Genomic impact of stress-induced transposable element mobility in Arabidopsis

Transposable elements (TEs) have long been known to be major contributors to plant evolution, adaptation and crop domestication. Stress-induced TE mobilization is of particular interest because it may result in novel gene regulatory pathways responding to stresses and thereby contribute to stress adaptation. Here, we investigated the genomic impacts of stress induced TE mobilization in wild type Arabidopsis plants. We find that the heat-stress responsive ONSEN TE displays an insertion site preference that is associated with specific chromatin states, especially those rich in H2A.Z histone variant and H3K27me3 histone mark. In order to better understand how novel ONSEN insertions affect the plant's response to heat stress, we carried out an in-depth transcriptomic analysis. We find that in addition to simple gene knockouts, ONSEN can produce a plethora of gene expression changes such as: constitutive activation of gene expression, alternative splicing, acquisition of heat-responsiveness, exonisation and genesis of novel non-coding and antisense RNAs. This report shows how the mobilization of a single TE-family can lead to a rapid rise of its copy number increasing the host's genome size and contribute to a broad range of transcriptomic novelty on which natural selection can then act.

Hydrogen Peroxide Ammonium Citrate Extraction: Mineral Decomposition and Preliminary Waste Rock Characterization

A commonly-used method in ore exploration is hydrogen peroxide ammonium citrate (HA) extraction, which has not typically been used in waste rock characterization. In this study, the sulfide specificity and leaching of other minerals in HA extraction was evaluated and its performance was compared with the aqua regia (AR) extraction for preliminary assessment of harmful element mobility. Samples collected from several different mine sites in Finland were utilized. The waste rock sample S contents ranged from 0.3% to 5.3%, and sums of the AR extractable elements As, Cd, Co, Cu, Ni and Zn range from 120 to 8040 mg/kg. The drainage types ranged from acid high-metal to neutral low-metal, with pH’s of 3.3–7.7. Mineralogical changes that took place in the HA solution were investigated by the field emission scanning electron microscope (FE-SEM) equipped with an energy-dispersive X-ray spectroscopy analyzer (EDS) and X-ray diffraction (XRD) methods. Results of the study showed that the HA extraction appears to be a more specific method for sulfide decomposition compared with AR extraction. Sulfide minerals, especially base metal sulfides pentlandite, chalcopyrite and sphalerite, decomposed efficiently in HA extraction. However, the Fe-sulfides pyrrhotite and pyrite only decomposed incompletely. The study showed that the HA extraction results can be used in the preliminary prediction of element mobility. Based on the results, the elevated As, Cd, Co, Cu, Ni, S and Zn leachability in the HA extraction appears to predict elevated drainage concentrations. If the HA-extractable sum of As, Cd, Co, Cu, Ni and Zn is >750 mg/kg, there is an increased risk of high-metal (>1000 µg/L) drainage. Therefore, the HA extraction data, e.g., produced during ore exploration, can be utilized to preliminary screen the risks of sulfide related element mobilities from waste rock material.

Trace Element Mobility during Corg-Enhanced Denitrification in Two Different Aquifers

Nitrate (NO3−)-polluted groundwater treatment by enhanced denitrification is becoming increasingly important due to rising NO3− concentrations and decreasing degradation capacities in aquifers. Besides evaluating the efficacy of substrates added to trigger denitrification, secondary reactions must be closely monitored. Biodenitrification by applied organic carbon (Corg) can lead to considerable changes in redox potential (Eh) and pH, two decisive parameters for trace element mobility. In this study, two geologically and hydrogeochemically different groundwater catchments important for drinking water production were investigated and compared. Sediments were analyzed for trace elements as well as sulfur (S) and carbon (C) contents. Ongoing hydrogeochemical reactions were evaluated with depth-specific isotope characterization, and the potential for trace element mobilization by Corg addition was determined in column experiments. Results for enhanced denitrification showed up to 3.8 times lower reaction rates with respect to comparable studies, probably due to incomplete formation of the necessary denitrifying bacteria. Concentrations of trace elements such as nickel (Ni) must also be considered when evaluating enhanced denitrification, as these can negatively affect microorganisms. Added ethanol led to Ni concentrations dropping from 0.013 mg/L to below the detection limit. Thus, Corg addition may not only induce denitrification, but also lead to the immobilization of previously released trace elements.