Research

18 pages, 3964 KiB

Open AccessArticle

Crude Oil Degradation in Temperatures Below the Freezing Point by Bacteria from Hydrocarbon-Contaminated Arctic Soils and the Genome Analysis of Sphingomonas sp. AR_OL41

by Ekaterina M. Semenova, Tatyana P. Tourova, Tamara L. Babich, Ekaterina Y. Logvinova, Diyana S. Sokolova, Nataliya G. Loiko, Vladimir A. Myazin, Maria V. Korneykova, Andrey V. Mardanov and Tamara N. Nazina

Microorganisms 2024, 12(1), 79; https://doi.org/10.3390/microorganisms12010079 - 30 Dec 2023

Viewed by 1327

Abstract

Intensive human activity in the Arctic region leads to hydrocarbon pollution of reservoirs and soils. Isolation of bacteria capable of growing at low temperatures and degrading oil and petroleum products is of scientific and practical value. The aim of this work was to [...] Read more.

Intensive human activity in the Arctic region leads to hydrocarbon pollution of reservoirs and soils. Isolation of bacteria capable of growing at low temperatures and degrading oil and petroleum products is of scientific and practical value. The aim of this work was to study the physiology and growth in oil at temperatures below 0 °C of four strains of bacteria of the genera Pseudomonas, Rhodococcus, Arthrobacter, and Sphingomonas—previously isolated from diesel-contaminated soils of the Franz Josef Land archipelago—as well as genomic analysis of the Sphingomonas sp. AR_OL41 strain. The studied strains grew on hydrocarbons at temperatures from −1.5 °C to 35 °C in the presence of 0–8% NaCl (w/v). Growth at a negative temperature was accompanied by visual changes in the size of cells as well as a narrowing of the spectrum of utilized n-alkanes. The studied strains were psychrotolerant, degraded natural biopolymers (xylan, chitin) and n-alkanes of petroleum, and converted phosphates into a soluble form. The ability to degrade n-alkanes is rare in members of the genus Sphingomonas. To understand how the Sphingomonas sp. AR_OL41 strain has adapted to a cold, diesel-contaminated environment, its genome was sequenced and analyzed. The Illumina HiSeq 2500 platform was used for AR_OL41 genome strain sequencing. The genome analysis of the AR_OL41 strain showed the presence of genes encoding enzymes of n-alkane oxidation, pyruvate metabolism, desaturation of membrane lipids, and the formation of exopolysaccharides, confirming the adaptation of the strain to hydrocarbon pollution and low habitat temperature. Average nucleotide identity and digital DNA–DNA hybridization values for genomes of the AR_OL41 strain with that of the phylogenetically relative Sphingomonas alpine DSM 22537^T strain were 81.9% and 20.9%, respectively, which allows the AR_OL41 strain to be assigned to a new species of the genus Sphingomonas. Phenomenological observations and genomic analysis indicate the possible participation of the studied strains in the self-purification of Arctic soils from hydrocarbons and their potential for biotechnological application in bioremediation of low-temperature environments. Full article

(This article belongs to the Special Issue Petroleum Microbiology 2.0)

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14 pages, 1974 KiB

Open AccessArticle

Horizontal and Vertical Comparison of Microbial Community Structures in a Low Permeability Reservoir at the Local Scale

by Zena Zhi, Ziwei Bian, Yuan Chen, Xiangchun Zhang, Yifei Wu and Hanning Wu

Microorganisms 2023, 11(12), 2862; https://doi.org/10.3390/microorganisms11122862 - 26 Nov 2023

Viewed by 636

Abstract

Petroleum microorganisms play a crucial role in the application of microbial-enhanced oil recovery, and the community structures of petroleum microorganisms have been widely studied. Due to variations in reservoir geological conditions, reservoir microbial communities exhibit unique characteristics. However, previous studies have primarily focused [...] Read more.

Petroleum microorganisms play a crucial role in the application of microbial-enhanced oil recovery, and the community structures of petroleum microorganisms have been widely studied. Due to variations in reservoir geological conditions, reservoir microbial communities exhibit unique characteristics. However, previous studies have primarily focused on microbial community changes within a single well, a single block, and before and after water flooding, and thus, cross-horizon and cross-regional comparative studies of in situ microbial communities are lacking. In this study, the 16S rRNA full-length sequencing method was adopted to study bacterial communities in crude oil samples taken from two wells at the same depths (depths of 2425 m and 2412 m) but approximately 20 km apart in the Hujianshan oilfield, located in the Ordos Basin. At the same time, the results were combined with another layer of research data from another article (from a depth of 2140 m). The aim was to compare the differences in the microbial community structures between the oil wells on a horizontal scale and a vertical scale. The results revealed that there were minimal differences in the microbial community structures that were influenced by the horizontal distances within a small range (<20 km), while differences were observed at a larger spatial scale. However, the dominant bacteria (Proteobacteria and Bacteroidetes) in the different oilfields were similar. Vertical depth variations (>300 m) had significant impacts on the communities, and this was mainly controlled by temperature. The greater the depth, the higher formation temperature, leading to an increase in thermophilic and anaerobic bacteria within a community. Full article

(This article belongs to the Special Issue Petroleum Microbiology 2.0)

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17 pages, 5518 KiB

Open AccessArticle

Pore- and Core-Scale Recovery Performance of Consortium Bacteria from Low-Permeability Reservoir

by Ziwei Bian, Zhiyong Song, Zena Zhi, Xiangchun Zhang, Yiqian Qu, Ruiyang Chai, Hanning Wu and Yifei Wu

Microorganisms 2023, 11(11), 2738; https://doi.org/10.3390/microorganisms11112738 - 09 Nov 2023

Viewed by 619

Abstract

Performance evaluation of microorganisms that have emulsifying and degrading effects on crude oil has been extensively conducted in the laboratory. However, the ultimate goal of microbial enhanced oil recovery is field application, so the pilot simulation experiments are crucial. In this study, a [...] Read more.

Performance evaluation of microorganisms that have emulsifying and degrading effects on crude oil has been extensively conducted in the laboratory. However, the ultimate goal of microbial enhanced oil recovery is field application, so the pilot simulation experiments are crucial. In this study, a micro-visualization model and the real cores were chosen to investigate the actual recovery efficiency and the mechanism of the consortium bacteria B-ALL, which has been proven to have good emulsification and degradation effects in lab studies in porous media. At the same time, the cast thin sections and rate-controlled porosimetry were combined to analyze the pore throat structure of the displacement core. It was found that the recovery efficiency was positively correlated with the microbial injection volume as well as the incubation time. For the microscopic model with high pores and high permeability, the efficiency of secondary water flooding can be increased by 44.77% after six days of incubation with two pore volume microbes. For the real tight cores, the maximum secondary water flooding efficiency under the same condition was 6.98%. Through visual modeling, microorganisms increase the oil washing efficiency mainly by emulsification and changing the wettability. The generated oil droplets will play a role in plugging and improving the wave efficiency. However, tight reservoirs have the characteristics of large pores and small throats, and curved and necking throats are developed, greatly reducing permeability. The microbial recovery efficiency was lower under shorter cultivation times. This study provides a practical basis for the application of consortium bacteria in tight oil fields to enhance recovery. Full article

(This article belongs to the Special Issue Petroleum Microbiology 2.0)

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12 pages, 1845 KiB

Open AccessArticle

Improving Rhamnolipids Biosynthesis in Pseudomonas sp. L01 through Atmospheric and Room-Temperature Plasma (ARTP) Mutagenesis

by Ying Xu, Yali Jing, Qun Zhang, Jianlong Xiu, Maozhang Tian, Qingfeng Cui, Yuandong Ma, Lina Yi, Lu Han, Yuchen Qian, Yaqian Zhang, Yong Nie and Xiao-Lei Wu

Microorganisms 2023, 11(5), 1182; https://doi.org/10.3390/microorganisms11051182 - 30 Apr 2023

Cited by 3 | Viewed by 1433

Abstract

Biosurfactants have significant applications in various industries, including microbial-enhanced oil recovery (MEOR). While the state-of-the-art genetic approaches can generate high-yield strains for biosurfactant production in fermenters, there remains a critical challenge in enhancing biosurfactant-producing strains for use in natural environments with minimal ecological [...] Read more.

Biosurfactants have significant applications in various industries, including microbial-enhanced oil recovery (MEOR). While the state-of-the-art genetic approaches can generate high-yield strains for biosurfactant production in fermenters, there remains a critical challenge in enhancing biosurfactant-producing strains for use in natural environments with minimal ecological risks. The objectives of this work are enhancing the strain’s capacity for rhamnolipids production and exploring the genetic mechanisms for its improvement. In this study, we employed atmospheric and room-temperature plasma (ARTP) mutagenesis to enhance the biosynthesis of rhamnolipids in Pseudomonas sp. L01, a biosurfactant-producing strain isolated from petroleum-contaminated soil. Following ARTP treatment, we identified 13 high-yield mutants, with the highest yield of 3.45 ± 0.09 g/L, representing a 2.7-fold increase compared to the parent strain. To determine the genetic mechanisms behind the enhanced rhamnolipids biosynthesis, we sequenced the genomes of the strain L01 and five high-yield mutants. A comparative genomic analysis suggested that mutations in genes related to the synthesis of lipopolysaccharides (LPS) and the transport of rhamnolipids may contribute to the improved biosynthesis. To the best of our knowledge, this is the first instance of utilizing the ARTP approach to improve rhamnolipid production in Pseudomonas strains. Our study provides valuable insights into the enhancement of biosurfactant-producing strains and the regulatory mechanisms of rhamnolipids biosynthesis. Full article

(This article belongs to the Special Issue Petroleum Microbiology 2.0)

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19 pages, 5455 KiB

Open AccessArticle

Effective Biocorrosive Control in Oil Industry Facilities: 16S rRNA Gene Metabarcoding for Monitoring Microbial Communities in Produced Water

by Joyce Dutra, Glen García, Rosimeire Gomes, Mariana Cardoso, Árley Côrtes, Tales Silva, Luís de Jesus, Luciano Rodrigues, Andria Freitas, Vinicius Waldow, Juliana Laguna, Gabriela Campos, Monique Américo, Rubens Akamine, Maíra de Sousa, Claudia Groposo, Henrique Figueiredo, Vasco Azevedo and Aristóteles Góes-Neto

Microorganisms 2023, 11(4), 846; https://doi.org/10.3390/microorganisms11040846 - 27 Mar 2023

Cited by 4 | Viewed by 1823

Abstract

Microbiologically influenced corrosion (MIC) or biocorrosion is a complex biological and physicochemical process, Strategies for monitoring MIC are frequently based on microbial cultivation methods, while microbiological molecular methods (MMM) are not well-established in the oil industry in Brazil. Thus, there is a high [...] Read more.

Microbiologically influenced corrosion (MIC) or biocorrosion is a complex biological and physicochemical process, Strategies for monitoring MIC are frequently based on microbial cultivation methods, while microbiological molecular methods (MMM) are not well-established in the oil industry in Brazil. Thus, there is a high demand for the development of effective protocols for monitoring biocorrosion with MMM. The main aim of our study was to analyze the physico-chemi- cal features of microbial communities occurring in produced water (PW) and in enrichment cultures in oil pipelines of the petroleum industry. In order to obtain strictly comparable results, the same samples were used for both culturing and metabarcoding. PW samples displayed higher phylogenetic diversity of bacteria and archaea whereas PW enrichments cultures showed higher dominance of bacterial MIC-associated genera. All samples had a core community composed of 19 distinct genera, with MIC-associated Desulfovibrio as the dominant genus. We observed significant associations between the PW and cultured PW samples, with a greater number of associations found between the cultured sulfate-reducing bacteria (SRB) samples and the uncultured PW samples. When evaluating the correlation between the physicochemical characteristics of the environment and the microbiota of the uncultivated samples, we suggest that the occurrence of anaerobic digestion metabolism can be characterized by well-defined phases. Therefore, the detection of microorganisms in uncultured PW by metabarcoding, along with physi-cochemical characterization, can be a more efficient method compared to the culturing method, as it is a less laborious and cost-effective method for monitoring MIC microbial agents in oil industry facilities. Full article

(This article belongs to the Special Issue Petroleum Microbiology 2.0)

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15 pages, 803 KiB

Open AccessArticle

Use of Shotgun Metagenomics to Assess the Microbial Diversity and Hydrocarbons Degrading Functions of Auto-Mechanic Workshops Soils Polluted with Gasoline and Diesel Fuel

by Emerance Jessica Claire D’Assise Goma-Tchimbakala, Ilaria Pietrini, Joseph Goma-Tchimbakala and Stefano Paolo Corgnati

Microorganisms 2023, 11(3), 722; https://doi.org/10.3390/microorganisms11030722 - 10 Mar 2023

Cited by 2 | Viewed by 1993

Abstract

Bioaugmentation is a valuable technique for oil recovery. This study investigates the composition and functions of microbial communities in gasoline- and diesel-contaminated soils of garages Matoko (SGM) and Guy et Paul (SGP) originating from auto mechanic workshops as well as the concentration of [...] Read more.

Bioaugmentation is a valuable technique for oil recovery. This study investigates the composition and functions of microbial communities in gasoline- and diesel-contaminated soils of garages Matoko (SGM) and Guy et Paul (SGP) originating from auto mechanic workshops as well as the concentration of soil enzymes β-glucosidase, β-glucosaminidase, and acid phosphatase. The work aimed to evaluate the presence of petroleum-hydrocarbon-degrading bacteria for the development of foreseen bioremediation of oil-contaminated soils. Microbial diversity, as given by shotgun metagenomics, indicated the presence of 16 classes, among which Actinobacteria and Gammaproteobacteria dominated, as well as more than 50 families, including the dominant Gordoniaceae (26.63%) in SGM and Pseudomonadaceae (57.89%) in SGP. The dominant bacterial genera in the two soils were, respectively, Gordonia (26.7%) and Pseudomonas (57.9%). The exploration of the bacterial metabolic abilities using HUMANn2 allowed to detect genes and pathways involved in alkanes and aromatic hydrocarbons in the two contaminated soils. Furthermore, enzymes β-glucosidase, β-glucosaminidase, and acid phosphatase were found in high concentrations ranging between 90.27 ± 5.3 and 804.17 ± 20.5 µg pN/g soil/h, which indicated active microbial metabolism. The high diversity of microorganisms with a hydrocarbon degradation genetic package revealed that the bacteria inhabiting the two soils are likely good candidates for the bioaugmentation of oil-contaminated soils. Full article

(This article belongs to the Special Issue Petroleum Microbiology 2.0)

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13 pages, 7746 KiB

Open AccessArticle

Succession Patterns of Microbial Composition and Activity following the Diesel Spill in an Urban River

by Ruiyu Yang, Chao Peng, Yuqiu Ye, Yun Tang and Lu Lu

Microorganisms 2023, 11(3), 698; https://doi.org/10.3390/microorganisms11030698 - 08 Mar 2023

Viewed by 1268

Abstract

Diesel spills in freshwater systems have adverse impacts on the water quality and the shore wetland. Microbial degradation is the major and ultimate natural mechanism that can clean the diesel from the environment. However, which, and how fast, diesel-degrading microorganisms could degrade spilled [...] Read more.

Diesel spills in freshwater systems have adverse impacts on the water quality and the shore wetland. Microbial degradation is the major and ultimate natural mechanism that can clean the diesel from the environment. However, which, and how fast, diesel-degrading microorganisms could degrade spilled diesel has not been well-documented in river water. Using a combination of ¹⁴C-/³H--based radiotracer assays, analytical chemistry, MiSeq sequencing, and simulation-based microcosm incubation approaches, we demonstrated succession patterns of microbial diesel-degrading activities, and bacterial and fungal community compositions. The biodegradation activities of alkanes and polycyclic aromatic hydrocarbons (PAHs) were induced within 24 h after diesel addition, and reached their maximum after incubation for 7 days. Potential diesel-degrading bacteria Perlucidibaca, Acinetobacter, Pseudomonas, Acidovorax, and Aquabacterium dominated the community initially (day 3 and day 7), but later community structure (day 21) was dominated by bacteria Ralstonia and Planctomyces. The key early fungi responders were Aspergillus, Mortierella, and Phaeoacremonium by day 7, whereas Bullera and Basidiobolus dominated the fungal community at day 21. These results directly characterize the rapid response of microbial community to diesel spills, and suggest that the progression of diesel microbial degradation is performed by the cooperative system of the versatile obligate diesel-degrading and some general heterotrophic microorganisms in river diesel spills. Full article

(This article belongs to the Special Issue Petroleum Microbiology 2.0)

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21 pages, 2746 KiB

Open AccessArticle

Interaction between Illite and a Pseudomonas stutzeri-Heavy Oil Biodegradation Complex

by Lei Li, Yun Yang Wan, Hong Mei Mu, Sheng Bao Shi and Jian Fa Chen

Microorganisms 2023, 11(2), 330; https://doi.org/10.3390/microorganisms11020330 - 28 Jan 2023

Cited by 1 | Viewed by 1545

Abstract

Illite is a widely distributed clay mineral with huge reserves in Earth’s crust, but its effect on heavy oil biodegradation is rarely reported. This study made an investigation of the interactions between illite and a Pseudomonas stutzeri-heavy oil complex (PstHO). [...] Read more.

Illite is a widely distributed clay mineral with huge reserves in Earth’s crust, but its effect on heavy oil biodegradation is rarely reported. This study made an investigation of the interactions between illite and a Pseudomonas stutzeri-heavy oil complex (PstHO). Results showed that, although illite exerted a negative effect on P. stutzeri degrading heavy oil by inhibiting the biodegradation of 64 saturated hydrocarbons (SHs) and 50 aromatic hydrocarbons (AHs), it selectively stimulated the biodegradation of 45 AHs with a specific structure, and its biogenic kaolinization at room temperature (35 °C) and pressure (1 atm) was observed in PstHO for the first time. The finding points out for the first time that, in PstHO, illite may change the quasi-sequential of AHs biodegradation of heavy oil, as well as its kaolinization without clay intermediate. Full article

(This article belongs to the Special Issue Petroleum Microbiology 2.0)

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15 pages, 30746 KiB

Open AccessArticle

Comparative Genomic Analysis of the Hydrocarbon-Oxidizing Dibenzothiophene-Desulfurizing Gordonia Strains

by Ekaterina Frantsuzova, Yanina Delegan, Alexander Bogun, Diyana Sokolova and Tamara Nazina

Microorganisms 2023, 11(1), 4; https://doi.org/10.3390/microorganisms11010004 - 20 Dec 2022

Cited by 4 | Viewed by 1911

Abstract

A number of actinobacteria of the genus Gordonia are able to use dibenzothiophene (DBT) and its derivatives as the only source of sulfur, which makes them promising agents for the process of oil biodesulfurization. Actinobacteria assimilate sulfur from condensed thiophenes without breaking the [...] Read more.

A number of actinobacteria of the genus Gordonia are able to use dibenzothiophene (DBT) and its derivatives as the only source of sulfur, which makes them promising agents for the process of oil biodesulfurization. Actinobacteria assimilate sulfur from condensed thiophenes without breaking the carbon–carbon bonds, using the 4S pathway encoded by the dszABC operon-like structure. The genome of the new dibenzothiophene-degrading hydrocarbon-oxidizing bacterial strain Gordonia amicalis 6-1 was completely sequenced and the genes potentially involved in the pathways of DBT desulfurization, oxidation of alkanes and aromatic compounds, as well as in the osmoprotectant metabolism in strain 6-1 and other members of the genus Gordonia, were analyzed. The genome of G. amicalis strain 6-1 consists of a 5,105,798-bp circular chromosome (67.3% GC content) and an 86,621-bp circular plasmid, pCP86 (65.4% GC content). This paper presents a comparative bioinformatic analysis of complete genomes of strain 6-1 and dibenzothiophene-degrading Gordonia strains 1D and 135 that do not have the dsz operon. The assumption is made about the participation in this process of the region containing the sfnB gene. Genomic analysis supported the results of phenomenological studies of Gordonia strains and the possibility of their application in the bioremediation of oil-contaminated environments and in the purification of oil equipment from oil and asphalt-resin-paraffin deposits. Full article

(This article belongs to the Special Issue Petroleum Microbiology 2.0)

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13 pages, 11093 KiB

Open AccessArticle

Single-Cell-Based High-Throughput Cultivation and Functional Characterization of Biosurfactant-Producing Bacteria from Soil and Oilfield-Produced Water

by Ying Xu, Yali Jing, Yaqian Zhang, Qingjie Liu, Jianlong Xiu, Ke Zhang, Ninghong Jia, Minghui Zhou, Xinyu Zhou, Jia Huang, Yong Nie and Xiao-Lei Wu

Microorganisms 2022, 10(11), 2216; https://doi.org/10.3390/microorganisms10112216 - 09 Nov 2022

Cited by 2 | Viewed by 1365

Abstract

Biosurfactants are a group of surface-active compounds that can be produced by diverse microorganisms. They have been widely used in various industrial fields. Reducing production costs, improving efficiency, and collecting more diverse producing strains have become major challenges in the biosurfactant industry. These [...] Read more.

Biosurfactants are a group of surface-active compounds that can be produced by diverse microorganisms. They have been widely used in various industrial fields. Reducing production costs, improving efficiency, and collecting more diverse producing strains have become major challenges in the biosurfactant industry. These challenges could be overcome by screening for more diverse and efficient biosurfactant-producing strains. The conventional methods for the isolation and functional characterization of microorganisms are laborious and biased toward fast-growing or strongly competitive microorganisms. Here, we established a high-throughput approach of single-cell-based cultivation and functional characterization of biosurfactant-producing bacteria (SCCBB). This approach combines single-cell cultivation with the detection of optical distortions. Using this approach, we isolated 431 strains with biosurfactant production potential from petroleum-contaminated soil and oilfield-produced water. The surfactant production capabilities of the strains were subsequently validated using surface tension measurements, TLC, and CMC measurements. To investigate the industrial production potential, we optimized the production conditions of a representative glycolipids-producing strain, Pseudomonas sp. L01, using response surface methodology (RSM). Optimal conditions yielded a crude biosurfactant yield of 8.43 g/L in a flask. Our work provides a high-throughput approach to the isolation and screening of biosurfactant-producing bacteria, as well as other functional bacteria in a wide range of fields. Full article

(This article belongs to the Special Issue Petroleum Microbiology 2.0)

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