The dominant microbial metabolic pathway of the petroleum hydrocarbons in the soil of shale gas field: Carbon fixation instead of CO2 emissions

doi:10.1016/j.scitotenv.2021.151074

Science of The Total Environment

Volume 807, Part 2, 10 February 2022, 151074

https://doi.org/10.1016/j.scitotenv.2021.151074 Get rights and content

Highlights

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The natural attenuation law of petroleum hydrocarbon pollution was explored.
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Carbon Fixation associated microbiota were assessed by 16S rRNA and PICRUSt.
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The main carbon fixation pathway in this study was the reductive citric acid cycle.

Abstract

In shale gas mining areas, indigenous microorganisms degrade organic pollutants such as petroleum hydrocarbons into carbon dioxide (CO₂) and water (H₂O) through aerobic metabolism. A large quantity of CO₂ emissions will exacerbate the “Greenhouse effect”. Based on the clean sieved soil and oil-based drilling fluid in the shale gas mining area, this experiment set three concentration gradients (3523 ± 159 mg/kg, 8715 ± 820 mg/kg and 22,031 ± 1533 mg/kg) to treat the soil, and each group was disposed for the same amount of time (63 days). By analyzing the dynamic changes of microbial diversity and the abundance of key functional genes for carbon fixation, the impact of petroleum hydrocarbons on carbon fixation potential was discovered, and the natural attenuation law of petroleum hydrocarbons in contaminated soil was explored. It provided the scientific research basis of ecology for the carbon cycle, carbon allocation, and carbon fixation in microbial remediation of petroleum hydrocarbon contaminated soil. The results obtained indicated the following: i) The removal rate of petroleum hydrocarbons under high-concentration pollution (45.33 ± 3.90%) was significantly lower than low and medium-concentration pollution. The TPH concentration removal rate of each group was the largest in the early stage of culture (1-5d), and there was no significant correlation between the TPH content and the community composition (R² = 0.0736, P > 0.05). ii) Composition and function of Carbon Fixation associated microbiota were assessed by 16S rRNA sequencing and PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) analysis. The main carbon fixation pathway in this study is the reductive citric acid cycle, because there was no shortage of enzymes that can affect subsequent reactions.

Graphical abstract

Introduction

The shale gas resources of the world are very rich and widely distributed (Ma et al., 2017; Zeng et al., 2018). With the development of shale gas, the research on modification of the pollution caused by the mining process has received much attention. Various studies were conducted on soil petroleum hydrocarbon pollution caused by shale gas development (Li et al., 2020b; Wang et al., 2019), which found that the soils have a high risk of total petroleum hydrocarbons (TPH) contamination. TPH, a mixture mainly composed of organic compounds, typically contains alkanes and aromatic hydrocarbons including BTEX (benzene, toluene, ethylbenzene, xylene) or PAH (polycyclic aromatic hydrocarbons). These compounds are highly toxicity and may perniciously affect human health and ecosystems (El-Alam et al., 2018; El-Hashemy and Ali, 2018; Liang et al., 2015). Due to its lipophilicity, TPH in terrestrial ecosystems mainly exists in the soil, and then poses a potential threat to human health through inhalation, contact, and ingestion (Gao et al., 2019).

Soil microbes, as the primary TPH decomposers, are associated with the environmental conditions and thereby can serve as a sensitive environmental indicator in the contaminated soil of petroleum hydrocarbons (Khan et al., 2013). Furthermore, compared with fungi and archaea, bacteria were more sensitive to soil TPH pollution (Zhou et al., 2017). As suitable indicators for assessment of soil TPH stress on the soil ecosystem, the TPH-degrading bacteria such as Arthrobacter, Pseudomonas, Mycobacterium, Bacillus, Rhodococcus, Streptomyces, Polaromonas, Comamonas, Sphingomonas, etc. were detected in the oil contaminated soil (Han et al., 2014; Li et al., 2015; Sun et al., 2015). These microorganisms degrade TPH into carbon dioxide (CO₂) and water (H₂O) through aerobic metabolism. The release of large amounts of CO₂ will aggravate the “Greenhouse effect” (Hamamura et al., 2013). Therefore, studying the metabolic fate of carbon in the microbial remediation of TPH has important significance for ecology and environment. Being consistent with the alteration of soil greenhouse gas fluxes from oil-contaminated soils, related genes played a key role in microbial carbon metabolism (Yang et al., 2018). Simultaneously, the petroleum contamination significantly altered the interactions between genes related to carbon cycling and other soil functions (Li et al., 2020a). However, the function of the carbon fixation potential genes, which regulate the carbon cycle during the decomposition of soil organic matters, is still far from clear. Therefore, it is necessary to use the abundance of key functional genes to evaluate the potential for microbes to fix carbon dioxide in the soil contaminated by petroleum hydrocarbons, which can explore the relationship between the abundance of key functional genes and the removal of petroleum hydrocarbons.

To provide the scientific research basis of ecology for the regulation of carbon metabolism and carbon cycle in TPH-polluted soil, we expect to add oil-based drilling fluids of different contents into clean soil in shale gas mining areas, which can carry out concentration gradient pollution simulation experiments. It is important to discover the impact of petroleum hydrocarbons on carbon fixation potential, which could explore the natural attenuation law of petroleum hydrocarbons in contaminated soil. Therefore，we analyzed the dynamic changes of microbial diversity and the abundance of key functional genes for carbon fixation. Through the PICRUSt function prediction method, the potential pathways of carbon metabolism, the corresponding microbial metabolism modules and carbon fixation genes were explored.

Section snippets

The source of the samples

The soil not contaminated by petroleum hydrocarbons was collected from the surface layer at the Shale gas mining area in Chongqing, Southwest China. The soil was a sandy yellow soil (silty clay). The coordinates of the sampling point were E107°34′43″, N29°41′58″, and the altitude was 488 m. A small part of the soil was used for the extraction of total microbial DNA, and the remaining soil samples were used to remove plant residues and debris in the laboratory. These soil samples were then

Temporal changes of petroleum hydrocarbons

After adding oil-based drilling fluid, the actual measured petroleum hydrocarbon content in the soils of the group L, M, and H were 3523 ± 159 mg/kg, 8715 ± 820 mg/kg, and 22,031 ± 1533 mg/kg, respectively.

The change of TPH content in the soil of L, M, and H groups over time was shown in Fig. 1(a). After 63 days of cultivation, the TPH content of L, M, and H groups decreased to 1593 ± 58 mg/kg, 3577 ± 820 mg/kg and 12,047 ± 118 mg/kg, respectively. The removal rates of L, M, and H groups were

Conclusions

After 63 days of cultivation, the degradation rates of TPH in the group L and group M were 56.02% and 57.64%, respectively, which were significantly higher than those of the group H (47.22%). The degradation rate decreased with the increase of the alkane chain length. The TPH concentration has a very significant positive correlation with the Pseudomonas in each group. Alkane 1-monooxygenase (EC: 1.14.15.3), often existed in Pseudomonas, had a well relative abundance in the experiment. The main

CRediT authorship contribution statement

Kejin Chen: Data curation (scrub data and maintain research data for initial use and later reuse), Writing-Original draft preparation, Visualization.

Rong He: Conceptualization (formulation or evolution of overarching research goals and aims), Methodology.

Li’ao Wang: Provision of study materials, reagents, instrumentation, computing resources, or other analysis tools.

Lingyue Liu: Application of statistical, mathematical, computational, or other formal techniques to analyze or synthesize study

Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgments

This research was supported by the National Key Research and Development Project (Project No. 2018YFC1800300), the Fundamental Research Funds for the Central Universities (Project No. 2021CDJQY-044) and the Graduate Scientific Research and Innovation Foundation of Chongqing, China (Grant No. CYB21039 and No. CYS21033).

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The dominant microbial metabolic pathway of the petroleum hydrocarbons in the soil of shale gas field: Carbon fixation instead of CO2 emissions

Highlights

Abstract

Graphical abstract

Introduction

Section snippets

The source of the samples

Temporal changes of petroleum hydrocarbons

Conclusions

CRediT authorship contribution statement

Declaration of competing interest

Acknowledgments

Environ. Int.

Sci. Total Environ.

Appl. Soil Ecol.

Sci. Total Environ.

J. Microbiol. Methods

Syst. Appl. Microbiol.

Chemosphere

Int. Biodeterior. Biodegradation

Renew. Sustain. Energy Rev.

J. Hazard. Mater.

Sci. Total Environ.

Chem. Eng. J.

Syst. Appl. Microbiol.

Front. Microbiol.

J. Clean. Prod.

J. Hazard. Mater.

Sci. Total Environ.

Gene

Energy

Measurements of physicochemical, elemental, and total petroleum hydrocarbon contents as pollution indicators of soils in petroleum products retailing station surrounding areas

Alkanindiges illinoisensis gen. Nov., sp nov., an obligately hydrocarbonoclastic, aerobic squalane-degrading bacterium isolated from oilfield soils

Int. J. Syst. Evol. Microbiol.

The dominant microbial metabolic pathway of the petroleum hydrocarbons in the soil of shale gas field: Carbon fixation instead of CO₂ emissions