Changes of sensitive microbial community in oil polluted soil in the coastal area in Shandong, China for ecorestoration

Exploring the diversity and functional profile of microbial communities of Brazilian soils with high salinity and oil contamination

Environmental pollution associated with the petroleum industry is a major problem worldwide. Microbial degradation is extremely important whether in the extractive process or in bioremediation of contaminants. Assessing the local microbiota and its potential for degradation is crucial for implementing effective bioremediation strategies. Herein, contaminated soil samples of onshore oil fields from a semiarid region in the Northeast of Brazil were investigated using metagenomics and metataxonomics. These soils exhibited hydrocarbon contamination and high salinity indices, while a control sample was collected from an uncontaminated area. The shotgun analysis revealed the predominance of Actinomycetota and Pseudomonadota, while 16S rRNA gene amplicon analysis of the samples showed Actinomycetota, Bacillota, and Pseudomonadota as the most abundant. The Archaea domain phylotypes were assigned to Thermoproteota and Methanobacteriota. Functional analysis and metabolic profile of the soil microbiomes exhibited a broader metabolic repertoire in the uncontaminated soil, while degradation pathways and surfactant biosynthesis presented higher values in the contaminated soils, where degradation pathways of xenobiotic and aromatic compounds were also present. Biosurfactant synthetic pathways were abundant, with predominance of lipopeptides. The present work uncovers several microbial drivers of oil degradation and mechanisms of adaptation to high salinity, which are pivotal traits for sustainable soil recovery strategies.

Characterization and identification of long-chain hydrocarbon-degrading bacterial communities in long-term chronically polluted soil in Ogoniland: an integrated approach using culture-dependent and independent methods

Escalating oil consumption has resulted in an increase in accidental spills of petroleum hydrocarbons, causing severe environmental degradation, notably in vulnerable regions like the Niger Delta. Complex mixture of these hydrocarbons particularly long-chain alkanes presents unique challenges in restoration of polluted environment due to their chemical properties. This study aimed to investigate the long-chain hydrocarbon-degrading bacterial communities within long-term chronically polluted soil in Ogoniland, by utilizing both traditional cultivation methods and modern culture-independent techniques. Results revealed that surface-polluted soil (SPS) and subsurface soil (SPSS) exhibit significantly higher total organic carbon (TOC) ranging from 5.64 to 5.06% and total petroleum hydrocarbons (TPH) levels ranging from 36,775 ppm to 14,087 ppm, compared to unpolluted soil (UPS) with 1.97% TOC and 479 ppm TPH, respectively. Analysis of carbon chain lengths reveals the prevalence of longer-chain alkanes (C20-28) in the surface soil. Culture-dependent methods, utilizing crude oil enrichment (COE) and paraffin wax enrichment (PWE), yield 47 bacterial isolates subjected to a long-chain alkane degradation assay. Twelve bacterial strains demonstrate significant degradation abilities across all enriched media. Three bacterial members, namely Pseudomonas sp. (almA), Marinomonas sp. (almA), and Alteromonas (ladA), exhibit genes responsible for long-chain alkane degradation, demonstrating efficiency between 50 and 80%. Culture-independent analysis reveals that surface SPS samples exhibit greater species richness and diversity compared to subsurface SPSS samples. Proteobacteria dominates as the phylum in both soil sample types, ranging from 22.23 to 82.61%, with Firmicutes (0.2-2.22%), Actinobacteria (0.4-3.02%), and Acidobacteria (0.1-3.53%) also prevalent. Bacterial profiles at genus level revealed that distinct variations among bacterial populations between SPS and SPSS samples comprising number of hydrocarbon degraders and the functional predictions also highlight the presence of potential catabolic genes (nahAa, adh2, and cpnA) in the polluted soil. However, culture-dependent analysis only captured a few of the dominant members found in culture-independent analysis, implying that more specialized media or environments are needed to isolate more bacterial members. The findings from this study contribute valuable information to ecological and biotechnological aspects, aiding in the development of more effective bioremediation applications for restoring oil-contaminated environments.

Biogeochemical modelling to assess the effect of bioclogging on multiple electron acceptor-mediated petroleum hydrocarbon bioremediation in vadose zone

Bioremediation is an economically viable and sustainable clean-up strategy. Hydrodynamic, as well as transport characteristics of the porous medium, can evolve over the period as a result of biological clean-up activities. The present study proposes a 2-D numerical framework to simulate the effect of bioclogging on multiple electron acceptor-mediated petroleum hydrocarbon bioremediation in the vadose zone. For modelling, a spill of BTEX (benzene, toluene, ethylbenzene and xylene) is assumed near source zone. The developed model results are validated using three previously published datasets on flow, transport and biodegradation in the vadose zone. Simulations are performed for three types of soil, including clay, sand and loam. The analysis shows that sand has a maximum infiltration rate and clay has a minimum. Hydraulic conductivity and saturation profile peaks reach their minimal value at a shallower depth (around four times) when bioclogging is present compared to when it is absent. The migration depth and concentration of BTEX are observed to be restricted to a shallower depth in aquifers with the presence of microbial clogging. The outcome shows that electron acceptor consumption is more (around sevenfold for oxygen, fourfold for nitrate and threefold for sulphate) in the presence of bioclogging at the shallower zone. Zeroth order spatial moment and sensitivity analyses show that biological clogging, number of electron acceptors and inhibition constant substantially affect BTEX bioremediation in the vadose zone.

Microbial remediation of oil-contaminated shorelines: a review

Frequent marine oil spills have led to increasingly serious oil pollution along shorelines. Microbial remediation has become a research hotspot of intertidal oil pollution remediation because of its high efficiency, low cost, environmental friendliness, and simple operation. Many microorganisms are able to convert oil pollutants into non-toxic substances through their growth and metabolism. Microorganisms use enzymes' catalytic activities to degrade oil pollutants. However, microbial remediation efficiency is affected by the properties of the oil pollutants, microbial community, and environmental conditions. Feasible field microbial remediation technologies for oil spill pollution in the shorelines mainly include the addition of high-efficiency oil degrading bacteria (immobilized bacteria), nutrients, biosurfactants, and enzymes. Limitations to the field application of microbial remediation technology mainly include slow start-up, rapid failure, long remediation time, and uncontrolled environmental impact. Improving the environmental adaptability of microbial remediation technology and developing sustainable microbial remediation technology will be the focus of future research. The feasibility of microbial remediation techniques should also be evaluated comprehensively.

Characterization of the biosurfactant production and enzymatic potential of bacteria isolated from an oil-contaminated saline soil

Biosurfactants are amphiphilic compounds with extensive applications in oily contaminated environments to remove hydrocarbons. Moreover, enzymes such as laccase and manganese peroxidase are responsible for the oxidation of a variety of phenolic compounds and aromatic amines. Therefore, in the present study, bacteria with the potential to produce biosurfactants and enzymes (namely, laccase, manganese peroxidase, and endoglucanase carboxymethyl cellulose (CMCase)) were isolated from petroleum oil-contaminated soil. From 15 isolated bacteria, three isolates were selected as the best producers of biosurfactants according to the related tests, such as tests for surface tension reduction. These three bacteria indicated tolerance to a salinity test and were classified as resistant and very resistant. The isolates 3, 12, 13, and 14 showed positive results for the degradation of guaiacol, phenol red, and carboxymethylcellulose, as well as the decoloration of methylene blue by the creation of a clear halo around the bacterial colony. Upon the quantitation of the laccase and manganese peroxidase activities, 22.58 U/L and 21.81 U/L, respectively, were measured by isolate 13. Furthermore, CMCase activity was recorded with 0.057436 U/ml belonging to isolate 14. Bacterial strains with appreciable laccase, peroxidase, CMCase activity, and biosurfactant production potentials were identified through 16S rDNA sequence analysis as Bacillus sp. (isolate 3), Bacillus toyonensis (isolate 12), Bacillus cereus (isolate 13), and Bacillus tropicus (isolate 14), and their nucleotide sequences were deposited in the GenBank. The potentials for the industrial applicability of the biosurfactants and enzymes abound, and production needs to be optimized by the selected bacterial strains.

Seasonal Dynamics of Bacterial Community Structure in Diesel Oil-Contaminated Soil Cultivated with Tall Fescue (Festuca arundinacea)

The objective of this study was to explore the seasonal characteristics of rhizoremediation and the bacterial community structure over the course of a year in soil contaminated with diesel oil. The soil was contaminated with diesel oil at a total petroleum hydrocarbon (TPH) concentration of 30,000 mg-TPH·kg-soil⁻¹. Tall fescue seedlings were planted in the contaminated soil and rhizoremediation performance was monitored for 317 days. The TPH concentration gradually declined, reaching 75.6% after day 61. However, the TPH removability decreased by up to 30% after re-contamination in the fall and winter. The bacterial community structure exhibited distinct seasonal dynamics. Genus Pseudomonas significantly increased up to 55.7% in the winter, while the genera Immundisolibacter and Lysobacter, well-known petroleum hydrocarbon (PH)-degrading bacteria, were found to be positively linked to the TPH removal rate. Consequently, knowledge of this seasonal variation in rhizoremediation performance and the bacterial community structure is useful for the improvement of rhizoremediation in PH-contaminated environments.

Strategic implementation of integrated bioaugmentation and biostimulation for efficient mitigation of petroleum hydrocarbon pollutants from terrestrial and aquatic environment

Release of petroleum hydrocarbon pollutants poses a serious problem to the terrestrial as well as marine ecosystem. This study investigated and compared the potency of different biodegradation strategies for mitigating total petroleum hydrocarbon (TPH) of petroleum refinery sludge by an integrated action of bioaugmentation and biostimulation vis-à-vis separate bioaugmentation and biostimulation approaches. The implementation of a concomitant bioaugmentation-biostimulation strategy (BABSS) involving the indigenously developed bacterial consortium and poultry litter extract showed the best performance by mitigating the TPH up to 90.3 ± 3.7% in 21 days. The GC-FID analysis confirmed the efficacy of different TPH degradation strategies. The kinetic study of TPH degradation of BABSS resulted first-order with rate 0.11 day^-1. Thus, the BABSS proved to be more efficient in degrading TPH in an eco-friendly manner and hence, may pave the way for better management of petroleum hydrocarbon pollutants, while providing a sustainable solution to the disposal of poultry wastes.

Impacts of earthworm casts on atrazine catabolism and bacterial community structure in laterite soil

Atrazine accumulation in agricultural soil is prone to cause serious environmental problems and pose risks to human health. Vermicomposting is an eco-friendly approach to accelerating atrazine biodegradation, but the roles of earthworm cast in the accelerated atrazine removal remains unclear. This work aimed to investigate the roles of earthworm cast in promoting atrazine degradation performance by comprehensively exploring the change in atrazine metabolites and bacterial communities. Our results showed that earthworm cast amendment significantly increased soil pH, organic matters, humic acid, fulvic acid and humin, and achieved a significantly higher atrazine removal efficiency. Earthworm cast addition also remarkably changed soil microbial communities by enriching potential soil atrazine degraders (Pseudomonadaceae, Streptomycetaceae, and Thermomonosporaceae) and introducing cast microbial degraders (Saccharimonadaceae). Particularly, earthworm casts increased the production of metabolites deethylatrazine and deisopropylatrazine, but not hydroxyatrazine. Some bacterial taxa (Gaiellaceaea and Micromonosporaceae) and humus (humic acid, fulvic acid and humin) were strongly correlated with atrazine metabolism into deisopropylatrazine and deethylatrazine, whereas hydroxyatrazine production was benefited by higher pH. Our findings verified the accelerated atrazine degradation with earthworm cast supplement, providing new insights into the influential factors on atrazine bioremediation in vermicomposting.

Effect of petroleum hydrocarbon pollution levels on the soil microecosystem and ecological function

Petroleum hydrocarbon pollution is a global problem. However, the effects of different petroleum pollution levels on soil microbial communities and ecological functions are still not clear. In this study, we analyzed the changes in microbial community structures and carbon and nitrogen transformation functions in oil-contaminated soils at different concentrations by chemical analysis, high-throughput sequencing techniques, cooccurrence networks, and KEGG database comparison functional gene annotation. The results showed that heavy petroleum concentrations (petroleum concentrations greater than 20,000 mg kg^-1) significantly decreased soil microbial diversity (p = 0.01), soil microbiome network complexity, species coexistence patterns, and prokaryotic carbon and nitrogen fixation genes. In medium petroleum contamination (petroleum concentrations of between 4000 mg kg^-1 and 20,000 mg kg^-1), microbial diversity (p > 0.05) and carbon and nitrogen transformation genes showed no evident change but promoted species coexistence patterns. Heavy petroleum contamination increased the Proteobacteria phylum abundance by 3.91%-57.01%, while medium petroleum contamination increased the Actinobacteria phylum abundance by 1.69%-0.26%. The results suggested that petroleum concentrations played a significant role in shifting soil microbial community structures, ecological functions, and species diversities.

Identification of pyrene degraders via DNA-SIP in oilfield soil during natural attenuation, bioaugmentation and biostimulation

Pyrene is a model contaminant of high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs), which are compounds that have potential carcinogenic effects and pose a serious threat to human health. Finding effective pyrene-degrading bacteria is crucial for removing PAHs from soil. In this study, DNA-based stable isotope probing (DNA-SIP) technology was used to investigate pyrene degraders in PAH-contaminated oilfield soil during natural attenuation (NA), bioaugmentation (BA) and biostimulation (BS). The results show that BA played an important role in pyrene degradation with the highest pyrene removal rate (~95%) after 12 days incubation, followed by removal rates of ~90% for NA and ~30% for BS. In addition, 6 novel pyrene degraders were identified, while 12 well-known PAH degraders were demonstrated to participate in the biodegradation of pyrene. Additionally, the external homologous strains introduced during BA promoted the degradation of pyrene, but not by directly participating in the metabolism of the target compound. Rhamnolipid supplementation during BS promoted the involvement of more microorganisms in the degradation of pyrene, which was beneficial to identifying more pyrene degraders via DNA-SIP. These findings provide new insight into the effects of external homologous strains and supplementary rhamnolipids on pyrene degradation.

Ecological criteria for assessing the content of petroleum hydrocarbons in the main soils of coniferous-deciduous forests and forest steppe

The effect of pollution of Albicluvisols/Retisols, Calcaric Leptosols, Luvic Phaeozems, Greyzamic Phaeozems and Folic Fluvisols with oil (Solovatovsky oil field, Perm region) added in amounts of 1, 2, 3 and 5 g oil/kg of soil on the organisms was studied in a model laboratory experiment. Oil addition showed phytotoxic effects on root length in Triticum aestivum L., Lepidium sativum L., Picea obovata Ledeb. and Pinus sylvestris L. in all soils. However, oil contamination of Calcaric Leptosols and Greyzamic Phaeozems led to growth stimulation in Picea obovata seedlings. A remarkable shift in the diversity and number of colony-forming units of heterotrophic and oil-oxidizing bacteria was detected in all soil types. The maximum decrease in biodiversity (45%) was noted for heterotrophic bacteria in Luvic Phaeozems. Aqueous extracts from all oil-contaminated soils had a toxic effect on Chlorella vulgaris Beijer, causing an increase in biomass by more than 30%, but did not show acute toxicity on Daphnia magna Straus. Oil addition in the range of 1-3 g oil/kg soil posed no environmental risk to human health. However, oil addition at 5 g oil/kg of soil led to an increase in the level of carcinogenic risk to children to the threshold values of acceptable risk and ranged from 0.95 × 10^-4 for Greyzamic Phaeozems and Folic Fluvisols to 1.098 × 10^-4 for Luvic Phaeozems. Our results suggest that the reaction of test organisms to oil pollution depends on the soil type, and their complex application makes it possible to identify the most sensitive factor and assess the dangerous level of pollution.

Oil contamination drives the transformation of soil microbial communities: Co-occurrence pattern, metabolic enzymes and culturable hydrocarbon-degrading bacteria

The land-based oil extraction activity has led to serious pollution of the soil. While microbes may play an important role in the remediation of contaminated soils, ecological effects of oil pollution on soil microbial relationships remain poorly understood. Here, typical contaminated soils and undisturbed soils from seven oilfields of China were investigated in terms of their physicochemical characteristics, indigenous microbial assemblages, bacterial co-occurrence patterns, and metabolic enzymes. Network visualization based on k-core decomposition illustrated that oil pollution reduced correlations between co-existing bacteria. The core genera were altered to those related with oil metabolism (Pseudarthrobacter, Alcanivorax, Sphingomonas, Chromohalobacter and Nocardioides). Under oil pollution pressure, the indigenous bacteria Gammaproteobacteria was domesticated as biomarker and the enzyme expression associated with the metabolism of toxic benzene, toluene, ethylbenzene, xylene and polycyclic aromatic hydrocarbons was enhanced. Functional pathways of xenobiotics biodegradation were also stimulated under oil contamination. Finally, twelve culturable hydrocarbon-degrading microbes were isolated from these polluted soils and classified into Stenotrophomonas, Delftia, Pseudomonas and Bacillus. These results show that the soil microbial communities are transformed under oil pollution stress, and also provide useful information for future bioremediation processes.

Safety and efficiency of sewage sludge and garden waste compost as a soil amendment based on the field application in woodland

Sewage sludge (SS) and garden waste (GW) compost can be used as soil amendments to improve the soil environment. Studies done till date have been focused on the changes of harmful substances during sludge composting, but the safety and efficacy of SS and GW composting on woodland soil environment are still unclear. In the study, a field experiment was performed using to investigate the safety and efficacy of SS and GW compost as a soil amendment on woodland soil. Soil nutrients (such as nitrogen, phosphorus and potassium), organic matter and electrical conductivity were significantly increased after the addition of the SS and GW compost, while there were no significant changes in soil heavy metals content and soil enzyme activities. From these soil properties, it was found that SS and GW compost was safe and efficacious in improving the soil environment. The application of SS and GW compost had no significant effect on microbial diversity. Co-occurrence network analysis revealed that SS and GW compost efficaciously enhanced the interaction between bacterial communities, which proved that it was safe and efficacious. Furthermore, SS and GW compost enhanced ABC transporters and carbohydrate metabolism of bacterial community, while reduced the pathotroph action (such as the plant pathogen) and wood saprotrophs. Overall, these results proved the safety and efficacy of SS and GW compost as soil amendments after being added to the soil. This study contributes to the use of harmless treatments and reutilization processes of SS and GW.

Molecular Characterization of Fungal Biodiversity in Long-Term Polychlorinated Biphenyl-Contaminated Soils

Polychlorinated biphenyls (PCBs) belong to the organic pollutants that are toxic to humans and harmful to environments. Numerous studies dealing with the impact of PCBs on soil microorganisms have focused on bacterial communities. The effects of PCBs on fungal communities in three different PCB-polluted soils from former industrial sites were investigated using high-throughput sequencing of the internal transcribed spacer 1 region. Significant differences in fungal alpha diversity were observed mainly due to soil physico-chemical properties. PCBs only influenced the richness of the fungal communities by increasing it. Fungal composition was rather strongly influenced by both PCBs and soil properties, resulting in different communities associated with each soil. Sixteen Ascomycota species were present in all three soils, including Stachybotrys chartarum, Fusarium oxysporum, Penicillium canescens, Penicillium chrysogenum,Penicillium citrosulfuratum and Penicillium brevicompactum, which are usually found in PCB-polluted soils, and Fusarium solani, Penicillium canescens, Penicillium citrosulfuratum and Penicillium chrysogenum, which are known PCB degraders. This study demonstrated that PCBs influence the richness and the composition of fungal communities. Their influence, associated with that of soil physico-chemical properties, led to distinct fungal communities, but with sixteen species common to the three soils which could be considered as ubiquitous species in PCB-polluted soils.