Toxicity of pyrene on the denitrifiers was studied by spiking an agricultural soil with pyrene to a series of concentrations (0–500mgkg⁻¹) followed by dose–response and dynamic incubation experiments. Results showed a positive correlation between potential denitrification activity and copy numbers of denitrifying functional genes (nirK, nirS and nosZ), and were both negatively correlated with pyrene concentrations. Based on the comparison of EC₅₀ values, denitrifiers harboring nirK, nirS or nosZ gene were more sensitive than denitrification activity, and denitrifiers harboring nirS gene were more sensitive than that harboring nirK or nosZ genes. Seven days after spiking with EC₅₀ concentration of pyrene, denitrifiers diversity decreased and community composition changed in comparison with the control. Phylogenetic analyses of three genes showed that the addition of pyrene increased the proportion of Bradyrhizobiaceae, Rhodospirillales, Burkholderiales and Pseudomonadales. Some species belonging to these groups were reported to be able to degrade PAHs.

We evaluated the molecular diversity of narG gene from Suquía River sediments to assess the impact of the nitrate concentration and water quality on the composition and structure of the nitrate-reducing bacterial community. To this aim, a library of one of the six monitoring stations corresponding to the highest nitrate concentration was constructed and 118 narG clones were screened. Nucleotide sequences were associated to narG gene from alpha-, beta-, delta-, gammaproteobacteria and Thermus thermophilus. Remarkably, 18% of clones contained narG genes with less than 69% similarity to narG sequences available in databases. Thus, indicating the presence of nitrate-reducing bacteria with novel narG genes, which were quantified by real-time PCR. Results show a variable number of narG copies, ranging from less than 1.0 × 102 to 5.0 × 104 copies per ng of DNA, which were associated with a decreased water quality index monitored along the basin at different times.

Antibiotics are among the most successful drugs used for human therapy. However, since they can challenge microbial populations, they must be considered as important pollutants as well. Besides being used for human therapy, antibiotics are extensively used for animal farming and for agricultural purposes. Residues from human environments and from farms may contain antibiotics and antibiotic resistance genes that can contaminate natural environments. The clearest consequence of antibiotic release in natural environments is the selection of resistant bacteria. The same resistance genes found at clinical settings are currently disseminated among pristine ecosystems without any record of antibiotic contamination. Nevertheless, the effect of antibiotics on the biosphere is wider than this and can impact the structure and activity of environmental microbiota. Along the article, we review the impact that pollution by antibiotics or by antibiotic resistance genes may have for both human health and for the evolution of environmental microbial populations. The article reviews the current knowledge on the effects that pollution by antibiotics and antibiotic resistance genes may have for the microbiosphere.

For phytoremediation of organic contaminants, plants have to host an efficiently degrading microflora. To assess the role of endophytes in alkane degradation, Italian ryegrass was grown in sterile soil with 0, 1 or 2% diesel and inoculated either with an alkane degrading bacterial strain originally derived from the rhizosphere of Italian ryegrass or with an endophyte. We studied plant colonization of these strains as well as the abundance and expression of alkane monooxygenase (alkB) genes in the rhizosphere, shoot and root interior. Results showed that the endophyte strain better colonized the plant, particularly the plant interior, and also showed higher expression of alkB genes suggesting a more efficient degradation of the pollutant. Furthermore, plants inoculated with the endophyte were better able to grow in the presence of diesel. The rhizosphere strain colonized primarily the rhizosphere and showed low alkB gene expression in the plant interior. Bacterial alkane degradation genes are expressed in the rhizosphere and in the plant interior.

The impact of Bt proteins on non-target arthropods is less understood than their effects on target organisms where the mechanism of toxic action is known. Here, we report the effects of two Bt proteins, Cry1Ab and Cry1Ac, on gene expression in the non-target collembolan, Folsomia candida. A customized microarray was used to study gene expression in F. candida specimens that were exposed to Cry1Ab and Cry1Ac. All selected transcripts were subsequently confirmed by qPCR. Eleven transcripts were finally verified, and three of them were annotated. The responses of all eleven transcripts were tested in specimens for both Cry1Ab and Cry1Ac at a series of concentrations. These transcripts were separated into two and three groups for Cry1Ab and Cry1Ac, respectively, depend on their expression levels. However, those eleven transcripts did not respond to the Bt proteins in Bt-rice residues.

The genetically modified maize MON89034 × MON88017 expresses different crystal (Cry) proteins with pesticidal activity against the European corn borer (Cry1.105; Cry2Ab2) and the Western corn root worm (Cry3Bb1). Non-target organisms, such as soil nematodes, might be exposed to the Cry proteins that enter the soil in course of crop growing. Therefore, the risk of those proteins for nematodes was assessed by testing their toxic effects on Caenorhabditis elegans. All three insecticidal Cry proteins showed dose-dependent inhibitory effects on C. elegans reproduction (EC50: 0.12–0.38 μmol L−1), however, at concentrations that were far above the expected soil concentrations. Moreover, a reduced toxicity was observed when Cry proteins were added jointly. A C. elegans mutant strain deficient for receptors for the nematicidal Cry5B was also resistant against Cry1.105 and Cry2Ab2, suggesting that these Cry proteins bound to the same or similar receptors as nematicidal Cry proteins and thereby affect the reproduction of C. elegans.

We investigated the influence of elevated CO₂ and O₃ on soil N cycling within the soybean growing season and across soil environments (i.e., rhizosphere and bulk soil) at the Soybean Free Air Concentration Enrichment (SoyFACE) experiment in Illinois, USA. Elevated O₃ decreased soil mineral N likely through a reduction in plant material input and increased denitrification, which was evidenced by the greater abundance of the denitrifier gene nosZ. Elevated CO₂ did not alter the parameters evaluated and both elevated CO₂ and O₃ showed no interactive effects on nitrifier and denitrifier abundance, nor on total and mineral N concentrations. These results indicate that elevated CO₂ may have limited effects on N transformations in soybean agroecosystems. However, elevated O₃ can lead to a decrease in soil N availability in both bulk and rhizosphere soils, and this likely also affects ecosystem productivity by reducing the mineralization rates of plant-derived residues.

Here we report the effects of three Bt-rice varieties and their non-Bt conventional isolines on biological traits including survival, reproduction, and the activities of three antioxidant enzymes superoxide dismutase, catalase and peroxidase, in the Collembolan, Folsomia candida. The reproduction was significantly lower when fed Kemingdao and Huahui1 than those feeding on their non-GM near-isogenic varieties Xiushui and Minghui63 respectively, this can be explained by the differences of plant compositions depended on variety of rice. The catalase activity of F. candida was significantly lower when fed the Bt-rice variety Kemingdao compared to the near-isogenic non-Bt-rice variety Xiushui. This suggests that some Bt-rice varieties may impose environmental stress to collembolans. We emphasize that changes in activity of antioxidant enzymes of non-target organisms are important in understanding the ecological consequences for organisms inhabiting transgenic Bt-rice plantations.