.