Crop residue management and tillage are known to affect the soil bacterial community, but when and which bacterial groups are enriched by application of ammonium in soil under different agricultural practices from a semi-arid ecosystem is still poorly understood. Soil was sampled from a long-term agronomic experiment with conventional tilled beds and crop residue retention (CT treatment), permanent beds with crop residue burned (PBB treatment) or retained (PBC) left unfertilized or fertilized with 300 kg urea-N ha−1 and cultivated with wheat (Triticum durum L.)/maize (Zea mays L.) rotation. Soil samples, fertilized or unfertilized, were amended or not (control) with a solution of (NH4)2SO4 (300 kg N ha−1) and were incubated aerobically at 25 ± 2 °C for 56 days, while CO2 emission, mineral N and the bacterial community were monitored. Application of NH4+ significantly increased the C mineralization independent of tillage-residue management or N fertilizer. Oxidation of NH4+ and NO2− was faster in the fertilized soil than in the unfertilized soil. The relative abundance of Nitrosovibrio, the sole ammonium oxidizer detected, was higher in the fertilized than in the unfertilized soil; and similarly, that of Nitrospira, the sole nitrite oxidizer. Application of NH4+ enriched Pseudomonas, Flavisolibacter, Enterobacter and Pseudoxanthomonas in the first week and Rheinheimera, Acinetobacter and Achromobacter between day 7 and 28. The application of ammonium to a soil cultivated with wheat and maize enriched a sequence of bacterial genera characterized as rhizospheric and/or endophytic independent of the application of urea, retention or burning of the crop residue, or tillage.

Hydrocarbon contamination cause serious environmental damage and human health problems, therefore, to resolve this problem has been proposed diversely remediation techniques friendly with the environment i.e. bioaugmentation, biostimulation, natural attenuation and phytoremediation. Among options, the phytoremediation causes minimum alterations to soil, low cost, it has proved good eff iciency and gained public acceptation. In the present study, the capacity of Mimosa pigra to restore a contaminated soil with both anthracene and phenanthrene was evaluated, along with the soil physicochemical changes due to both plant and contaminant presence in the soil. A silt-loam contaminated soil with 100 mg kg-1 (dry weight) anthracene and 200 mg kg-1 (dry weight) phenanthrene was used in all three treatments: Contaminated soil with M. pigra (C1), contaminated soil without M. pigra (C2), and not contaminated soil with M. pigra (C0) as control. After 70 days of experimentation both biomass and height of M. pigra was not affected due to soil contaminants. There was no difference among treatments for some physicochemical characteristics e.g. soil pH, electrolytic conductivity, soil-texture, and total nitrogen content throughout the experiment. M. pigra increased the soil water holding capacity after 50 and 70 days of the experiment, however, total organic carbon content was lower after 70 days compared to the control treatment. The higher contaminant removal rate was before 7 days of experimentation for all treatments. Anthracene and phenanthrene content were lower in treatments with the presence of M. pigra: 92% of phenanthrene and 80% of anthracene were removed in C1 while nearly 77% of phenanthrene and 60% of anthracene were removed in C2. This suggest a greater removal of contaminants using M. pigra. Total removal of contaminants was not achieved. However, M. pigra was able to accumulate both compounds, showing the M. pigra capability for bioremediation use in contaminated soils.

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A modified method for the direct extraction of DNA from alkaline-saline soils with minimum DNA fragmentation and a possible reduction in chimera formation during polymerase chain reaction (PCR) was developed. The commercial extraction kit Power Soil DNA (Mo Bio™ Laboratories, Inc.) was used as a reference technique. The method reported here was based on cell lysis employing ethylenediaminetetraacetic acid (EDTA), sodium dodecyl sulfate (SDS), and cell disruption with mechanical force with FastPrep-24™ equip followed by one cycle of freezing at -40 °C for 60 min and thawing at 65 °C for 20 min. The extraction method was tested for allophonic soils with large concentrations of organic matter, fulvic and humic acids, electrolytic conductivity (EC) ranging between 2.6 dS m-1 and 39.9 dS m-1, and pH between 8.8 and 10.9. The yield of DNA extracted depended on soil type, i.e., DNA extracted from soil varied between 2.35 (Texcoco-2) to 3.66 (Texcoco-1) μg DNA g-1 soil. The proposed method in this study produced enough DNA with yield and quality for PCR amplification of 16S rDNA when bovine serum albumin (BSA) was added to the reaction buffer. The DNA obtained had sufficient quality and yield for later use for 16S sequencing or possible use in other sequencing technologies, e.g. whole metagenome shotgun sequencing.