Distribution of PAH-ring hydroxylating dioxygenase genes in bacteria isolated from two illegal oil refining sites in the Niger Delta, Nigeria

Catalytic resilience of multicomponent aromatic ring-hydroxylating dioxygenases in Pseudomonas for degradation of polycyclic aromatic hydrocarbons

Hydrophobic organic compounds, either natural or introduced through anthropogenic activities, pose a serious threat to all spheres of life, including humankind. These hydrophobic compounds are recalcitrant and difficult to degrade by the microbial system; however, microbes have also evolved their metabolic and degradative potential. Pseudomonas species have been reported to have a multipotential role in the biodegradation of aromatic hydrocarbons through aromatic ring-hydroxylating dioxygenases (ARHDs). The structural complexity of different hydrophobic substrates and their chemically inert nature demands the explicit role of evolutionary conserved multicomponent enzyme ARHDs. These enzymes catalyze ring activation and subsequent oxidation by adding two molecular oxygen atoms onto the vicinal carbon of the aromatic nucleus. This critical metabolic step in the aerobic mode of degradation of polycyclic aromatic hydrocarbons (PAHs) catalyzed by ARHDs can also be explored through protein molecular docking studies. Protein data analysis enables an understanding of molecular processes and monitoring complex biodegradation reactions. This review summarizes the molecular characterization of five ARHDs from Pseudomonas species already reported for PAH degradation. Homology modeling for the amino acid sequences encoding the catalytic α-subunit of ARHDs and their docking analyses with PAHs suggested that the enzyme active sites show flexibility around the catalytic pocket for binding of low molecular weight (LMW) and high molecular weight (HMW) PAH substrates (naphthalene, phenanthrene, pyrene, benzo[α]pyrene). The alpha subunit harbours variable catalytic pockets and broader channels, allowing relaxed enzyme specificity toward PAHs. ARHD's ability to accommodate different LMW and HMW PAHs demonstrates its 'plasticity', meeting the catabolic demand of the PAH degraders.

Effect of crude oil exploration and exploitation activities on soil, water and air in a Nigerian community

The continuous degradation of environmental ecosystems (land, water and soil) resulting from crude oil exploration and exploitation activities continues to gain global attention. This study investigates the effects of crude oil exploration and exploitation activities on soil, water and air in the study area. Soil samples were collected in three replicates at depths of 0-15 and 15-30 cm at sampling distances of 20, 100 and 200 m a from core oil exploitation operation area and a control point. Water samples were also taken from within the study area and analyzed using standard procedures. Major pollutants concentrations of particulate matter (PM_2.5 and PM₁₀) of the air were also measured using Air Quality Index (AQI). The results reveal that the soil, water and air parameters measured mostly at 20 m from the core oil operation area compromise the allowable standards provided for healthy living. In the same manner, some results at 100 and 200 m were slightly higher than the recommended values in some cases of heavy metals and bacteria activities in the soil. The AQI at 20 m was far above the permissible limit provided by the Environmental Protection Agency while others are gradually drawing towards the limit given for each pollutant. To safeguard the health of the residents of the host community and oil field workers, there is a need for proper and frequent environmental monitoring and assessment by authorized regulatory bodies in Nigeria. This will prevent any future exposure which may endanger the lives of the dwellers.

Effects of Salinity on the Biodegradation of Polycyclic Aromatic Hydrocarbons in Oilfield Soils Emphasizing Degradation Genes and Soil Enzymes

The biodegradation of organic pollutants is the main pathway for the natural dissipation and anthropogenic remediation of polycyclic aromatic hydrocarbons (PAHs) in the environment. However, in the saline soils, the PAH biodegradation could be influenced by soil salts through altering the structures of microbial communities and physiological metabolism of degradation bacteria. In the worldwide, soils from oilfields are commonly threated by both soil salinity and PAH contamination, while the influence mechanism of soil salinity on PAH biodegradation were still unclear, especially the shifts of degradation genes and soil enzyme activities. In order to explain the responses of soils and bacterial communities, analysis was conducted including soil properties, structures of bacterial community, PAH degradation genes and soil enzyme activities during a biodegradation process of PAHs in oilfield soils. The results showed that, though low soil salinity (1% NaCl, w/w) could slightly increase PAH degradation rate, the biodegradation in high salt condition (3% NaCl, w/w) were restrained significantly. The higher the soil salinity, the lower the bacterial community diversity, copy number of degradation gene and soil enzyme activity, which could be the reason for reductions of degradation rates in saline soils. Analysis of bacterial community structure showed that, the additions of NaCl increase the abundance of salt-tolerant and halophilic genera, especially in high salt treatments where the halophilic genera dominant, such as Acinetobacter and Halomonas. Picrust2 and redundancy analysis (RDA) both revealed suppression of PAH degradation genes by soil salts, which meant the decrease of degradation microbes and should be the primary cause of reduction of PAH removal. The soil enzyme activities could be indicators for microorganisms when they are facing adverse environmental conditions.

The environmental fate of phenanthrene in paddy field system and microbial responses in rhizosphere interface: Effect of water-saving patterns

The effects of water-saving patterns (Semi-dry water-saving, B; Shallow-wet control irrigation, Q; Traditional flooding irrigation, C; and Moistening irrigation, S) on the environmental fate of phenanthrene (Phe) and microbial responses in rhizosphere were investigated in paddy field system. Results showed the rice grain in Q treatment was more high production and safety with less Phe residue (up to 18%-49%) than other treatments, and the residual Phe in soil declined in the order: C (14.17%) > S (13.36%) > B (5.86%)>Q (2.70%), which proves the existence of optimal water conditions for PAHs degradation and rhizosphere effect during rice cultivation. Laccase (LAC) and dioxygenase (C23O) played important roles in Phe degradation, which were significantly positively correlated with Phe dissipation rate in soil (p < 0.01). Moreover, their activities in Q treatment, rhizosphere and subsoil were higher than those in C treatment, non-rhizoshere and upper layer soil. The introduction of Phe and rice into paddy field system decreased the microorganism diversity, and promoted the activities of enzymes and some PAHs degrading bacteria, such as Delftia, Serratia, Enterobacter, Pseudomonas, norank_f_Rhodospirillaceae, norank_f_Nitrosomonadaceae and so on. According to the cluster analysis, redundancy analysis and correlation analysis between bacterial community composition and environmental factors, water-saving patterns markedly impacted the relative abundance and bacterial community structure by the regulating and controlling on environmental conditions of paddy field. The dioxygenase activity, laccase activity, oxidation-reduction potential and conductivity were the main affecting factors on Phe dissipation during growth stage of rice.

Whole genome characterization and phenanthrene catabolic pathway of a biofilm forming marine bacterium Pseudomonas aeruginosa PFL-P1

Pseudomonas aeruginosa is a small rod shaped Gram-negative bacterium of Gammaproteobacteria class known for its metabolic versatility. P. aeruginosa PFL-P1 was isolated from Polycyclic Aromatic Hydrocarbons (PAHs) contaminated site of Paradip Port, Odisha Coast, India. The strain showed excellent biofilm formation and could retain its ability to form biofilm grown with different PAHs in monoculture as well as co-cultures. To explore mechanistic insights of PAHs metabolism, the whole genome of the strain was sequenced. Next generation sequencing unfolded a genome size of 6,333,060 bp encoding 5857 CDSs. Gene ontology distribution assigned to a total of 2862 genes, wherein 2235 genes were allocated to biological process, 1549 genes to cellular component and 2339 genes to molecular function. A total of 318 horizontally transferred genes were identified when the genome was compared with the reference genomes of P. aeruginosa PAO1 and P. aeruginosa DSM 50071. Further comparison of P. aeruginosa PFL-P1 genome with P. putida containing TOL plasmids revealed similarities in the meta cleavage pathway employed for degradation of aromatic compounds like xylene and toluene. Gene annotation and pathway analysis unveiled 145 genes involved in xenobiotic biodegradation and metabolism. The biofilm cultures of P. aeruginosa PFL-P1 could degrade ~74% phenanthrene within 120 h while degradation increased up to ~76% in co-culture condition. GC-MS analysis indicated presence of diverse metabolites indicating the involvement of multiple pathways for one of the PAHs (phenanthrene) degradation. The strain also possesses the genetic machinery to utilize diverse toxic aromatic compounds such as naphthalene, benzoate, aminobenzoate, fluorobenzoate, toluene, xylene, styrene, atrazine, caprolactam etc. Common catabolic gene clusters such as benABCD, xylXYZ and catAB were observed within the genome of P. aeruginosa PFL-P1 which play key roles in the degradation of various toxic aromatic compounds.

Enhanced biodegradation of crude oil in soil by a developed bacterial consortium and indigenous plant growth promoting bacteria

AIMS

This study aimed to develop an efficient, cost-effective and eco-friendly bacterial consortium to degrade petroleum sludge.

METHODS AND RESULTS

Four bacterial strains belonging to genera Acinetobacter and Pseudomonas were selected to constitute three different consortia based on their initial concentration. The highest degradation rate (78%) of 1% (v/v) crude oil after 4 weeks of incubation was recorded when the concentration of biosurfactant (BS) producing isolate was high. Genes, such as alkB, almA, cyp153, pah-rhdGN, nah, phnAC and cat23 were detected using the polymerase chain reaction method and their induction levels were optimal at pH 7·0. A crude oil sludge was artificially constituted, and its bacterial composition was investigated using 16S rRNA gene amplicon sequencing. The results showed that the soil bacterial community was dominated by plant growth-promoting bacteria (PGPB) after crude oil treatment.

CONCLUSIONS

Our findings indicate the decontamination of the crude oil contaminated soil was more effective in the presence of both the constituted consortium and PGPB compared to the presence of PGPB alone.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study showed that the PGPB (Taibaiella) present in petroleum uncontaminated soil can promote the soil decontamination. The addition of both efficient hydrocarbon-degrading and BS producing bacteria is also necessary to improve the decontamination.

Sustained impact of the activities of local crude oil refiners on their host communities in Nigeria

The local refining of crude oil has become a lucrative but disturbing business in the Niger Delta region of Nigeria. Deep inside the forest of the Niger Delta camps are built and used for the local refining of crude oil. The economic benefits this brings to the refiners are clear, however the host communities are severely hit by the activities of the 'local crude oil refiners'. Farmlands have been destroyed and fishing settlements evacuated as a result of pollution of the rivers and estuaries, with loss of lives and properties. This research investigates the impact of the activities of the local refiners on their host communities' farmlands, rivers and estuaries. A quantitative research method was adopted in this study through the administration of questionnaires to local stakeholders (chiefs, the youth, farmers, traders, fishermen/fisherwomen and residents of affected communities). Quantitative data was collected from three communities in the Niger Delta with local refineries and the data was analysed using descriptive and inferential (Chi Square and Correlation) methods. The study demonstrates the high impact of the activities of the refiners on farmlands and fishing areas of the host communities and makes recommendations to all stakeholders in the upstream and downstream sectors of the petroleum industry. In addition, recommendations are made to the Nigerian government, on ways to address the impact of local refining on host communities.

High Throughput Sediment DNA Sequencing Reveals Azo Dye Degrading Bacteria Inhabit Nearshore Sediments

Estuaries and coastal environments are often regarded as a critical resource for the bioremediation of organic pollutants such as azo dyes due to their high abundance and diversity of extremophiles. Bioremediation through the activities of azoreductase, laccase, and other associated enzymes plays a critical role in the removal of azo dyes in built and natural environments. However, little is known about the biodegradation genes and azo dye degradation genes residing in sediments from coastal and estuarine environments. In this study, high-throughput sequencing (16S rRNA) of sediment DNA was used to explore the distribution of azo-dye degrading bacteria and their functional genes in estuaries and coastal environments. Unlike laccase genes, azoreductase (azoR), and naphthalene degrading genes were ubiquitous in the coastal and estuarine environments. The relative abundances of most functional genes were higher in the summer compared to winter at locations proximal to the mouths of the Hanjiang River and its distributaries. These results suggested inland river discharges influenced the occurrence and abundance of azo dye degrading genes in the nearshore environments. Furthermore, the azoR genes had a significant negative relationship with total organic carbon, Hg, and Cr (p < 0.05). This study provides critical insights into the biodegradation potential of indigenous microbial communities in nearshore environments and the influence of environmental factors on microbial structure, composition, and function which is essential for the development of technologies for bioremediation in azo dye contaminated sites.