Accurate quantification of gene and transcript-specific expression, with the underlying knowledge of precise transcript isoforms, is crucial to understanding many biological processes. Analysis of RNA sequencing data has benefited from the development of alignment-free algorithms which enhance the precision and speed of expression analysis. However, such algorithms require a reference transcriptome. Here we generate a reference transcript dataset (LsRTDv1) for lettuce (cv. Saladin), combining long- and short-read sequencing with publicly available transcriptome annotations, and filtering to keep only transcripts with high-confidence splice junctions and transcriptional start and end sites. LsRTDv1 identifies novel genes (mostly long non-coding RNAs) and increases the number of transcript isoforms per gene in the lettuce genome from 1.4 to 2.7. We show that LsRTDv1 significantly increases the mapping rate of RNA-seq data from a lettuce time-series experiment (mock- and Botrytis cinerea-inoculated) and enables detection of genes that are differentially alternatively spliced in response to infection as well as transcript-specific expression changes. LsRTDv1 is a valuable resource for investigation of transcriptional and alternative splicing regulation in lettuce.

The irrigation of soils with reclaimed contaminated wastewater or its amendment with sewage sludge contributes to the uptake of pharmaceuticals by vegetables growing in the soil. A multiresidue method has been devised to determine five pharmaceuticals and nine of their main metabolites in leafy and root vegetables. The method employs ultrasound-assisted extraction, clean-up via dispersive solid-phase extraction, and analysis through liquid chromatography-tandem mass spectrometry. Box-Behnken design was used to refine variables such as extraction solvent volume, time of extraction, number of extraction cycles, and the type and amount of d-SPE sorbent. The method achieved linearity (R2) greater than 0.994, precision (relative standard deviation) under 16% for most compounds, and detection limits ranging from 0.007 to 2.25 ng g-1 dry weight. This method was applied to a leafy vegetable (lettuce) and to a root vegetable (carrot) sourced from a local market. Parent compounds were detected at higher concentrations than their metabolites, with the exception of carbamazepine-10,11-epoxide.

Systemic plant protection products, such as neonicotinoids (NIs), are capable of being translocated throughout a plant. Although NIs are less toxic to mammals, fish, and birds, their impact on microbial and non-target insects is of concern. This study investigates the uptake, translocation, and accumulation of the NI, imidacloprid (IMI), in romaine lettuce (Lactuca sativa L. var. longipolia). Exposing 15-day-old seedlings to \"10 mg/L\" of IMI, the effects on microbial communities in both cultivated (CS) and non-cultivated soil (NCS) were studied along with IMI translocation within plant tissues. The concentrations of IMI in soil varied temporally and between soil types after initial application, with a decrease from 2.0 and 7.7 mg/kg on the first day of sampling to 0.5 and 2.6 mg/kg on the final sampling day (day 35) for CS and NCS, respectively. The half-life of IMI soil was 10.7 and 72.5 days in CS and NCS, respectively, indicating that IMI degraded more quickly in CS, possibly due to smaller grain size, aeration, microbial degradation, and water flow. The accumulated concentrations of IMI in lettuce tissues ranged from 12.4 ± 0.2 and 18.7± 0.9 mg/kg in CS and NCS, respectively. The highest concentration of IMI was found in the shoots, followed by the roots, whereas the soil showed the lowest IMI residuals at the end of the trial. Soil bacteria and fungi were altered by the application of IMI, with a lower abundance index within the bacterial community, indicating a negative impact on the distribution of bacteria in the soil.

Biofortification of green leafy vegetables with pro-vitamin A carotenoids, such as β-carotene, has remained challenging to date. Here, we combined two strategies to achieve this goal. One of them involves producing β-carotene in the cytosol of leaf cells to avoid the negative impacts on photosynthesis derived from changing the balance of carotenoids and chlorophylls in chloroplasts. The second approach involves the conversion of chloroplasts into non-photosynthetic, carotenoid-overaccumulating chromoplasts in leaves agroinfiltrated or infected with constructs encoding the bacterial phytoene synthase crtB, leaving other non-engineered leaves of the plant to sustain normal growth. A combination of these two strategies, referred to as strategy C (for cytosolic production) and strategy P (for plastid conversion mediated by crtB), resulted in a 5-fold increase in the amount of β-carotene in Nicotiana benthamiana leaves. Following several attempts to further improve β-carotene leaf contents by metabolic engineering, hormone treatments and genetic screenings, it was found that promoting the proliferation of plastoglobules with increased light-intensity treatments not only improved β-carotene accumulation but it also resulted in a much higher bioaccessibility. The combination of strategies C and P together with a more intense light treatment increased the levels of accessible β-carotene 30-fold compared to controls. We further demonstrated that stimulating plastoglobule proliferation with strategy P, but also with a higher-light treatment alone, also improved β-carotene contents and bioaccessibility in edible lettuce (Lactuca sativa) leaves.

Salinization poses a significant challenge in agriculture, exacerbated by anthropogenic global warming. Biostimulants, derived from living microorganisms or natural extracts, have emerged as valuable tools for conventional and organic agriculture. However, our understanding of the molecular mechanisms underlying the effects of biostimulants is very limited, especially in crops under real cultivation conditions. In this study, we adopted an integrative approach to investigate the effectiveness of the combined application of plant growth-promoting bacterium (Bacillus megaterium strain BM08) and a non-microbial biostimulant under control conditions (normal watering) and salt stress. After confirming the yield increase under both conditions, we investigated the molecular mechanisms underlying the observed effect by measuring a number of physiological parameters (i.e., lipid peroxidation, antioxidants, chlorophylls, total phenolics and phytohormone content), as well as RNA sequencing and primary metabolite analyses. Our findings reveal that the combined effect of the microbial and non-microbial biostimulants led to a decrease in the antioxidant response and an up-regulation of genes involved in cytokinin biosynthesis under salt stress conditions. This, in turn, resulted in a higher concentration of the bioactive cytokinin, isopentenyladenosine, in roots and leaves and an increase in γ-aminobutyric acid, a non-proteic amino acid related to abiotic stress responses. In addition, we observed a decrease in malic acid, along with an abscisic acid (ABA)-independent up-regulation of SR-kinases, a family of protein kinases associated with abiotic stress responses. Furthermore, we observed that the single application of the non-microbial biostimulant triggers an ABA-dependent response under salt stress; however, when combined with the microbial biostimulant, it potentiated the mechanisms triggered by the BM08 bacterial strain. This comprehensive investigation shows that the combination of two biostimulants is able to elicit a cytokinin-dependent response that may explain the observed yield increase under salt stress conditions.

Plants must cope with ever-changing temperature conditions in their environment. In many plant species, suboptimal high and low temperatures can induce adaptive mechanisms that allow optimal performance. Thermomorphogenesis is the acclimation to high ambient temperature, whereas cold acclimation refers to the acquisition of cold tolerance following a period of low temperatures. The molecular mechanisms underlying thermomorphogenesis and cold acclimation are increasingly well understood but neither signalling components that have an apparent role in acclimation to both cold and warmth, nor factors determining dose-responsiveness, are currently well defined. This can be explained in part by practical limitations, as applying temperature gradients requires the use of multiple growth conditions simultaneously, usually unavailable in research laboratories. Here we demonstrate that commercially available thermal gradient tables can be used to grow and assess plants over a defined and adjustable steep temperature gradient within one experiment. We describe technical and thermodynamic aspects and provide considerations for plant growth and treatment. We show that plants display the expected morphological, physiological, developmental and molecular responses that are typically associated with high temperature and cold acclimation. This includes temperature dose-response effects on seed germination, hypocotyl elongation, leaf development, hyponasty, rosette growth, temperature marker gene expression, stomatal conductance, chlorophyll content, ion leakage and hydrogen peroxide levels. In conclusion, thermal gradient table systems enable standardized and predictable environments to study plant responses to varying temperature regimes and can be swiftly implemented in research on temperature signalling and response.

Most nitrogen (N) applied to plants as fertilizer is lost through leaching. Here, nanocellulose was used in mitigating N leaching loss. Lettuce-cropped soil was treated with unmodified or Zn-modified nanocellulose (1-2% by wt) in combination with NPK, compared with urea and NPK-only treatments. Consecutive leaching, plant growth, plant N uptake, and soil nitrogen retention were assessed. Nanocellulose + NPK significantly (p ≤ 0.05) reduced N leaching, compared with urea and NPK-only. 1-and-2 wt % nanocellulose, as well as Zn-modified 1-and-2 wt % nanocellulose, reduced N leaching by 45, 38, 39, and 49% compared with urea and by 43, 36, 37, and 47% compared with NPK-only, respectively. Nitrogen leached mainly as NO3- (98.4%). Compared with urea and NPK, lettuce shoot mass was significantly (p ≤ 0.05) increased by 30-42% and by 44-57%, respectively, by all nanocellulose treatments, except for the Zn-modified 1 wt % nanocellulose. Leached N negatively correlated to biomass yield. Soil N retention was enhanced by the pristine and Zn-modified nanocelluloses between 27 and 94%. Demonstrably, nanocellulose can be utilized for mitigating N loss in soil and supporting crop production, resource management, and environmental sustainability.

Phosphorus (P) plays an important role in immobilizing heavy metals (HMs), thereby preventing their accumulation, especially in edible parts of crops. In this study, vermicompost (VM) and chemical fertilizers (CFs) were used as soil amendments to increase the available P concentration in soil contaminated with cadmium (Cd) and nickel (Ni), with the aim of reducing their bioavailability, uptake, and bioaccessibility. Using CF and VM as soil amendments substantially increased the available P and exchangeable potassium concentrations in the soil. Furthermore, VM addition led to an increase in OM content and in exchangeable calcium and magnesium, resulting in the improved growth of lettuce. It also reduced the uptake of Cd and Ni in the two lettuce cultivars tested in the study. However, CF addition boosted the accumulation of Cd and Ni by increasing the soil acidity. CF addition, and especially VM addition, altered the chemical forms of Cd and Ni from active to inactive. Overall, the results of this study underscore the positive impact of using VM as a soil amendment on lettuce growth and the prevention of HM accumulation in edible parts of lettuce. VM addition led to decreased bioavailability, uptake, and bioaccessibility of HMs in soil, which could improve food safety and reduce potential risks associated with HM contamination.

Heat shock protein 20 (Hsp20) plays a very important role in response to abiotic stressors such as drought; however, in lettuce (Lactuca sativa L.), this gene family is poorly understood. This study used bioinformatics methods to identify 36 members of the lettuce Hsp20 family, which were named LsHsp20-1~LsHsp20-36. Subcellular localization results revealed that 26 members of the LsHsp20 protein family localized to the cytoplasm and nucleus. Additionally, 15 conserved domains were identified in the LsHsp20 protein family, with the number of amino acids ranging from 8 to 50. Gene structure analysis revealed that 15 genes (41.7%) had no introns, and 20 genes (55.5%) had one intron. The proportion of the LsHsp20 secondary structure was random coil > alpha helix > extended strand > beta turn. Chromosome positioning analysis indicated that 36 genes were unevenly distributed on nine chromosomes, and four pairs of genes were collinear. The Ka/Ks ratio of the collinear genes was less than 1, indicating that purifying selection dominated during L. sativa evolution. Thirteen pairs of genes were collinear in lettuce and Arabidopsis, and 14 pairs of genes were collinear in lettuce and tomato. A total of 36 LsHsp20 proteins were divided into 12 subgroups based on phylogenetic analysis. Three types of cis-acting elements, namely, abiotic and biotic stress-responsive, plant hormone-responsive, and plant development-related elements, were identified in the lettuce LsHsp20 family. qRT-PCR was used to analyze the expression levels of 23 LsHsp20 genes that were significantly upregulated on the 7th or 14th day of drought treatment, and the expression levels of two genes (LsHsp20-12 and LsHsp20-26) were significantly increased by 153-fold and 273-fold on the 14th and 7th days of drought treatment, respectively. The results of this study provide comprehensive information for research on the LsHsp20 gene family in lettuce and lay a solid foundation for further elucidation of Hsp20 biological functions, providing valuable information on the regulatory mechanisms of the LsHsp20 family in lettuce drought resistance.

Listeria monocytogenes is a foodborne pathogen that lives in nature as a saprophyte. Two of the three most common serotypes that cause foodborne listeriosis are 1/2a and 4b. Within serotype 4b, there is a variant called 4bv-1. In the last decade, several produce-related outbreaks (linked to leafy salad, caramel apples, and stone fruit) were linked to 4bv-1 strains, specifically those of Sequence Type 382. This study assessed the fitness of ST 382 strains on lettuce leaf sections to determine if they are more fit on produce than strains of other serotypes. Strains of serotypes 1/2a, 4b, and ST 382 were inoculated as mixtures onto lettuce and incubated at 4 °C for 7 days or 25 °C for 24 h. Thirty L. monocytogenes colonies resulting from the growth on each lettuce piece were characterized for serotype by multiplex PCR, and the percentages of each serotype recovered were compared. In the individual mixtures with three strains, none of the ST 382 strains showed better fitness for growth on lettuce at either 4 °C or 25 °C. Overall, ST 382 strains showed better recovery from lettuce sections grown at 4 °C than at 25 °C. Statistical analysis of the recovery of twelve strains tested in competition experiments indicated that ST 382 strains were less fit for lettuce growth when competing against the other serotypes. The data indicate that ST 382 strains do not have a competitive fitness advantage on cut lettuce sections.