Evidence for co-selection of antibiotic resistance genes and mobile genetic elements in metal polluted urban

Plants interact closely with microbes, which are partly responsible for plant growth, health, and adaptation to stressful environments. Engineering the plant-associated microbiome could improve plant survival and performance in stressful environments such as contaminated soils. Here, willow cuttings were planted into highly petroleum-contaminated soils that had been gamma-irradiated and subjected to one of four treatments: inoculation with rhizosphere soil from a willow that grew well (LA) or sub-optimally (SM) in highly contaminated soils or with bulk soil in which the planted willow had died (DE) or no inoculation (CO). Samples were taken from the starting inoculum, at the beginning of the experiment (T0) and after 100 days of growth (TF). Short hypervariable regions of archaeal/bacterial 16S rRNA genes and the fungal ITS region were amplified from soil DNA extracts and sequenced on the Illumina MiSeq. Willow growth was monitored throughout the experiment, and plant biomass was measured at TF. CO willows were significantly smaller throughout the experiment, while DE willows were the largest at TF. Microbiomes of different treatments were divergent at T0, but for most samples, had converged on highly similar communities by TF. Willow biomass was more strongly linked to overall microbial community structure at T0 than to microbial community structure at TF, and the relative abundance of many genera at T0 was significantly correlated to final willow root and shoot biomass. Although microbial communities had mostly converged at TF, lasting differences in willow growth were observed, probably linked to differences in T0 microbial communities.

The interaction between plants and microorganisms, which is the driving force behind the decontamination of petroleum hydrocarbon (PHC) contamination in phytoremediation technology, is poorly understood. Here, we aimed at characterizing the variations between plant compartments in the microbiome of two willow cultivars growing in contaminated soils. A field experiment was set-up at a former petrochemical plant in Canada and after two growing seasons, bulk soil, rhizosphere soil, roots, and stems samples of two willow cultivars (Salix purpurea cv. FishCreek, and Salix miyabeana cv. SX67) growing at three PHC contamination concentrations were taken. DNA was extracted and bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) regions were amplified and sequenced using an Ion Torrent Personal Genome Machine (PGM). Following multivariate statistical analyses, the level of PHC-contamination appeared as the primary factor influencing the willow microbiome with compartment-specific effects, with significant differences between the responses of bacterial, and fungal communities. Increasing PHC contamination levels resulted in shifts in the microbiome composition, favoring putative hydrocarbon degraders, and microorganisms previously reported as associated with plant health. These shifts were less drastic in the rhizosphere, root, and stem tissues as compared to bulk soil, probably because the willows provided a more controlled environment, and thus, protected microbial communities against increasing contamination levels. Insights from this study will help to devise optimal plant microbiomes for increasing the efficiency of phytoremediation technology.

Mobility of heavy metals at contaminated sites is mainly influenced by the soil physicochemical properties and environmental conditions, therefore assessing heavy metals (HMs) and metalloids fractionation can provide insights into their potential risk and the mechanisms that regulate bioavailability. A 12-months mesocosms experiment was setup to investigate the effect of physicochemical factors (pH, moisture, and temperature) and weathering (time) on HMs and metalloids fractionation in three different multi-contaminated soil matrices (low, medium, and high contamination) collected from a soil treatment facility located in the United Kingdom, and two rural contaminated soil samples. The study demonstrates that even though Pb and Zn were found associated with the exchangeable fraction in the soil with the highest contamination (total average Pb 3400 mg/kg, and total average Zn 2100 mg/kg in Soil C), neither the condition applied nor the weathering caused an increase in their mobility. Although it was expected that lower pH (4.5) would favours the dissociation of HMs and metalloids, no significant differences were observed, potentially due to the initial alkaline pH of the genuine-contaminated soil samples. The results show that even though total concentration of Pb, Cu, and Zn exceed the soil standards and guideline values, HMs were predominantly associated with the non-exchangeable fraction, while only 5% were dissolved in the pore water fraction (potentially bioavailable). In addition, the mobility and bioavailability of HMs remained constant over the 12 months monitoring, suggesting that these soils pose negligible risk to the environment.

Highlights  Chromate copper arsenate (CCA) contaminated soils pose risks to the environment  In-situ stabilization of CCA contaminated soil was tested with biochar and ZVI  Soil remediation was evaluated based on chemical and microbiological techniques  Biochar reduced bioavailable (Cu bio), but not water-extractable Cu (Cu water)  Combination of biochar and ZVI most effectively reduced toxic effects of CCA