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.

Modelling botanical biofiltration of indoor air streams contaminated by volatile organic compounds.

Botanical filtration is a biological-based treatment method suitable for removing hazardous volatile organic compounds (VOCs) from air streams, based on forcing an air flow through a porous substrate and foliage of a living botanical compartment. The pathways and removal mechanisms during VOC bioremediation have been largely investigated; however, their mathematical representation is well established only for the non-botanical components of the system. In this study, we evaluated the applicability of such a modelling scheme to systems which include a botanical compartment. We implemented a one-dimensional numerical model and performed a global sensitivity analysis to measure the input parameters influence on the transient and steady biofilter responses. We found that the most sensitive parameters on the transient-state behaviour were the mass transfer coefficient between gas and solid surfaces, and the fraction of solid surfaces covered by the biofilm; the steady-state response was primarily influenced by the biofilm specific surface area and the fraction of surfaces covered by the biofilm. We calibrated the identified set of parameters and successfully validated the model against data from a pilot-scale installation. The results showed that the application of the model to systems with a botanical compartment is feasible, although under a strict set of assumptions.

Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants.

Metatranscriptomic study of nonmodel organisms requires strategies that retain the highly resolved genetic information generated from model organisms while allowing for identification of the unexpected. A real-world biological application of phytoremediation, the field growth of 10 Salix cultivars on polluted soils, was used as an exemplar nonmodel and multifaceted crop response well-disposed to the study of gene expression. Sequence reads were assembled de novo to create 10 independent transcriptomes, a global transcriptome, and were mapped against the Salix purpurea 94006 reference genome. Annotation of assembled contigs was performed without a priori assumption of the originating organism. Global transcriptome construction from 3.03 billion paired-end reads revealed 606,880 unique contigs annotated from 1588 species, often common in all 10 cultivars. Comparisons between transcriptomic and metatranscriptomic methodologies provide clear evidence that nonnative RNA can mistakenly map to reference genomes, especially to conserved regions of common housekeeping genes, such as actin, α/ß-tubulin, and elongation factor 1-α. In Salix, Rubisco activase transcripts were down-regulated in contaminated trees across all 10 cultivars, whereas thiamine thizole synthase and CP12, a Calvin Cycle master regulator, were uniformly up-regulated. De novo assembly approaches, with unconstrained annotation, can improve data quality; care should be taken when exploring such plant genetics to reduce de facto data exclusion by mapping to a single reference genome alone. Salix gene expression patterns strongly suggest cultivar-wide alteration of specific photosynthetic apparatus and protection of the antenna complexes from oxidation damage in contaminated trees, providing an insight into common stress tolerance strategies in a real-world phytoremediation system.

Potential of selected Canadian plant species for phytoextraction of trace elements from selenium-rich soil contaminated by industrial activity.

In this preliminary screening study, we tested the phytoextraction potential of nine Canadian native/well-adapted plant species on a soil highly polluted by trace elements (TE) from a copper refinery. Plant physiological parameters and soil cover index were monitored for a 12-week period. At the end of the trial, biomass yield, bioconcentration (BFC) and translocation (TF) factors for the main TE as well as phytoextraction potential were determined. Most plants were severely injured by the high pollution levels, showing symptoms of toxicity including chlorosis, mortality and very low biomass yield. However, Indian mustard showed the highest selenium extraction potential (65 mg m(-2)), even under harsh growing conditions. Based on our results, tall fescue and ryegrass, which mainly stored As, Cu, Pb and Zn within roots, could be used effectively for phytostabilization.

Early response of willow to increasing silver concentration exposure.

This is a preliminary hydroponic study to test willow sensitivity to silver nitrate, a highly toxic chemical compound. We grew willow cuttings for a period of three weeks in the presence of increasing AgNO(3) concentrations and assessed the response in terms of growth and physiology. We found that AgNO(3) is generally extremely harmful to willow. AgNO(3) concentration as high as 0.027 muM may result in a significant reduction of biomass productivity and a decrease in stomatal conductance over the first week of exposure. However, willows seem able to adapt to high AgNO(3) concentrations on a longer timeline.