Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach.

Soil pollution occurring at mining sites has adverse impacts on soil microbial diversity. New approaches, such as metagenomics approach, have become a powerful tool to investigate biodiversity of soil microbial communities. In the current study, metagenomics approach was used to investigate the microbial diversity of soils contaminated with different concentrations of lead (Pb) and zinc (Zn). The contaminated soils were collected from a Pb and Zn mine. The soil total DNA was extracted and 16S rDNA genes were amplified using universal primers. The PCR amplicons were sequenced and bioinformatic analysis of metagenomes was conducted to identify prokaryotic diversity in the Pb- and Zn-contaminated soils. The results indicated that the ten most abundant bacteria in all samples were Solirubrobacter (Actinobacteria), Geobacter (Proteobacteria), Edaphobacter (Acidobacteria), Pseudomonas (Proteobacteria), Gemmatiomonas (Gemmatimonadetes), Nitrosomonas, Xanthobacter, and Sphingomonas (Proteobacteria), Pedobacter (Bacterioidetes), and Ktedonobacter (Chloroflexi), descendingly. Archaea were also numerous, and Nitrososphaerales which are important in the nitrogen cycle had the highest abundance in the samples. Although, alpha and beta diversity showed negative effects of Pb and Zn contamination on soil microbial communities, microbial diversity of the contaminated soils was not subjected to a significant change. This study provided valuable insights into microbial composition in heavy metals-contaminated soils.

Impact of calcium carbonate and temperature on survival of Escherichia coli in soil.

Spreading of waste organic matter on agricultural lands is considered to enhance soil microbial activities and physical properties and improves soil nutrient status. However, organic wastes have also been shown to be a source of microbial contaminants including pathogens. Related risks are governed by pathogens' survival and transport particularities. We evaluated the significance of high levels of CaCO3, common in arid and semi-arid soils, on survival of Escherichia coli NAR at different temperatures. Amendments of 0, 5, 10, 15 or 25 g CaCO3 were mixed into variable soil amounts to obtain 100 g soil-CaCO3 mixtures. Both sterile and non-sterile soil mixtures were tested. Suspensions of a nalidixic acid-resistant E. coli strain (E. coli NAR) were added to the mixtures at a rate of 10(6) cell g(-1) soil. Mixtures were incubated at 4, 15, or 37 °C at the soil's field capacity for water (i.e. 0.13 g g(-1)). Each treatment was tested in triplicate. Persistence of culturable E. coli NAR was verified throughout the incubation period. The recovery rates of culturable E. coli NAR were significantly correlated to CaCO3 concentrations (P < 0.05). Incubation temperature (T) was the most significant factor (P < 0.01). In non-sterile mixtures the largest decline in survival rates of E. coli NAR was measured for treatments with larger CaCO3 content (i.e. 15 and 25%). Interaction of temperature and CaCO3 was significant for E. coli NAR die-off. Sterilization of soil caused non-uniform fluctuations in the effect of treatments. The maximum calculated decay rate for E. coli NAR was 0.83 d(-1) for the 15 g CaCO3 non-sterile mixture incubated at 37 °C while the minimum was 0.09 d(-1) for the control unamended sterile soil incubated at 15 °C. A combination of high temperature, large CaCO3 concentrations and a non-sterile, biologically active soil created the least favorable conditions for E. coli survival.