Metagenomic Analysis of the Bioremediation of Diesel-Contaminated Canadian High Arctic Soils

As human activity in the Arctic increases, so does the risk of hydrocarbon pollution events. On site bioremediation of contaminated soil is the only feasible clean up solution in these remote areas, but degradation rates vary widely between bioremediation treatments. Most previous studies have focused on the feasibility of on site clean-up and very little attention has been given to the microbial and functional communities involved and their ecology. Here, we ask the question: which microorganisms and functional genes are abundant and active during hydrocarbon degradation at cold temperature? To answer this question, we sequenced the soil metagenome of an ongoing bioremediation project in Alert, Canada through a time course. We also used reverse-transcriptase real-time PCR (RT-qPCR) to quantify the expression of several hydrocarbon-degrading genes. Pseudomonas species appeared as the most abundant organisms in Alert soils right after contamination with diesel and excavation (t = 0) and one month after the start of the bioremediation treatment (t = 1m), when degradation rates were at their highest, but decreased after one year (t = 1y), when residual soil hydrocarbons were almost depleted. This trend was also reflected in hydrocarbon degrading genes, which were mainly affiliated with Gammaproteobacteria at t = 0 and t = 1m and with Alphaproteobacteria and Actinobacteria at t = 1y. RT-qPCR assays confirmed that Pseudomonas and Rhodococcus species actively expressed hydrocarbon degradation genes in Arctic biopile soils. Taken together, these results indicated that biopile treatment leads to major shifts in soil microbial communities, favoring aerobic bacteria that can degrade hydrocarbons

Microbiology of Eutrophic (Ornithogenic and Hydrocarbon-Contaminated) Soil

Antarctic soils are typically low in carbon, nitrogen and phosphorus.Ornithogenic and hydrocarbon-contaminated soils, however, could be consideredeutrophic. In this chapter, we review the microbial composition of ornithogenicand hydrocarbon-contaminated soils. Ornithogenic soils form in soils under birdnesting sites. These include those that form under penguin colonies of coastal soilsand under bird nests in coastal soils and on nunataks. The soils currently occupiedby birds have high levels of C, N and P and a low C:N ratio. The diversity andabundance of microbes in the soils depends on whether they are currently occupiedby birds have been abandoned or are adjacent to the colony. Bacteria dominateoccupied soils with Firmicutes reported to be prevalent, but in abandoned soils,Proteobacteria are dominant. Among the nematodes Panagrolaimus is mostcommonly reported from ornithogenic soils. Extensive areas of growth of visiblephotosynthetic microbes occupy soils adjacent to ornithogenic soils. Prasiola sppand Phormidium spp. are the dominant algae and cyanobacteria, respectively, thatare reported. Most investigations of hydrocarbon-contaminated Antarctic soilshave focused on heterotrophic bacteria, with a few reports of fungi. Hydrocarbonspills on soils typically occur next to research stations and result in an increase insoil C and a high C:N ratio. The result is a shift in microbial communities towardshydrocarbon-degrading species, predominantly from the Proteobacteria phylum.Among the hydrocarbon-degrading bacteria isolated from Antarctic soils aremembers of the genera Pseudomonas, Sphingomonas and Rhodococcus. These genera have been observed widely in contaminated temperate soils and have thecapability to degrade hydrocarbons. Filamentous fungi from the Ascomycotaphylum commonly isolated from contaminated soils include those from the Cadophora,Trichoderma and Mortierella genera, but their ability to degradehydrocarbons is not always known. There is limited knowledge on the effect ofhydrocarbons on Archaea, invertebrates or photosynthetic microbes in hydrocarbon-contaminated Antarctic soil. Our knowledge of eutrophic soils of Antarctica issparse