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Mbow FT, Akbari A, Dopffel N, Schneider K, Mukherjee S, Meckenstock RU. Insights into the effects of anthropogenic activities on oil reservoir microbiome and metabolic potential. N Biotechnol 2024; 79:30-38. [PMID: 38040289 DOI: 10.1016/j.nbt.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 11/21/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Microbial communities have long been observed in oil reservoirs, where the subsurface conditions are major drivers shaping their structure and functions. Furthermore, anthropogenic activities such as water flooding during oil production can affect microbial activities and community compositions in oil reservoirs through the injection of recycled produced water, often associated with biocides. However, it is still unclear to what extent the introduced chemicals and microbes influence the metabolic potential of the subsurface microbiome. Here we investigated an onshore oilfield in Germany (Field A) that undergoes secondary oil production along with biocide treatment to prevent souring and microbially induced corrosion (MIC). With the integrated approach of 16 S rRNA gene amplicon and shotgun metagenomic sequencing of water-oil samples from 4 production wells and 1 injection well, we found differences in microbial community structure and metabolic functions. In the injection water samples, amplicon sequence variants (ASVs) belonging to families such as Halanaerobiaceae, Ectothiorhodospiraceae, Hydrogenophilaceae, Halobacteroidaceae, Desulfohalobiaceae, and Methanosarcinaceae were dominant, while in the production water samples, ASVs of families such as Thermotogaceae, Nitrospiraceae, Petrotogaceae, Syntrophaceae, Methanobacteriaceae, and Thermoprotei were also dominant. The metagenomic analysis of the injection water sample revealed the presence of C1-metabolism, namely, genes involved in formaldehyde oxidation. Our analysis revealed that the microbial community structure of the production water samples diverged slightly from that of injection water samples. Additionally, a metabolic potential for oxidizing the applied biocide clearly occurred in the injection water samples indicating an adaptation and buildup of degradation capacity or resistance against the added biocide.
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Affiliation(s)
- Fatou T Mbow
- University of Duisburg-Essen - Environmental Microbiology and Biotechnology - Aquatic Microbiology, Universitätsstraße 5, 45141 Essen, Germany
| | - Ali Akbari
- University of Duisburg-Essen - Environmental Microbiology and Biotechnology - Aquatic Microbiology, Universitätsstraße 5, 45141 Essen, Germany
| | - Nicole Dopffel
- BASF SE, Carl-Bosch-Straße 38, 67056 Ludwigshafen am Rhein, Germany
| | | | | | - Rainer U Meckenstock
- University of Duisburg-Essen - Environmental Microbiology and Biotechnology - Aquatic Microbiology, Universitätsstraße 5, 45141 Essen, Germany.
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Liu XJ, Zhu KL, Ye YQ, Han ZT, Tan XY, Du ZJ, Ye MQ. Phenotypic and genotypic characterization of Marinobacterium weihaiense sp. nov. and Marinobacterium marinum sp. nov., isolated from marine sediment, and genomic properties of the genus Marinobacterium. Microb Genom 2024; 10:001182. [PMID: 38265428 PMCID: PMC10868613 DOI: 10.1099/mgen.0.001182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/04/2024] [Indexed: 01/25/2024] Open
Abstract
In this study, two novel bacterial strains were isolated from coastal sediment of Weihai, China. The two strains were Gram-stain-negative and facultatively aerobic, designated 3-1745T and A346T. Based on phenotypic, genetic and phylogenetic properties, strains 3-1745T and A346T represent two novel species of the genus Marinobacterium. The results of genome analysis revealed many central carbohydrate metabolism pathways such as gluconeogenesis, pyruvate oxidation, tricyclic acid cycle, pentose phosphate pathway and PRPP biosynthesis in the genus Marinobacterium. The ability of strains 3-1745T and A346T to utilize volatile fatty acids was experimentally confirmed. Polyhydroxyalkanoate synthases (PhaA, PhaB and PhaC) for the synthesis of polyhydroxyalkanoates were prevalent in the genus Marinobacterium. Multiple BGCs (biosynthetic gene clusters) including betalactone, ectoine, ranthipeptide, redox-cofactor, RiPPs (ribosomally synthesized post-translationally modified peptides) and T3PKS (polyketide synthases) in the genome of the genus Marinobacterium were found. Additional genome analyses suggested that the genus Marinobacterium contained diverse potential mechanisms of salt tolerance and mainly utilized oligosaccharides. This is the first report on broad genomic analyses of the genus Marinobacterium with the description of two novel species and potential ecological and biotechnological implications.
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Affiliation(s)
- Xin-Jiang Liu
- Shenzhen Research Institute of Shandong University, Shenzhen, Guangdong, 518057, PR China
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Ke-Lei Zhu
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Yu-Qi Ye
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Ze-Tian Han
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Xin-Yun Tan
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, PR China
| | - Meng-Qi Ye
- Shenzhen Research Institute of Shandong University, Shenzhen, Guangdong, 518057, PR China
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, PR China
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3
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Zhi Z, Bian Z, Chen Y, Zhang X, Wu Y, Wu H. Horizontal and Vertical Comparison of Microbial Community Structures in a Low Permeability Reservoir at the Local Scale. Microorganisms 2023; 11:2862. [PMID: 38138006 PMCID: PMC10745628 DOI: 10.3390/microorganisms11122862] [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: 10/24/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
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 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.
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Affiliation(s)
- Zena Zhi
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi’an 710069, China; (Z.Z.); (Z.B.)
| | - Ziwei Bian
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi’an 710069, China; (Z.Z.); (Z.B.)
| | - Yuan Chen
- College of Food Science and Technology, Northwest University, Xi’an 710069, China;
| | - Xiangchun Zhang
- College of Biology and Agriculture, Zunyi Normal University, Zunyi 563006, China;
| | - Yifei Wu
- College of Food Science and Technology, Northwest University, Xi’an 710069, China;
| | - Hanning Wu
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi’an 710069, China; (Z.Z.); (Z.B.)
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Kadnikov VV, Ravin NV, Sokolova DS, Semenova EM, Bidzhieva SK, Beletsky AV, Ershov AP, Babich TL, Khisametdinov MR, Mardanov AV, Nazina TN. Metagenomic and Culture-Based Analyses of Microbial Communities from Petroleum Reservoirs with High-Salinity Formation Water, and Their Biotechnological Potential. BIOLOGY 2023; 12:1300. [PMID: 37887010 PMCID: PMC10604348 DOI: 10.3390/biology12101300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/15/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
The reserves of light conditional oil in reservoirs with low-salinity formation water are decreasing worldwide, necessitating the extraction of heavy oil from petroleum reservoirs with high-salinity formation water. As the first stage of defining the microbial-enhanced oil recovery (MEOR) strategies for depleted petroleum reservoirs, microbial community composition was studied for petroleum reservoirs with high-salinity formation water located in Tatarstan (Russia) using metagenomic and culture-based approaches. Bacteria of the phyla Desulfobacterota, Halanaerobiaeota, Sinergistota, Pseudomonadota, and Bacillota were revealed using 16S rRNA-based high-throughput sequencing in halophilic microbial communities. Sulfidogenic bacteria predominated in the studied oil fields. The 75 metagenome-assembled genomes (MAGs) of prokaryotes reconstructed from water samples were assigned to 16 bacterial phyla, including Desulfobacterota, Bacillota, Pseudomonadota, Thermotogota, Actinobacteriota, Spirochaetota, and Patescibacteria, and to archaea of the phylum Halobacteriota (genus Methanohalophilus). Results of metagenomic analyses were supported by the isolation of 20 pure cultures of the genera Desulfoplanes, Halanaerobium, Geotoga, Sphaerochaeta, Tangfeifania, and Bacillus. The isolated halophilic fermentative bacteria produced oil-displacing metabolites (lower fatty acids, alcohols, and gases) from sugar-containing and proteinaceous substrates, which testify their potential for MEOR. However, organic substrates stimulated the growth of sulfidogenic bacteria, in addition to fermenters. Methods for enhanced oil recovery should therefore be developed, combining the production of oil-displacing compounds with fermentative bacteria and the suppression of sulfidogenesis.
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Affiliation(s)
- Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.V.K.); (N.V.R.); (A.V.B.); (A.V.M.)
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.V.K.); (N.V.R.); (A.V.B.); (A.V.M.)
| | - 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.); (A.P.E.); (T.L.B.)
| | - 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.); (A.P.E.); (T.L.B.)
| | - 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.); (A.P.E.); (T.L.B.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.V.K.); (N.V.R.); (A.V.B.); (A.V.M.)
| | - 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.); (A.P.E.); (T.L.B.)
| | - 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.); (A.P.E.); (T.L.B.)
| | - Marat R. Khisametdinov
- Tatar Scientific Research and Design Institute of Oil “Tatneft”, 423236 Bugulma, Russia;
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (V.V.K.); (N.V.R.); (A.V.B.); (A.V.M.)
| | - 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.); (A.P.E.); (T.L.B.)
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Alibrandi A, di Primio R, Bartholomäus A, Kallmeyer J. A modified isooctane-based DNA extraction method from crude oil. MLIFE 2023; 2:328-338. [PMID: 38817811 PMCID: PMC10989908 DOI: 10.1002/mlf2.12081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/09/2023] [Accepted: 07/29/2023] [Indexed: 06/01/2024]
Abstract
Microbes from oil reservoirs shape petroleum composition through processes such as biodegradation or souring. Such processes are considered economically detrimental and might pose health and safety hazards. It is therefore crucial to understand the composition of a reservoir's microbial community and its metabolic capabilities. However, such analyses are hindered by difficulties in extracting DNA from such complex fluids as crude oil. Here, we present a novel DNA extraction method from oils with a wide American Petroleum Institute (API) gravity (density) range. We investigated the ability to extract cells from oils with different solvents and surfactants, the latter both nonionic and ionic. Furthermore, we evaluated three DNA extraction methods. Overall, the best DNA yields and the highest number of 16S rRNA reads were achieved with isooctane as a solvent, followed by an ionic surfactant treatment using sodium dodecyl sulfate and DNA extraction using the PowerSoil Pro Kit (Qiagen). The final method was then applied to various oils from oil reservoirs collected in aseptic conditions. Despite the expected low cell density of 101-103 cells/ml, the new method yielded reliable results, with average 16S rRNA sequencing reads in the order of 41431 (±8860) per sample. Thermophilic, halophilic, and anaerobic taxa, which are most likely to be indigenous to the oil reservoir, were found in all samples. API gravity and DNA yield, despite the sufficient DNA obtained, did not show a correlation.
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Affiliation(s)
- Armando Alibrandi
- GFZ German Research Centre for Geoscience, Section GeomicrobiologyPotsdamGermany
| | | | | | - Jens Kallmeyer
- GFZ German Research Centre for Geoscience, Section GeomicrobiologyPotsdamGermany
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6
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Pavlova ON, Izosimova ON, Chernitsyna SM, Ivanov VG, Pogodaeva TV, Khabuev AV, Gorshkov AG, Zemskaya TI. Anaerobic oxidation of petroleum hydrocarbons in enrichment cultures from sediments of the Gorevoy Utes natural oil seep under methanogenic and sulfate-reducing conditions. MICROBIAL ECOLOGY 2022; 83:899-915. [PMID: 34255112 DOI: 10.1007/s00248-021-01802-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
This article presents the first experimental data on the ability of microbial communities from sediments of the Gorevoy Utes natural oil seep to degrade petroleum hydrocarbons under anaerobic conditions. Like in marine ecosystems associated with oil discharge, available electron acceptors, in particular sulfate ions, affect the composition of the microbial community and the degree of hydrocarbon conversion. The cultivation of the surface sediments under sulfate-reducing conditions led to the formation of a more diverse bacterial community and greater loss of n-alkanes (28%) in comparison to methanogenic conditions (6%). Microbial communities of both surface and deep sediments are more oriented to degrade polycyclic aromatic hydrocarbons (PAHs), to which the degree of the PAH conversion testifies (up to 46%) irrespective of the present electron acceptors. Microorganisms with the uncultured closest homologues from thermal habitats, sediments of mud volcanoes, and environments contaminated with hydrocarbons mainly represented microbial communities of enrichment cultures. The members of the phyla Firmicutes, Chloroflexi, and Caldiserica (OP5), as well as the class Deltaproteobacteria and Methanomicrobia, were mostly found in enrichment cultures. The influence of gas-saturated fluids may be responsible for the presence in the bacterial 16S rRNA gene libraries of the sequences of "rare taxa": Planctomycetes, Ca. Atribacteria (OP9), Ca. Armatimonadetes (OP10), Ca. Latescibacteria (WS3), Ca. division (AC1), Ca. division (OP11), and Ca. Parcubacteria (OD1), which can be involved in hydrocarbon oxidation.
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Affiliation(s)
- O N Pavlova
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia.
| | - O N Izosimova
- Laboratory of Chromatography, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - S M Chernitsyna
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - V G Ivanov
- Laboratory of Hydrology and Hydrophysics, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - T V Pogodaeva
- Laboratory of Hydrochemistry and Atmosphere Chemistry, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - A V Khabuev
- Laboratory of Lake Baikal Geology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - A G Gorshkov
- Laboratory of Chromatography, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
| | - T I Zemskaya
- Laboratory of Hydrocarbon Microbiology, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russia
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Tiburcio SRG, Macrae A, Peixoto RS, da Costa Rachid CTC, Mansoldo FRP, Alviano DS, Alviano CS, Ferreira DF, de Queiroz Venâncio F, Ferreira DF, Vermelho AB. Sulphate-reducing bacterial community structure from produced water of the Periquito and Galo de Campina onshore oilfields in Brazil. Sci Rep 2021; 11:20311. [PMID: 34645885 PMCID: PMC8514479 DOI: 10.1038/s41598-021-99196-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 09/09/2021] [Indexed: 12/28/2022] Open
Abstract
Sulphate-reducing bacteria (SRB) cause fouling, souring, corrosion and produce H2S during oil and gas production. Produced water obtained from Periquito (PQO) and Galo de Campina (GC) onshore oilfields in Brazil was investigated for SRB. Produced water with Postgate B, Postgate C and Baars media was incubated anaerobically for 20 days. DNA was extracted, 16S rDNA PCR amplified and fragments were sequenced using Illumina TruSeq. 4.2 million sequence reads were analysed and deposited at NCBI SAR accession number SRP149784. No significant differences in microbial community composition could be attributed to the different media but significant differences in the SRB were observed between the two oil fields. The dominant bacterial orders detected from both oilfields were Desulfovibrionales, Pseudomonadales and Enterobacteriales. The genus Pseudomonas was found predominantly in the GC oilfield and Pleomorphominas and Shewanella were features of the PQO oilfield. 11% and 7.6% of the sequences at GC and PQO were not classified at the genus level but could be partially identified at the order level. Relative abundances changed for Desulfovibrio from 29.8% at PQO to 16.1% at GC. Clostridium varied from 2.8% at PQO and 2.4% at GC. These data provide the first description of SRB from onshore produced water in Brazil and reinforce the importance of Desulfovibrionales, Pseudomonadales, and Enterobacteriales in produced water globally. Identifying potentially harmful microbes is an important first step in developing microbial solutions that prevent their proliferation.
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Affiliation(s)
- Samyra Raquel Gonçalves Tiburcio
- Post Graduate Program in Plant Biotechnology and Bioprocesses, Decania, Center for Health Sciences, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Andrew Macrae
- Post Graduate Program in Plant Biotechnology and Bioprocesses, Decania, Center for Health Sciences, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- Institute of Microbiology Paulo de Góes, Brasil, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Raquel Silva Peixoto
- Post Graduate Program in Plant Biotechnology and Bioprocesses, Decania, Center for Health Sciences, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Institute of Microbiology Paulo de Góes, Brasil, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Felipe Raposo Passos Mansoldo
- Institute of Microbiology Paulo de Góes, Brasil, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- BIOINOVAR - Biocatalysis, Bioproducts and Bioenergy Lab, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Daniela Sales Alviano
- Post Graduate Program in Plant Biotechnology and Bioprocesses, Decania, Center for Health Sciences, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Institute of Microbiology Paulo de Góes, Brasil, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Celuta Sales Alviano
- Post Graduate Program in Plant Biotechnology and Bioprocesses, Decania, Center for Health Sciences, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Institute of Microbiology Paulo de Góes, Brasil, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Davis Fernandes Ferreira
- Post Graduate Program in Plant Biotechnology and Bioprocesses, Decania, Center for Health Sciences, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | | | | | - Alane Beatriz Vermelho
- Post Graduate Program in Plant Biotechnology and Bioprocesses, Decania, Center for Health Sciences, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Institute of Microbiology Paulo de Góes, Brasil, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- BIOINOVAR - Biocatalysis, Bioproducts and Bioenergy Lab, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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Pal S, Dutta A, Sarkar J, Roy A, Sar P, Kazy SK. Exploring the diversity and hydrocarbon bioremediation potential of microbial community in the waste sludge of Duliajan oil field, Assam, India. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:50074-50093. [PMID: 33945094 DOI: 10.1007/s11356-021-13744-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Microbial community analysis of crude oil containing sludge collected from Duliajan oil field, Assam, India, showed the predominance of hydrocarbon-degrading bacteria such as Pseudomonas (20.1%), Pseudoxanthomonas (15.8%), Brevundimonas (1.6%), and Bacillus (0.8%) alongwith anaerobic, fermentative, nitrogen-fixing, nitrate-, sulfate-, and metal-reducing, syntrophic bacteria, and methanogenic archaea. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis indicated gene collection for potential hydrocarbon degradation, lipid, nitrogen, sulfur, and methane metabolism. The culturable microbial community was predominated by Pseudomonas and Bacillus with the metabolic potential for utilizing diverse hydrocarbons, crude oil, and actual petroleum sludge as sole carbon source during growth and tolerating various environmental stresses prevailing in such contaminated sites. More than 90% of the isolated strains could produce biosurfactant and exhibit catechol 2,3-dioxygenase activity. Nearly 30% of the isolates showed alkane hydroxylase activity with the maximum specific activity of 0.54 μmol min-1 mg-1. The study provided better insights into the microbial diversity and functional potential within the crude oil containing sludge which could be exploited for in situ bioremediation of contaminated sites.
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Affiliation(s)
- Siddhartha Pal
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Avishek Dutta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
- School of Bio Science, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Jayeeta Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Ajoy Roy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Sufia K Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India.
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Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide. Microorganisms 2021; 9:microorganisms9091812. [PMID: 34576708 PMCID: PMC8465018 DOI: 10.3390/microorganisms9091812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 11/30/2022] Open
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.
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Taxogenomic and Metabolic Insights into Marinobacterium ramblicola sp. nov., a New Slightly Halophilic Bacterium Isolated from Rambla Salada, Murcia. Microorganisms 2021; 9:microorganisms9081654. [PMID: 34442733 PMCID: PMC8398569 DOI: 10.3390/microorganisms9081654] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 11/17/2022] Open
Abstract
A Gram-negative, motile, rod-shaped bacteria, designated D7T, was isolated by using the dilution-to-extinction method, from a soil sample taken from Rambla Salada (Murcia, Spain). Growth of strain D7T was observed at 15–40 °C (optimum, 37 °C), pH 5–9 (optimum, 7) and 0–7.5% (w/v) NaCl (optimum, 3%). It is facultatively anaerobic. Phylogenetic analysis based on 16S rRNA gene sequence showed it belongs to the genus Marinobacterium. The in silico DDH and ANI against closest Marinobacterium relatives support its placement as a new species within this genus. The major fatty acids of strain D7T were C16:0, summed feature 3 (C16:1 ω7c/C16:1 ω6c) and summed feature 8 (C18:1 ω7c/C18:1 ω6c). The polar lipid profile consists of phosphatidylethanolamine, phosphatidylglycerol and two uncharacterized lipids. Ubiquinone 8 was the unique isoprenoid quinone detected. The DNA G + C content was 59.2 mol%. On the basis of the phylogenetic, phenotypic, chemotaxonomic and genomic characterization, strain D7T (= CECT 9818T = LMG 31312T) represents a novel species of the genus Marinobacterium for which the name Marinobacterium ramblicola sp. nov. is proposed. Genome-based metabolic reconstructions of strain D7T suggested a heterotrophic and chemolitotrophic lifestyle, as well as the capacity to biosynthetize and catabolize compatible solutes, and to degrade hydrocarbon aromatic compounds.
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Zemskaya TI, Bukin SV, Lomakina AV, Pavlova ON. Microorganisms in the Sediments of Lake Baikal, the Deepest and Oldest Lake in the World. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721030140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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12
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Shlimon A, Mansurbeg H, Othman R, Head I, Kjeldsen KU, Finster K. Identity and hydrocarbon degradation activity of enriched microorganisms from natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI). Biodegradation 2021; 32:251-271. [PMID: 33782778 DOI: 10.1007/s10532-021-09931-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 02/19/2021] [Indexed: 10/21/2022]
Abstract
A previous cultivation-independent investigation of the microbial community structure of natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI) revealed the dominance of uncultured bacterial taxa belonging to the phyla Deferribacterota and Coprothermobacterota and the orders Thermodesulfobacteriales, Thermales, and Burkholderiales. Here we report on a cultivation-dependent approach to identify members of these groups involved in hydrocarbon degradation in the KRI oil and asphalt seeps. For this purpose, we set up anoxic crude oil-degrading enrichment cultures based on cultivation media known to support the growth of members of the above-mentioned taxonomic groups. During 100-200 days incubation periods, nitrate-reducing and fermentative enrichments showed up to 90% degradation of C8-C17 alkanes and up to 28% degradation of C18-C33 alkanes along with aromatic hydrocarbons. Community profiling of the enrichment cultures showed that they were dominated by diverse bacterial taxa, which were rare in situ community members in the investigated seeps. Groups initially targeted by our approach were not enriched, possibly because their members are slow-growing and involved in the degradation of recalcitrant hydrocarbons. Nevertheless, the enriched taxa were taxonomically related to phylotypes recovered from hydrocarbon-impacted environments as well as to characterized bacterial isolates not previously known to be involved in hydrocarbon degradation. Marker genes (assA and bssA), diagnostic for fumarate addition-based anaerobic hydrocarbon degradation, were not detectable in the enrichment cultures by PCR. We conclude that hydrocarbon biodegradation in our enrichments occurred via unknown pathways and synergistic interactions among the enriched taxa. We suggest, that although not representing abundant populations in situ, studies of the cultured close relatives of these taxa will reveal an unrecognized potential for anaerobic hydrocarbon degradation, possibly involving poorly characterized mechanisms.
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Affiliation(s)
- Adris Shlimon
- Department of Biology, Soran University, Soran, Iraq. .,Section of Microbiology, Department of Biology, Aarhus University, Ny Munkegade 116, 8000, Aarhus, Denmark.
| | - Howri Mansurbeg
- Department of Petroleum Geoscience, Soran University, Soran, Iraq.,Department of Earth and Environmental Sciences, University of Windsor, Windsor, ON, Canada
| | - Rushdy Othman
- Department of Petroleum Geoscience, Soran University, Soran, Iraq
| | - Ian Head
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Kasper U Kjeldsen
- Section of Microbiology, Department of Biology, Aarhus University, Ny Munkegade 116, 8000, Aarhus, Denmark
| | - Kai Finster
- Section of Microbiology, Department of Biology, Aarhus University, Ny Munkegade 116, 8000, Aarhus, Denmark
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13
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Hidalgo KJ, Sierra-Garcia IN, Dellagnezze BM, de Oliveira VM. Metagenomic Insights Into the Mechanisms for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Oil Supply Chain. Front Microbiol 2020; 11:561506. [PMID: 33072021 PMCID: PMC7530279 DOI: 10.3389/fmicb.2020.561506] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/24/2020] [Indexed: 02/01/2023] Open
Abstract
Petroleum is a very complex and diverse organic mixture. Its composition depends on reservoir location and in situ conditions and changes once crude oil is spilled into the environment, making the characteristics associated with every spill unique. Polycyclic aromatic hydrocarbons (PAHs) are common components of the crude oil and constitute a group of persistent organic pollutants. Due to their highly hydrophobic, and their low solubility tend to accumulate in soil and sediment. The process by which oil is sourced and made available for use is referred to as the oil supply chain and involves three parts: (1) upstream, (2) midstream and (3) downstream activities. As consequence from oil supply chain activities, crude oils are subjected to biodeterioration, acidification and souring, and oil spills are frequently reported affecting not only the environment, but also the economy and human resources. Different bioremediation techniques based on microbial metabolism, such as natural attenuation, bioaugmentation, biostimulation are promising approaches to minimize the environmental impact of oil spills. The rate and efficiency of this process depend on multiple factors, like pH, oxygen content, temperature, availability and concentration of the pollutants and diversity and structure of the microbial community present in the affected (contaminated) area. Emerging approaches, such as (meta-)taxonomics and (meta-)genomics bring new insights into the molecular mechanisms of PAH microbial degradation at both single species and community levels in oil reservoirs and groundwater/seawater spills. We have scrutinized the microbiological aspects of biodegradation of PAHs naturally occurring in oil upstream activities (exploration and production), and crude oil and/or by-products spills in midstream (transport and storage) and downstream (refining and distribution) activities. This work addresses PAH biodegradation in different stages of oil supply chain affecting diverse environments (groundwater, seawater, oil reservoir) focusing on genes and pathways as well as key players involved in this process. In depth understanding of the biodegradation process will provide/improve knowledge for optimizing and monitoring bioremediation in oil spills cases and/or to impair the degradation in reservoirs avoiding deterioration of crude oil quality.
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Affiliation(s)
- Kelly J. Hidalgo
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Isabel N. Sierra-Garcia
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
- Biology Department & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Bruna M. Dellagnezze
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
| | - Valéria Maia de Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
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14
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Sierra-Garcia IN, Belgini DRB, Torres-Ballesteros A, Paez-Espino D, Capilla R, Santos Neto EV, Gray N, de Oliveira VM. In depth metagenomic analysis in contrasting oil wells reveals syntrophic bacterial and archaeal associations for oil biodegradation in petroleum reservoirs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 715:136646. [PMID: 32014760 DOI: 10.1016/j.scitotenv.2020.136646] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
Microbial biodegradation of hydrocarbons in petroleum reservoirs has major consequences in the petroleum value and quality. The identification of microorganisms capable of in-situ degradation of hydrocarbons under the reservoir conditions is crucial to understand microbial roles in hydrocarbon transformation and the impact of oil exploration and production on energy resources. The aim of this study was to profile the metagenome of microbial communities in crude oils and associated formation water from two high temperature and relatively saline oil-production wells, where one has been subjected to water flooding (BA-2) and the other one is considered pristine (BA-1). The microbiome was studied in the fluids using shotgun metagenome sequencing. Distinct microbial compositions were revealed when comparing pristine and water flooded oil wells in contrast to the similar community structures observed between the aqueous and oil fluids from the same well (BA-2). The equal proportion of archaea and bacteria together with the greater anaerobic hydrocarbon degradation potential in the BA-1 pristine but degraded reservoir contrasted with the predominance of bacteria over archaea, aerobic pathways and lower frequency of anaerobic degradation genes in the BA-2 water flooded undegraded well. Our results suggest that Syntrophus, Syntrophomonas, candidatus Atribacteria and Synergistia, in association with mainly acetoclastic methanogenic archaea of the genus Methanothrix, were collectively responsible for the oil biodegradation observed in the pristine petroleum well BA-1. Conversely, the microbial composition of the water flooded oil well BA-2 was mainly dominated by the fast-growing and putatively aerobic opportunists Marinobacter and Marinobacterium. This presumable allochthonous community introduced a greater metabolic versatility, although oil biodegradation has not been detected hitherto perhaps due to in-reservoir unfavorable physicochemical conditions. These findings provide a better understanding of the petroleum reservoir microbiomes and their potential roles in biogeochemical processes occurring in environments with different geological and oil recovery histories.
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Affiliation(s)
- Isabel Natalia Sierra-Garcia
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, Campinas, Brazil; Institute of Biology, University of Campinas - UNICAMP, Campinas, Brazil.
| | - Daiane R B Belgini
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, Campinas, Brazil; Institute of Biology, University of Campinas - UNICAMP, Campinas, Brazil
| | - Adriana Torres-Ballesteros
- Sustainable Agriculture Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | | | | | | | - Neil Gray
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Valeria Maia de Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, Campinas, Brazil
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15
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Pannekens M, Kroll L, Müller H, Mbow FT, Meckenstock RU. Oil reservoirs, an exceptional habitat for microorganisms. N Biotechnol 2018; 49:1-9. [PMID: 30502541 PMCID: PMC6323355 DOI: 10.1016/j.nbt.2018.11.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 01/21/2023]
Abstract
Water-containing parts within oil reservoirs extend the zone of biodegradation. Biodegradation is controlled by environmental factors. Proteobacteria and Euryarchaeota are ubiquitous in oil reservoirs over all temperature ranges. Biofilms as microbial adaption in oil reservoirs. Viruses as potential control for microbial activity and function.
Microorganisms are present in oil reservoirs around the world where they degrade oil and lead to changes in oil quality. Unfortunately, our knowledge about processes in deep oil reservoirs is limited due to the lack of undisturbed samples. In this review, we discuss the distribution of microorganisms at the oil-water transition zone as well as in water saturated parts of the oil leg and their possible physiological adaptations to abiotic and biotic ecological factors such as temperature, salinity and viruses. We show the importance of studying the water phase within the oil, because small water inclusions and pockets within the oil leg provide an exceptional habitat for microorganisms within a natural oil reservoir and concurrently enlarge the zone of oil biodegradation. Environmental factors such as temperature and salinity control oil biodegradation. Temperature determines the type of microorganisms which are able to inhabit the reservoir. Proteobacteria and Euryarchaeota, are ubiquitous in oil reservoirs over all temperature ranges, whereas some others are tied to specific temperatures. It is proposed that biofilm formation is the dominant way of life within oil reservoirs, enhancing nutrient uptake, syntrophic interactions and protection against environmental stress. Literature shows that viruses are abundant in oil reservoirs and the possible impact on microbial community composition due to control of microbial activity and function is discussed.
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Affiliation(s)
- Mark Pannekens
- University of Duisburg-Essen, Biofilm Centre, Universitätsstr. 5, 41451, Essen, Germany
| | - Lisa Kroll
- University of Duisburg-Essen, Biofilm Centre, Universitätsstr. 5, 41451, Essen, Germany
| | - Hubert Müller
- University of Duisburg-Essen, Biofilm Centre, Universitätsstr. 5, 41451, Essen, Germany
| | - Fatou Tall Mbow
- University of Duisburg-Essen, Biofilm Centre, Universitätsstr. 5, 41451, Essen, Germany
| | - Rainer U Meckenstock
- University of Duisburg-Essen, Biofilm Centre, Universitätsstr. 5, 41451, Essen, Germany.
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16
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Multidisciplinary involvement and potential of thermophiles. Folia Microbiol (Praha) 2018; 64:389-406. [PMID: 30386965 DOI: 10.1007/s12223-018-0662-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/25/2018] [Indexed: 12/15/2022]
Abstract
The full biotechnological exploitation of thermostable enzymes in industrial processes is necessary for their commercial interest and industrious value. The heat-tolerant and heat-resistant enzymes are a key for efficient and cost-effective translation of substrates into useful products for commercial applications. The thermophilic, hyperthermophilic, and microorganisms adapted to extreme temperatures (i.e., low-temperature lovers or psychrophiles) are a rich source of thermostable enzymes with broad-ranging thermal properties, which have structural and functional stability to underpin a variety of technologies. These enzymes are under scrutiny for their great biotechnological potential. Temperature is one of the most critical parameters that shape microorganisms and their biomolecules for stability under harsh environmental conditions. This review describes in detail the sources of thermophiles and thermostable enzymes from prokaryotes and eukaryotes (microbial cell factories). Furthermore, the review critically examines perspectives to improve modern biocatalysts, its production and performance aiming to increase their value for biotechnology through higher standards, specificity, resistance, lowing costs, etc. These thermostable and thermally adapted extremophilic enzymes have been used in a wide range of industries that span all six enzyme classes. Thus, in particular, target of this review paper is to show the possibility of both high-value-low-volume (e.g., fine-chemical synthesis) and low-value-high-volume by-products (e.g., fuels) by minimizing changes to current industrial processes.
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Complete Genome Sequence of Marinobacterium aestuarii ST58-10 T, a Benzene-Degrading Bacterium Isolated from Estuarine Sediment. Microbiol Resour Announc 2018; 7:MRA00971-18. [PMID: 30533631 PMCID: PMC6256654 DOI: 10.1128/mra.00971-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 08/27/2018] [Indexed: 11/20/2022] Open
Abstract
Marinobacterium aestuarii ST58-10T was identified as a benzene-degrading aerobic bacterium isolated from estuarine sediment in the Republic of Korea. The genome of strain ST58-10T was found to be composed of a single circular chromosome (5,191,608 bp) with a G+C content of 58.78% and harboring 4,473 protein-coding genes. Marinobacterium aestuarii ST58-10T was identified as a benzene-degrading aerobic bacterium isolated from estuarine sediment in the Republic of Korea. The genome of strain ST58-10T was found to be composed of a single circular chromosome (5,191,608 bp) with a G+C content of 58.78% and harboring 4,473 protein-coding genes. The assembled sequence data will help elucidate potential metabolic pathways and mechanisms responsible for the hydrocarbon-degrading ability of M. aestuarii ST58-10T.
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18
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Liang B, Zhang K, Wang LY, Liu JF, Yang SZ, Gu JD, Mu BZ. Different Diversity and Distribution of Archaeal Community in the Aqueous and Oil Phases of Production Fluid From High-Temperature Petroleum Reservoirs. Front Microbiol 2018; 9:841. [PMID: 29755446 PMCID: PMC5934436 DOI: 10.3389/fmicb.2018.00841] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/12/2018] [Indexed: 11/13/2022] Open
Abstract
To get a better knowledge on how archaeal communities differ between the oil and aqueous phases and whether environmental factors promote substantial differences on microbial distributions among production wells, we analyzed archaeal communities in oil and aqueous phases from four high-temperature petroleum reservoirs (55–65°C) by using 16S rRNA gene based 454 pyrosequencing. Obvious dissimilarity of the archaeal composition between aqueous and oil phases in each independent production wells was observed, especially in production wells with higher water cut, and diversity in the oil phase was much higher than that in the corresponding aqueous phase. Statistical analysis further showed that archaeal communities in oil phases from different petroleum reservoirs tended to be more similar, but those in aqueous phases were the opposite. In the high-temperature ecosystems, temperature as an environmental factor could have significantly affected archaeal distribution, and archaeal diversity raised with the increase of temperature (p < 0.05). Our results suggest that to get a comprehensive understanding of petroleum reservoirs microbial information both in aqueous and oil phases should be taken into consideration. The microscopic habitats of oil phase, technically the dispersed minuscule water droplets in the oil could be a better habitat that containing the indigenous microorganisms.
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Affiliation(s)
- Bo Liang
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, China
| | - Kai Zhang
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, China
| | - Li-Ying Wang
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, China
| | - Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, China.,Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, China.,Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, China.,Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China
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Ridley CM, Voordouw G. Aerobic microbial taxa dominate deep subsurface cores from the Alberta oil sands. FEMS Microbiol Ecol 2018; 94:4983121. [DOI: 10.1093/femsec/fiy073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 04/22/2018] [Indexed: 01/13/2023] Open
Affiliation(s)
- Christina M Ridley
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Gerrit Voordouw
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
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20
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Zuñiga C, Zaramela L, Zengler K. Elucidation of complexity and prediction of interactions in microbial communities. Microb Biotechnol 2017; 10:1500-1522. [PMID: 28925555 PMCID: PMC5658597 DOI: 10.1111/1751-7915.12855] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 12/11/2022] Open
Abstract
Microorganisms engage in complex interactions with other members of the microbial community, higher organisms as well as their environment. However, determining the exact nature of these interactions can be challenging due to the large number of members in these communities and the manifold of interactions they can engage in. Various omic data, such as 16S rRNA gene sequencing, shotgun metagenomics, metatranscriptomics, metaproteomics and metabolomics, have been deployed to unravel the community structure, interactions and resulting community dynamics in situ. Interpretation of these multi-omic data often requires advanced computational methods. Modelling approaches are powerful tools to integrate, contextualize and interpret experimental data, thus shedding light on the underlying processes shaping the microbiome. Here, we review current methods and approaches, both experimental and computational, to elucidate interactions in microbial communities and to predict their responses to perturbations.
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Affiliation(s)
- Cristal Zuñiga
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
| | - Livia Zaramela
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
| | - Karsten Zengler
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
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21
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Michas A, Vestergaard G, Trautwein K, Avramidis P, Hatzinikolaou DG, Vorgias CE, Wilkes H, Rabus R, Schloter M, Schöler A. More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis. MICROBIOME 2017; 5:118. [PMID: 28893308 PMCID: PMC5594585 DOI: 10.1186/s40168-017-0337-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 09/03/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Natural oil seeps offer the opportunity to study the adaptation of ecosystems and the associated microbiota to long-term oil exposure. In the current study, we investigated a land-to-sea transition ecosystem called "Keri Lake" in Zakynthos Island, Greece. This ecosystem is unique due to asphalt oil springs found at several sites, a phenomenon already reported 2500 years ago. Sediment microbiomes at Keri Lake were studied, and their structure and functional potential were compared to other ecosystems with oil exposure histories of various time periods. RESULTS Replicate sediment cores (up to 3-m depth) were retrieved from one site exposed to oil as well as a non-exposed control site. Samples from three different depths were subjected to chemical analysis and metagenomic shotgun sequencing. At the oil-exposed site, we observed high amounts of asphalt oil compounds and a depletion of sulfate compared to the non-exposed control site. The numbers of reads assigned to genes involved in the anaerobic degradation of hydrocarbons were similar between the two sites. The numbers of denitrifiers and sulfate reducers were clearly lower in the samples from the oil-exposed site, while a higher abundance of methanogens was detected compared to the non-exposed site. Higher abundances of the genes of methanogenesis were also observed in the metagenomes from other ecosystems with a long history of oil exposure, compared to short-term exposed environments. CONCLUSIONS The analysis of Keri Lake metagenomes revealed that microbiomes in the oil-exposed sediment have a higher potential for methanogenesis over denitrification/sulfate reduction, compared to those in the non-exposed site. Comparison with metagenomes from various oil-impacted environments suggests that syntrophic interactions of hydrocarbon degraders with methanogens are favored in the ecosystems with a long-term presence of oil.
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Affiliation(s)
- Antonios Michas
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Kathleen Trautwein
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - Pavlos Avramidis
- Department of Geology, University of Patras, Panepistimioupoli Patron, 26504 Rio-Patras, Greece
| | - Dimitris G. Hatzinikolaou
- Department of Biology, National and Kapodistrian University of Athens, Zografou University Campus, 15784 Athens, Greece
| | - Constantinos E. Vorgias
- Department of Biology, National and Kapodistrian University of Athens, Zografou University Campus, 15784 Athens, Greece
| | - Heinz Wilkes
- Organic Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Anne Schöler
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
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