Metagenomic analysis revealed highly diverse carbon fixation microorganisms in a petroleum-hydrocarbon-contaminated aquifer

Ning, Zhuo; Cai, Pingping; Zhang, Min

doi:10.1016/j.envres.2024.118289

Cited by 10 publications

(3 citation statements)

References 63 publications

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“…The DNA was then collected by a vacuum pump (SHB-III A) onto filter membranes with a pore size of 0.22 μm. After the collected DNA was extracted, fragmented, and sequenced on the Illumina HiSeq4000 platform (Illumina Inc., San Diego, CA, USA) at Majorbio Bio-Pharm Technology Co., Ltd., (Shanghai, China) data quality control was performed [ 30 ]. The gene prediction was carried out after assembling the short sequences obtained from the quality control.…”

Section: Methodsmentioning

confidence: 99%

“…The non-redundant gene set sequences were compared with KEGG’s gene database (GENES) using BLASTP. Here, ppm was used to calculate the abundance of functional genes, i.e., the number of reads corresponding to a gene per million sequenced reads [ 30 ]. The specific method for functional gene determination is the same as the previous metagenomic testing techniques using conventional experimental techniques [ 31 , 32 , 33 ].…”

Section: Methodsmentioning

confidence: 99%

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Assessing the Natural Source Zone Depletion of a Petroleum-Contaminated Clayey Soil Site in Southern China Combining Concentration Gradient Method and Metagenomics

Xu,

Zhang,

Ning

et al. 2024

Life

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Natural source zone depletion (NSZD) is the main process of LNAPL (Light Non-Aqueous Phase Liquid) removal under natural conditions. The NSZD rates assessed ranged from 0.55 to 11.55 kg·m−2·a−1 (kilograms per square meter per year) in previous studies. However, most of these data were obtained from sandy sites, with few clayey sites. To gain knowledge of NSZD in clayey soil sites, the study assessed the NSZD of a petroleum hydrocarbon-contaminated clayey soil site in China, combining the concentration gradient method with metagenomic sequencing technology. The results show that the abundance of methane-producing key enzyme mcrA gene in the source zone was more abundant than in background areas, which suggests that there was methanogenesis, the key process of NSZD. The concentration gradients of oxygen and carbon dioxide existed only in shallow soil (<0.7 m), which suggests that there was a thin methane oxidation zone in the shallow zone. The calculated NSZD rates range from 0.23 to 1.15 kg·m−2·a−1, which fall within the moderate range compared to previous NSZD sites. This study expands the knowledge of NSZD in clayey soil and enriches the attenuation rate data for contaminated sites, which is of significant importance in managing petroleum contaminants.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Assessing the Natural Source Zone Depletion of a Petroleum-Contaminated Clayey Soil Site in Southern China Combining Concentration Gradient Method and Metagenomics

Xu,

Zhang,

Ning

et al. 2024

Life

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“…Differences in enzyme response to contamination by both petroleum-derived products are likely to be due to the nature of the hydrocarbons they contain. Some microorganisms use these hydrocarbons as a source of carbon and energy [29,34,105], leading to increased proliferation [106] and expansion of the enzyme pool [107]. However, certain fractions of petroleum-derived products may contaminate microbial cells, perforate their cell membrane, and thus exert a toxic effect on them.…”

Section: Plant and Enzyme Response To Petrochemical Productsmentioning

confidence: 99%

The Potential for Restoring the Activity of Oxidoreductases and Hydrolases in Soil Contaminated with Petroleum Products Using Perlite and Dolomite

Wyszkowska,

Borowik,

Zaborowska

et al. 2024

Applied Sciences

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The research focused on assessing the response of oxidoreductases (dehydrogenases and catalase) and hydrolases (urease, acid phosphatase, alkaline phosphatase, arylsulfatase, and β-glucosidase) to diesel oil (DO) and gasoline (G) contamination of soils subjected to phytoremediation with Zea mays. The activity of enzymes constitutes one of the fundamental mechanisms for the removal of contaminants from soil, which have the potential to contaminate not only the soil but also groundwater and water reservoirs. Additionally, correlations between enzyme activity and the basic physicochemical properties of the soil were determined. The interaction of perlite and dolomite with soil enzymes and the cultivated plant was also tested. The study was carried out in a pot experiment, where soil contaminated with DO or G was artificially treated at doses of 0, 8 cm3, and 16 cm3 kg−1. Perlite and dolomite were applied for remediation at doses of 0 and 10 g kg−1 of soil. Zea mays was found to respond to the tested pollutant with a reduction in biomass. DO affected the growth of this plant more than G. DO reduced the yield of aerial parts by 86% and G by 74%. The negative effects of these pollutants on the growth and development of Zea mays were mitigated by both perlite and dolomite. DO exerted greater pressure than G on the activity of oxidoreductases and hydrolases, as well as on the physicochemical properties of the soil. DO enhanced the activity of oxidoreductases and most hydrolases, whereas G inhibited them. The implementation of dolomite intensified the activity of all enzymes, except AcP (acid phosphatase) and Glu (ß-glucosidase), in soil contaminated with DO and G, and also improved its physicochemical properties. Perlite induced less significant effects than dolomite on soil enzymes and the physicochemical properties of the soil.

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Identification of carbon fixation microorganisms and pathways in an aquifer contaminated with long‐chain petroleum hydrocarbons

Gan,

Ning,

Wang

et al. 2024

Water Environment Research

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Petroleum hydrocarbons (PHCs) can be biodegraded into CO2, and PHC‐contaminated aquifers are always deemed as carbon sources. Fortunately, some carbon fixation microorganisms have been found in PHC‐contaminated sites. However, most of the studies are related to volatile short‐chain PHC, and few studies focus on long‐chain PHC‐contaminated sites. To reveal the carbon fixation microorganisms in these sites, in the study, a long‐chain PHC polluted site in North China was selected. Through hydrochemical and metagenomics analysis, the structure and capacity of carbon fixing microorganisms in the site were revealed. Results showed that there were many kinds of carbon fixed microorganisms that were identified such as Flavobacterium, Pseudomonas. HP/4HB, rTCA, and DC/4HB cycles were dominated carbon fixation pathways. The long‐chain PHC were weakly correlated with carbon fixation microorganisms, but it may stimulate the growth of some carbon fixation microorganisms, such as microorganisms involved in rTCA cycle.Practitioner Points The microorganisms with carbon fixation gene exist in the aquifer contaminated by long‐chain petroleum hydrocarbon. Microorganisms that have the ability to degrade petroleum also have the ability to carbon fixation. Long‐chain petroleum hydrocarbon may promote the growth of carbon fixation microorganisms.

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Metagenomic analysis revealed highly diverse carbon fixation microorganisms in a petroleum-hydrocarbon-contaminated aquifer

Cited by 10 publications

References 63 publications

Assessing the Natural Source Zone Depletion of a Petroleum-Contaminated Clayey Soil Site in Southern China Combining Concentration Gradient Method and Metagenomics

Assessing the Natural Source Zone Depletion of a Petroleum-Contaminated Clayey Soil Site in Southern China Combining Concentration Gradient Method and Metagenomics

The Potential for Restoring the Activity of Oxidoreductases and Hydrolases in Soil Contaminated with Petroleum Products Using Perlite and Dolomite

Identification of carbon fixation microorganisms and pathways in an aquifer contaminated with long‐chain petroleum hydrocarbons

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