Assessment of co-contaminated soil amended by graphene oxide: Effects on pollutants, microbial communities and soil health.

Graphene oxide (GOx) is a nanomaterial with demonstrated capacity to remove metals from water. However, its effects on organic pollutants and metal(loid)s present in polluted soils when used for remediation purposes have not been extensively addressed. Likewise, few studies describe the effects of GOx on edaphic properties and soil biology. In this context, here we assessed the potential of GOx for remediating polluted soil focusing also on different unexplored effects of GOx in soil. To achieve this, we treated soil contaminated with concurrent inorganic (As and metals) and organic pollution (TPH and PAHs), using GOx alone and in combination with nutrients (N and P sources). In both cases increased availability of As and Zn was observed after 90 days, whereas Cu and Hg availability was reduced and the availability of Pb and the concentration of organic pollutants were not significantly affected. The application of GOx on the soil induced a significant and rapid change (within 1 week) in microbial populations, leading to a transient reduction in biodiversity, consistent with the alteration of several soil properties. Concurrently, the combination with nutrients exhibited a distinct behaviour, manifesting a more pronounced and persistent shift in microbial populations without a decrease in biodiversity. On the basis of these findings, GOx emerges as a versatile amendment for soil remediation approaches.

Goethite-based carbon foam nanocomposites for concurrently immobilizing arsenic and metals in polluted soils.

Although different amendments have been used for the immobilization of metals and metalloids in contaminated soils, in most of them there are still important challenges that need to be faced in order to achieve an optimal result. In this work, a new material based on a carbon foam impregnated with goethite nanoneedles has been developed with the aim of evaluating its effect on the mobility and availability of As, Cd, Cu, Pb and Zn in an industrial soil. For this purpose, leaching, sequential extraction and phytotoxicity studies have been carried out. The results were compared with the same carbon foam without goethite impregnation. When the soil was treated with goethite-based carbon foam nanocomposite, the mobility of metal(loid)s was markedly reduced, with the exception of Zn, which showed moderate immobilization. The presence of acid groups on the surface of the carbon foam, together with a high surface area, led to a strong immobilization of pollutants. Moreover, the modification of the foams using goethite nanoneedles, imply that the novel nanocomposite obtained is effective to remediate simultaneously metal and metalloid-polluted soils, without any relevant effect on soil toxicity.

Design and field-scale implementation of an "on site" bioremediation treatment in PAH-polluted soil.

An "on site" bioremediation program was designed and implemented in soil polluted with polycyclic aromatic hydrocarbons (PAHs), especially naphthalene. We began by characterizing the soil's physical and chemical properties. A microbiological screening corroborated the presence of microorganisms capable of metabolizing PAHs. We then analyzed the viability of bioremediation by developing laboratory microcosms and pilot scale studies, to optimize the costs and time associated with remediation. The treatment assays were based on different types of biostimulants, such as a slow or fast-release fertilizer, combined with commercial surfactants. Once the feasibility of the biostimulation was confirmed, a real-scale bioremediation program was undertaken in 900 m(3) of contaminated soil. The three-step design reduced PAH contamination by 94.4% at the end of treatment (161 days). The decrease in pollutants was concomitant with the selection of autochthonous bacteria capable of degrading PAHs, with Bacillus and Pseudomonas the most abundant genera.

Structural and functional characterization of the recR gene of Streptomyces.

The recR gene product is necessary for homologous recombination and recombinational DNA repair in eubacteria. We report the isolation and sequencing of the recR gene from Streptomyces coelicolor. It encodes a protein of 198 amino acids, with a predicted molecular mass of 22 kDa. The deduced amino acid sequence shows significant similarity to that of RecR proteins from other bacteria, including Escherichia coli and Bacillus subtilis. Like these, Streptomyces RecR contains potential helix-hairpin-helix, zinc finger and ATP-binding motifs, as well as the Toprim domain which is present also in topoisomerases of Types IA and II, primases and nucleases of the OLD family. The recR genes of Escherichia coli and Bacillus subtilis are immediately preceded by a small ORF (orf12 and orf107, respectively). An equivalent ORF (orf1) is also found in Streptomyces. S. lividans recR mutants, obtained either by insertional inactivation of recR or by deletion of the gene together with the preceding ORF, displayed increased sensitivity to DNA-damaging agents (such as UV light and methylmethanesulfonate), when compared with the wild-type strain. Both mutants could be complemented by the wild-type orflrecR genes and also by the recR gene alone. Based on these results, orf1 appears to be dispensable for the repair function of Streptomyces RecR. In studies of heterologous complementation, the B. subtilis recR region (orf107recR) was found to complement the S. lividans deltaorflrecR mutant, but the equivalent region from E. coli (orf12recR) could not. However, in the absence of orf107, B. subtilis recR was unable to restore the wild-type phenotype to the Streptomyces deletion mutant.

Characterization of IS1389, a new member of the IS3 family of insertion sequences isolated from Xanthomonas campestris pv. amaranthicola.

IS1389, a new insertion sequence belonging to the IS3 family, has been identified in Xanthomonas campestris pv. amaranthicola. The genome of this bacterium contains at least 11 copies of the element, whereas no hybridizing sequences were detected in other Xanthomonas species [X. axonopodis, X. fragaridae, X. phaseoli, and X. (Stenotrophomonas) maltophila]. Two nearly identical copies of the element (IS1389-A and IS1389-B) were characterized. According to analysis of sequence alignments and similar structural features, IS1389 belongs to the IS407 subgroup of the IS3 family, which duplicates 4 bp of target DNA upon insertion. IS1389-A was found in the proximity of the modification gene of the XamI restriction-modification system.

Establishment of a hybrid SalI-HgiDII type II restriction-modification system.

In the SalI system, endonuclease activity can be only achieved in the presence of a functional modification gene. Thus, the DNA methyltransferase is involved in the control of restriction. By fusion of the restriction gene of the SalI system to the modification gene of the isospecific HgiDII system a hybrid type II restriction-modification system was created. Although in the hybrid situation the level of endonuclease activity was significantly lower than in the natural system, the HgiDII modification enzyme clearly supports SalI restriction. The mechanism by which the two isospecific methyltransferases control restriction is currently under study.

Isolation and nucleotide sequence of the gene encoding the XamI DNA methyltransferase of Xanthomonas campestris pv. amaranthicola.

The gene (xamIM) encoding the DNA methyltransferase of the XamI restriction-modification system from Xanthomonas campestris pv. amaranithicola (M.XamI) has been cloned in Escherichia coli and its nucleotide sequence determined. The sequence predicts a protein of 527 amino acids that contains nine conserved motifs characteristic of DNA amino methyltransferases. In fact, M.XamI shows significant similarity with N6-adenine methyltransferases of the gamma group of amino methyltransferases, including M.SalI (from the isoschizomeric SalI restriction-modification system) and M.TaqI (the only N6-adenine methyltransferase for which a three-dimensional structure is available). M.XamI and M.SalI share two highly conserved regions within the C-terminal domain, one of which aligns with one of the DNA recognition loops proposed for M.TaqI. Analysis of the chromosomal DNA adjacent to xamIM led to the identification of an additional ORF (275 codons), downstream, in the same transcriptional orientation. Although some limited similarities between the SalI restriction enzyme and the product deduced from this ORF were found, the clone carrying xamIM did not express the expected endonuclease function.