Microbial communities in petroleum-contaminated seasonally frozen soil and their response to temperature changes

Diversity of hydrocarbon-degrading bacteria in mangroves rhizosphere as an indicator of oil-pollution bioremediation in mangrove forests

Mangrove ecosystems, characterized by high levels of productivity, are susceptible to anthropogenic activities, notably oil pollution arising from diverse origins including spills, transportation, and industrial effluents. Owing to their role in climate regulation and economic significance, there is a growing interest in developing mangrove conservation strategies. In the Arabian Gulf, mangroves stand as the sole naturally occurring green vegetation due to the region's hot and arid climate. However, they have faced persistent oil pollution for decades. This review focuses on global mangrove distribution, with a specific emphasis on Qatar's mangroves. It highlights the ongoing challenges faced by mangroves, particularly in relation to the oil industry, and the impact of oil pollution on these vital ecosystems. It outlines major oil spill incidents worldwide and the diverse hydrocarbon-degrading bacterial communities within polluted areas, elucidating their potential for bioremediation. The use of symbiotic interactions between mangrove plants and bacteria offers a more sustainable, cost-effective and environmentally friendly alternative. However, the success of these bioremediation strategies depends on a deep understanding of the dynamics of bacterial communities, environmental factors and specific nature of the pollutants.

Metagenomics-metabolomics analysis of microbial function and metabolism in petroleum-contaminated soil

Contamination of soil by petroleum is becoming increasingly serious in the world today. However, the research on gene functional characteristics, metabolites and distribution of microbial genomes in oil-contaminated soil is limited. Considering that, metagenomic and metabonomic were used to detect microbes and metabolites in oil-contaminated soil, and the changes of functional pathways were analyzed. We found that oil pollution significantly changed the composition of soil microorganisms and metabolites, and promoted the relative abundance of Pseudoxanthomonas, Pseudomonas, Mycobacterium, Immundisolibacter, etc. The degradation of toluene, xylene, polycyclic aromatic hydrocarbon and fluorobenzoate increased in Xenobiotics biodegradation and metabolism. Key monooxygenases and dioxygenase systems were regulated to promote ring opening and degradation of aromatic hydrocarbons. Metabolite contents of polycyclic aromatic hydrocarbons (PAHs) such as 9-fluoronone and gentisic acid increased significantly. The soil microbiome degraded petroleum pollutants into small molecular substances and promoted the bioremediation of petroleum-contaminated soil. Besides, we discovered the complete degradation pathway of petroleum-contaminated soil microorganisms to generate gentisic acid from the hydroxylation of naphthalene in PAHs by salicylic acid. This study offers important insights into bioremediation of oil-contaminated soil from the aspect of molecular regulation mechanism and provides a theoretical basis for the screening of new oil degrading bacteria.

Fingerprint characteristics of refined oils and their traceability in the groundwater environment

Chemical fingerprinting is essential for identifying the presence and responding to oil spills that frequently contaminate the groundwater environment of refineries. In this study, crude oil and oil products from the atmospheric and vacuum distillation units of a refinery were analyzed by gas chromatography-mass spectrometry (GC-MS) to evaluate their chemical variability before and after refinery. A series of experiments involving evaporation and soil column penetration were conducted to simulate refined oil spilling into groundwater and determine appropriate characteristic ratios (CRs) for principal component analysis (PCA) for oil source identification. The simulated study demonstrated that all products had bell-shaped n-alkane distributions, with dominant peaks that remained unchanged or shifted towards longer chain lengths compared to the source oil. Similarly, naphthalene and dibenzothiophene series remained the main PAH components like the source oil. Ten relatively stable CRs were selected for PCA to identify different oil products through the simulated experiments. The chosen CRs were then utilized to identify the sources for two groundwater oil spills recently occurred, one that occurred in an oil depot area, and another near a continuous catalytic reforming unit in a refinery. This study showed that the components with long-chain n-alkanes (n ≥ C₁₈), pristane, phytane, and phenanthrene and dibenzothiophene series PAHs played an important role in the identification of refined oil products spilling into the groundwater environment. The selected CRs provide an effective tool for rapid and accurate identification of oil spills, especially for newly occurring spills in the groundwater environment, which can aid in developing appropriate response strategies.

Impacts of Arctic diesel contamination on microbial community composition and degradative gene abundance during hydrocarbon biodegradation with and without nutrients: A case study of seven sub-Arctic soils

Although a number of studies have assessed hydrocarbon degradation or microbial responses in petroleum contaminated soils, few have examined both and/or assessed impacts in multiple soils simultaneously. In this study petroleum hydrocarbon biodegradation and microbial activity was monitored in seven sub-Arctic soils at similar levels (∼3500-4000 mg/kg) of Arctic diesel (DSL), amended with moisture and nutrients (70 mg-N/kg, 78 mg-P/kg), and incubated at site-representative summer temperatures (∼7 °C) under water unsaturated conditions. Total petroleum hydrocarbon (TPH) biodegradation extents (42.7-85.4 %) at 50 days were slightly higher in nutrient amended (DSL + N,P) than unamended (DSL) systems in all but one soil. Semi-volatile (C₁₀-C₁₆) hydrocarbons were degraded to a greater extent (40-80 %) than non-volatile (C₁₆-C₂₄) hydrocarbons (20-40 %). However, more significant shifts in microbial diversity and relative abundance of genera belonging to Actinobacteria and Proteobacteria phyla were observed in DSL + N,P than in DSL systems in all soils. Moreover, higher abundance of the alkane degrading gene alkB were observed in DSL + N,P systems than in DSL systems for all soils. The more significant microbial community response in the DSL + N,P systems indicate that addition of nutrients may have influenced the microbial community involved in degradation of carbon sources other than the diesel compounds, such as the soil organic matter or degradation intermediates of diesel compounds. Nocardioides, Arthrobacter, Marmoricola, Pseudomonas, Polaromonas, and Massilia genera were present in high relative abundance in the DSL systems suggesting those genera contained hydrocarbon degraders. Overall, the results suggest that the extents of microbial community shifts or alkB copy number increases may not be closely correlated to the increase in hydrocarbon biodegradation and thus bioremediation performance between various treatments or across different soils.

Contrasting responses of bacterial community to 4,4'-dibromodiphenyl ether (BDE-15) contamination in soil microcosms at different temperatures

Polybrominated diphenyl ethers (PBDEs) are biodegradable organic pollutants and pose potential risks to microorganisms exposed to the contamination, which are also affected by a variety of factors, such as temperature, in real environmental settings. A better understanding of the microbial community responses to PBDEs at different temperatures has practical significance for assessing ecological risks or possible degraders of these widely used flame retardants. In this study, soil microcosms spiked with or without 100 mg kg^-1 4,4'-dibromodiphenyl ether (BDE-15) were established and incubated at four different temperatures (4 °C, 20 °C, 37 °C, and varying ambient temperature) for up to 180 days. Concentration and carbon isotope analyses were used to verify the transformation of BDE-15. Bacterial communities were monitored during the incubation to evaluate the community succession under the PBDE stress. The results showed the majority of added BDE-15 remained after the incubation period, with limited degradation occurred at all four temperatures. Temperature significantly shaped the richness, diversity, composition and co-occurrence network of soil bacterial community, while the impacts of PBDE on soil bacteria were temperature dependent. When incubated at 4 °C, BDE-15 substantially reduced the network complexity and changed the ratio of negative to positive interactions between taxa (nodes), highlighting the PBDE-associated risks at low temperature. At higher temperatures, BDE-15 had negligible influence on the community characteristics and network. Random forest model identified distinct taxa that might be related to PBDE degradation at different incubation temperatures. These findings demonstrate contrasting bacterial community effects of PBDE at different temperatures, thus attention should be paid to the ecological impacts of soil pollution under real environmental conditions.

The role of microorganisms in petroleum degradation: Current development and prospects

Petroleum hydrocarbon compounds are persistent organic pollutants, which can cause permanent damage to ecosystems due to their biomagnification. Bioremediation of oil is currently the main solution for the remediation of petroleum hydrocarbon pollutants in ecosystems. Despite several lab studies on oil microbial biodegradation efficiency, still there are various challenges for microorganisms to perform efficiently in outside environments. Herewith, investigating efficient biodegradation technologies through discovering new microorganisms, biodegradation pathways modification, and new bioremediations technologies are in great demand. The degradation of petroleum pollutants by microorganisms and the remediation of contaminated soils are achieved through their key enzymes and metabolic pathways. Although, several challenges hinder the effective biodegradation processes such as the toxic environment, long chains and versatility of petroleum hydrocarbons and the existence of the full metabolism pathways in a single microorganism. There are several developed oil biodegradation strategies by microorganisms such as synthetic biology, biofilm, recombinant technology and microbial consortia. Herewith, the application of multi-omics technology to discover oil-contaminated environments microbial communities, synthetic biology, microbial consortia, and other technologies would help improve the efficiency of microbial remediation.

Comparing the indigenous microorganism system in typical petroleum-contaminated groundwater

The environmental conditions at a contaminated site will impact on the indigenous microbial communities, with implications for the removal of pollutants. An analysis of the characteristics of microbial communities in petroleum-contaminated groundwater can give insights into the relationships between microbial community and environmental factors, and provide guidance about how microbes can be used to remediate and regulate petroleum-contaminated groundwater. This study focuses on two petroleum-contaminated sites in northeast China, the physico-chemical-biological changes in petroleum-contaminated groundwater were analyzed, the response relationship between hydro-chemical indicators and microbial communities was characterized, and the bioindicator that can reflect the petroleum contamination status were established for environmental monitoring and management. The results showed that Proteobacteria was the dominant bacteria in petroleum-contaminated groundwater, with a relative abundance of 42.45%-91.19%. pH, TDS, DO, NO3-, NO2-, SO42-, NH4+, Al, and Mn have significant effects on microbial community. The effect of petroleum pollutants on microbial communities is not only related to the concentration and composition of the pollutants themselves, but also could indirectly affect microbial communities by changing the content of inorganic electron acceptor components such as iron, manganese, sulfate and nitrate in groundwater, and this indirect effect is significantly greater than the direct impact of pollutants on microbial communities. In petroleum-contaminated groundwater, the dominant genera (Polaromonas, Caulobacter) and microbial metabolic functions (methanol oxidation, methylotrophy, ureolysis, and reductive biosynthesis) of the indigenous microbial community can be used as bioindicators to indicate petroleum contamination status. The higher abundance of these bioindicators in petroleum-contaminated groundwater, the more serious petroleum pollution in groundwater.

Microbial community succession during crude oil-degrading bacterial enrichment cultivation and construction of a degrading consortium

Microbial community succession during the enrichment of crude-oil-degrading bacteria was analyzed using Illumina high-throughput sequencing to guide bacterial isolation and construction of a bacterial consortium. Community change occurred in 6 days; the most abundant phylum changed from Proteobacteria to Actinobacteria; the most abundant genera were Dietzia and unspecified_Idiomarinaceae. Two crude oil-degrading strains, Rhodococcus sp. OS62-1 and Dietzia sp. OS33, and one weak-crude-oil-degrading strain, Pseudomonas sp. P35, were isolated. A consortium comprising Rhodococcus sp. OS62-1 and Pseudomonas sp. P35 showed the highest crude-oil-degrading efficiency, reaching 85.72 ± 3.21% within 7 days, over a wide pH range (5–11) and salinity (0–80 g·L−1). Consumption of saturated hydrocarbons, aromatic hydrocarbons, and resins was greater by the consortium than by a single strain, as was degradation of short-chain-alkanes (C13–C17) according to gas-chromatography. The bacterial consortium provides technical support for bioremediation of crude oil pollution.

A unique microbiome in a highly polluted and alkalic lake in a seasonally frozen area

Highly polluted waters profoundly promoted microbial activities and vice versa. Although microbial community structures and bioprocesses in polluted environments have been fully investigated, they are rarely uncovered in abandoned and highly polluted aquatic environment, especially in a seasonally frozen area. East Lake had been polluted by surrounding paper mills and dairy plants from the 1960s to the early 2000s. Under low biodegradability (BOD₅/COD ratio<0.2) and alkalic (pH > 9) conditions, a unique microbiome was discovered in East lake. Proteobacteria was the largest taxonomic group in the microbial community, covering almost half of the top-100 genera. Among them, seven genera are sulfate-reducing bacteria, including Desulfuromusa, Desulfuromonas, Desulfobulbus, Desulfocapsa, Desulfurivibrio, Desulfatiglans, and Desulfomicrobium. Functional analysis revealed abundant predicted functional genes for the respiration of sulfur compounds and sulfate respiration. Great vertical variations were found to both microbial community structures and predicted functions. This work provides unique evidence for future microbiome studies of nutrient-rich, alkalic, and seasonally frozen water habitats.

Insights into the kinetic processes of solute migration by unidirectional freezing in porous media with micromodel visualization at the pore-scale

Field investigations have proved that frozen soil does not act as a completely impermeable barrier for contaminants in cold regions. However, the subsurface behaviors of solutes in freezing and frozen porous media are still unclear. To unveil their nature, the pore-scale behavior of potassium permanganate in saturated porous media subjected to the unidirectional freezing was investigated using micromodel visualizations. An optical microscope was applied to obtain the pore-scale kinetics of solute redistribution in a two-dimensional micromodel using a calibration curve between the color intensity and concentration. We found that (1) the solute migration was not only limited to the ice-water interface but also occurred in the freezing area; (2) the redistribution of solutes had a significant hysteresis effect relative to the freezing front movement during the freezing of the porous media. By combining these results with the theory of sea ice, we suggested that the formation and re-motion of solute-rich inclusions in the mushy layer appear to be vital processes responsible for these phenomena. It was believed that the major mechanism for the re-motion of liquid inclusions was brine diffusion and expulsion in this experiment. The results of this study provide a better understanding of the physics of contaminant migration and their complex kinetics at the pore scale, which has important implications for the assessment and remediation of contaminated soils in seasonal frozen soils and permafrost.

Anthropogenic activities change the relationship between microbial community taxonomic composition and functional attributes

Functional redundancy is considered common in microbial systems, but recent studies have challenged this idea. The mechanism for this contradictory result is not clear. However, in this study, we hypothesize that strong environmental filtering which links to the anthropogenic activities is able to weaken microbial functional redundancy. We used metagenome and 16S rRNA gene high-throughput sequencing to investigate planktonic microbial communities in a subtropical river. We found that the weak anthropogenic activities might result in a low selection pressure in the river upstream area. Therefore, the microbial community functional attributes were stable although the community composition changed with the water temperature and NO₃ -N in upstream area (this indicates functional redundancy). However, the strong anthropogenic activities in river downstream area selected pollutant-degraded functions (e.g. nitrogen metabolism, toluene, xylenes and ethylbenzene degradation) and potentially pollutant-degraded (tolerant) microbes, and therefore caused the microbial community composition synchronously changed with the variation of community functional attributes. Our results reveal that strong environmental filtering which associates with the anthropogenic activities not only has effects on microbial community composition and community functional attributes but also on their relationships. These results provide a new insight to refine the functional redundancy idea.

Petroleum contamination significantly changes soil microbial communities in three oilfield locations in Delta State, Nigeria

Soil microbial community structure is altered by petroleum contamination in response to compound toxicity and degradation. Understanding the relation between petroleum contamination and soil microbial community structure is crucial to determine the amenability of contaminated soils to bacterial- and fungal-aided remediation. To understand how petroleum contamination and soil physicochemical properties jointly shaped the microbial structure of soils from different oilfields, high-throughput sequencing of 16S and ITS amplicons were used to evaluate the shifts of microbial communities in the petroleum-contaminated soils in Ughelli East (UE), Utorogu (UT), and Ughelli West (UW) oilfields located in Delta State, Nigeria. The results showed 1515 bacteria and 919 fungal average OTU number, and community richness and diversity, trending as AL > UT > UW > UE and AL > UW > UT > UE for bacteria, and AL > UW > UT > UE and UW > UT > AL > UE for fungi, respectively. The bacterial taxa KCM-B-112, unclassified Saccharibacteria, unclassified Rhizobiales, Desulfurellaceae, and Acidobacteriaceae and fungal Trichocomaceae, unclassified Ascomycota, unclassified Sporidiobolales, and unclassified Fungi were found to be the dominant families in petroleum-contaminated soils. Redundancy analysis (RDA) and Spearman's correlation analysis revealed that total carbon (TC), electric conductivity (EC), pH, and moisture content (MO) were the major drivers of bacterial and fungal communities, respectively. Gas chromatography-mass spectrophotometer (GC-MS) analysis exhibited that the differences in C₇-C₁₀, C₁₁-C₁₆, and C₁₂-C₂₉ compounds in the crude oil composition and soil MO content jointly constituted the microbial community variance among the contaminated soils. This study revealed the bacterial and fungal communities responsible for the biodegradation of petroleum contamination from these oilfields, which could serve as biomarkers to monitor oil spill site restoration within these areas. Further studies on these contaminated sites could offer useful insights into other contributing factors such as heavy metals.