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Ershov AP, Babich TL, Grouzdev DS, Sokolova DS, Semenova EM, Avtukh AN, Poltaraus AB, Ianutsevich EA, Nazina TN. Genome Analysis and Potential Ecological Functions of Members of the Genus Ensifer from Subsurface Environments and Description of Ensifer oleiphilus sp. nov. Microorganisms 2023; 11:2314. [PMID: 37764159 PMCID: PMC10538136 DOI: 10.3390/microorganisms11092314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/06/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
The current work deals with genomic analysis, possible ecological functions, and biotechnological potential of two bacterial strains, HO-A22T and SHC 2-14, isolated from unique subsurface environments, the Cheremukhovskoe oil field (Tatarstan, Russia) and nitrate- and radionuclide-contaminated groundwater (Tomsk region, Russia), respectively. New isolates were characterized using polyphasic taxonomy approaches and genomic analysis. The genomes of the strains HO-A22T and SHC 2-14 contain the genes involved in nitrate reduction, hydrocarbon degradation, extracellular polysaccharide synthesis, and heavy metal detoxification, confirming the potential for their application in various environmental biotechnologies. Genomic data were confirmed by cultivation studies. Both strains were found to be neutrophilic, chemoorganotrophic, facultatively anaerobic bacteria, growing at 15-33 °C and 0-1.6% NaCl (w/v). The 16S rRNA gene sequences of the strains were similar to those of the type strains of the genus Ensifer (99.0-100.0%). Nevertheless, genomic characteristics of strain HO-A22T were below the thresholds for species delineation: the calculated average nucleotide identity (ANI) values were 83.7-92.4% (<95%), and digital DNA-DNA hybridization (dDDH) values were within the range of 25.4-45.9% (<70%), which supported our conclusion that HO-A22T (=VKM B-3646T = KCTC 92427T) represented a novel species of the genus Ensifer, with the proposed name Ensifer oleiphilus sp. nov. Strain SHC 2-14 was assigned to the species 'Ensifer canadensis', which has not been validly published. This study expanded the knowledge about the phenotypic diversity among members of the genus Ensifer and its potential for the biotechnologies of oil recovery and radionuclide pollution treatment.
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Affiliation(s)
- Alexey P. Ershov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
| | - Tamara L. Babich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
| | | | - Diyana S. Sokolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
| | - Ekaterina M. Semenova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
| | - Alexander N. Avtukh
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Andrey B. Poltaraus
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Elena A. Ianutsevich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
| | - Tamara N. Nazina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
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Dutra J, Gomes R, Yupanqui García GJ, Romero-Cale DX, Santos Cardoso M, Waldow V, Groposo C, Akamine RN, Sousa M, Figueiredo H, Azevedo V, Góes-Neto A. Corrosion-influencing microorganisms in petroliferous regions on a global scale: systematic review, analysis, and scientific synthesis of 16S amplicon metagenomic studies. PeerJ 2023; 11:e14642. [PMID: 36655046 PMCID: PMC9841911 DOI: 10.7717/peerj.14642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/05/2022] [Indexed: 01/15/2023] Open
Abstract
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.
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Affiliation(s)
- Joyce Dutra
- Graduate Program in Microbiology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rosimeire Gomes
- Graduate Program in Microbiology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Glen Jasper Yupanqui García
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Mariana Santos Cardoso
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vinicius Waldow
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Rubens N. Akamine
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maira Sousa
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Henrique Figueiredo
- Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Aristóteles Góes-Neto
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Guo G, Li Z, Chen L, Ling Q, Zan F, Isawi H, Hao T, Ma J, Wang Z, Chen G, Lu H. Advances in elemental sulfur-driven bioprocesses for wastewater treatment: From metabolic study to application. WATER RESEARCH 2022; 213:118143. [PMID: 35149365 DOI: 10.1016/j.watres.2022.118143] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/17/2022] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
Elemental sulfur (S0) is known to be an abundant, non-toxic material with a wide range of redox states (-2 to +6) and may serve as an excellent electron carrier in wastewater treatment. In turn, S0-driven bioprocesses, which employ S0 as electron donor or acceptor, have recently established themselves as cost-effective therefore attractive solutions for wastewater treatment. Numerous related processes have, to date, been developed from laboratory experiments into full-scale applications, including S0-driven autotrophic denitrification for nitrate removal and S0-reducing organic removal. Compared to the conventional activated sludge process, these bioprocesses require only a small amount of organic matter and produce very little sludge. There have been great efforts to characterize chemical and biogenic S0 and related functional microorganisms in order to identify the biochemical pathways, upgrade the bioprocesses, and assess the impact of the operating factors on process performance, ultimately aiming to better understand and to optimize the processes. This paper is therefore a comprehensive overview of emerging S0-driven biotechnologies, including the development of S0-driven autotrophic denitrification and S0-based sulfidogenesis, as well as the associated microbiology and biochemistry. Also reviewed here are the physicochemical characteristics of S0 and the effects that environmental factors such as pH, influent sulfur/nitrate ratio, temperature, S0 particle size and reactor configurations have on the process. Research gaps, challenges of process applications and potential areas for future research are further proposed and discussed.
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Affiliation(s)
- Gang Guo
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Zhaoling Li
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Lei Chen
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Qingshan Ling
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Feixiang Zan
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Heba Isawi
- Desert Research Center, Water Resources and Desert Soils Division, Egyptian Desalination Research Center of Excellence (EDRC), Cairo, Egypt
| | - Tianwei Hao
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China.
| | - Jie Ma
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Zongping Wang
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Guanghao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.
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Sokolova DS, Semenova EM, Grouzdev DS, Bidzhieva SK, Babich TL, Loiko NG, Ershov AP, Kadnikov VV, Beletsky AV, Mardanov AV, Zhaparov NS, Nazina TN. Sulfidogenic Microbial Communities of the Uzen High-Temperature Oil Field in Kazakhstan. Microorganisms 2021; 9:1818. [PMID: 34576714 PMCID: PMC8467725 DOI: 10.3390/microorganisms9091818] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022] Open
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.
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Affiliation(s)
- Diyana S. Sokolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (D.S.S.); (E.M.S.); (S.K.B.); (T.L.B.); (N.G.L.); (A.P.E.)
| | - Ekaterina M. Semenova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (D.S.S.); (E.M.S.); (S.K.B.); (T.L.B.); (N.G.L.); (A.P.E.)
| | | | - Salimat K. Bidzhieva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (D.S.S.); (E.M.S.); (S.K.B.); (T.L.B.); (N.G.L.); (A.P.E.)
| | - Tamara L. Babich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (D.S.S.); (E.M.S.); (S.K.B.); (T.L.B.); (N.G.L.); (A.P.E.)
| | - Nataliya G. Loiko
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (D.S.S.); (E.M.S.); (S.K.B.); (T.L.B.); (N.G.L.); (A.P.E.)
| | - Alexey P. Ershov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (D.S.S.); (E.M.S.); (S.K.B.); (T.L.B.); (N.G.L.); (A.P.E.)
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.V.K.); (A.V.B.); (A.V.M.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.V.K.); (A.V.B.); (A.V.M.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.V.K.); (A.V.B.); (A.V.M.)
| | - Nurlan S. Zhaparov
- Branch of the Limited Liability Partnership “KazMunaiGas Engineering”, Aktau 130000, Kazakhstan;
| | - Tamara N. Nazina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (D.S.S.); (E.M.S.); (S.K.B.); (T.L.B.); (N.G.L.); (A.P.E.)
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Nazina TN, Bidzhieva SK, Grouzdev DS, Sokolova DS, Tourova TP, Parshina SN, Avtukh AN, Poltaraus AB, Talybly AK. Soehngenia longivitae sp. nov., a Fermenting Bacterium Isolated from a Petroleum Reservoir in Azerbaijan, and Emended Description of the Genus Soehngenia. Microorganisms 2020; 8:E1967. [PMID: 33322329 PMCID: PMC7763609 DOI: 10.3390/microorganisms8121967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 02/05/2023] Open
Abstract
A methanogenic enrichment growing on a medium with methanol was obtained from a petroleum reservoir (Republic of Azerbaijan) and stored for 33 years without transfers to fresh medium. High-throughput sequencing of the V4 region of the 16S rRNA gene revealed members of the genera Desulfovibrio, Soehngenia, Thermovirga, Petrimonas, Methanosarcina, and Methanomethylovorans. A novel gram-positive, rod-shaped, anaerobic fermentative bacterium, strain 1933PT, was isolated from this enrichment and characterized. The strain grew at 13-55 °C (optimum 35 °C), with 0-3.0% (w/v) NaCl (optimum 0-2.0%) and in the pH range of 6.7-8.0 (optimum pH 7.0). The 16S rRNA gene sequence similarity, the average nucleotide identity (ANI) and in silico DNA-DNA hybridization (dDDH) values between strain 1933PT and the type strain of the most closely related species Soehngenia saccharolytica DSM 12858T were 98.5%, 70.5%, and 22.6%, respectively, and were below the threshold accepted for species demarcation. Genome-based phylogenomic analysis and physiological and biochemical characterization of the strain 1933PT (VKM B-3382T = KCTC 15984T) confirmed its affiliation to a novel species of the genus Soehngenia, for which the name Soehngenia longivitae sp. nov. is proposed. Genome analysis suggests that the new strain has potential in the degradation of proteinaceous components.
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Affiliation(s)
- Tamara N. Nazina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 117312 Moscow, Russia; (S.K.B.); (D.S.S.); (T.P.T.); (S.N.P.)
| | - Salimat K. Bidzhieva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 117312 Moscow, Russia; (S.K.B.); (D.S.S.); (T.P.T.); (S.N.P.)
| | | | - Diyana S. Sokolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 117312 Moscow, Russia; (S.K.B.); (D.S.S.); (T.P.T.); (S.N.P.)
| | - Tatyana P. Tourova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 117312 Moscow, Russia; (S.K.B.); (D.S.S.); (T.P.T.); (S.N.P.)
| | - Sofiya N. Parshina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 117312 Moscow, Russia; (S.K.B.); (D.S.S.); (T.P.T.); (S.N.P.)
| | - Alexander N. Avtukh
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Andrey B. Poltaraus
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Azhdar K. Talybly
- Institute of Microbiology of the National Academy of Sciences of Azerbaijan, Baku AZ1073, Azerbaijan;
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