Impact of diesel and biodiesel contamination on soil microbial community activity and structure

Integration of physiology, genomics and microbiomics analyses reveal the biodegradation mechanism of petroleum hydrocarbons by Medicago sativa L. and growth-promoting bacterium Rhodococcus erythropolis KB1

Despite the effectiveness of microbial-phytoremediation for remediating total petroleum hydrocarbons (TPH)-contaminated soil, the underlying mechanisms remain elusive. This study investigated the whole-genome and biological activity of Rhodococcus erythropolis KB1, revealing its plant growth promotion (PGP), TPH degradation, and stress resistance capabilities. Phytoremediation (using alfalfa) and plant-microbial remediation (using alfalfa and KB1) were employed to degrade TPH. The highest TPH degradation rate, reaching 95%, was observed with plant-microbial remediation. This is attributed to KB1's ability to promote alfalfa growth, induce the release of signaling molecules to activate plant antioxidant enzymes, actively recruit TPH-degrading bacteria (e.g., Sphingomonas, Pseudomonas, C1-B045), and increase soil nitrogen and phosphorus levels, thereby accelerating TPH degradation by both plants and microorganisms. This study demonstrates that R. erythropolis KB1 holds great potential for enhancing the remediation of TPH-contaminated soil through its multifaceted mechanisms, particularly in plant-microbial remediation strategies, providing valuable theoretical support for the application of this technology.

Functional microbiome and phytoremediation enhance soil diesel degradation via enzyme activity

This study investigates the enhancement of diesel degradation in contaminated soil through the synergistic effects of functional microbiomes and phytoremediation, emphasizing increased enzyme activity. The approach integrates a hydrogen-producing microbiome (HMb) with phytoremediation techniques. Observations revealed changes in soil conditions, including increases in moisture levels from 12.5% to 20% and a shift in pH from 6.9 to an alkaline range of 8.0-8.5 due to the treatment. Organic matter content also improved, supporting microbial activity. These modifications were closely monitored to evaluate their impact on microbial growth and enzyme activity. The findings showed that total petroleum hydrocarbons (TPH) in diesel-contaminated soil decreased by 78.1% using the combined HMb and phytoremediation method. This decrease was markedly higher than the 30.4% achieved through water drenching and the 30.9% with HMb alone. Central to this success were Clostridium sp. and Sporolactobacillus sp., which played essential roles in hydrocarbon degradation. Improved soil conditions supported an increase in microbial populations, with bacterial counts peaking at 6.0 x 1011 by day 4, enhancing degradation. Additionally, Bermuda grass survival rates increased to 35% by day 35. In the HMb and planting combination, amylase activity peaked at 100% by day 10, significantly aiding degradation, although it later decreased to 1% by day 35. This research presents a robust strategy for diesel-contaminated soil remediation, highlighting significant advancements in microbial growth and degradation efficiency.

Depletion of hydrocarbons and concomitant shift in bacterial community structure of a diesel-spiked tropical agricultural soil

Bacterial community of a diesel-spiked agricultural soil was monitored over a 42-day period using the metagenomic approach in order to gain insight into key phylotypes impacted by diesel contamination and be able to predict end point of bioattenuation. Soil physico-chemical parameters showed significant differences (P < 0.05) between the Polluted Soil (PS) and the Unpolluted control (US)across time points. After 21 days, the diesel content decreased by 27.39%, and at the end of 42 days, by 57.11%. Aromatics such as benzene, anthanthrene, propylbenzene, phenanthrenequinone, anthraquinone, and phenanthridine were degraded to non-detected levels within 42 days, while some medium range alkanes and polyaromatics such as acenaphthylene, naphthalene, and anthracene showed significant levels of degradation. After 21 days (LASTD21), there was a massive enrichment of the phylum Proteobacteria (72.94%), a slight decrease in the abundance of phylum Actinobacteriota (12.74%), and > 500% decrease in the abundance of the phylum Acidobacteriodota (5.26%). Day 42 (LASTD42) saw establishment of the dominance of the Proteobacteria (34.95%), Actinobacteriota, (21.71%), and Firmicutes (32.14%), and decimation of phyla such as Gemmatimonadota, Planctomycetota, and Verrucromicrobiota which play important roles in the cycling of elements and soil health. Principal component analysis showed that in PS moisture contents, phosphorus, nitrogen, organic carbon, had greater impacts on the community structure in LASTD21, while acidity, potassium, sodium, calcium and magnesium impacted the control sample. Recovery time of the soil based on the residual hydrocarbons at Day 42 was estimated to be 229.112 d. Thus, additional biostimulation may be required to achieve cleanup within one growing season.

Assessing Diesel Tolerance of Chromobacterium violaceum: Insights from Growth Kinetics, Substrate Utilization, and Implications for Microbial Adaptation

This study aimed to determine the tolerance of Chromobacterium violaceum ATCC 12472 to diesel. The growth of the strain was evaluated through exposure to various diesel concentrations (1, 2.5, 5, 7.5, and 10% v/v), with continuous monitoring of growth via optical density measurements until the death phase was reached. Employing a logistic model, we analyzed the growth kinetics of C. violaceum and compared them with five other models to comprehend substrate utilization dynamics. Our results indicate that optimal bacterial growth occurred at 2.5% (v/v) or 18,125 mg/L diesel, while both higher and lower concentrations manifested inhibitory and increasingly stressful effects. The Aiba model emerged as the most fitting representation of substrate utilization by C. violaceum. In addition, our findings underscore the remarkable diesel tolerance of C. violaceum ATCC 12472, despite the inherently stressful nature of the medium. This study contributes to the understanding of microbial responses to environmental stressors and highlights the pivotal role of the substrate concentration in influencing microbial growth. These insights have implications for bioremediation strategies and enhance our understanding of bacterial ecological resilience in the presence of hydrocarbon pollutants.

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome

BACKGROUND

Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome.

RESULTS

After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments).

CONCLUSION

Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.

An integrated metagenomic model to uncover the cooperation between microbes and magnetic biochar during microplastics degradation in paddy soil

The free radicals released from the advanced oxidation processes can enhance microplastics degradation, however, the existence of microbes acting synergistically in this process is still uncertain. In this study, magnetic biochar was used to initiate the advanced oxidation process in flooded soil. paddy soil was contaminated with polyethylene and polyvinyl chloride microplastics in a long-term incubation experiment, and subsequently subjected to bioremediation with biochar or magnetic biochar. After incubation, the total organic matter present in the samples containing polyvinyl chloride or polyethylene, and treated with magnetic biochar, significantly increased compared to the control. In the same samples there was an accumulation of "UVA humic" and "protein/phenol-like" substances. The integrated metagenomic investigation revealed that the relative abundance of some key genes involved in fatty acids degradation and in dehalogenation changed in different treatments. Results from genome-centric investigation suggest that a Nocardioides species can cooperate with magnetic biochar in the degradation of microplastics. In addition, a species assigned to the Rhizobium taxon was identified as a candidate in the dehalogenation and in the benzoate metabolism. Overall, our results suggest that cooperation between magnetic biochar and some microbial species involved in microplastic degradation is relevant in determining the fate of microplastics in soil.

Contrasting Responses and Phytoremediation Potential of Two Poplar Species to Combined Strontium and Diesel Oil Stress

The soil pollution caused by diesel oil and heavy metals has become an increasingly serious environmental issue, with negative global-scale impacts. The remediation of contaminated soil requires special attention, in which phytoremediation has emerged as an ecofriendly solution. However, the response of plants to the combined stress of diesel oil and heavy metals remains largely unknown. In this study, the aim was to investigate the potential of Populus alba and P. russkii for phytoremediation by examining their response to combined diesel oil and heavy metal stress. In a greenhouse experiment using soil contaminated with 15 mg kg^-1 of diesel oil and varying concentrations of Sr (0, 10, or 100 mg kg^-1), we studied the physiological and biochemical changes, as well as the Sr absorption, of P. alba and P. russkii. The results showed that at high concentrations of Sr and diesel oil, the growth of both species was substantially inhibited, but P. alba exhibited higher resistance due to its higher antioxidant enzyme activities and increased accumulation of soluble sugar and proline. Additionally, P. alba concentrated Sr in the stem, whereas P. russkii accumulated Sr in the leaf, exacerbating its negative effects. Diesel oil treatments were beneficial for Sr extraction due to cross-tolerance. Our findings indicate that P. alba is more suitable for the phytoremediation of Sr contamination due to its superior tolerance to combined stress, and we identified potential biomarkers for monitoring pollution. Therefore, this study provides a theoretical basis and implementation strategy for the remediation of soil contaminated by both heavy metals and diesel oil.

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.

Soil contamination by diesel fuel destabilizes the soil microbial pools: Insights from permafrost soil incubations

Arctic contamination by diesel fuel (DF) is of great concern because of the uncertain feedback of permafrost carbon (C) and soil microbiota to DF in the context of climate change in high latitudes. We conducted a laboratory incubation experiment with a gradient of DF addition ratios to examine the responses of the soil microbiota of the typical permafrost soils in the tundra ecosystems of the Norilsk region (Siberia). The study revealed initial heterogeneity in the microbial activity of the studied soils (Histic Gleyic Cryosols (CR-hi,gl), Turbic Cryosols (CR-tu), Turbic Spodic Folic Cryosols (CR-tu,sd,fo), Gleyic Fluvisols (FL-gl)). We applied the two-pool model for evaluation of the effect of DF on the proportions of C pools and revealed significant differences between soil types in the fast and slow C pools in response to DF addition. The results showed that DF addition treatments had varying effects on the fast and slow C pools, microbial activity, and microbial community structure in the studied soils. For minor exceptions, DF dramatically accelerated C loss from the slow C pool in all soil types. We assume that differences in C pool and microbiota responses to DF addition were caused by soil texture and changes in microbial community structure. We isolated Serratia proteamaculans, S. liquefaciens, S. plymuthica, Rhodococcus erythropolis, Pseudomonas antarctica, P. libanensis, P. brassicacearum, and P. chlororaphis from the DF-polluted soils. These species are recommended for bioremediation to mitigate the DF contamination of permafrost soils, especially regarding climate change and the sustainable well-being of Arctic ecosystems.

The combined enhancement of RL, nZVI and AQDS on the microbial anaerobic-aerobic degradation of PAHs in soil

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous persistent organic pollutants in soil, which have carcinogenic, teratogenic and mutagenic hazards. The effects of rhamnolipid (RL), nano zero-valent iron (nZVI), and anthraquinone-2,6-disulfonic acid (AQDS) on the degradation of PAHs in soil were studied. It was found that the treatment of 5 mg·kg^-1RL + 1% nZVI +0.2 mmol·kg^-1AQDS had the highest degradation rate. The degradation rate of total PAHs and HMW-PAHs was 72.81% and 79.47% respectively after 90 days. High-throughput sequencing showed that in RL + nZVI + AQDS enhanced soil, Clostridium, Geobacter, Anaeromyxobacter and Sphingomonas were the dominant species for anaerobic degradation of PAHs. Rhodococcus, Nocardioides, and Microvirga are the dominant species for aerobic degradation of PAHs. The activities of methyltransferase, dehydrogenase and catechol 1,2-dioxygenase in the anaerobic-aerobic degradation process of PAHs were consistent with the degradation process of PAHs, indicating the role of these enzymes in the degradation of PAHs. RL, nZVI, and AQDS combined enhanced microbial anaerobic-aerobic degradation has great application potential in remediation of PAHs-contaminated soil.

Effect of Process Parameters on the Graphite Expansion Produced by a Green Modification of the Hummers Method

Adsorption stand out among other standard techniques used for water treatment because of its remarkable simplicity, easy operation, and high removal capability. Expanded graphite has been selected as a promising agent for oil spill adsorption, but its production involves the generation of corrosive remnants and massive amounts of contaminated washing waters. Although the advantageous use of the H2O2–H2SO4 mixture was described in 1978, reported works using this method are scarce. This work deals with the urgent necessity for the development of alternative chemical routes decreasing their environmental impact (based on green chemistry concepts), presenting a process for expanded graphite production using only two intercalation chemicals, reducing the consumption of sulfuric acid to only 10% and avoiding the use of strong oxidant salts (both environmentally detrimental). Three process parameters were evaluated: milling effect, peroxide concentration, and microwave expansion. Some remarkable results were obtained following this route: high specific volumes elevated oil adsorption rate exhibiting a high oil–water selectivity and rapid adsorption. Furthermore, the recycling capability was checked using up to six adsorption cycles. Results showed that milling time reduces the specimen’s expansion rate and oil adsorption capacity due to poor intercalant insertion and generation of small particle sizes.

Thermal desorption optimization for the remediation of hydrocarbon-contaminated soils by a self-built sustainability evaluation tool

Current thermal desorption practices of hydrocarbon-contaminated soils focus on remediation efficiency and cost, with little systematic assessment of the reuse value of treated soils. This study evaluated various integrated indices of treatment cost and reuse of treated soils at three desorption temperatures. Various typical engineering and ecological characteristics closely related to soil reusability were selected to analyze the changes in various treated soils, including shear strength, Atterberg limits, particle size distribution, permeability, soil carbon, and soil biomass. A sustainability evaluation tool was developed for the greener disposal of hazardous soils considering both the treatment cost and reuse indices. Such an evaluation led to the conclusion that the contaminated soils treated at 350 °C generated the highest soil reusability with an excellent remediation efficiency. The sensitivity analysis confirmed that the tool had better stability in a common situation where the weight of the remediation cost was heavier than the soil reusability. Meanwhile, published data were input into the tool to validate its applicability under different scenarios. The results were consistent with the qualitative assessment of the literature. The tool can quantitatively select a more sustainable desorption method for the disposal and reuse of hazardous soils.

Vertical distribution characteristics and interactions of polycyclic aromatic compounds and bacterial communities in contaminated soil in oil storage tank areas

Polycyclic aromatic compound (PAC) contamination in soil as a result of oil spills is a serious issue because of the huge global demand for fossil energy. This study assessed the vertical variation in polycyclic aromatic hydrocarbons (PAHs), derivatives of PAHs (dPAHs) and bacterial community structure in deep soil with long-term contamination by oil spillage. Our results suggest that the content of total PACs ranged from 1196.6 μg/kg to 14980.9 μg/kg and decreased with depth at all sites. PAHs were the most abundant PACs, with a mean concentration of 6640.7 μg/kg, followed by oxygenated PAHs (mean 156.3 μg/kg) and nitrated PAHs (mean 33.4 μg/kg). PAHs are mainly low molecular weight PACs such as naphthalene, fluorene and phenanthrene, while derivatives of PAHs are all low molecular weight PACs and mainly oxygenated PAHs. Low molecular weight PAHs were an important source of dPAHs under specific conditions. The bacterial community structure showed higher bacterial diversity and lower bacterial richness in shallow soil (2-6 m in depth) than in deep soil (8-10 m in depth). Spearman's analysis confirmed that dramatic bacterial community shifts are a response to contamination. At the genus level, the presence of PACs highly selected for Pseudomonas, belonging to Proteobacteria. Moreover, functional predictions based on Tax4Fun revealed that soil with long-term contamination had a strong potential for PAC degradation. In addition, statistical analysis showed that oxidation-reduction potential (Eh) was closely related to variations of bacterial community composition and function. Finally, Ramlibacter, Pseudomonas, Pseudonocardia, c_MB-A2-108, f_Amb-16S-1323, and Qipengyuania were identified by cooccurrence network analysis as keystone taxa contributing to the maintenance of bacterial ecological function. Together, our results provide evidence of tight bacterial effects of PAHs and dPAHs and a more complete understanding of the fate of PACs in deep contaminated soils.

Microbial contamination of diesel-biodiesel blends in storage tank; an analysis of colony morphology

Fuel contamination is a major issue that comes with the utilization of biodiesel. Microbial growth is one of the primary causes of contamination during fuel handling and storage. This work attempts to identify the types, shapes, and growth profiles of microorganisms on fuel samples. The morphology of microbial colonies is presented in order to analyze the potential of fuel contamination. The diesel, biodiesel, and blends are stored in stainless steel (SS) and glass tanks, where each is placed indoors and outdoors during the 90 days of storage time. The morphology of microbial colonies is observed through a microscope with a magnification of 1000× and the quantity is calculated by a digital colony counter. Microbial contamination in all samples is considered as high contamination where the Colony Forming Unit (CFU) is greater than 10⁵ L⁻¹. Colony forms are far more assorted in blends than in pure diesel (B0) and neat biodiesel (B100). The transformation of microbial colonies accelerates after 60 days of storage time. The results reveal that the number of bacterial colonies that grow in B20 is higher and more varied, nevertheless, the contamination in B100 is significantly higher. This is indicated by a 1.5-fold rise in B20 acidity and a 2.5-fold increase in water content compared to the initial condition.

The Influence of Kerosene on Microbiomes of Diverse Soils

One of the most important challenges for soil science is to determine the limits for the sustainable functioning of contaminated ecosystems. The response of soil microbiomes to kerosene pollution is still poorly understood. Here, we model the impact of kerosene leakage on the composition of the topsoil microbiome in pot and field experiments with different loads of added kerosene (loads up to 100 g/kg; retention time up to 360 days). At four time points we measured kerosene concentration and sequenced variable regions of 16S ribosomal RNA in the microbial communities. Mainly alkaline Dystric Arenosols with low content of available phosphorus and soil organic matter had an increased fraction of Actinobacteriota, Firmicutes, Nitrospirota, Planctomycetota, and, to a lesser extent, Acidobacteriota and Verrucomicobacteriota. In contrast, in highly acidic Fibric Histosols, rich in soil organic matter and available phosphorus, the fraction of Acidobacteriota was higher, while the fraction of Actinobacteriota was lower. Albic Luvisols occupied an intermediate position in terms of both physicochemical properties and microbiome composition. The microbiomes of different soils show similar response to equal kerosene loads. In highly contaminated soils, the proportion of anaerobic bacteria-metabolizing hydrocarbons increased, whereas the proportion of aerobic bacteria decreased. During the field experiment, the soil microbiome recovered much faster than in the pot experiments, possibly due to migration of microorganisms from the polluted area. The microbial community of Fibric Histosols recovered in 6 months after kerosene had been loaded, while microbiomes of Dystric Arenosols and Albic Luvisols did not restore even after a year.

Effects of Coal and Sewage Sludge Ashes on Macronutrient Content in Maize (Zea mays L.) Grown on Soil Contaminated with Eco-Diesel Oil

Petroleum hydrocarbons, as aggressive components of diesel oils, after migration to the land environment can alter the activity and efficiency of ecosystems. They can also be dangerous to animal and human health. Eco-friendly methods for the reclamation of affected soils is necessary to manage degraded lands. One such method is the use of ashes. The aim of this research was to determine how soil pollution with diesel oil (brand name, Eco-Diesel) affects the chemical composition of maize (Zea mays L.) and whether the application of ash from a combined heat and power plant, as well as from sewage sludge incineration, could reduce the potentially adverse impact of diesel oil on plants. The research results demonstrated that soil contamination with Eco-Diesel oil modified the content of selected macronutrients in the analyzed crop plant. Eco-Diesel oil had a negative effect on maize yield. The highest diesel oil dose in a series without neutralizing substances had a positive effect on the accumulation of most elements, except nitrogen and sodium. Soil enrichment with ash differentiated the content of macronutrients, mainly nitrogen and phosphorus, in the aerial biomass of maize. The ashes increased the yield of maize and content of some macronutrients, mainly nitrogen but also calcium, the latter in a series where soil was treated with ash from sewage sludge thermal recycling. Both types of ash also resulted in a decrease in the plant content of phosphorus, while ash from hard coal caused a slight reduction in the content of potassium in maize. Ash of different origins can be an effective solution in the reclamation of degraded soils, which may then be used for growing energy crops.

In situ Fenton remediation for diesel contaminated clayey zone assisted by thermal plasma blasting: Synergism and cost estimation

Thermal plasma blasting technology has been widely applied for rock cracking. Though, the application for environmental remediation has yet to be reported. Since the delivery of remediation agents into diesel contaminated clayey zones are exceptionally challenging, herein, this study explores the effect of pilot-scale thermal plasma blasting for soil fracturing and concurrently dispersing the Fenton reagent into the diesel contaminated silty soils. Six times plasma blasting with sole H₂O₂ at 20 kV had the highest degradation of diesel (>97%) with an equilibrium time of 3 h, and the final diesel concentration was below the South Korean regulated health standard (500 mg kg^-1). This study highlights plasma blasting able to deliver H₂O₂ instantaneously and homogeneously into contaminated zone while promoting Fenton reaction synergism (f_syn: 2.04) between H₂O₂ and ≡Fe surface for effective remediation. Furthermore, the remediation cost (USD 4 metric ton^-1) is much lower than most reported in situ technologies.