Characterization of microbial communities in heavy crude oil from Saudi Arabia

Simultaneous removal of crude oil and heavy metals by highly adapted bacterial strain Cutibacterium sp. NL2 isolated from Algerian oilfield

Investigating the ability of bacteria to simultaneously enhance hydrocarbon removal and reduce heavy metals' toxicity is necessary to design more effective bioremediation strategies. A bacterium (NL2 strain) isolated from an Algerian oilfield was cultivated on crude oil as sole carbon and energy sources. Molecular analyses of the 16S rRNA gene sequence placed the strain within the Cutibacterium genera. This isolate was able to tolerate up to 60% of crude oil as sole carbon source. Chemical analyses (GC-MS) evidenced that strain NL2 was able to degrade 92.22% of crude oil (at optimal growing conditions: pH 10, 44 °C, 50 g L-1 NaCl, and 20% of crude oil (v/v) as sole carbon source) in only 7 days. NL2 isolate was also able to produce biosurfactants with reduction of surface tension of growing media (29.4 mN m-1). On the other hand, NL2 strain was able to tolerate high lead (Pb) and copper (Cu) concentrations (up to 60 mM). In fact, NL2 cultivated in the presence of 20% of crude oil, and 0.48 mM of Pb was able to reduce Pb concentration by a 41.36%. In turn, when cultivated on high Pb concentration (15 mM), the strain was able to remove 35.19% of it and 86.25% of crude oil, both in a time frame of 7 days. Our findings suggest that Cutibacterium strain NL2 is able to efficiently use and remove a wide range of crude oil substrates in presence of high Pb concentration. Accordingly, NL2 strain is of extreme interest from a biotechnological standpoint.

Isolation, identification, and screening of biosurfactant-producing and hydrocarbon-degrading bacteria from oil and gas industrial waste

Qatar is one of the biggest oil and gas producers in the world, coupled with it is challenging environmental conditions (high average temperature: >40 °C, low annual rainfall: 46.71 mm, and high annual evaporation rate: 2200 mm) harbors diverse microbial communities that are novel and robust, with the potential to biodegrade hydrocarbons. In this study, we collected hydrocarbon contaminated sludge, wastewater and soil samples from oil and gas industries in Qatar. Twenty-six bacterial strains were isolated in the laboratory from these samples using high saline conditions and crude oil as the sole carbon source. A total of 15 different bacterial genera were identified in our study that have not been widely reported in the literature or studied for their usage in the biodegradation of hydrocarbons. Interestingly, some of the bacteria that were identified belonged to the same genus however, demonstrated variable growth rates and biosurfactant production. This indicates the possibility of niche specialization and specific evolution to acquire competitive traits for better survival. The most potent strain EXS14, identified as Marinobacter sp., showed the highest growth rate in the oil-containing medium as well as the highest biosurfactant production. When this strain was further tested for biodegradation of hydrocarbons, the results showed that it was able to degrade 90 to 100% of low and medium molecular weight hydrocarbons and 60 to 80% of high molecular weight (C35 to C50) hydrocarbons. This study offers many promising leads for future studies of microbial species and their application for the treatment of hydrocarbon contaminated wastewater and soil in the region and in other areas with similar environmental conditions.

Corrosion-influencing microorganisms in petroliferous regions on a global scale: systematic review, analysis, and scientific synthesis of 16S amplicon metagenomic studies

The objective of the current systematic review was to evaluate the taxonomic composition and relative abundance of bacteria and archaea associated with the microbiologically influenced corrosion (MIC), and the prediction of their metabolic functions in different sample types from oil production and transport structures worldwide. To accomplish this goal, a total of 552 published studies on the diversity of microbial communities using 16S amplicon metagenomics in oil and gas industry facilities indexed in Scopus, Web of Science, PubMed and OnePetro databases were analyzed on 10th May 2021. The selection of articles was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Only studies that performed amplicon metagenomics to obtain the microbial composition of samples from oil fields were included. Studies that evaluated oil refineries, carried out amplicon metagenomics directly from cultures, and those that used DGGE analysis were removed. Data were thoroughly investigated using multivariate statistics by ordination analysis, bivariate statistics by correlation, and microorganisms' shareability and uniqueness analysis. Additionally, the full deposited databases of 16S rDNA sequences were obtained to perform functional prediction. A total of 69 eligible articles was included for data analysis. The results showed that the sulfidogenic, methanogenic, acid-producing, and nitrate-reducing functional groups were the most expressive, all of which can be directly involved in MIC processes. There were significant positive correlations between microorganisms in the injection water (IW), produced water (PW), and solid deposits (SD) samples, and negative correlations in the PW and SD samples. Only the PW and SD samples displayed genera common to all petroliferous regions, Desulfotomaculum and Thermovirga (PW), and Marinobacter (SD). There was an inferred high microbial activity in the oil fields, with the highest abundances of (i) cofactor, (ii) carrier, and (iii) vitamin biosynthesis, associated with survival metabolism. Additionally, there was the presence of secondary metabolic pathways and defense mechanisms in extreme conditions. Competitive or inhibitory relationships and metabolic patterns were influenced by the physicochemical characteristics of the environments (mainly sulfate concentration) and by human interference (application of biocides and nutrients). Our worldwide baseline study of microbial communities associated with environments of the oil and gas industry will greatly facilitate the establishment of standardized approaches to control MIC.

Correlation of soil microbiome with crude oil contamination drives detection of hydrocarbon degrading genes which are independent to quantity and type of contaminants

The impacts of crude oil contamination on soil microbial populations were explored in seven different polluted areas near oil and gas drilling sites and refineries of Assam, India. Using high-throughput sequencing techniques, the functional genes and metabolic pathways involved in the bioconversion of crude oil contaminants by the indigenous microbial community were explored. Total petroleum hydrocarbon (TPH) concentrations in soil samples ranged from 1109.47 to 75,725.33 mg/kg, while total polyaromatic hydrocarbon (PAH) concentrations ranged from 0.780 to 560.05 mg/kg. Pyrene, benzo[a]anthracene, naphthalene, phenanthrene, and anthracene had greater quantities than the maximum permitted limits, suggesting a greater ecological risk, in comparison to other polyaromatic hydrocarbons. According to the metagenomic data analysis, the bacterial phyla Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroides were the most prevalent among all polluted areas. The most prominent hydrocarbon degraders in the contaminated sites included Burkholderia, Mycobacterium, Polaromonas, and Pseudomonas. However, the kinds of pollutants and their concentrations did not correlate with the abundances of respective degrading genes for all polluted locations, as some of the sites with little to low PAH contamination had significant abundances of corresponding functional genes for degradation. Thus, the findings of this study imply that the microbiome of hydrocarbon-contaminated areas, which are biologically involved in the degradation process, has various genes, operons and catabolic pathways that are independent of the presence of a specific kind of contaminant.

Microbiome Studies from Saudi Arabia over the Last 10 Years: Achievements, Gaps, and Future Directions

In the past ten years, microbiome studies have shown tremendous potentiality for implementation of understanding microbiome structures and functions of various biomes and application of this knowledge for human betterment. Saudi Arabia is full of geographical, ecological, ethnical, and industrial diversities and scientific capacities. Therefore, there is a great potential in Saudi Arabia to conduct and implement microbiome-based research and applications. However, there is no review available on where Saudi Arabia stands with respect to global microbiome research trends. This review highlights the metagenome-assisted microbiome research from Saudi Arabia compared to the global focuses on microbiome research. Further, it also highlights the gaps and areas that should be focused on by Saudi microbiome researchers and the possible initiatives to be taken by Saudi government and universities. This literature review shows that the global trends of microbiome research cover a broad spectrum of human and animal health conditions and diseases, environmental and antimicrobial resistance surveillance, surveillance of food and food processing, production of novel industrial enzymes and bioactive pharmaceutical products, and space applications. However, Saudi microbiome studies are mostly confined to very few aspects of health (human and animal) and environment/ecology in last ten years, without much application. Therefore, Saudi Arabia should focus more on applied microbiome research through government, academic, and industry initiatives and global cooperation to match the global trends.

Exploiting Microbes in the Petroleum Field: Analyzing the Credibility of Microbial Enhanced Oil Recovery (MEOR)

Crude oil is a major energy source that is exploited globally to achieve economic growth. To meet the growing demands for oil, in an environment of stringent environmental regulations and economic and technical pressure, industries have been required to develop novel oil salvaging techniques. The remaining ~70% of the world’s conventional oil (one-third of the available total petroleum) is trapped in depleted and marginal reservoirs, and could thus be potentially recovered and used. The only means of extracting this oil is via microbial enhanced oil recovery (MEOR). This tertiary oil recovery method employs indigenous microorganisms and their metabolic products to enhance oil mobilization. Although a significant amount of research has been undertaken on MEOR, the absence of convincing evidence has contributed to the petroleum industry’s low interest, as evidenced by the issuance of 400+ patents on MEOR that have not been accepted by this sector. The majority of the world’s MEOR field trials are briefly described in this review. However, the presented research fails to provide valid verification that the microbial system has the potential to address the identified constraints. Rather than promising certainty, MEOR will persist as an unverified concept unless further research and investigations are carried out.

Characterization of microbial response to petroleum hydrocarbon contamination in a lacustrine ecosystem

Microbiomes of freshwater basins intended for human use remain poorly studied, with very little known about the microbial response to in situ oil spills. Lake Pertusillo is an artificial freshwater reservoir in Basilicata, Italy, and serves as the primary source of drinking water for more than one and a half million people in the region. Notably, it is located in close proximity to one of the largest oil extraction plants in Europe. The lake suffered a major oil spill in 2017, where approximately 400 tons of crude oil spilled into the lake; importantly, the pollution event provided a rare opportunity to study how the lacustrine microbiome responds to petroleum hydrocarbon contamination. Water samples were collected from Lake Pertusillo 10 months prior to and 3 months after the accident. The presence of hydrocarbons was verified and the taxonomic and functional aspects of the lake microbiome were assessed. The analysis revealed specialized successional patterns of lake microbial communities that were potentially capable of degrading complex, recalcitrant hydrocarbons, including aromatic, chloroaromatic, nitroaromatic, and sulfur containing aromatic hydrocarbons. Our findings indicated that changes in the freshwater microbial community were associated with the oil pollution event, where microbial patterns identified in the lacustrine microbiome 3 months after the oil spill were representative of its hydrocarbonoclastic potential and may serve as effective proxies for lacustrine oil pollution.

Bacterial Community Legacy Effects Following the Agia Zoni II Oil-Spill, Greece

In September 2017 the Agia Zoni II sank in the Saronic Gulf, Greece, releasing approximately 500 tonnes of heavy fuel oil, contaminating the Salamina and Athens coastlines. Effects of the spill, and remediation efforts, on sediment microbial communities were quantified over the following 7 months. Five days post-spill, the concentration of measured hydrocarbons within surface sediments of contaminated beaches was 1,093-3,773 μg g-1 dry sediment (91% alkanes and 9% polycyclic aromatic hydrocarbons), but measured hydrocarbons decreased rapidly after extensive clean-up operations. Bacterial genera known to contain oil-degrading species increased in abundance, including Alcanivorax, Cycloclasticus, Oleibacter, Oleiphilus, and Thalassolituus, and the species Marinobacter hydrocarbonoclasticus from approximately 0.02 to >32% (collectively) of the total bacterial community. Abundance of genera with known hydrocarbon-degraders then decreased 1 month after clean-up. However, a legacy effect was observed within the bacterial community, whereby Alcanivorax and Cycloclasticus persisted for several months after the oil spill in formerly contaminated sites. This study is the first to evaluate the effect of the Agia Zoni II oil-spill on microbial communities in an oligotrophic sea, where in situ oil-spill studies are rare. The results aid the advancement of post-spill monitoring models, which can predict the capability of environments to naturally attenuate oil.

The effect of bioaugmentation with Exiguobacterium sp. AO-11 on crude oil removal and the bacterial community in sediment microcosms, and the development of a liquid ready-to-use inoculum

This study demonstrates the feasibility of using Exiguobacterium sp. AO-11 to remediate oil-contaminated environments. Bioaugmentation using AO-11 showed the best removal percentage, 75%, of 4% (w/w) crude oil in sediment microcosms in 100 days. In terms of the bacterial community structure during crude oil degradation, the addition of AO-11 did not change the indigenous bacterial community, while the addition of urea fertilizer induced structural shift of indigenous bacterial community. Exiguobacterium sp. AO-11 was developed as a bioremediation product, and a liquid formulation of AO-11 was developed. Coconut milk residue and soybean oil mill sludge were used for bacterial cultivation to reduce the production cost, and they could enhance bacterial cell growth. The liquid formulation of AO-11 prepared in phosphate buffer could be stored at 4 °C for at least 2 months, and it maintained efficacy in the treatment of crude oil-contaminated seawater. Overall, bioaugmentation with strain AO-11 could be an effective solution for the bioremediation of crude oil-contaminated environments.

Comparative analysis of bacterial community and functional species in oil reservoirs with different in situ temperatures

Temperature is supposed to be one of the primary drivers for the bacterial diversification as well as hydrocarbon formation process of oil reservoirs. However, the bacterial community compositions are not systematically elucidated in oil reservoirs with different temperatures. Herein, the diversity of indigenous bacteria and the functional species in the water samples from oil reservoirs with different in situ temperatures was investigated by high-throughput sequencing technology. The results showed that samples in the high (65 °C) and super high (80 °C) temperature oil reservoir had significantly high bacterial richness, even more than twice as much as moderate temperature (36 °C) ones, which showed relatively high bacterial diversity. Meanwhile, the bacterial compositions were almost similar in the high temperature oil reservoirs but there were different relative abundances of the bacterial communities. Phylogenetic analysis revealed that indigenous bacteria fell into 20 phylotypes in which Proteobacteria were the principal phylum in all of samples. At the genus level, 10 out of 22 major genera displayed statistically significant differences. Among of them, Pseudomonas was extremely dominant in all of samples, while Halomonas, Caldicoprobacter, Arcobacter, and Marinobacter tended to be enriched in the high temperature oil reservoirs. Moreover, the abundance of bacterial populations exhibited important distinction in oil reservoir such as hydrocarbon-oxidizing, fermentative, nitrate-reducing, sulfate-reducing, and methanogenic bacteria. Those bacteria were strongly correlated to in situ temperature variation.

Analysis of Bacterial Diversity in Different Heavy Oil Wells of a Reservoir in South Oman with Alkaline pH

The identification of potential hydrocarbon utilizing bacteria is an essential requirement in microbial enhanced oil recovery (MEOR). Molecular approaches like proteomic and genomic characterization of the isolates are replacing the traditional method of identification with systemic classification. Genotypic profiling of the isolates includes fingerprint or pattern-based technique and sequence-based technique. Understanding community structure and dynamics is essential for studying diversity profiles and is challenging in the case of microbial analysis. The present study aims to understand the bacterial community composition from different heavy oil contaminated soil samples collected from geographically related oil well areas in Oman and to identify spore-forming hydrocarbon utilizing cultivable bacteria. V4 region of 16S rDNA gene was the target for Ion PGM™. A total of 825081 raw sequences were obtained from Ion torrent from all the 10 soil samples. The species richness and evenness were found to be moderate in all the samples with four main phyla, Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria, the most abundant being Firmicutes. Bacillus sp. ubiquitously dominated in all samples followed by Paenibacillus, which was followed by Brevibacillus, Planococcus, and Flavobacterium. Principal Coordinate Analysis (PCoA) and UPGMA dendrogram clustered the 10 soil samples into four main groups. Weighted UniFrac significance test determined that there was significant difference in the communities present in soil samples examined. It can be concluded that the microbial community was different in all the 10 soil samples with Bacillus and Paenibacillus sp. as predominating genus. The 16S rDNA sequencing of cultivable spore-forming bacteria identified the hydrocarbon utilizing bacteria as Bacillus and Paenibacillus sp. and the nucleotide sequences were submitted to NCBI GenBank under accession numbers KP119097-KP119115. Bacillus and Paenibacillus sp., which were relatively abundant in the oil fields, can be recommended to be chosen as candidates for hydrocarbon utilization study.

Determination of petroleum biodegradation by bacteria isolated from drilling fluid, waste mud pit and crude oil

Objective:

In this study, the aim was to isolate and identify bacterial strains in crude oil, drilling fluid and waste mud pit samples collected from the same oil field, determine the petroleum biodegradation and find the most effective bacteria in the samples in petroleum biodegradation.

Methods:

The contents of crude oil, drilling fluid and waste mud pit samples were enriched in appropriate conditions. Upon identification of the isolated bacteria, the incubations in petroleum containing media were performed at 150 rpm at 30°C for 7 days. Petroleum biodegradations by bacteria were measured by using colorimetric, spectrophotometric and gravimetric methods.

Results:

were isolated from the crude oil sample;

Conclusion:

In literature, no study was encountered showing biodegradation efficiencies of

Considering the Specific Impact of Harsh Conditions and Oil Weathering on Diversity, Adaptation, and Activity of Hydrocarbon-Degrading Bacteria in Strategies of Bioremediation of Harsh Oily-Polluted Soils

Weathering processes change properties and composition of spilled oil, representing the main reason of failure of bioaugmentation strategies. Our purpose was to investigate the metabolic adaptation of hydrocarbon-degrading bacteria at harsh conditions to be considered to overcome the limitations of bioaugmentation strategies at harsh conditions. Polluted soils, exposed for prolonged periods to weathered oil in harsh soils and weather conditions, were used. Two types of enrichment cultures were employed using 5% and 10% oil or diesel as sole carbon sources with varying the mineral nitrogen sources and C/N ratios. The most effective isolates were obtained based on growth, tolerance to toxicity, and removal efficiency of diesel hydrocarbons. Activities of the newly isolated bacteria, in relation to the microenvironment from where they were isoalted and their interaction with the weathered oil, showed individual specific ability to adapt when exposed to such factors, to acquire metabolic potentialities. Among 39 isolates, ten identified ones by 16S rDNA genes similarities, including special two Pseudomonas isolates and one Citrobacter isolate, showed particularity of shifting hydrocarbon-degrading ability from short chain n-alkanes (n-C12-n-C16) to longer chain n-alkanes (n-C21-n-C25) and vice versa by alternating nitrogen source compositions and C/N ratios. This is shown for the first time.

Effect of Biostimulation Using Sewage Sludge, Soybean Meal, and Wheat Straw on Oil Degradation and Bacterial Community Composition in a Contaminated Desert Soil

Waste materials have a strong potential in the bioremediation of oil-contaminated sites, because of their richness in nutrients and their economical feasibility. We used sewage sludge, soybean meal, and wheat straw to biostimulate oil degradation in a heavily contaminated desert soil. While oil degradation was assessed by following the produced CO₂ and by using gas chromatography–mass spectrometry (GC–MS), shifts in bacterial community composition were monitored using illumina MiSeq. The addition of sewage sludge and wheat straw to the desert soil stimulated the respiration activities to reach 3.2–3.4 times higher than in the untreated soil, whereas the addition of soybean meal resulted in an insignificant change in the produced CO₂, given the high respiration activities of the soybean meal alone. GC–MS analysis revealed that the addition of sewage sludge and wheat straw resulted in 1.7–1.8 fold increase in the degraded C₁₄ to C₃₀ alkanes, compared to only 1.3 fold increase in the case of soybean meal addition. The degradation of ≥90% of the C₁₄ to C₃₀ alkanes was measured in the soils treated with sewage sludge and wheat straw. MiSeq sequencing revealed that the majority (76.5–86.4% of total sequences) of acquired sequences from the untreated soil belonged to Alphaproteobacteria, Gammaproteobacteria, and Firmicutes. Multivariate analysis of operational taxonomic units placed the bacterial communities of the soils after the treatments in separate clusters (ANOSIM R = 0.66, P = 0.0001). The most remarkable shift in bacterial communities was in the wheat straw treatment, where 95–98% of the total sequences were affiliated to Bacilli. We conclude that sewage sludge and wheat straw are useful biostimulating agents for the cleanup of oil-contaminated desert soils.