A polyphasic approach for assessing the suitability of bioremediation for the treatment of hydrocarbon-impacted soil

Exploiting the intrinsic microbial degradative potential for field-based in situ dechlorination of trichloroethene contaminated groundwater

“…DNA sequences were annotated with MetaGenomics Rapid Annotation Subsystem Technology (MG-RAST) pipeline version 3.5 as described in [33] using a minimum alignment length of 15 bp and a maximum E-value cut off of 1 × 10 −5 [34]. Taxonomic profiles were constructed with normalised abundance of sequences matched to M5NR database.…”

Response of soil microorganisms to radioactive oil waste: results from a leaching experiment

“…To investigate the microbial community, shifts in soils, culture-independent molecular techniques such as clone libraries, gradient gel electrophoresis, single strand polymorphisms, terminal restriction fragment length polymorphism, deep sequencing, and quantitative real-time polymerase chain reaction are used (Adetutu et al, 2013;Bacosa et al, 2012;Liu et al, 2013).…”

“…Recently, culture-independent methods were used to estimate the number of strains belonging to different ecological or systematic groups (Adetutu et al, 2013). In this study, PCR-SSCP was used to describe the changes in microbial community structure (Schwieger and Tebbe, 1998).…”

“…Clones of band 1 (KF926419-KF926422) were phylogenetically similar to Burkholderia strains found in unpolluted and polluted sites (AF247491, DQ465451, FJ210816; Weisskopf et al, 2011;Friedrich et al, 2000), while clones of band 2 (KF926423-926425) were similar to strains of Burkholderia and Bradyrhizobium jicamae (JX010967, JN662515). Bacteria from the genus Burkholderia are typical soil inhabitants, and certain Burkholderia strains are resistant to hydrocarbons and are used in the bioremediation of oil-polluted sites (Bacosa et al, 2012;Weisskopf et al, 2011;Hamamura et al, 2008;Adetutu et al, 2013). Band 3 (KF926426-KF926429), which is sensitive to oily and radioactive components in the waste samples (not seen in contaminated H -and R-samples), was genetically similar to Hydrogenobacter hydrogenophilus (Z30242) uncultured Acidobacteria isolated from unpolluted grassland and forest soils (HQ598830, HQ599021; Naether et al, 2012) and an uncultured Chlorobiales bacterium found in a uranium mining waste pile (AJ295649, AJ536877; Selenska-Pobell, 2002).…”

Evaluation of constraints in bioremediation of weathered hydrocarbon-contaminated arid soils through microcosm biopile study

“…16S RNA-based pyrosequencing data have shown that the diversity of Proteobacteria and Actinobacteria may increase in hydrocarbon-contaminated soils. Several members of the Proteobacteria and Actinobacteria have been demonstrated to be involved in hydrocarbon degradation (Adetutu et al 2013). The Proteobacteria are subdivided into three classes: Alpha-, Beta-and Gammaproteobacteria, and their ability to utilise both aliphatic and aromatic compounds has already been established (Greer et al 2010).…”