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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 34984

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Special Issue Editors

Dr. Tamara N. Nazina

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Guest Editor

Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya, 7/2, 117312 Moscow, Russia
Interests: petroleum microbiology; crude oil pollution
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Bo-Zhong Mu

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Guest Editor

Institute of Applied Chemistry, East China University of Science and Technology, Shanghai 200237, China
Interests: petroleum microbiology; microbially enhanced oil recovery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In 2026, it will be 100 years since the first articles on petroleum microbiology were published. This was the year when Bastin E.S. and Beckman J.W. in the USA and Ginzburg-Karagicheva T.L. in the USSR outlined the range of basic and applied issues within the scope of petroleum microbiology, including the microbial ecology of petroleum reservoirs and involvement of microorganisms in oil transformation, corrosion of steel equipment, and oil-souring. Petroleum reservoirs are now recognized as integrated ecosystems, where microbial populations interact with the environment and with each other, while the energy flows are based on biotransformation of oil and exogenous trophic substrates in a trophic change and may be regulated.

This Special Issue will publish papers that address a wide range of problems of petroleum microbiology: (1) phylogenetic and functional microbial diversity in petroleum and gas reservoirs and underground gas storage; (2) the new taxa of prokaryotes from petroleum reservoirs; (3) CO₂ sequestration in petroleum reservoirs and its influence on microbial communities; (4) aerobic and anaerobic biotransformation of crude oil and bitumen; (5) impact of metagenomics approaches in ecology of microorganisms in petroleum reservoirs; and (6) biotechnologies for the oil industry, including microbial enhanced energy recovery, microbiologically influenced corrosion and souring, etc.

Dr. Tamara N. Nazina
Prof. Dr. Bo-Zhong Mu
Guest Editors

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Published Papers (11 papers)

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Editorial

Jump to: Research, Review, Other

5 pages, 194 KiB

Open AccessEditorial

Recent Advances in Petroleum Microbiology

by Bo-Zhong Mu and Tamara N. Nazina

Microorganisms 2022, 10(9), 1706; https://doi.org/10.3390/microorganisms10091706 - 24 Aug 2022

Cited by 5 | Viewed by 2606

Abstract

Petroleum reservoirs are unique deep-subsurface ecosystems that are generally characterized by such extreme conditions as high temperature, high pressure, high salinity, and anoxia [...] Full article

(This article belongs to the Special Issue Petroleum Microbiology)

Research

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13 pages, 1784 KiB

Open AccessArticle

Hydrocarbon Cycling in the Tokamachi Mud Volcano (Japan): Insights from Isotopologue and Metataxonomic Analyses

by Alexis Gilbert, Mayuko Nakagawa, Koudai Taguchi, Naizhong Zhang, Akifumi Nishida and Naohiro Yoshida

Microorganisms 2022, 10(7), 1417; https://doi.org/10.3390/microorganisms10071417 - 14 Jul 2022

Cited by 12 | Viewed by 2578

Abstract

Understanding hydrocarbon cycling in the subsurface is important in various disciplines including climate science, energy resources and astrobiology. Mud volcanoes provide insights into biogeochemical processes occurring in the subsurface. They are usually associated with natural gas reservoirs consisting mainly of methane and other hydrocarbons as well as CO₂. Stable isotopes have been used to decipher the sources and sinks of hydrocarbons in the subsurface, although the interpretation can be ambiguous due to the numerous processes involved. Here we report new data for hydrocarbon isotope analysis, including position-specific isotope composition of propane, for samples from the Tokamachi mud volcano area, Japan. The data suggest that C₂₊ hydrocarbons are being biodegraded, with indirect production of methane (“secondary methanogenesis”). Data from chemical and isotopic composition are discussed with regard to 16S rRNA analysis, which exhibits the presence of hydrogenotrophic and acetoclastic methoanogens. Overall, the combination of isotopologue analysis with 16S rRNA gene data allows refining of our understanding of hydrocarbon cycling in subsurface environments. Full article

(This article belongs to the Special Issue Petroleum Microbiology)

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20 pages, 4270 KiB

Open AccessArticle

Assessing Microbial Corrosion Risk on Offshore Crude Oil Production Topsides under Conditions of Nitrate and Nitrite Treatment for Souring

by Danika Nicoletti, Mohita Sharma and Lisa M. Gieg

Microorganisms 2022, 10(5), 932; https://doi.org/10.3390/microorganisms10050932 - 29 Apr 2022

Cited by 6 | Viewed by 3101

Abstract

Oilfield souring is a detrimental effect caused by sulfate-reducing microorganisms that reduce sulfate to sulfide during their respiration process. Nitrate or nitrite can be used to mitigate souring, but may also impart a corrosion risk. Produced fluids sampled from the topside infrastructure of two floating, production, storage, and offloading (FPSO) vessels (Platform A and Platform B) were assessed for microbial corrosion under nitrate and nitrite breakthrough conditions using microcosm tests incubated at 54 °C. Microbial community compositions on each individual FPSO were similar, while those between the two FPSO vessels differed. Platform B microbial communities responded as expected to nitrate breakthrough conditions, where nitrate-reducing activity was enhanced and sulfate reduction was inhibited. In contrast, nitrate treatments of Platform A microbial communities were not as effective in preventing sulfide production. Nitrite breakthrough conditions had the strongest sulfate reduction inhibition in samples from both platforms, but exhibited the highest pitting density. Live experimental replicates with no nitrate or nitrite additive yielded the highest general corrosion rates in the study (up to 0.48 mm/year), while nitrate- or nitrite-treated fluids revealed general corrosion rates that are considered low or moderate (<0.12 mm/year). Overall, the results of this study provide a description of nitrogen- and sulfur-based microbial activities under thermophilic conditions, and their risk for MIC that can occur along fluid processing lines on FPSO topsides that process fluids during offshore oil production operations. Full article

(This article belongs to the Special Issue Petroleum Microbiology)

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22 pages, 2924 KiB

Open AccessArticle

Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae

by Ekaterina M. Semenova, Denis S. Grouzdev, Diyana S. Sokolova, Tatiyana P. Tourova, Andrey B. Poltaraus, Natalia V. Potekhina, Polina N. Shishina, Maria A. Bolshakova, Alexander N. Avtukh, Elena A. Ianutsevich, Vera M. Tereshina and Tamara N. Nazina

Microorganisms 2022, 10(2), 378; https://doi.org/10.3390/microorganisms10020378 - 6 Feb 2022

Cited by 11 | Viewed by 3206 | Correction

Abstract

The goal of the present work was to determine the diversity of prokaryotes involved in anaerobic oil degradation in oil fields. The composition of the anaerobic oil-degrading methanogenic enrichment obtained from an oil reservoir was determined by 16S rRNA-based survey, and the facultatively anaerobic chemoorganotrophic bacterial strain HO-Ch2^T was isolated and studied using polyphasic taxonomy approach and genome sequencing. The strain HO-Ch2^T grew optimally at 28 °C, pH 8.0, and 1–2% (w/v) NaCl. The 16S rRNA gene sequence of the strain HO-Ch2^T had 98.8% similarity with the sequence of Actinotalea ferrariae CF5-4^T. The genomic DNA G + C content of strain HO-Ch2^T was 73.4%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the genome of strain HO-Ch2^T and Actinotalea genomes were 79.8–82.0% and 20.5–22.2%, respectively, i.e., below the thresholds for species delineation. Based on the phylogenomic, phenotypic, and chemotaxonomic characterization, we propose strain HO-Ch2^T (= VKM Ac-2850^T = KCTC 49656^T) as the type strain of a new species within the genus Actinotalea, with the name Actinotalea subterranea sp. nov. Based on the phylogenomic analysis of 187 genomes of Actinobacteria we propose the taxonomic revision of the genera Actinotalea and Pseudactinotalea and of the family Actinotaleaceae. We also propose the reclassification of Cellulomonas carbonis as Actinotalea carbonis comb. nov., Cellulomonas bogoriensis as Actinotalea bogoriensis comb. nov., Actinotalea caeni as Pseudactinotalea caeni comb. nov., and the transfer of the genus Pseudactinotalea to the family Ruaniaceae of the order Ruaniales. Full article

(This article belongs to the Special Issue Petroleum Microbiology)

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21 pages, 2430 KiB

Open AccessArticle

Metagenomic Investigation of a Low Diversity, High Salinity Offshore Oil Reservoir

by Gabrielle Scheffer, Casey R. J. Hubert, Dennis R. Enning, Sven Lahme, Jaspreet Mand and Júlia R. de Rezende

Microorganisms 2021, 9(11), 2266; https://doi.org/10.3390/microorganisms9112266 - 31 Oct 2021

Cited by 11 | Viewed by 3788

Abstract

Oil reservoirs can represent extreme environments for microbial life due to low water availability, high salinity, high pressure and naturally occurring radionuclides. This study investigated the microbiome of saline formation water samples from a Gulf of Mexico oil reservoir. Metagenomic analysis and associated anaerobic enrichment cultures enabled investigations into metabolic potential for microbial activity and persistence in this environment given its high salinity (4.5%) and low nutrient availability. Preliminary 16S rRNA gene amplicon sequencing revealed very low microbial diversity. Accordingly, deep shotgun sequencing resulted in nine metagenome-assembled genomes (MAGs), including members of novel lineages QPJE01 (genus level) within the Halanaerobiaceae, and BM520 (family level) within the Bacteroidales. Genomes of the nine organisms included respiratory pathways such as nitrate reduction (in Arhodomonas, Flexistipes, Geotoga and Marinobacter MAGs) and thiosulfate reduction (in Arhodomonas, Flexistipes and Geotoga MAGs). Genomic evidence for adaptation to high salinity, withstanding radioactivity, and metal acquisition was also observed in different MAGs, possibly explaining their occurrence in this extreme habitat. Other metabolic features included the potential for quorum sensing and biofilm formation, and genes for forming endospores in some cases. Understanding the microbiomes of deep biosphere environments sheds light on the capabilities of uncultivated subsurface microorganisms and their potential roles in subsurface settings, including during oil recovery operations. Full article

(This article belongs to the Special Issue Petroleum Microbiology)

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18 pages, 2536 KiB

Open AccessArticle

Bioemulsification and Microbial Community Reconstruction in Thermally Processed Crude Oil

by Bing Hu, Jie-Yu Zhao, Yong Nie, Xiao-Yu Qin, Kai-Duan Zhang, Jian-Min Xing and Xiao-Lei Wu

Microorganisms 2021, 9(10), 2054; https://doi.org/10.3390/microorganisms9102054 - 29 Sep 2021

Cited by 2 | Viewed by 2374

Abstract

Utilization of low-cost, environmental-friendly microbial enhanced oil recovery (MEOR) techniques in thermal recovery-processed oil reservoirs is potentially feasible. However, how exogenous microbes facilitate crude oil recovery in this deep biosphere, especially under mesophilic conditions, is scarcely investigated. In this study, a thermal treatment and a thermal recurrence were processed on crude oil collected from Daqing Oilfield, and then a 30-day incubation of the pretreated crude oil at 37 °C was operated with the addition of two locally isolated hydrocarbon-degrading bacteria, Amycolicicoccus subflavus DQS3-9A1^T and Dietzia sp. DQ12-45-1b, respectively. The pH, surface tension, hydrocarbon profiles, culture-dependent cell densities and taxonomies, and whole and active microbial community compositions were determined. It was found that both A. subflavus DQS3-9A1^T and Dietzia sp. DQ12-45-1b successfully induced culture acidification, crude oil bioemulsification, and residual oil sub-fraction alteration, no matter whether the crude oil was thermally pretreated or not. Endogenous bacteria which could proliferate on double heated crude oil were very few. Compared with A. subflavus, Dietzia sp. was substantially more effective at inducing the proliferation of varied species in one-time heated crude oil. Meanwhile, the effects of Dietzia sp. on crude oil bioemulsification and hydrocarbon profile alteration were not significantly influenced by the ploidy increasing of NaCl contents (from 5 g/L to 50 g/L), but the reconstructed bacterial communities became very simple, in which the Dietzia genus was predominant. Our study provides useful information to understand MEOR trials on thermally processed oil reservoirs, and proves that this strategy could be operated by using the locally available hydrocarbon-degrading microbes in mesophilic conditions with different salinity degrees. Full article

(This article belongs to the Special Issue Petroleum Microbiology)

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11 pages, 20823 KiB

Open AccessArticle

Composition and Corrosivity of Extracellular Polymeric Substances from the Hydrocarbon-Degrading Sulfate-Reducing Bacterium Desulfoglaeba alkanexedens ALDC

by Irene A. Davidova, Tiffany R. Lenhart, Mark A. Nanny and Joseph M. Suflita

Microorganisms 2021, 9(9), 1994; https://doi.org/10.3390/microorganisms9091994 - 21 Sep 2021

Cited by 5 | Viewed by 2213

Abstract

Sulfate-reducing bacteria (SRB) often exist as cell aggregates and in biofilms surrounded by a matrix of extracellular polymeric substances (EPSs). The chemical composition of EPSs may facilitate hydrophobic substrate biodegradation and promote microbial influenced corrosion (MIC). Although EPSs from non-hydrocarbon-degrading SRB have been studied; the chemical composition of EPSs from hydrocarbon-degrading SRBs has not been reported. The isolated EPSs from the sulfate-reducing alkane-degrading bacterium Desulfoglaeba alkanexedens ALDC was characterized with scanning and fluorescent microscopy, nuclear magnetic resonance spectroscopy (NMR), and by colorimetric chemical assays. Specific fluorescent staining and ¹H NMR spectroscopy revealed that the fundamental chemical structure of the EPS produced by D. alkanexedens is composed of pyranose polysaccharide and cyclopentanone in a 2:1 ratio. NMR analyses indicated that the pyranose ring structure is bonded by 1,4 connections with the cyclopentanone directly bonded to one pyranose ring. The presence of cyclopentanone presumably increases the hydrophobicity of the EPS that may facilitate the accessibility of hydrocarbon substrates to aggregating cells or cells in a biofilm. Weight loss and iron dissolution experiments demonstrated that the EPS did not contribute to the corrosivity of D. alkanexedens cells. Full article

(This article belongs to the Special Issue Petroleum Microbiology)

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20 pages, 10784 KiB

Open AccessArticle

Sulfidogenic Microbial Communities of the Uzen High-Temperature Oil Field in Kazakhstan

by Diyana S. Sokolova, Ekaterina M. Semenova, Denis S. Grouzdev, Salimat K. Bidzhieva, Tamara L. Babich, Nataliya G. Loiko, Alexey P. Ershov, Vitaly V. Kadnikov, Alexey V. Beletsky, Andrey V. Mardanov, Nurlan S. Zhaparov and Tamara N. Nazina

Microorganisms 2021, 9(9), 1818; https://doi.org/10.3390/microorganisms9091818 - 26 Aug 2021

Cited by 15 | Viewed by 3281

Abstract

Application of seawater for secondary oil recovery stimulates the development of sulfidogenic bacteria in the oil field leading to microbially influenced corrosion of steel equipment, oil souring, and environmental issues. The aim of this work was to investigate potential sulfide producers in the high-temperature Uzen oil field (Republic of Kazakhstan) exploited with seawater flooding and the possibility of suppressing growth of sulfidogens in both planktonic and biofilm forms. Approaches used in the study included 16S rRNA and dsrAB gene sequencing, scanning electron microscopy, and culture-based techniques. Thermophilic hydrogenotrophic methanogens of the genus Methanothermococcus (phylum Euryarchaeota) predominated in water from the zone not affected by seawater flooding. Methanogens were accompanied by fermentative bacteria of the genera Thermovirga, Defliviitoga, Geotoga, and Thermosipho (phylum Thermotogae), which are potential thiosulfate- or/and sulfur-reducers. In the sulfate- and sulfide-rich formation water, the share of Desulfonauticus sulfate-reducing bacteria (SRB) increased. Thermodesulforhabdus, Thermodesulfobacterium, Desulfotomaculum, Desulfovibrio, and Desulfoglaeba were also detected. Mesophilic denitrifying bacteria of the genera Marinobacter, Halomonas, and Pelobacter inhabited the near-bottom zone of injection wells. Nitrate did not suppress sulfidogenesis in mesophilic enrichments because denitrifiers reduced nitrate to dinitrogen; however, thermophilic denitrifiers produced nitrite, an inhibitor of SRB. Enrichments and a pure culture Desulfovibrio alaskensis Kaz19 formed biofilms highly resistant to biocides. Our results suggest that seawater injection and temperature of the environment determine the composition and functional activity of prokaryotes in the Uzen oil field. Full article

(This article belongs to the Special Issue Petroleum Microbiology)

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21 pages, 4266 KiB

Open AccessArticle

Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide

by Kelly J. Hidalgo, Isabel N. Sierra-Garcia, German Zafra and Valéria M. de Oliveira

Microorganisms 2021, 9(9), 1812; https://doi.org/10.3390/microorganisms9091812 - 26 Aug 2021

Cited by 8 | Viewed by 4847

Abstract

Microorganisms inhabiting subsurface petroleum reservoirs are key players in biochemical transformations. The interactions of microbial communities in these environments are highly complex and still poorly understood. This work aimed to assess publicly available metagenomes from oil reservoirs and implement a robust pipeline of genome-resolved metagenomics to decipher metabolic and taxonomic profiles of petroleum reservoirs worldwide. Analysis of 301.2 Gb of metagenomic information derived from heavily flooded petroleum reservoirs in China and Alaska to non-flooded petroleum reservoirs in Brazil enabled us to reconstruct 148 metagenome-assembled genomes (MAGs) of high and medium quality. At the phylum level, 74% of MAGs belonged to bacteria and 26% to archaea. The profiles of these MAGs were related to the physicochemical parameters and recovery management applied. The analysis of the potential functional core in the reservoirs showed that the microbiota was specialized for each site, with 31.7% of the total KEGG orthologies annotated as functions (1690 genes) common to all oil fields, while 18% of the functions were site-specific, i.e., present only in one of the oil fields. The oil reservoirs with a lower level of intervention were the most similar to the potential functional core, while the oil fields with a long history of water injection had greater variation in functional profile. These results show how key microorganisms and their functions respond to the distinct physicochemical parameters and interventions of the oil field operations such as water injection and expand the knowledge of biogeochemical transformations in these ecosystems. Full article

(This article belongs to the Special Issue Petroleum Microbiology)

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Review

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15 pages, 1171 KiB

Open AccessReview

Microbial Lipopeptide-Producing Strains and Their Metabolic Roles under Anaerobic Conditions

by Jia-Yi Li, Lu Wang, Yi-Fan Liu, Lei Zhou, Hong-Ze Gang, Jin-Feng Liu, Shi-Zhong Yang and Bo-Zhong Mu

Microorganisms 2021, 9(10), 2030; https://doi.org/10.3390/microorganisms9102030 - 25 Sep 2021

Cited by 15 | Viewed by 3109

Abstract

The lipopeptide produced by microorganisms is one of the representative biosurfactants and is characterized as a series of structural analogues of different families. Thirty-four families covering about 300 lipopeptide compounds have been reported in the last decades, and most of the reported lipopeptides produced by microorganisms were under aerobic conditions. The lipopeptide-producing strains under anaerobic conditions have attracted much attention from both the academic and industrial communities, due to the needs and the challenge of their applications in anaerobic environments, such as in oil reservoirs and in microbial enhanced oil recovery (MEOR). In this review, the fifty-eight reported bacterial strains, mostly isolated from oil reservoirs and dominated by the species Bacillus subtilis, producing lipopeptide biosurfactants, and the species Pseudomonas aeruginosa, producing glycolipid biosurfactants under anaerobic conditions were summarized. The metabolic pathway and the non-ribosomal peptide synthetases (NRPSs) of the strain Bacillus subtilis under anaerobic conditions were analyzed, which is expected to better understand the key mechanisms of the growth and production of lipopeptide biosurfactants of such kind of bacteria under anaerobic conditions, and to expand the industrial application of anaerobic biosurfactant-producing bacteria. Full article

(This article belongs to the Special Issue Petroleum Microbiology)

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