Uptake of different pharmaceuticals in soil and mycorrhizal artichokes from wastewater

The irrigation with treated wastewater is among the main anthropogenic sources for the release of pharmaceuticals (PhACs) into the soils and their translocation into crops, with possible toxic and adverse effects on humans. The arbuscular mycorrhizal fungi (AMF) can be employed for the reduction of organic soil pollutants, even if their efficiency depends on the mycorrhizal fungi, the plant colonized, and the type and concentration of the contaminant. This study aimed to evaluate the uptake of PhACs from wastewaters of different qualities used for the irrigation of mycorrhizal artichoke plants, the presence in their edible parts and the role of the arbuscular mycorrhizal fungi. The research was carried out on artichoke plants not inoculated and inoculated with two different AMF and irrigated with treated wastewater (TW), groundwater (GW) or GW spiked with different and selected PhACs (SGW). The inocula were a crude inoculum of Septoglomus viscosum (MSE) and a commercial inoculum of Glomus intraradices and Glomus mosseae (MSY). The results of the present study showed that carbamazepine and fluconazole were found in the artichoke only with SGW irrigation. The mycorrhizal plants showed a reduction of the pharmaceutical's uptake, and within the AMF, MSE was more effective in preventing their absorption and translocation.

Exploiting Genomic Features to Improve the Prediction of Transcription Factor-Binding Sites in Plants

The identification of transcription factor (TF) target genes is central in biology. A popular approach is based on the location by pattern matching of potential cis-regulatory elements (CREs). During the last few years, tools integrating next-generation sequencing data have been developed to improve the performance of pattern matching. However, such tools have not yet been comprehensively evaluated in plants. Hence, we developed a new streamlined method aiming at predicting CREs and target genes of plant TFs in specific organs or conditions. Our approach implements a supervised machine learning strategy, which allows decision rule models to be learnt using TF ChIP-chip/seq experimental data. Different layers of genomic features were integrated in predictive models: the position on the gene, the DNA sequence conservation, the chromatin state and various CRE footprints. Among the tested features, the chromatin features were crucial for improving the accuracy of the method. Furthermore, we evaluated the transferability of predictive models across TFs, organs and species. Finally, we validated our method by correctly inferring the target genes of key TFs controlling metabolite biosynthesis at the organ level in Arabidopsis. We developed a tool-Wimtrap-to reproduce our approach in plant species and conditions/organs for which ChIP-chip/seq data are available. Wimtrap is a user-friendly R package that supports an R Shiny web interface and is provided with pre-built models that can be used to quickly get predictions of CREs and TF gene targets in different organs or conditions in Arabidopsis thaliana, Solanum lycopersicum, Oryza sativa and Zea mays.

Influence of soil pollution on the morphology of roots and leaves of Verbascum thapsus L

The impact of inorganic pollutants in the zone of industrial wastewater settling tanks (South of Russia) was studied. The levels of Mn, Cr, Ni, Cu, Zn, Pb, Cd were determined for Verbascum thapsus L., which are part of the mesophilic succession of wild plants in the studied technogenically polluted territory. The bioavailability of heavy metals (HM) for plants from transformed soils has been established. Anatomical and morphological features in the tissues of the plants affected by HM were analyzed using light-optical and electron microscopic methods. Contamination of the soil cover with Mn, Cr, Ni, Cu, Zn, Pb and Cd has been established with maximum content of Zn. It was revealed that the HM content in the V. thapsus plants exceeded the maximum permissible levels (Russian state standard): Zn by 23, Pb by 2, Cr by 31 and Cd by 3 times. The lower level of HM content in the inflorescences of mullein plants in comparison with the root system, stems and leaves indicates the resistance of generative organs to technogenic pollution. In the root and leaves of the V. thapsus, the anatomical and ultrastructural observation were carried out using light-optical and transmission electron microscopy. Changes in the ultrastructure of plants under the influence of anthropogenic impact have been revealed. The most significant changes of the ultrastructure of the polluted plants were found in the cell organelles of leaves (mitochondria, plastids, peroxisomes, etc.) including spatial transformation of the thylakoid system of plastids during the metal accumulation by plants, which may determine the mechanism of plant adaptation to technogenic pollution.

Coupling of different plant functional group, soil, and litter nutrients in a natural secondary mixed forest in the Qinling Mountains, China

Soil and litter play important roles in ecosystem nutrient storage and cycling, which both affect plant growth and ecosystem productivity. However, the potential linkages between soil and litter nutrient characteristics and nutrient characteristics of different plant functional groups (PFGs) remain unclear. In this study, we investigated the carbon (C), nitrogen (N), and phosphorus (P) concentrations and stoichiometric ratios in different organs of three PFGs (trees, shrubs, and herbs), litter, and soil in nine natural secondary mixed forests in the Qinling Mountains. Leaves N and P concentrations and N:P ratios, varied from 15.6 to 18.97 mg·g^-1, 1.86 to 2.01 mg·g^-1, and 7.34 to 8.72, were highest at the organ level, whereas the C:N and C:P values were lowest in leaves. At the PFG level, N and P concentrations of herbaceous were 1.23 to 3.69 and 1.42 to 1.93 times higher than those in same organs of woody species, while the N:P ratio was significantly lower in herb leaves than in tree and shrub leaves. Tree organs had significantly higher C concentrations and C:N and C:P ratios than shrub and herb organs. The leaf N:P ratios of all PFGs were less than 14, suggesting that plant growth was limited by N in the study region. The nutrient contents and stoichiometric ratios in plant organs had different degrees of linkages with those in litter and soil. Soil nutrient characteristics mainly affected (23.9 to 56.4%) the nutrient characteristics of the different PFGs, and litter nutrient characteristics also had important contributions (4.5 to 49.7%) to the nutrient characteristics of PFGs, showing the following order: herbs > trees > shrubs. Our results indicate that the functional difference in plant organs resulted in diverse nutrient concentrations; and varied nutrient connections exist among different ecosystem components. Furthermore, nutrient characteristics of litter and soil can together affect the nutrient characteristics of PFGs.

C:N:P stoichiometry responses to 10 years of nitrogen addition differ across soil components and plant organs in a subtropical Pleioblastus amarus forest

How stoichiometry in different ecosystem components responds to long-term nitrogen (N) addition is crucial for understanding within-ecosystem biogeochemistry cycling processes in the context of global change. To explore the effects of long-term N addition on nutrient stoichiometry in soil and plant components in forest ecosystem, a 10-year N addition experiment using ammonium nitrate (NH₄NO₃) was conducted in a bamboo forest in the Rainy Zone of West China, where the background N deposition is the highest in the world. Four N treatment levels (+0, +50, +150, +300 kg N ha^-1 yr^-1) (CK, LN, MN, HN) were applied monthly since November 2007, and then, the C:N:P stoichiometry of soil, microbial biomass, and enzymes in rhizosphere soil and bulk soil, and plant organs were measured. N addition decreased the stoichiometry of C:N:P of soil, microbial biomass, and enzymes. Soil C:N:P change under N addition treatments was stronger in bulk soil, while C:N:P changes for microbial biomass and enzyme activity were significant in rhizosphere soil. N addition significantly decreased TOC in bulk soil. Changes in MBC:MBN:MBP in rhizosphere and bulk soil were mainly caused by MBN and MBP, and MBP performance was consistent with that of AP. The main variable leading to the change of enzyme C:N:P in rhizosphere soil was BG and AP, and in bulk soil was LAP + NAG activity. Plant root C:P and N:P increased with N addition, while those for leaves and twigs did not. N addition significantly reduced the pH of both rhizosphere and bulk soils. These results suggest that the stoichiometry responses of rhizosphere and bulk soils were different due to the influence of plant roots. Soil acidification, enhanced aluminum toxicity potential, decreased root biomass and enhanced microbial P limitation caused by N addition were the important mechanisms that promoted stoichiometry changes in this ecosystem. Under the chronic input of N deposition, the stoichiometry between plant and soil evolved in different directions, which may lead to the decoupling of plants from soils.

C:N:P stoichiometry in terrestrial ecosystems in China

Ecological stoichiometry is an efficient tool for exploring the balance and cycling of coupled elements (e.g., carbon [C], nitrogen [N], and phosphorus [P]). Therefore, C:N:P ratios are essential input parameters in most ecological models of productivity or C cycling. However, previous C:N:P ratios estimated using the species arithmetic means exhibit high uncertainty when used as direct model parameters. In this study, we comprehensively calculated C:N:P ratios from organs to ecosystems for 66 typical natural ecosystems in China (e.g., forests, grasslands, and deserts) using the community biomass-weighted mean (CWM), with the consistently measured element data of 3229 site-species combination. The C:N:P ratios were 427:19:1, 885:13:1, 9549:33:1, and 797:18:1 in the leaves, branches, trunks, and roots of terrestrial ecosystems, respectively. Furthermore, the ratios were 91:4:1, 919:17:1, 1121:25:1, and 55:4:1 in ecosystems, plant communities, litter, and soils, respectively. Significant differences were observed in C:N:P ratios among different ecosystem types and biomes, with generally higher ratios in forests. Moreover, the latitudinal patterns of C:N ratios exhibited no obvious trends, whereas both C:P and N:P ratios decreased significantly with increasing latitude, especially in forests. Environmental conditions explained 15.4-86.6% of the spatial variation of C:N:P ratios from organs to ecosystems. In summary, this study systematically demonstrates the variations in biome-scale C:N:P stoichiometry in terrestrial ecosystems, as well as their influencing factors, using the CWM. More importantly, this study provides a systematic dataset of C:N:P ratios from plot to biome scale that can be used to improve relevant ecological models.

Study of Potentially Toxic Elements Uptake into Organs of Quercus spp. from Copper Deposits in Slovakia, Italy and Portugal

The article is focused on the application of Energy dispersive micro X-ray fluorescence spectroscopy as a specific method to determine the contents of potentially toxic elements and its spread in plant tissues. As a model species, Quercus spp. were selected. In order to compare the obtained results with previous research, four well-described abandoned Cu-deposits were selected for sampling: Ľubietová (Slovakia), Libiola and Caporciano (Italy), and São Domingos (Portugal). The results of micro X-ray fluorescence spectrometry confirm the irregular contamination of Quercus spp. by potentially toxic elements. The level of contamination is the highest predominantly in the root cortex, where is also the highest Ca contents (with exception of São Domingos). At Ľubietová and Caporciano, high Ni content was described in branches cortex, in branches mesoderm also Fe, Cu and Zn. At the same time, the inhibition influence of Ca was also confirmed regarding the input of these elements into plants.

Effects of benzo[a]pyrene toxicity on morphology and ultrastructure of Hordeum sativum

Many studies have been devoted to investigation of toxic benzo(a)pyrene (BaP) compound, but studies involving changes at the cellular level are insufficient to understand the mechanisms of polycyclic aromatic hydrocarbons (PAHs) effect on plants. To study the toxicity of BaP, a model vegetation experiment was conducted on cultivation of spring barley (Hordeum sativum distichum) on artificially polluted BaP soil at different concentrations. The article discusses the intake of BaP from the soil into the plant and its effect on the organismic and cellular levels of plant organization. The BaP content in the organs of spring barley was determined by the method of saponification. With an increase in the concentration of BaP in the soil, its content in plants also rises, which leads to inhibition of growth processes. The BaP content in the green part of Hordeum sativum increased from 0.3 µg kg^-1 in control soil up to 2.6 µg kg^-1 and 16.8 µg kg^-1 under 20 and 400 ng/g BaP applying in soil, as well as in roots: 0.9 µg kg^-1, 7.7 µg kg^-1, 42.8 µg kg^-1, respectively. Using light and electron microscopy, changes in the tissues and cells of plants were found and it was established that accumulation of BaP in plant tissues caused varying degrees of ultrastructural damage depending on the concentration of pollutant. BaP had the greatest effect on the root, significant changes were found in it both at histological and cytological levels, while changes in the leaves were observed only at the cytological level. The results provide significant information about the mechanism of action of BaP on agricultural plants.

Culture-independent analysis of an endophytic core microbiome in two species of wheat: Triticum aestivum L. (cv. 'Hondia') and the first report of microbiota in Triticum spelta L. (cv. 'Rokosz')

The main goal of the study was to determine the structure of endophytic bacteria inhabiting different parts (endosperm, germ, roots, coleoptiles, and leaves) of two wheat species, Triticum aestivum L. (cv. 'Hondia') and Triticum spelta L. (cv. 'Rokosz'), in order to provide new knowledge about the stability and/or changeability of the core microbiome in different plant organs. The endophytic core microbiome is associated with plants throughout their whole life cycle; however, plant organs can determine the actual endophytic community. Therefore, next generation sequencing with MiSeq Illumina technology was applied to identify the endophytic microbiome of T. aestivum and T. spelta. Bioinformatic analyses were performed with the use of the DADA2(1.8) package and R software (3.5.1). It was demonstrated that wheat, which is an important crop plant, was associated with beneficial endophytic bacteria inside the endosperms, germs, roots, leaves, and coleoptiles. Importantly, for the first time, biodiversity was recognized in the coleoptiles of the investigated wheat species. Flavobacterium, Pseudomonas and Janthinobacterium were shown to be common genera for both tested wheat cultivars. Among them, Pseudomonas was found to be the only endophytic genus accompanying both wheat species from the endosperm stage to the development of the leaf. Paenibacillus was recognized as a core genus for the 'Hondia' cv., whereas Pedobacter and Duganella constituted the core microbiome in the 'Rokosz' cv. In addition, the first insight into the unique and yet unrecognized endophytic microbiome of T. spelta is presented.

Plant Structure and Specificity - Challenges and Sample Preparation Considerations for Proteomics

Plants are considered as a simple structured organism when compared to humans and other vertebrates. The number of organs and tissue types is very limited. Instead the origin of the complexity comes from the high number and variety of plant species that exist, with >300,000 compared to 5000 in mammals. Proteomics, defined as the large-scale study of the proteins present in a tissue, cell or cellular compartment at a defined time point, was introduced in 1994. However, the first publications reported in the plant proteomics field only appeared at the beginning of the twenty-first century. Since these early years, the increase of proteomic studies in plants has only followed a linear trend. The main reason for this stems from the challenges specific to studying plants, those of protein extraction from cells with variously strengthened cellulosic cell walls, and a high abundance of interfering compounds, such as phenolic compounds and pigments located in plastids throughout the plant. Indeed, the heterogeneity between different organs and tissue types, between species and different developmental stages, requires the use of optimized plant protein extraction methods as described in this section. The second bottleneck of plant proteomics, which will not be discussed or reviewed here, is the lack of genomic information. Without sequence databases of the >300,000 species, proteomic studies of plants, especially of those that are not considered economically relevant, are impossible to accomplish.

Comparative LC-MS-based metabolite profiling of the ancient tropical rainforest tree Symphonia globulifera

In the last few years, several phytochemical studies have been undertaken on the tropical tree Symphonia globulifera leading to the isolation and characterisation of several compounds exhibiting antiparasitic activities against Plasmodium falciparum, Trypanosoma brucei and Leishmania donovani. The comparative LC-MS based metabolite profiling study conducted on the tree led to the identification of compounds originating from specific tissues. The results showed that renewable organs/tissues can be used as the starting material for the production of polycyclic poly-prenylated-acylphloroglucinols, therefore reducing impacts on biodiversity. This study also underlined the lack of knowledge on the secondary metabolites produced by S. globulifera since only a small number of the total detected features were putatively identified using the database of known compounds for the species.