Identification and analysis of polyaromatic hydrocarbons (PAHs)--biodegrading bacterial strains from refinery soil of India

Bacterial crude oil and polyaromatic hydrocarbon degraders from Kazakh oil fields as barley growth support

Bacterial strains of the genera Arthrobacter, Bacillus, Dietzia, Kocuria, and Micrococcus were isolated from oil-contaminated soils of the Balgimbaev, Dossor, and Zaburunye oil fields in Kazakhstan. They were selected from 1376 isolated strains based on their unique ability to use crude oil and polyaromatic hydrocarbons (PAHs) as sole source of carbon and energy in growth experiments. The isolated strains degraded a wide range of aliphatic and aromatic components from crude oil to generate a total of 170 acid metabolites. Eight metabolites were detected during the degradation of anthracene and of phenanthrene, two of which led to the description of a new degradation pathway. The selected bacterial strains Arthrobacter bussei/agilis SBUG 2290, Bacillus atrophaeus SBUG 2291, Bacillus subtilis SBUG 2285, Dietzia kunjamensis SBUG 2289, Kocuria rosea SBUG 2287, Kocuria polaris SBUG 2288, and Micrococcus luteus SBUG 2286 promoted the growth of barley shoots and roots in oil-contaminated soil, demonstrating the enormous potential of isolatable and cultivable soil bacteria in soil remediation. KEY POINTS: • Special powerful bacterial strains as potential crude oil and PAH degraders. • Growth on crude oil or PAHs as sole source of carbon and energy. • Bacterial support of barley growth as resource for soil remediation.

Exploring the potential of Diplosphaera mucosa VSPA for the treatment of petroleum effluent with simultaneous lipid production

The discovery of unexplored, robust microalgal strains will assist in treating highly polluted industrial effluent, including petroleum effluent. In the current analysis, a newly isolated microalgal strain, Diplosphaera mucosa VSPA, was used to treat petroleum effluent in a lab-scale raceway bioreactor. Its treatment efficiency was compared with a well-known species, Chlorella pyrenoidosa. The D. mucosa VSPA strain proliferated in petroleum effluent at a high growth rate, with final biomass, and lipid concentrations reaching 6.93 g/L and 2.72 g/L, respectively. Treatment efficiency was calculated based on the final removal efficiency of ammonium nitrogen, phosphate phosphorus, and chemical oxygen demand, which was more than 90%. Control experiments suggested that the maximum removal of pollutants from petroleum effluent was due to microalgae growth. Some growth models, including the Gompertz, Logistic, Stannard, Richard, and Schnute, were used to simulate the experimental data, verifying the results. Good fitting of all models was obtained, with the R2 value reaching more than 0.90. The development of a suitable model can help in decreasing the efforts required for the scale-up of the process.

The role of predicted chemotactic and hydrocarbon degrading taxa in natural source zone depletion at a legacy petroleum hydrocarbon site

Petroleum hydrocarbon contamination is a global problem which can cause long-term environmental damage and impacts water security. Natural source zone depletion (NSZD) is the natural degradation of such contaminants. Chemotaxis is an aspect of NSZD which is not fully understood, but one that grants microorganisms the ability to alter their motion in response to a chemical concentration gradient potentially enhancing petroleum NSZD mass removal rates. This study investigates the distribution of potentially chemotactic and hydrocarbon degrading microbes (CD) across the water table of a legacy petroleum hydrocarbon site near Perth, Western Australia in areas impacted by crude oil, diesel and jet fuel. Core samples were recovered and analysed for hydrocarbon contamination using gas chromatography. Predictive metagenomic profiling was undertaken to infer functionality using a combination of 16 S rRNA sequencing and PICRUSt2 analysis. Naphthalene contamination was found to significantly increase the occurrence of potential CD microbes, including members of the Comamonadaceae and Geobacteraceae families, which may enhance NSZD. Further work to explore and define this link is important for reliable estimation of biodegradation of petroleum hydrocarbon fuels. Furthermore, the outcomes suggest that the chemotactic parameter within existing NSZD models should be reviewed to accommodate CD accumulation in areas of naphthalene contamination, thereby providing a more accurate quantification of risk from petroleum impacts in subsurface environments, and the scale of risk mitigation due to NSZD.

Microbial diversity drives pyrene dissipation in soil

Soil microbial diversity is an essential driver of multiple ecosystem functions and services. However, the role and mechanisms of microbial diversity in the dissipation of persistent organic pollutants in soil are largely unexplored. Here, a gradient of soil microbial diversity was constructed artificially by a dilution-to-extinction approach to assess the role of soil microbial diversity in the dissipation of pyrene, a high molecular weight polycyclic aromatic hydrocarbon (PAH), in a 42-day microcosm experiment. The results showed that pyrene dissipation (98.1%) and the abundances of pyrene degradation genes (the pyrene dioxygenase gene nidA and the gram-positive PAH-ring hydroxylating dioxygenase gene PAH-RHDα GP) were highest in soils with high microbial diversity. Random-forest machine learning was combined with linear regression analysis to identify a range of keystone taxa (order level) associated with pyrene dissipation, including Sphingobacteriales, Vampirovibrionales, Blastocatellales, Myxococcales, Micrococcales and Rhodobacterales. The diversity of these keystone taxa was significantly and positively correlated with the abundance of pyrene degradation genes and the removal rate of pyrene. According to (partial) Mantel tests, keystone taxa diversity was the dominant factor determining pyrene dissipation compared with total microbial diversity. Moreover, co-occurrence network analysis revealed that diverse keystone taxa may drive pyrene dissipation via more positive interactions between keystone species and with other species in soil. Taken together, these findings provide new insights on the regulation of keystone taxa diversity to promote the dissipation of PAH in soil.

Microbial Degradation of Azo Dyes: Approaches and Prospects for a Hazard-Free Conversion by Microorganisms

Azo dyes have become a staple in various industries, as colors play an important role in consumer choices. However, these dyes pose various health and environmental risks. Although different wastewater treatments are available, the search for more eco-friendly options persists. Bioremediation utilizing microorganisms has been of great interest to researchers and industries, as the transition toward greener solutions has become more in demand through the years. This review tackles the health and environmental repercussions of azo dyes and its metabolites, available biological approaches to eliminate such dyes from the environment with a focus on the use of different microorganisms, enzymes that are involved in the degradation of azo dyes, and recent trends that could be applied for the treatment of azo dyes.

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.

Phenanthrene removal and response of bacterial community in the combined system of photocatalysis and PAH-degrading microbial consortium in laboratory system

This work aimed to study the removal of phenanthrene, change of bacterial community and microbial functions through combined photocatalysis and biodegradation under ultraviolet (UV) and visible light illumination. Results showed that phenanthrene removal was enhanced in combined system irradiated by UV and visible light. High-throughput sequencing of 16S rRNA gene manifested that alpha diversity (richness, evenness and diversity) got promoted and data of relative abundance reported that Planococcaceae as the dominant bacteriawas replaced by Pseudomonadaceae, with some other functional bacteria quickly acclimatizing. Difference analysis indicated that top fifteen genera were generally different significantly (p < 0.001) among two distinct samples, particularly for Pseudomonas on relative abundance. Functional features' regulation suggested that the bacterial community not only protected itself well but also participated in degrading phenanthrene. Selecting suitable degrading microbial consortium from natural environment and understanding deeply on performance of bacterial community contribute to assemble effective and directional combined system.

The impact of calcium peroxide on groundwater bacterial diversity during naphthalene removal by permeable reactive barrier (PRB)

Oxygen-releasing compounds (ORCs) have recently gained much attention in contaminated groundwater remediation. We investigated the impact of calcium peroxide nanoparticles on the groundwater indigenous bacteria in a bioremediation process by permeable reactive barrier (PRB). Three sand-packed columns were applied, including (1) control column (fresh groundwater), (2) natural remediation column (contaminated groundwater), and (3) biostimulation column (contaminated groundwater amended with CaO₂). Actinobacteria and Proteobacteria constituted the main phyla among the identified isolates. According to the results of next-generation sequencing, Proteobacteria was the dominant phylum (81% relative abundance) in the natural remediation condition. But, it was declined to 38.1% in the biostimulation column. Meanwhile, the abundance of Actinobacteria and Bacteroidetes were increased to 25.9% and 15.4%, respectively, by exposing the groundwater microbial structure to CaO₂ nanoparticles. Furthermore, orders Chlamydiales, Nitrospirales, and Oceanospirillales existing in the control column were detected in the presence of naphthalene. Shannon index was 4.32 for the control column samples, while it was reduced to 2.73 and 2.00 in the natural and biostimulation columns, respectively. Therefore, the present study provides a considerable insight into the impact of ORCs on the groundwater microbial community during the bioremediation process.

Housefly larvae (Musca domestica) significantly accelerates degradation of monensin by altering the structure and abundance of the associated bacterial community

Vermicomposting of livestock manure using housefly larvae is a promising biotechnology for waste reduction and control of antibiotic pollution. Monensin (MON), an ionophore polyether antibiotic (IPA), is widely used in broiler feed to control coccidiosis. However, MON residues in litter have become a major source of pollution in the environment. In this work, we studied the efficiency of housefly larvae (Musca domestica) on monensin attenuation during a 12-day laboratory scale vermicomposting experiment. We observed a 94.99% reduction in MON concentration after four days in treatment groups, while it took twelve days to remove more than 94.71% of MON in the control group. We found that the bacterial community composition of the substrate was reshaped by housefly larvae. From the treatment groups, three MON-degrading bacterial strains were isolated and identified as Acinetobacter sp., Stenotrophomonas sp. and Alcaligenes sp. based on 16 S rRNA gene sequence analysis. These three strains were among dominant the bacteria in treated substrates, showing between 52.80% and 89.25% degradation of MON in mineral salt medium within 28 days. Furthermore, two MON-degrading bacteria (Stenotrophomonas sp. and Alcaligenes sp.) were more abundant in treatment groups and larvae gut groups compared with those in control groups. The abundance enhancement of MON-degrading bacteria was related to the change in ambient temperature and pH in the substrates, which were affected by housefly larvae activities. Our results confirm that housefly larvae can significantly accelerate degradation of MON in chicken manure by increasing the abundance of MON-degrading bacteria.

Degradation of fluorene and phenanthrene in PAHs-contaminated soil using Pseudomonas and Bacillus strains isolated from oil spill sites

Biodegradation of 3-ring and 4-ring polycyclic aromatic hydrocarbons (PAHs) model (fluorene, phenanthrene, fluoranthene and pyrene) were investigated. Twenty-seven bacterial strains were isolated from contaminated-site by oil spills. PAHs-degrading bacteria were screened to select high tolerant species for ensuring an efficient bioremediation. Each of the isolated bacterial strains was grown under different PAHs concentrations (250, 500, 1000 and 1500 mg/L). Among the 27 strains, 8 resulted to be resistant to high concentration level of PAHs (1500 mg/L) and thereof can use PAHs as sole source of carbon and energy. The most tolerant strains were molecularly identified using mass spectrometer MALDI-TOF VITEK MS and 16S rDNA sequencing approaches. The identified bacterial strains Pseudomonas stutzeri (P. stutzeri), Bacillus simplex (B. simplex) and Bacillus pumilus (B. pumilus) were used for the bioremediation experiment of soils contaminated by PAHs. The studies were conducted under controlled conditions using soil spiked with a mixture of the target PAHs and the three microcosm strains. The results revealed that only fluorene and phenanthrene, which are low molecular weight PAHs, were degraded efficiently within 72 days of test organism incubation. These degradations were about 65-86% and 86-95% for fluorene and phenanthrene, respectively. At the same time and conversely to fluorene and phenanthrene, the high molecular weight PAHs, pyrene and fluoranthene were recalcitrant to these selected microbial strains. The biodegradation kinetics of both fluorene and phenanthrene were fit a first order rate with R² values ranging from 0.88 to 0.92. The half-lives of phenanthrene (2.4-2.7 days) and those of fluorene (3.5-4.6 days) were all less than 10 days, delineating therefore acclimatization with the strains.

Hydrocarbonoclastic Ascomycetes to enhance co-composting of total petroleum hydrocarbon (TPH) contaminated dredged sediments and lignocellulosic matrices

Four new Ascomycete fungi capable of degrading diesel oil were isolated from sediments of a river estuary mainly contaminated by shipyard fuels or diesel oil. The isolates were identified as species of Lambertella, Penicillium, Clonostachys, and Mucor. The fungal candidates degraded and adsorbed the diesel oil in suspension cultures. The Lambertella sp. isolate displayed the highest percentages of oxidation of diesel oil and was characterised by the capacity to utilise the latter as a sole carbon source. This isolate showed extracellular laccase and Mn-peroxidase activities in the presence of diesel oil. It was tested for capacity to accelerate the process of decontamination of total petroleum hydrocarbon contaminated sediments, co-composted with lignocellulosic residues and was able to promote the degradation of 47.6% of the TPH contamination (54,074 ± 321 mg TPH/Kg of sediment) after two months of incubation. The response of the bacterial community during the degradation process was analysed by 16S rRNA gene meta-barcoding.

Comparative metagenomics reveals different hydrocarbon degradative abilities from enriched oil-drilling waste

The oil drilling process generates large volumes of waste with inadequate treatments. Here, oil drilling waste (ODW) microbial communities demonstrate different hydrocarbon degradative abilities when exposed to distinct nutrient enrichments as revealed by comparative metagenomics. The ODW was enriched in Luria Broth (LBE) and Potato Dextrose (PDE) media to examine the structure and functional variations of microbial consortia. Two metagenomes were sequenced on Ion Torrent platform and analyzed using MG-RAST. The STAMP software was used to analyze statistically significant differences amongst different attributes of metagenomes. The microbial diversity presented in the different enrichments was distinct and heterogeneous. The metabolic pathways and enzymes were mainly related to the aerobic hydrocarbons degradation. Moreover, our results showed efficient biodegradation after 15 days of treatment for aliphatic hydrocarbons (C8-C33) and polycyclic aromatic hydrocarbons (PAHs), with a total of about 50.5% and 46.4% for LBE and 44.6% and 37.9% for PDE, respectively. The results obtained suggest the idea that the enzymatic apparatus have the potential to degrade petroleum compounds.

From oil spills to barley growth - oil-degrading soil bacteria and their promoting effects

Heavy contamination of soils by crude oil is omnipresent in areas of oil recovery and exploitation. Bioremediation by indigenous plants in cooperation with hydrocarbon degrading microorganisms is an economically and ecologically feasible means to reclaim contaminated soils. To study the effects of indigenous soil bacteria capable of utilizing oil hydrocarbons on biomass production of plants growing in oil-contaminated soils eight bacterial strains were isolated from contaminated soils in Kazakhstan and characterized for their abilities to degrade oil components. Four of them, identified as species of Gordonia and Rhodococcus turned out to be effective degraders. They produced a variety of organic acids from oil components, of which 59 were identified and 7 of them are hitherto unknown acidic oil metabolites. One of them, Rhodococcus erythropolis SBUG 2054, utilized more than 140 oil components. Inoculating barley seeds together with different combinations of these bacterial strains restored normal growth of the plants on contaminated soils, demonstrating the power of this approach for bioremediation. Furthermore, we suggest that the plant promoting effect of these bacteria is not only due to the elimination of toxic oil hydrocarbons but possibly also to the accumulation of a variety of organic acids which modulate the barley's rhizosphere environment.