Unravelling DNA methylation dynamics during developmental stages in Quercus ilex subsp. ballota [Desf.] Samp.

BACKGROUND: DNA methylation is a critical factor influencing plant growth, adaptability, and phenotypic plasticity. While extensively studied in model and crop species, it remains relatively unexplored in holm oak and other non-domesticated forest trees. This study conducts a comprehensive in-silico mining of DNA methyltransferase and demethylase genes within the holm oak genome to enhance our understanding of this essential process in these understudied species. The expression levels of these genes in adult and seedling leaves, as well as embryos, were analysed using quantitative real-time PCR (qRT-PCR). Global DNA methylation patterns were assessed through methylation-sensitive amplified polymorphism (MSAP) techniques. Furthermore, specific methylated genomic sequences were identified via MSAP sequencing (MSAP-Seq). RESULT: A total of 13 DNA methyltransferase and three demethylase genes were revealed in the holm oak genome. Expression levels of these genes varied significantly between organs and developmental stages. MSAP analyses revealed a predominance of epigenetic over genetic variation among organs and developmental stages, with significantly higher global DNA methylation levels observed in adult leaves. Embryos exhibited frequent demethylation events, while de novo methylation was prevalent in seedling leaves. Approximately 35% of the genomic sequences identified by MSAP-Seq were methylated, predominantly affecting nuclear genes and intergenic regions, as opposed to repetitive sequences and chloroplast genes. Methylation was found to be more pronounced in the exonic regions of nuclear genes compared to their promoter and intronic regions. The methylated genes were predominantly associated with crucial biological processes such as photosynthesis, ATP synthesis-coupled electron transport, and defence response. CONCLUSION: This study opens a new research direction in analysing variability in holm oak by evaluating the epigenetic events and mechanisms based on DNA methylation. It sheds light on the enzymatic machinery governing DNA (de)methylation, and the changes in the expression levels of methylases and demethylases in different organs along the developmental stages. The expression level was correlated with the DNA methylation pattern observed, showing the prevalence of de novo methylation and demethylation events in seedlings and embryos, respectively. Several methylated genes involved in the regulation of transposable element silencing, lipid biosynthesis, growth and development, and response to biotic and abiotic stresses are highlighted. MSAP-seq integrated with whole genome bisulphite sequencing and advanced sequencing technologies, such as PacBio or Nanopore, will bring light on epigenetic mechanisms regulating the expression of specific genes and its correlation with the phenotypic variability and the differences in the response to environmental cues, especially those related to climate change.

Antibiotic Resistance in Urban Soils: Dynamics and Mitigation Strategies.

Antibiotic resistance (AR) is a critical global health issue with significant clinical and economic implications. AR occurs when microorganisms develop mechanisms to withstand the effects of antibiotics, reducing treatment efficacy and increasing the risk of mortality and healthcare costs. While the connection between antibiotic use in clinical and agricultural settings and the emergence of AR is well-established, the role of urban soils as reservoirs and spreaders of AR is underexplored. This review examines the complex dynamics of AR in urban soils, highlighting the various sources of antibiotics, including domestic wastewater, industrial effluents, urban agricultural practices, but also microplastics and domestic animal excrements. The selective pressure exerted by these anthropogenic sources promotes the proliferation of antibiotic-resistant bacteria, particularly through horizontal gene transfer, which facilitates the transmission of resistance genes among soil microorganisms in urban environments. About that, the presence of antibiotics in urban soils poses a significant threat to public health by potentially transferring resistance genes to human pathogens through multiple pathways, including direct contact, food consumption, and water ingestion. Furthermore, AR in urban soils disrupts microbial community dynamics, impacting soil fertility, plant growth, and overall environmental quality. Therefore, this review aims to address gaps in understanding AR in urban soils, offering insights into its implications for human health and ecosystem integrity. By identifying these gaps and suggesting evidence-based strategies, this review proposes valid and sustainable solutions to mitigate and counteract the spread of AR in urban environments.

Landfill leachate treatment by a combination of a multiple plant hybrid constructed wetland system with a solar photoFenton process in a raceway pond reactor.

The sustainable and green treatment of landfill leachate (LL), produced by municipal solid waste, represents one of the most relevant challenges in the integrated waste management systems. Accordingly, in this work a green solution was investigated by coupling an innovative hybrid constructed wetland (HCW) to a solar photo-Fenton (SPF) process. A multiple layers HCW pilot plant including different medium substrates (sand, solid compost and carriers) and plant species (Phragmites australis, Arundo donax and A. plinii) was designed. The HCW was functionalised with compost tea solution to simultaneously provide high nutrient content for plants and increase the microorganism biodiversity. Process efficiency was investigated using different real LLs (young and mature) in terms of chemical oxygen demand (COD), nitrogen compounds, chlorides and metals. Removals in the range 75-95% were observed for all the parameters after ten days of leachate recirculation in the pilot plant. Subsequently, the SPF process was carried out in a raceway pond reactor (RPR) as polishing step, significantly improving COD removal (further 49%). HCW combined with SPF in RPR would allow to meet the corresponding limits according to the final use/fate of the effluent by modulating the main parameters of the process.

Botanical, Phytochemical, Anti-Microbial and Pharmaceutical Characteristics of Hawthorn (Crataegusmonogyna Jacq.), Rosaceae.

Hawthorn (Crataegus monogyna Jacq.) is a wild edible fruit tree of the genus Crataegus, one of the most interesting genera of the Rosaceae family. This review is the first to consider, all together, the pharmaceutical, phytochemical, functional and therapeutic properties of C. monogyna based on numerous valuable secondary metabolites, including flavonoids, vitamin C, glycoside, anthocyanin, saponin, tannin and antioxidants. Previous reviews dealt with the properties of all species of the entire genera. We highlight the multi-therapeutic role that C. monogyna extracts could have in the treatment of different chronic and degenerative diseases, mainly focusing on flavonoids. In the first part of this comprehensive review, we describe the main botanical characteristics and summarize the studies which have been performed on the morphological and genetic characterization of the C. monogyna germplasm. In the second part, the key metabolites and their nutritional and pharmaceutical properties are described. This work could be an essential resource for promoting future therapeutic formulations based on this natural and potent bioactive plant extract.

The combined effect of Cr(III) and NaCl determines changes in metal uptake, nutrient content, and gene expression in quinoa (Chenopodium quinoa Willd.).

Many areas of the world are affected simultaneously by salinity and heavy metal pollution. Halophytes are considered as useful candidates in remediation of such soils due to their ability to withstand both osmotic stress and ion toxicity deriving from high salt concentrations. Quinoa (Chenopodium quinoa Willd) is a halophyte with a high resistance to abiotic stresses (drought, salinity, frost), but its capacity to cope with heavy metals has not yet been fully investigated. In this pot experiment, we investigated phytoextraction capacity, effects on nutrient levels (P and Fe), and changes in gene expression in response to application of Cr(III) in quinoa plants grown on saline or non-saline soil. Plants were exposed for three weeks to 500 mg kg-1 soil of Cr(NO3)3·9H2O either in the presence or absence of 150 mM NaCl. Results show that plants were able tolerate this soil concentration of Cr(III); the metal was mainly accumulated in roots where it reached the highest concentration (ca. 2.6 mg g-1 DW) in the presence of NaCl. On saline soil, foliar Na concentration was significantly reduced by Cr(III). Phosphorus translocation to leaves was reduced in the presence of Cr(III), while Fe accumulation was enhanced by treatment with NaCl alone. A real-time RT-qPCR analysis was conducted on genes encoding for sulfate, iron, and phosphate transporters, a phytochelatin, a metallothionein, glutathione synthetase, a dehydrin, Hsp70, and enzymes responsible for the biosynthesis of proline (P5CS), glycine betaine (BADH), tocopherols (TAT), and phenolic compounds (PAL). Cr(III), and especially Cr(III)+NaCl, affected transcript levels of most of the investigated genes, indicating that tolerance to Cr is associated with changes in phosphorus and sulfur allocation, and activation of stress-protective molecules. Moderately saline conditions, in most cases, enhanced this response, suggesting that the halophytism of quinoa could contribute to prime the plants to respond to chromium stress.

Epigenetic Analysis through MSAP-NGS Coupled Technology: The Case Study of White Poplar Monoclonal Populations/Stands.

Over the last several decades, several lines of evidence have shown that epigenetic modifications modulate phenotype and mediate an organism's response to environmental stimuli. Plant DNA is normally highly methylated, although notable differences exist between species. Many biomolecular techniques based on PCR have been developed to analyse DNA methylation status, however a qualitative leap was made with the advent of next-generation sequencing (NGS). In the case of large, repetitive, or not-yet-sequenced genomes characterised by a high level of DNA methylation, the NGS analysis of bisulphite pre-treated DNA is expensive and time consuming, and moreover, in some cases data analysis is a major challenge. Methylation-sensitive amplification polymorphism (MSAP) analysis is a highly effective method to study DNA methylation. The method is based on the comparison of double DNA digestion profiles (EcoRI-HpaII and EcoRI-MspI) to reveal methylation pattern variations. These are often attributable to pedoclimatic and stress conditions which affect all organisms during their lifetime. In our study, five white poplar (Populus alba L.) specimens were collected from different monoclonal stands in the Maltese archipelago, and their DNA was processed by means of an innovative approach where MSAP analysis was followed by NGS. This allowed us to identify genes that were differentially methylated among the different specimens and link them to specific biochemical pathways. Many differentially methylated genes were found to encode transfer RNAs (tRNAs) related to photosynthesis or light reaction pathways. Our results clearly demonstrate that this combinatorial method is suitable for epigenetic studies of unsequenced genomes like P. alba (at the time of study), and to identify epigenetic variations related to stress, probably caused by different and changing pedoclimatic conditions, to which the poplar stands have been exposed.

Admixture mapping in interspecific Populus hybrids identifies classes of genomic architectures for phytochemical, morphological and growth traits.

The genomic architecture of functionally important traits is key to understanding the maintenance of reproductive barriers and trait differences when divergent populations or species hybridize. We conducted a genome-wide association study (GWAS) to study trait architecture in natural hybrids of two ecologically divergent Populus species. We genotyped 472 seedlings from a natural hybrid zone of Populus alba and Populus tremula for genome-wide markers from reduced representation sequencing, phenotyped the plants in common gardens for 46 phytochemical (phenylpropanoid), morphological and growth traits, and used a Bayesian polygenic model for mapping. We detected three classes of genomic architectures: traits with finite, detectable associations of genetic loci with phenotypic variation in addition to highly polygenic heritability; traits with indications for polygenic heritability only; and traits with no detectable heritability. For the first class, we identified genome regions with plausible candidate genes for phenylpropanoid biosynthesis or its regulation, including MYB transcription factors and glycosyl transferases. GWAS in natural, recombinant hybrids represent a promising step towards resolving the genomic architecture of phenotypic traits in long-lived species. This facilitates the fine-mapping and subsequent functional characterization of genes and networks causing differences in hybrid performance and fitness.

Genetic characterization, micropropagation, and potential use for arsenic phytoremediation of Dittrichia viscosa (L.) Greuter.

In the last decade, many scientists have focused their attention on the search for new plant species that can offer improved capacities to reclaim polluted soils and waters via phytoremediation. In this study, seed batches from three natural populations of Dittrichia viscosa, harvested in rural, urban, and industrial areas of central and southern Italy, were used to: (i) evaluate the genetic and morphological diversity of the populations; (ii) develop an efficient protocol for in-vitro propagation from seedling microcuttings; (iii) achieve optimal acclimatization of micropropagated plants to greenhouse conditions; (iv) test the response to arsenic (As) soil contamination of micropropagated plants. The genetic biodiversity study, based on Random Amplification of Polymorphic DNA (RAPD), as well as the morphometric analysis of 20 seedlings from each population revealed some degree of differentiation among populations. Based on these data, the most biodiverse plants from the three populations (10 lines each) were clonally multiplied by micropropagation using microcuttings of in-vitro grown seedlings. Three culture media were tested and Mureshige and Skoog medium was chosen for both seedling growth and micropropagation. The micropropagated plants responded well to greenhouse conditions and over 95% survived the acclimatization phase. Four clones were tested for their capacity to grow on soil spiked with NaAsO2 and to absorb and accumulate the metalloid. All clones tolerated up to 1.0mg As. At the end of the trial (five weeks), As was detectable only in leaves of As-treated plants and concentration varied significantly among clones. The amount of As present in plants (leaves) corresponded to ca. 0.10-1.7% of the amount supplied. However, As was no longer detectable in soil suggesting that the metalloid was taken up, translocated and probably phytovolatilized.

Effects of heavy metals and chelants on phytoremediation capacity and on rhizobacterial communities of maize.

Heavy metals (HMs) are one of the major ecological problem related to human activities. Phytoremediation is a promising "green technology" for soil and water reclamation, and it can be improved by means of the use of chelants. In the past particular attention was paid on the effects of HMs and/or chelants on plant health, but much less on their effects on rhizosphere communities. To shed light on the interaction among plant-HM-chelant-rhizobacterial community a pot experiment was set up. Maize plants were grown on uncontaminated, multi-metal (copper and zinc) contaminated and chelants artificially amended soils. A high concentration of HMs was detected in the different maize organs; chelants improved the accumulation capacity of the maize plants. The rhizosphere bacterial community isolated from control plants showed the largest biodiversity in terms of bacterial genera. However, the addition of HMs reduced the number of taxa to three: Bacillus, Lysinibacillus and Pseudomonas. The effects of HM treatment were counteracted by the addition of chelants in terms of the genetic biodiversity. Furthermore, several bacterial strains particularly resistant to HMs and chelants were isolated and selected. Our study suggests that the combined use of resistant bacteria and chelants could improve the phytoremediation capacity of maize.

Genome-wide patterns of differentiation and spatially varying selection between postglacial recolonization lineages of Populus alba (Salicaceae), a widespread forest tree.

Studying the divergence continuum in plants is relevant to fundamental and applied biology because of the potential to reveal functionally important genetic variation. In this context, whole-genome sequencing (WGS) provides the necessary rigour for uncovering footprints of selection. We resequenced populations of two divergent phylogeographic lineages of Populus alba (n = 48), thoroughly characterized by microsatellites (n = 317), and scanned their genomes for regions of unusually high allelic differentiation and reduced diversity using > 1.7 million single nucleotide polymorphisms (SNPs) from WGS. Results were confirmed by Sanger sequencing. On average, 9134 high-differentiation (≥ 4 standard deviations) outlier SNPs were uncovered between populations, 848 of which were shared by ≥ three replicate comparisons. Annotation revealed that 545 of these were located in 437 predicted genes. Twelve percent of differentiation outlier genome regions exhibited significantly reduced genetic diversity. Gene ontology (GO) searches were successful for 327 high-differentiation genes, and these were enriched for 63 GO terms. Our results provide a snapshot of the roles of 'hard selective sweeps' vs divergent selection of standing genetic variation in distinct postglacial recolonization lineages of P. alba. Thus, this study adds to our understanding of the mechanisms responsible for the origin of functionally relevant variation in temperate trees.

Different behaviours in phytoremediation capacity of two heavy metal tolerant poplar clones in relation to iron and other trace elements.

Plant biodiversity and intra-population genetic variability have not yet been properly exploited in the framework of phytoremediation and soil reclamation. For this reason, iron and other metal accumulation capacity of two Cu and Zn tolerant poplar clones, namely AL22 (Populus alba L.) and N12 (Populus nigra L.), was investigated in a pot experiment. Cuttings of the two clones were planted in iron rich soil collected from an urban-industrial area. Concentrations of Cd, Cu, Fe, Pb and Zn were analysed in leaves (at different times), as well as in stems and in roots (at the end of the experiment), both in control plants and in plants grown on a soil whose Fe availability was artificially enhanced. Results showed that Cd and Zn were preferentially accumulated in leaves, whereas Cu, Fe and Pb were mainly accumulated in roots. The main differences in metal accumulation between clones were related to Cd (about tenfold higher concentrations in N12) and Cu (higher concentrations in AL22). Once soil Fe availability was enhanced, the uptake and accumulation of all metals declined, with the exception of Fe at the first sampling time in AL22 leaves. The different behaviour of the two poplar clones suggests that a thoughtful choice should be made for their use in relation to soil heavy metal remediation.

Polyaspartate, a biodegradable chelant that improves the phytoremediation potential of poplar in a highly metal-contaminated agricultural soil.

Phytoremediation is a cost-effective and environment friendly in situ technique for the reclamation of heavy metal-polluted soils. The efficacy of this technique, which relies on tolerant plant species, can be improved by the use of chelating agents. A pot experiment was carried out to evaluate the phytoextraction and phytostabilisation capacities of a white poplar (Populus alba L.) clone named AL35 previously selected for its marked tolerance to copper (Cu) and zinc (Zn). Cuttings were grown on agricultural soil highly contaminated with Cu and Zn, in the presence or not (controls) of a chelant mixture (EDTA/EDDS) known to enhance metal bioavailability and, hence, uptake by plant roots, or the not yet investigated synthetic, highly biodegradable polyaspartic acid (PASP). Both chelant treatments improved the phytostabilisation of Cu and Zn in AL35 plants, whilst the phytoextraction capacity was enhanced only in the case of Cu. Considering that the effectiveness of PASP as phytostabilizer was comparable or better than that of EDTA/EDDS, the low cost of its large-scale chemical synthesis and its biodegradability makes it a good candidate for chelant-enhanced metal phytoextraction from soil while avoiding the toxic side-effects previously described for both EDTA and EDDS.

Development of Broad-Range Microbial Minimal Culture Medium for Lanthanide Studies.

Rare Earth Elements (REE), also known as Lanthanides (Ln3+), are a group of 17 elements showing peculiar physical and chemical properties. Unlike technological applications, very little is known about the physiological role and toxicity of Ln3+ on biological systems, in particular on microorganisms (e.g., bacteria), which represent the most abundant domains on our planet. Up to now, very limited studies have been conducted due to Ln3+ precipitation with some anions commonly present in the culture media. Therefore, the development of a minimal medium is essential to allow the study of Ln3+-microbial interactions, limiting considerably the precipitation of insoluble salts. In this regard, a new minimal culture medium capable of solubilizing large amounts of Ln3+ and allowing the growth of different microbial taxa was successfully developed. Assays have shown that the medium is capable of solubilizing Ln3+ up to 100 times more than other common culture media and allowing the growth of 63 bacteria and 5 fungi. The kinetic growth of one yeast and one Gram-positive bacterium has been defined, proving to support superior growth and biomass compared to other commonly used minimal media. Moreover, the sensitivity and uptake/absorption of a Bacillus stratosphericus strain were tested, highlighting its capability to tolerate concentrations up to 10 mM of either Cerium, Gadolinium or Lanthanum and accumulate different quantities of the three.

Reduction of antimicrobial resistance: Advancements in nature-based wastewater treatment.

Water scarcity, affecting one-fifth of the global population, is exacerbated by industrial, agricultural, and population growth pressures on water resources. Wastewater, containing Contaminants of Emerging Concern (CECs) such as antibiotics, presents environmental and health hazards. This study explores a Nature-Based Solution (NBS) using Constructed Wetlands (CWs) for wastewater reclamation and CECs removal. Two CW configurations (Vertical-VCW and Hybrid-HCW) were tested for their efficacy. Results show significant reduction in for all the chemico-physical and biological parameters meeting Italian water reuse standards. Furthermore, Antibiotic Resistant Bacteria (ARB) and Antibiotic Resistant Genes (ARGs) were effectively reduced, emphasizing the potential of the CWs in mitigating Antimicrobial Resistance (AMR). Lettuce seedlings irrigated with the treated wastewater exhibited no ARB/ARGs transfer, indicating the safety of the reclaimed wastewater for agricultural use. Overall, CWs emerge as sustainable Nature Based Solutions (NBS) for wastewater treatment, contributing to global water conservation efforts amid escalating water scarcity challenges.

Epigenetic changes induced by chronic and acute chromium stress treatments in Arabidopsis thaliana identified by the MSAP-Seq.

Chromium (Cr) is an highly toxic metal to plants and causes severe damage to their growth, development, and reproduction. Plant exposure to chronic and acute Cr stress treatments results in significant changes at short time in the gene expression profile and at long time in the genomic DNA methylation profile at a transgenerational level and, consequently, in gene expression. These epigenetic modifications and their implications imposed by the Cr stress are not yet completely known in plants. Herein, were identified the epigenetic changes induced by chronic and acute Cr stress treatments in Arabidopsis thaliana plants using Methylation Sensitive Amplification Polymorphism coupled with next-generation sequencing (MSAP-Seq). First-generation Arabidopsis plants (termed F0 plants) kept under hoagland solution were subjected to Cr stress treatments. For chronic Cr stress, plants were treated through hoagland solution with 2.5 µM Cr during the entire cultivation period until seed harvest. Meanwhile, for acute Cr stress, plants were treated with 5 µM Cr during the first three weeks and returned to unstressful control condition until seed harvest. Seeds from F0 plants were sown and F1 plants were re-submitted to the same Cr stress treatments. The seed germination rate was evaluated from F-2 seeds harvested of F1 plants kept under different Cr stress treatments (0, 10, 20, and 40 µM) compared to the unstressful control condition. These data showed significant changes in the germination rate of F-2 seeds originating from stressed F1 plants compared to F-2 seeds harvested from unstressful control plants. Given this data, F1 plants kept under these chronic and acute Cr stress treatments and unstressful control condition were evaluated for the transgenerational epigenetic modifications using MSAP-Seq. The MSAP-Seq data showed that several genes were modified in their methylation status as a consequence of chronic and acute Cr stress treatment to maintain plant defenses activated. In particular, RNA processing, protein translation, photorespiration, energy production, transmembrane transport, DNA transcription, plant development, and plant resilience were the major biological processes modulated by epigenetic mechanisms identified in F1 plants kept under chronic and acute Cr stress. Therefore, collective data suggested that Arabidopsis plants kept under Cr stress regulate their epigenetic status over generations based on DNA methylation to modulate defense and resilience mechanisms.

Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species.

Recent advances in population genomics have triggered great interest in the genomic landscape of divergence in taxa with 'porous' species boundaries. One important obstable of previous studies of this topic was the low genomic coverage achieved. This issue can now be overcome by the use of 'next generation' or short-read DNA-sequencing approaches capable of assaying many thousands of single nucleotide polymorphisms (SNPs) in divergent species. We have scanned the 'porous' genomes of Populus alba and Populus tremula, two ecologically divergent hybridizing forest trees, using >38,000 SNPs assayed by restriction site associated DNA (RAD) sequencing. Windowed analyses indicate great variation in genetic divergence (e.g. the proportion of fixed SNPs) between species, and these results are unlikely to be strongly biased by genomic features of the Populus trichocarpa reference genome used for SNP calling. Divergence estimates were significantly autocorrelated (P < 0.01; Moran's I up to 0.6) along 11 of 19 chromosomes. Many of these autocorrelations involved low divergence blocks, thus suggesting that allele sharing was caused by recurrent gene flow rather than shared ancestral polymorphism. A conspicuous low divergence block of three megabases was detected on chromosome XIX, recently put forward as an incipient sex chromosome in Populus, and was largely congruent with introgression of mapped microsatellites in two natural hybrid zones (N > 400). Our results help explain the origin of the 'genomic mosaic' seen in these taxa with 'porous' genomes and suggest rampant introgression or extensive among-species conservation of an incipient plant sex chromosome. RAD sequencing holds great promise for detecting patterns of divergence and gene flow in highly divergent hybridizing species.

Beyond Cleansing: Ecosystem Services Related to Phytoremediation.

Phytotechnologies used for cleaning up urban and suburban polluted soils (i.e., brownfields) have shown some weakness in the excessive extent of the timeframe required for them to be effectively operating. This bottleneck is due to technical constraints, mainly related to both the nature of the pollutant itself (e.g., low bio-availability, high recalcitrance, etc.) and the plant (e.g., low pollution tolerance, low pollutant uptake rates, etc.). Despite the great efforts made in the last few decades to overcome these limitations, the technology is in many cases barely competitive compared with conventional remediation techniques. Here, we propose a new outlook on phytoremediation, where the main goal of decontaminating should be re-evaluated, considering additional ecosystem services (ESs) related to the establishment of a new vegetation cover on the site. The aim of this review is to raise awareness and stress the knowledge gap on the importance of ES associated with this technique, which can make phytoremediation a valuable tool to boost an actual green transition process in planning urban green spaces, thereby offering improved resilience to global climate change and a higher quality of life in cities. This review highlights that the reclamation of urban brownfields through phytoremediation may provide several regulating (i.e., urban hydrology, heat mitigation, noise reduction, biodiversity, and CO2 sequestration), provisional (i.e., bioenergy and added-value chemicals), and cultural (i.e., aesthetic, social cohesion, and health) ESs. Although future research should specifically be addressed to better support these findings, acknowledging ES is crucial for an exhaustive evaluation of phytoremediation as a sustainable and resilient technology.

Counteracting action of Bacillus stratosphericus and Staphylococcus succinus strains against deleterious salt effects on Zea mays L.

The salinization of soil is the process of progressive accumulation of salts such as sulfates, sodium, or chlorides into the soil. The increased level of salt has significant effects on glycophyte plants, such as rice, maize, and wheat, which are staple foods for the world's population. Consequently, it is important to develop biotechnologies that improve crops and clean up the soil. Among other remediation methods, there is an environmentally friendly approach to ameliorate the cultivation of glycophyte plants in saline soil, namely, the use of microorganisms tolerant to salt with growth-promoting features. Plant growth-promoting rhizobacteria (PGPR) can improve plant growth by colonizing their roots and playing a vital role in helping plants to establish and grow in nutrient-deficient conditions. Our research aimed to test in vivo halotolerant PGPR, isolated and characterized in vitro in a previous study conducted in our laboratory, inoculating them on maize seedlings to improve their growth in the presence of sodium chloride. The bacterial inoculation was performed using the seed-coating method, and the produced effects were evaluated by morphometric analysis, quantization of ion contents (sodium, potassium), produced biomass, both for epigeal (shoot) and hypogeal (root) organs, and by measuring salt-induced oxidative damage. The results showed an increase in biomass and sodium tolerance and even a reduction of oxidative stress in seedlings pretreated with a PGPR bacterial consortium (Staphylococcus succinus + Bacillus stratosphericus) over the control. Moreover, we observed that salt reduces growth and alters root system traits of maize seedlings, while bacterial treatment improves plant growth and partially restores the root architecture system in saline stress conditions. Therefore, the PGPR seed-coating or seedling treatment could be an effective strategy to enhance sustainable agriculture in saline soils due to the protection of the plants from their inhibitory effect.

Transgenerational effects of chromium stress at the phenotypic and molecular level in Arabidopsis thaliana.

In this study, we describe the results obtained in a study of the transgenerational phenotypic effects of chromium (Cr) stress on the model plant species Arabidopsis thaliana. The F1 generation derived from parents grown under chronic and medium chronic stress showed significantly higher levels of the maximal effective concentration (EC50) compared with F1 plants generated from unstressed parents. Moreover, F1 plants from Cr-stressed parents showed a higher germination rate when grown in the presence of Cr. F1 plants derived from parents cultivated under chronic Cr stress displayed reduced hydrogen peroxide levels under Cr stress compared to controls. At lower Cr stress levels, F1 plants were observed to activate promptly more genes involved in Cr stress responses than F0 plants, implying a memory effect linked to transgenerational priming. At higher Cr levels, and at later stages, F1 plants modulated significantly fewer genes than F0 plants, implying a memory effect leading to Cr stress adaptation. Several bHLH transcription factors were induced by Cr stress in F1 but not in F0 plants, including bHLH100, ORG2 and ORG3. F1 plants optimized gene expression towards pathways linked to iron starvation response. A model of the transcriptional regulation of transgenerational memory to Cr stress is presented here, and could be applied for other heavy metal stresses.

Exploring the crop epigenome: a comparison of DNA methylation profiling techniques.

Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.