Genotoxicity assessment of textile waste contaminated soil and characterization of textile dye degradation by a novel indigenous bacterium Ochrobactrum intermedium BS39

The harmful effects of textile wastewater irrigation practices on the crop productivity and soil nutrient levels are primarily related with the accumulation of recalcitrant azo dyes in the soil. Therefore, toxicity assessment of the textile waste contaminated soil along with the development of a powerful soil bioremediation strategy is a challenging task for the researchers. Present study aimed to evaluate potential toxicity of the textile wastewater irrigated soil collected from Panki industrial site 5, Kanpur, India employing Ames Salmonella/mammalian microsome test, Escherichia coli DNA repair defective mutation assay and Allium cepa chromosomal aberration assay. The results of the Ames test and DNA repair defective mutation test showed that all the organic extracts of the contaminated soil samples induced different degrees of DNA damage, indicating the existence of mutagenicity and genotoxicity. Additionally, in A. cepa root cells, the contaminated soil altered mitotic index and caused chromosomal abnormalities. Results of the study demonstrated potential health risks related with the irrigation of textile wastewater. Keeping in view of the above scenario, the study led to the isolation and characterization of a novel indigenous bacterium capable of tolerating very high concentration of reactive black 5 dye (500 μg-mL^-1) and salt (20 gL^-1) with concurrently high efficiency of the dye degradation i.e., 93% decolorization at temperature of 37 °C and in pH range of 5-9. Based on the 16S rRNA gene sequencing, the bacterium was identified as Ochrobactrum intermedium. Further, dye degradation products were identified as sodium-2-hydrosulfonylethyl sulphate and sodium-3-aminonaphthalene-2-sulfonate by Gas Chromatography-Mass spectrometry; and this isolate can be exploited for bioremediation of textile waste contaminated soils.

Impact of a G2-EPSPS & GAT Dual Transgenic Glyphosate-Resistant Soybean Line on the Soil Microbial Community under Field Conditions Affected by Glyphosate Application

In the past thirty years, the biosafety of the aboveground part of crops, including horizontal gene transferal through pollen dispersal and hybridization, has been the focus of research; however, microbial communities in the underground part are attracting increasing attention. In the present study, the soybean root-associated bacterial communities of the G2-EPSPS plus GAT transgenic soybean line Z106, its recipient variety ZH10, and Z106 treated with glyphosate (Z106J) were compared at the seedling, flowering, and seed filling stages by high-throughput sequencing of the V4 hypervariable regions of 16S rRNA gene amplicons using Illumina MiSeq. The results obtained showed no significant differences in the alpha/beta diversities of root-associated bacterial communities at the three stages among ZH10, Z106, and Z106J under field growth conditions; however, the relative abundance of four main nitrogen-fixing bacterial genera significantly differed among ZH10, Z106, and Z106J. Ternary plot results indicated that in the root compartment, the proportional contributions of rhizobial nitrogen-fixing Ensifer fredii and Bradyrhizobium elkanii, which exhibit an extremely broad nodulation host range, markedly differed among the three treatments at the three stages. Thus, the present results indicate that transgenic G2-EPSPS and GAT soybean may induce different changes in functional bacterial species in soil, such as E. fredii and B. elkanii, from ZH10, which were compensated for/enriched at the flowering and seed filling stages, respectively, to some extent through as of yet unknown mechanisms by transgenic soybean treated with glyphosate.

Comparative Analyses of the Microbial Communities Inhabiting Coal Mining Waste Dump and an Adjacent Acid Mine Drainage Creek

Microbial communities inhabiting the acid mine drainage (AMD) have been extensively studied, but the microbial communities in the coal mining waste dump that may generate the AMD are still relatively under-explored. In this study, we characterized the microbial communities within these under-explored extreme habitats and compared with those in the downstream AMD creek. In addition, the interplay between the microbiota and the environmental parameters was statistically investigated. A Random Forest ensemble model indicated that pH was the most important environmental parameter influencing microbial community and diversity. Parameters associated with nitrogen cycling were also critical factors, with positive effects on microbial diversity, while S-related parameters had negative effects. The microbial community analysis also indicated that the microbial assemblage was driven by pH. Various taxa were enriched in different pH ranges: Sulfobacillus was the indicator genus in samples with pH < 3 while Acidobacteriaceae-affiliated bacteria prevailed in samples with 3 < pH < 3.5. The detection of some lineages that are seldom reported in mining areas suggested the coal mining dumps may be a reservoir of phylogenetic novelty. For example, potential nitrogen fixers, autotrophs, and heterotrophs may form diverse communities that actively self-perpetuate pyrite dissolution and acidic waste generation, suggesting unique ecological strategies adopted by these innate microorganisms. In addition, co-occurrence network analyses suggest that members of Acidimicrobiales play important roles in interactions with other taxa, especially Fe- and S-oxidizing bacteria such as Sulfobacillus spp.

Identification and analysis of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene from glyphosate-resistant Ochrobactrum intermedium Sq20

BACKGROUND

Glyphosate is a herbicide that acts by inhibition of the enzyme, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), involved in the catalysis of an essential step in the biosynthesis of aromatic amino acids. The objective of this study was the isolation of glyphosate-resistant bacterial strains and subsequent characterization of the gene(s) encoding glyphosate resistance in these isolates. Using an enrichment culture technique, a glyphosate-resistant bacterium, Ochrobactrum intermedium Sq20 was isolated from glyphosate-contaminated indigenous soil and characterized.

RESULTS

An open reading frame (ORF) comprising of 1353 bp potentially encoding aroAO. intermediumSq20 was amplified from O. intermedium Sq20. It showed 97% homology with aroA genes from other Ochrobactrum spp. Physicochemical characterization revealed that aroAO. intermediumSq20 encodes a polypeptide of 450 amino acids with a calculated molecular mass of 48.9782 kDa and an isoelectric point of 5.21. Secondary structure prediction of AroAO. intermediumSq20 demonstrated a high percentage of random coils and α helices. Methodical optimization and validation of the protein structure helped to build a reliable protein model indicating the presence of 91.8% amino acid residues in most favoured regions. In addition, strain Sq20 was found to be capable of complete degradation of glyphosate at 500 mg L-1 initial concentration as the sole carbon and energy source within 4 days.

CONCLUSION

A glyphosate-resistant bacterial strain O. intermedium Sq20 was discovered. Sequence analysis and structure modelling demonstrated that AroAO. intermediumSq20 closely resembles class II EPSPS and possesses high glyphosate resistance. This provides a good foundation for functional analysis of experimentally derived crystal structures. The cloning and characterization of AroAO. intermediumSq20 will further help in understanding its role at the molecular level and its potential use in the production of glyphosate-resistant transgenic crops. © 2017 Society of Chemical Industry.

Niches, population structure and genome reduction in Ochrobactrum intermedium: clues to technology-driven emergence of pathogens

Ochrobactrum intermedium is considered as an emerging human environmental opportunistic pathogen with mild virulence. The distribution of isolates and sequences described in literature and databases showed frequent association with human beings and polluted environments. As population structures are related to bacterial lifestyles, we investigated by multi-locus approach the genetic structure of a population of 65 isolates representative of the known natural distribution of O. intermedium. The population was further surveyed for genome dynamics using pulsed-field gel electrophoresis and genomics. The population displayed a clonal epidemic structure with events of recombination that occurred mainly in clonal complexes. Concerning biogeography, clones were shared by human and environments and were both cosmopolitan and local. The main cosmopolitan clone was genetically and genomically stable, and grouped isolates that all harbored an atypical insertion in the rrs. Ubiquitism and stability of this major clone suggested a clonal succes in a particular niche. Events of genomic reduction were detected in the population and the deleted genomic content was described for one isolate. O. intermedium displayed allopatric characters associated to a tendancy of genome reduction suggesting a specialization process. Considering its relatedness with Brucella, this specialization might be a commitment toward pathogenic life-style that could be driven by technological selective pressure related medical and industrial technologies.