Insights into Bacterial Community Involved in Bioremediation of Aged Oil-Contaminated Soil in Arid Environment

Rahmeh, Rita; Akbar, Abrar; Kumar, Vinod; Al-Mansour, Hamad; Kishk, Mohamed; Ahmed, Nisar; Al-Shamali, Mustafa; Boota, A.; Al-Ballam, Zainab; Shajan, Anisha; Al-Okla, Naser

doi:10.1177/11769343211016887

Cited by 6 publications

(3 citation statements)

References 87 publications

(144 reference statements)

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“…Microorganisms that have recently been isolated from polluted soils may have unique catabolic capabilities and the resilience of thriving in harsh environments with a dearth of nutrients (Oves et al, 2012;Rahmeh et al, 2021). These organisms, which can also fail PAHs, can provide a costeffective and viable solution for remediation (Kuppusamy et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Molecular characterization of a polycyclic aromatic hydrocarbons (PAHs) degrader, Burkholderia contaminans strain P14, isolated from aged oil-contaminated soil in Kuwait

Akbar

Rahmeh

Kishk

et al. 2022

Appl Env Biotechnol

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Soil contamination by polycyclic aromatic hydrocarbons (PAHs) and heavy metals is a major concern affecting soil quality. Bioremediation is an efficient approach to decontaminate these pollutants while posing the lowest risk to the environment. This technique is based on identifying microorganisms with the metabolic potential to degrade the pollutants. In this study, the physiochemical properties of oil-contaminated soils in Kuwait were investigated. The soil had alkaline pH (8.36) with a salinity of 0.08% and PAHs compounds were detected at high concentrations (pyrene, 1212 mg/kg), (phenanthrene, 710 mg/kg) and (fluorene 326 mg/kg). Heavy metals such as iron, aluminum, sodium, magnesium, vanadium, copper, etc., were also detected in the soil samples. Then, selective screening for PAH degraders was performed and assessed by colony forming units (CFU) and 16S rDNA gene sequences to determine their growth profiles and taxonomical identification. In total, 21 strains were selected for their resistance to PAHs, which include Pseudomonas (9), Burkholderia (6), Bacillus (2), Bordetella (1), Microbacterium (1), Micrococcus (1), and Kocuria (1). Among all, the growth by Burkholderia sp. P14, in the presence of phenanthrene and fluorene, has maintained a stationary phase from day 5 to 8 with a 6 log CFU/ml bacterial count. The draft genome of the Burkholderia contaminans P14 strain comprised 68 contigs with 8,584,157bp, 66% GC content, 4 rRNA and 75 tRNA. A total of 80 genes were involved in the degradation of the benzoate, naphthalene, and PAH . Genes that encode the PAH degradation were clustered into four distinct groups, including pcaHG, pcaB, pcaIJ, and pcaKFR and were found to be in contigs 5, 11, 8 and 13 of B. contaminans P14, respectively. KEGG analysis suggested that PAHs were degraded in P14 via the protocatechuate and catechol branches of the β-ketoadipate protocatechuate degradation pathway. The genomic island regions in P14 differed from those in the reference genome of B. contaminans M14, indicating the novelty and genomic recombination of the strain. Genomic information on P14 has helped clarify the molecular mechanisms involved in PAH catabolism. Burkholderia contaminans P14 strain will enhance the bioremediation of oil-contaminated soils.

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Section: Discussionmentioning

confidence: 99%

Molecular characterization of a polycyclic aromatic hydrocarbons (PAHs) degrader, Burkholderia contaminans strain P14, isolated from aged oil-contaminated soil in Kuwait

Akbar

Rahmeh

Kishk

et al. 2022

Appl Env Biotechnol

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“…In a recent study, biostimulation was used for the remediation of a crude oil contaminated site via biodegradation of total petroleum hydrocarbons (TPHs) and PAHs by a consortium of bacteria observed using metagenomic analysis (Rahmeh et al, 2021). The diversity investigation revealed a group of microbes belonging to a diverse genus could be employed for remediation/restoration purposes especially in temperate regions.…”

Section: Bioremediation Of Organic Compoundsmentioning

confidence: 99%

Metagenomics: an emerging tool for the chemistry of environmental remediation

Offiong,

Edet,

Shaibu

et al. 2023

Front. Environ. Chem.

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Metagenomics is the study of genetic information, including the sequences and genomes of microorganisms present in an environment. Since 1998, the full-scale application of this technique to environmental chemistry has brought significant advances in the characterization of the nature and chemical composition/distribution of contaminants present in environmental matrices of contaminated and/or remediated sites. This has been critical in the selection of microorganisms and has contributed significantly to the success of this biological treatment over the years. Metagenomics has gone through different phases of development, which ranges from initial sequencing strategies to next-generation sequencing (NGS), which is a recently developed technology to obtain more robust deoxyribonucleic acid (DNA) profile of microorganisms devoid of chimeric sequences which reduces the quality of metagenomic data. Therefore, the objective of this review is to evaluate the applications of metagenomics in the understanding of environmental dynamics of chemical contaminants during remediation studies. Also, this review presents the relationship between biological characteristics of microorganisms and chemical properties of chemical compounds, which forms the basis of bioremediation and could be useful in developing predictive models that could enhance remediation efficiency. In conclusion, metagenomic techniques have improved the characterisation of chemical contaminants in the environment and provides a correlation for useful prediction of the type of contaminant expected in various environmental matrices.

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“…The organism in this taxon was first isolated from marine sediment and mangrove soil (Liu et al, 2006;Hong et al, 2023) and was among the tropical mangrove sediment communities demonstrated to readily degrade Enteromorpha prolifera (Zhao and Ruan, 2011). Similarly, with regard to the sharp increase in population of the genus observed in treated petroleum hydrocarboncontaminated soil, Rahmeh et al (2021) attributed this surge to the less complex ring structure derivatives resulting from the degradation of aromatic compounds with complex structures. A Frontiers in Environmental Science frontiersin.org 13 critical evaluation of the metagenome data clearly showed that among the population of bacterial phyla reported across the sites, none came close to the Bacteroidetes.…”

Section: Frontiers In Environmental Sciencementioning

confidence: 99%

Geochemistry and metagenomics analyses of bacterial community structure in selected waste dumpsites in Lagos Metropolis, Nigeria

Saibu,

Adebusoye,

Oyetibo

et al. 2023

Front. Environ. Sci.

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Dumpsites are reservoirs of persistent organic pollutants (POPs) and heavy metals (HMs), constituting environmental hazards to humanity. Autochthonous microorganisms in dumpsites exhibit various degrees of responses to contaminants. Unfortunately, there is a dearth of information on the types and concentration of pollutants and the array of microorganisms in these dumpsites which may play important roles in the metabolism of such pollutants or other community processes. Therefore, determining the microbial community structure in such contaminated sites across a municipality is essential for profiling the taxa that would serve as consensus degraders of the pollutants. In this study, soil samples from three dumpsites (Cele, CS; Solous, SS; and Computer Village, CVS) were characterized for geochemical properties using GC-MS, MP-AES, and other analytical protocols, while the dynamics of bacterial communities were evaluated based on their 16S rRNA gene barcodes. A significant difference in the bacterial communities was observed among the dumpsites in relation to the extent of pollution caused by POPs and HMs. CVS, with the highest HM contamination, was rich in Actinobacteria (41.7%) and Acidobacteria (10.2%), in contrast to CS and SS. Proteobacteria (34.1%) and Firmicutes (20%) were the dominant phyla in CS (highest POP contamination), while Bacteroidetes (45.5%) and Proteobacteria (39.9%) were dominant in SS soil. Bacillus was the dominant genus in the most polluted dumpsite. Canonical correspondence analysis revealed that polycyclic aromatic hydrocarbons (PAHs) and HMs shaped the structure of the bacterial operational taxonomic units (OTUs) in the most polluted dumpsite. Out of a total of 706 OTUs, 628 OTUs exhibited a significant correlation (>50%) with benzo(b)fluoranthene, azobenzene, dibenzofurans, pyrene, dibenzo(a,l)pyrene, Cu, and Zn. In particular, Proteobacteria (Achromobacter sp. and Serratia sp.), Bacteroidetes (Zhouia sp.), and Firmicutes (Bacillus sp.) were suggested to be pivotal to the ecophysiology of dumpsite soils contaminated with POPs and HMs. The results generally underscored the importance of metagenomic and physicochemical analyses of polluted systems in enabling correlations for useful prediction of drivers of such ecosystems. This will further improve our understanding of the metabolic potential and adaptation of organisms in such systems.

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Insights into Bacterial Community Involved in Bioremediation of Aged Oil-Contaminated Soil in Arid Environment

Cited by 6 publications

References 87 publications

Molecular characterization of a polycyclic aromatic hydrocarbons (PAHs) degrader, Burkholderia contaminans strain P14, isolated from aged oil-contaminated soil in Kuwait

Molecular characterization of a polycyclic aromatic hydrocarbons (PAHs) degrader, Burkholderia contaminans strain P14, isolated from aged oil-contaminated soil in Kuwait

Metagenomics: an emerging tool for the chemistry of environmental remediation

Geochemistry and metagenomics analyses of bacterial community structure in selected waste dumpsites in Lagos Metropolis, Nigeria

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