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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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Okamura Y, Shimizu R, Tominaga Y, Maki S, Aki T, Matsumura Y, Nakashimada Y. Characterization of Biogenic PbS Quantum Dots. Int J Mol Sci 2023; 24:14149. [PMID: 37762453 PMCID: PMC10531774 DOI: 10.3390/ijms241814149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Heavy metals in a polluted environment are toxic to life. However, some microorganisms can remove or immobilize heavy metals through biomineralization. These bacteria also form minerals with compositions similar to those of semiconductors. Here, this bioprocess was used to fabricate semiconductors with low energy consumption and cost. Bacteria that form lead sulfide (PbS) nanoparticles were screened, and the crystallinity and semiconductor properties of the resulting nanoparticles were characterized. Bacterial consortia that formed PbS nanoparticles were obtained. Extracellular particle size ranged from 3.9 to 5.5 nm, and lattice fringes were observed. The lattice fringes and electron diffraction spectra corresponded to crystalline PbS. The X-ray diffraction (XRD) patterns of bacterial PbS exhibited clear diffraction peaks. The experimental and theoretical data of the diffraction angles on each crystal plane of polycrystalline PbS were in good agreement. Synchrotron XRD measurements showed no crystalline impurity-derived peaks. Thus, bacterial biomineralization can form ultrafine crystalline PbS nanoparticles. Optical absorption and current-voltage measurements of PbS were obtained to characterize the semiconductor properties; the results showed semiconductor quantum dot behavior. Moreover, the current increased under light irradiation when PbS nanoparticles were used. These results suggest that biogenic PbS has band gaps and exhibits the general fundamental characteristics of a semiconductor.
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Affiliation(s)
- Yoshiko Okamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8530, Japan; (T.A.); (Y.N.)
- Graduate School of Advanced Science of Matter, Hiroshima University, Hiroshima 739-8530, Japan (Y.T.)
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo 102-0076, Japan;
- Consolidated Research for Biogenic Nanomaterials, Hiroshima University, Hiroshima 739-8530, Japan;
| | - Ryo Shimizu
- Graduate School of Advanced Science of Matter, Hiroshima University, Hiroshima 739-8530, Japan (Y.T.)
| | - Yoriko Tominaga
- Graduate School of Advanced Science of Matter, Hiroshima University, Hiroshima 739-8530, Japan (Y.T.)
- Consolidated Research for Biogenic Nanomaterials, Hiroshima University, Hiroshima 739-8530, Japan;
- Graduate School of Advanced Science and Engineering, Hiroshima University, Hiroshima 739-8527, Japan
| | - Sachiko Maki
- Consolidated Research for Biogenic Nanomaterials, Hiroshima University, Hiroshima 739-8530, Japan;
- Graduate School of Science, Hiroshima University, Hiroshima 739-8526, Japan
| | - Tsunehiro Aki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8530, Japan; (T.A.); (Y.N.)
- Graduate School of Advanced Science of Matter, Hiroshima University, Hiroshima 739-8530, Japan (Y.T.)
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo 102-0076, Japan;
| | - Yukihiko Matsumura
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo 102-0076, Japan;
- Graduate School of Advanced Science and Engineering, Hiroshima University, Hiroshima 739-8527, Japan
| | - Yutaka Nakashimada
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8530, Japan; (T.A.); (Y.N.)
- Graduate School of Advanced Science of Matter, Hiroshima University, Hiroshima 739-8530, Japan (Y.T.)
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo 102-0076, Japan;
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Farrell AA, Nesbø CL, Zhaxybayeva O. Early Divergence and Gene Exchange Highways in the Evolutionary History of Mesoaciditogales. Genome Biol Evol 2023; 15:evad156. [PMID: 37616556 PMCID: PMC10476701 DOI: 10.1093/gbe/evad156] [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: 06/23/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
The placement of a nonhyperthermophilic order Mesoaciditogales as the earliest branching clade within the Thermotogota phylum challenges the prevailing hypothesis that the last common ancestor of Thermotogota was a hyperthermophile. Yet, given the long branch leading to the only two Mesoaciditogales described to date, the phylogenetic position of the order may be due to the long branch attraction artifact. By testing various models and applying data recoding in phylogenetic reconstructions, we observed that early branching of Mesoaciditogales within Thermotogota is strongly supported by the conserved marker genes assumed to be vertically inherited. However, based on the taxonomic content of 1,181 gene families and a phylogenetic analysis of 721 gene family trees, we also found that a substantial number of Mesoaciditogales genes are more closely related to species from the order Petrotogales. These genes contribute to coenzyme transport and metabolism, fatty acid biosynthesis, genes known to respond to heat and cold stressors, and include many genes of unknown functions. The Petrotogales comprise moderately thermophilic and mesophilic species with similar temperature tolerances to that of Mesoaciditogales. Our findings hint at extensive horizontal gene transfer (HGT) between, or parallel independent gene gains by, the two ecologically similar lineages and suggest that the exchanged genes may be important for adaptation to comparable temperature niches.
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Affiliation(s)
- Anne A Farrell
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Camilla L Nesbø
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire, USA
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Complete Genome Sequence of Oceanotoga sp. Strain T3B (DSM 15011). Microbiol Resour Announc 2023; 12:e0002223. [PMID: 36856423 PMCID: PMC10112263 DOI: 10.1128/mra.00022-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
Oceanotoga sp. strain T3B was isolated from an estuarine sinkhole in the Bahamas. Here, we report its complete genome, which is currently the only sequenced genome from the genus Oceanotoga. The genome sequence provides new data for the genus Oceanotoga.
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Dohrmann AB, Krüger M. Microbial H 2 Consumption by a Formation Fluid from a Natural Gas Field at High-Pressure Conditions Relevant for Underground H 2 Storage. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:1092-1102. [PMID: 36599497 DOI: 10.1021/acs.est.2c07303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Underground hydrogen storage (UHS) has been proposed as one option for storage of excess energy from renewable sources. Depleted gas reservoirs appear suitable, but at the same time, they may be environments with potentially high microbial abundances and activities. Hydrogen (H2) is one of the most energetic substrates in such environments, and many microorganisms are able to oxidize H2, potentially leading to loss of H2 or other unwanted reactions like production of, e.g., H2S, clogging, or corrosion. This study addressed the potential of H2 consumption by naturally abundant microorganisms in formation fluid from a gas field at near in situ pressure and temperature conditions. Microbial H2 consumption was evident at ambient and 100 bar and tolerated pressure variations reflecting cycles of H2 storage. Temperature strongly influenced the activity with higher activity at 30 °C but lower activity at 60 °C. The activity was sulfate-dependent, and sulfide was produced. The microbial community composition changed during H2 consumption with an increase in sulfate-reducing prokaryotes (SRP). Thus, the presence of an SRP-containing, H2-consuming microbial community with activity at UHS-relevant pressure and temperature conditions was shown and should be taken into account when planning UHS at this and other sites.
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Affiliation(s)
- Anja B Dohrmann
- Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655Hannover, Germany
| | - Martin Krüger
- Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655Hannover, Germany
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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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Santos JCD, Lopes DRG, Silva LCF, Ramos JLL, Dias RS, Lima HS, Sousa MPD, Waldow VDA, Paula SOD, Ferreira SO, Silva CCD. Characterization of the biofilm structure and microbial diversity of sulfate-reducing bacteria from petroleum produced water supplemented by different carbon sources. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 304:114189. [PMID: 34864413 DOI: 10.1016/j.jenvman.2021.114189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/17/2021] [Accepted: 11/24/2021] [Indexed: 06/13/2023]
Abstract
Colonization by sulfate-reducing bacteria (SRB) in environments associated with oil is mainly dependent on the availability of sulfate and carbon sources. The formation of biofilms by SRB increases the corrosion of pipelines and oil storage tanks, representing great occupational and operational risks and respective economic losses for the oil industry. The aim of this study was to evaluate the influence of the addition of acetate, butyrate, lactate, propionate and oil on the structure of biofilm formed in carbon steel coupons, as well as on the diversity of total bacteria and SRB in the planktonic and sessile communities from petroleum produced water. The biofilm morphology, chemical composition, average roughness and the microbial diversity was analyzed. In all carbon sources, formation of dense biofilm without morphological and/or microbial density differences was detected, with the most of cells observed in the form of individual rods. The diversity and richness indices of bacterial species in the planktonic community was greater than in the biofilm. Geotoga was the most abundant genus, and more than 85% of SRB species were common to all treatments. The functional predicted profile shown that the observed genres in planktonic communities were related to the reduction of sulfate, sulfite, elementary sulfur and other sulfur compounds, but the abundance varied between treatments. For the biofilm, the functions predicted profile for the oil treatment was the one that most varied in relation to the control, while for the planktonic community, the addition of all carbon sources interfered in the predicted functional profile. Thus, although it does not cause changes in the structure and morphology biofilm, the supplementation of produced water with different carbon sources is associated with changes in the SRB taxonomic composition and functional profiles of the biofilm and the planktonic bacterial communities.
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Affiliation(s)
| | | | | | - José Luiz Lima Ramos
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
| | - Roberto Sousa Dias
- Department of General Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
| | - Helena Santiago Lima
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
| | - Maíra Paula de Sousa
- Petrobras Research and Development Center (CENPES), Petrobras, Rio de Janeiro, RJ, Brazil.
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Zeng Q, Zan F, Hao T, Khanal SK, Chen G. Sewage sludge digestion beyond biogas: Electrochemical pretreatment for biochemicals. WATER RESEARCH 2022; 208:117839. [PMID: 34801819 DOI: 10.1016/j.watres.2021.117839] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/15/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Low economic gains from biogas drive research on shifting to volatile fatty acid (VFA) production during anaerobic sludge digestion. pH control and methanogenesis inhibition are widely used strategies for VFA production via anaerobic digestion of sludge. However, these strategies require perpetual dosing of chemicals, increasing cost and operation complexity. Here, we applied electrochemical pretreatment (EPT) (12 V/30 min) for VFA production during anaerobic sludge digestion. The underlying mechanisms of the VFA production induced by EPT were explored systematically through analyses of the changes in the EPT operation parameters, the sludge characteristics, and the microbial community structure and functional enzymes involving in the subsequent sludge digestion. EPT with carbon-based electrodes selectively inhibited methanogenesis by down-regulating heterodisulfide reductase without affecting enzymatic acidogenesis and hydrolysis, resulting in accumulation of VFAs (up to 389±12 mg acetic acid equivalent/L). Propionate and acetate were, respectively enriched to 89 and 75% of the total VFAs after carbon- and graphite- EPT. Titanium-EPT produced lower levels of VFA; instead, biogas yield increased by ∼20%. We anticipate that EPT will advance VFA recovery from diverse organic wastes to meet the global challenge of resource supply and waste management.
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Affiliation(s)
- Qian Zeng
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Centre, Hong Kong University of Science and Technology, Hong Kong, China
| | - Feixiang Zan
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan, China
| | - Tianwei Hao
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China.
| | - Samir Kumar Khanal
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, United States
| | - Guanghao Chen
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Centre, Hong Kong University of Science and Technology, Hong Kong, China; Wastewater Treatment Laboratory, FYT Graduate School, Hong Kong University of Science and Technology, Guangzhou, China.
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Singh NK, Choudhary S. Bacterial and archaeal diversity in oil fields and reservoirs and their potential role in hydrocarbon recovery and bioprospecting. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:58819-58836. [PMID: 33410029 DOI: 10.1007/s11356-020-11705-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
Hydrocarbon is a primary source of energy in the current urbanized society. Considering the increasing demand, worldwide oil productions are declining due to maturity of oil fields and because of difficulty in discovering new oil fields to substitute the exploited ones. To meet current and future energy demands, further exploitation of oil resources is highly required. Microorganisms inhabiting in these areas exhibit highly diverse catabolic activities to degrade, transform, or accumulate various hydrocarbons. Enrichment of hydrocarbon-utilizing bacteria in oil basin is caused by continuous long duration and low molecular weight hydrocarbon microseepage which plays a very important role as an indicator for petroleum prospecting. The important microbial metabolic processes in most of the oil reservoir are sulfate reduction, fermentation, acetogenesis, methanogenesis, NO3- reduction, and Fe (III) and Mn (IV) reduction. The microorganisms residing in these sites have critical control on petroleum composition, recovery, and production methods. Physical characteristics of heavy oil are altered by microbial biotransformation and biosurfactant production. Considering oil to be one of the most vital energy resources, it is important to have a comprehensive understanding of petroleum microbiology. This manuscript reviews the recent research work referring to the diversity of bacteria in oil field and reservoir sites and their applications for enhancing oil transformation in the target reservoir and geomicrobial prospecting scope for petroleum exploration.
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Affiliation(s)
- Nishi Kumari Singh
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Vanasthali, Rajasthan, 304022, India
| | - Sangeeta Choudhary
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Vanasthali, Rajasthan, 304022, India.
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Mori K, Sakurai K, Hosoyama A, Kakegawa T, Hanada S. Vestiges of Adaptation to the Mesophilic Environment in the Genome of Tepiditoga spiralis gen. nov., sp. nov. Microbes Environ 2021; 35. [PMID: 32963207 PMCID: PMC7734402 DOI: 10.1264/jsme2.me20046] [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] [Indexed: 11/29/2022] Open
Abstract
A novel anaerobic heterotrophic strain, designated strain sy52T, was isolated from a hydrothermal chimney at Suiyo Seamount in the Pacific Ocean. A 16S rRNA gene analysis revealed that the strain belonged to the family Petrotogaceae in the phylum Thermotogae. The strain was mesophilic with optimum growth at 48°C and the phylum primarily comprised hyperthermophiles and thermophiles. Strain sy52T possessed unique genomic characteristics, such as an extremely low G+C content and 6 copies of rRNA operons. Genomic analyses of strain sy52T revealed that amino acid usage in the predicted proteins resulted from adjustments to mesophilic environments. Genomic features also indicated independent adaptions to the mesophilic environment of strain sy52T and Mesotoga species, which belong to the mesophilic lineage in the phylum Thermotogae. Based on phenotypic and phylogenetic evidence, strain sy52T is considered to represent a novel genus and species in the family Petrotogaceae with the proposed name Tepiditoga spiralis gen. nov., sp. nov.
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Affiliation(s)
- Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE)
| | - Kenta Sakurai
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE)
| | - Akira Hosoyama
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE)
| | | | - Satoshi Hanada
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).,Graduate School of Science and Engineering, Tokyo Metropolitan University
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Rajbongshi A, Gogoi SB. A review on anaerobic microorganisms isolated from oil reservoirs. World J Microbiol Biotechnol 2021; 37:111. [PMID: 34076736 DOI: 10.1007/s11274-021-03080-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/26/2021] [Indexed: 11/25/2022]
Abstract
The Role of microorganisms in the petroleum industry is wide-ranging. To understand the role of microorganisms in hydrocarbon transformation, identification of such microorganisms is vital, especially the ones capable of in situ degradation. Microorganisms play a pivotal role in the degradation of hydrocarbons and remediation of heavy metals. Anaerobic microorganisms such as Sulphate Reducing Bacteria (SRB), responsible for the production of hydrogen sulphide (H2S) within the reservoir, reduces the oil quality by causing reservoir souring and reduction in oil viscosity. This paper reviews the diversity of SRB, methanogens, Nitrogen Reducing Bacteria (NRB), and fermentative bacteria present in oil reservoirs. It also reviews the extensive diversity of these microorganisms, their applications in petroleum industries, characteristics and adaptability to survive in different conditions, the potential to alter the petroleum hydrocarbons properties, the propensity to petroleum hydrocarbon degradation, and remediation of metals.
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Affiliation(s)
- Amarjit Rajbongshi
- Brahmaputra Valley Fertilizer Corporation Limited, Namrup, Assam, India.
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Lanzilli M, Esercizio N, Vastano M, Xu Z, Nuzzo G, Gallo C, Manzo E, Fontana A, d’Ippolito G. Effect of Cultivation Parameters on Fermentation and Hydrogen Production in the Phylum Thermotogae. Int J Mol Sci 2020; 22:ijms22010341. [PMID: 33396970 PMCID: PMC7795431 DOI: 10.3390/ijms22010341] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 01/19/2023] Open
Abstract
The phylum Thermotogae is composed of a single class (Thermotogae), 4 orders (Thermotogales, Kosmotogales, Petrotogales, Mesoaciditogales), 5 families (Thermatogaceae, Fervidobacteriaceae, Kosmotogaceae, Petrotogaceae, Mesoaciditogaceae), and 13 genera. They have been isolated from extremely hot environments whose characteristics are reflected in the metabolic and phenotypic properties of the Thermotogae species. The metabolic versatility of Thermotogae members leads to a pool of high value-added products with application potentials in many industry fields. The low risk of contamination associated with their extreme culture conditions has made most species of the phylum attractive candidates in biotechnological processes. Almost all members of the phylum, especially those in the order Thermotogales, can produce bio-hydrogen from a variety of simple and complex sugars with yields close to the theoretical Thauer limit of 4 mol H2/mol consumed glucose. Acetate, lactate, and L-alanine are the major organic end products. Thermotagae fermentation processes are influenced by various factors, such as hydrogen partial pressure, agitation, gas sparging, culture/headspace ratio, inoculum, pH, temperature, nitrogen sources, sulfur sources, inorganic compounds, metal ions, etc. Optimization of these parameters will help to fully unleash the biotechnological potentials of Thermotogae and promote their applications in industry. This article gives an overview of how these operational parameters could impact Thermotogae fermentation in terms of sugar consumption, hydrogen yields, and organic acids production.
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Affiliation(s)
- Mariamichela Lanzilli
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Nunzia Esercizio
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Marco Vastano
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Zhaohui Xu
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA;
| | - Genoveffa Nuzzo
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Carmela Gallo
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Emiliano Manzo
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Angelo Fontana
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
| | - Giuliana d’Ippolito
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy; (M.L.); (N.E.); (M.V.); (G.N.); (C.G.); (E.M.); (A.F.)
- Correspondence: ; Tel.: +39-081-8675096
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Semenova EM, Grouzdev DS, Tourova TP, Nazina TN. Physiology and Genomic Characteristics of Geotoga petraea, a Bacterium Isolated from a Low-Temperature Petroleum Reservoir (Russia). Microbiology (Reading) 2020. [DOI: 10.1134/s0026261719060171] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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14
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Rubiano-Labrador C, Díaz-Cárdenas C, López G, Gómez J, Baena S. Colombian Andean thermal springs: reservoir of thermophilic anaerobic bacteria producing hydrolytic enzymes. Extremophiles 2019; 23:793-808. [PMID: 31555903 DOI: 10.1007/s00792-019-01132-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 09/13/2019] [Indexed: 11/25/2022]
Abstract
Anaerobic cultivable microbial communities in thermal springs producing hydrolytic enzymes were studied. Thermal water samples from seven thermal springs located in the Andean volcanic belt, in the eastern and central mountain ranges of the Colombian Andes were used as inocula for the growth and isolation of thermophilic microorganisms using substrates such as starch, gelatin, xylan, cellulose, Tween 80, olive oil, peptone and casamino acids. These springs differed in temperature (50-70 °C) and pH (6.5-7.5). The predominant ion in eastern mountain range thermal springs was sulphate, whereas that in central mountain range springs was bicarbonate. A total of 40 anaerobic thermophilic bacterial strains that belonged to the genera Thermoanaerobacter, Caloramator, Anoxybacillus, Caloranaerobacter, Desulfomicrobium, Geotoga, Hydrogenophilus, Desulfacinum and Thermoanaerobacterium were isolated. To investigate the metabolic potential of these isolates, selected strains were analysed for enzymatic activities to identify strains than can produce hydrolytic enzymes. We demonstrated that these thermal springs contained diverse microbial populations of anaerobic thermophilic comprising different metabolic groups of bacteria including strains belonging to the genera Thermoanaerobacter, Caloramator, Anoxybacillus, Caloranaerobacter, Desulfomicrobium, Geotoga, Hydrogenophilus, Desulfacinum and Thermoanaerobacterium with amylases, proteases, lipases, esterases, xylanases and pectinases; therefore, the strains represent a promising source of enzymes with biotechnological potential.
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Affiliation(s)
- Carolina Rubiano-Labrador
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, 56710, Bogotá DC, Colombia
- Facultad de Ciencias Básicas, Universidad Tecnológica de Bolívar, Cartagena de Indias D.T. y C., Colombia
| | - Carolina Díaz-Cárdenas
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, 56710, Bogotá DC, Colombia.
| | - Gina López
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, 56710, Bogotá DC, Colombia
| | - Javier Gómez
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, 56710, Bogotá DC, Colombia
| | - Sandra Baena
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, 56710, Bogotá DC, Colombia
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15
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Draft Genome Sequence of Geotoga petraea Strain HO-Geo1, Isolated from a Petroleum Reservoir in Russia. Microbiol Resour Announc 2019; 8:8/29/e00706-19. [PMID: 31320436 PMCID: PMC6639626 DOI: 10.1128/mra.00706-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The draft genome sequence of Geotoga petraea strain HO-Geo1, a bacterium isolated from production water of the Vostochno-Anzirskoe petroleum reservoir in Russia, is presented. The genome of strain HO-Geo1 is annotated for elucidation of the metabolic potential and its possible function in the subsurface microbial community and biotechnological application.
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Characterization of the GH13 and GH57 glycogen branching enzymes from Petrotoga mobilis SJ95 and potential role in glycogen biosynthesis. PLoS One 2019; 14:e0219844. [PMID: 31306450 PMCID: PMC6629080 DOI: 10.1371/journal.pone.0219844] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/03/2019] [Indexed: 01/19/2023] Open
Abstract
Glycogen is a highly branched α-glucan polymer widely used as energy and carbon reserve by many microorganisms. The branches are introduced by glycogen branching enzymes (EC 2.4.1.18), that are classified into glycoside hydrolase families 13 (GH13) and 57 (GH57). Most microorganisms have typically only a single glycogen branching enzyme (gbe) gene. Only a few microorganisms carry both GH13 and GH57 gbe genes, such as Petrotoga mobilis and Mycobacterium tuberculosis. Here we report the basic characteristics of the GH13 and GH57 GBE of P. mobilis, both heterologously expressed in E. coli. The GH13 GBE has a considerably higher branching activity towards the linear α-glucan amylose, and produces a highly branched α-glucan with a high molecular weight which is very similar to glycogen. The GH57 GBE, on the contrary, makes a much smaller branched α-glucan. While the GH13 GBE acts as a classical glycogen branching enzyme involved in glycogen synthesis, the role of GH57 GBE remains unclear.
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Morono Y, Wishart JR, Ito M, Ijiri A, Hoshino T, Torres M, Verba C, Terada T, Inagaki F, Colwell FS. Microbial Metabolism and Community Dynamics in Hydraulic Fracturing Fluids Recovered From Deep Hydrocarbon-Rich Shale. Front Microbiol 2019; 10:376. [PMID: 30915042 PMCID: PMC6422894 DOI: 10.3389/fmicb.2019.00376] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 02/13/2019] [Indexed: 11/29/2022] Open
Abstract
Hydraulic fracturing is a prominent method of natural gas production that uses injected, high-pressure fluids to fracture low permeability, hydrocarbon rich strata such as shale. Upon completion of a well, the fluid returns to the surface (produced water) and contains natural gas, subsurface constituents, and microorganisms (Barbot et al., 2013; Daly et al., 2016). While the microbial community of the produced fluids has been studied in multiple gas wells, the activity of these microorganisms and their relation to biogeochemical activity is not well understood. In this experiment, we supplemented produced fluid with 13C-labeled carbon sources (glucose, acetate, bicarbonate, methanol, or methane), and 15N-labeled ammonium chloride in order to isotopically trace microbial activity over multiple day in anoxic incubations. Nanoscale secondary ion mass spectrometry (NanoSIMS) was used to generate isotopic images of 13C and 15N incorporation in individual cells, while isotope ratio monitoring–gas chromatography–mass spectrometry (IRM–GC–MS) was used to measure 13CO2, and 13CH4 as metabolic byproducts. Glucose, acetate, and methanol were all assimilated by microorganisms under anoxic conditions. 13CO2 production was only observed with glucose as a substrate indicating that catabolic activity was limited to this condition. The microbial communities observed at 0, 19, and 32 days of incubation did not vary between different carbon sources, were low in diversity, and composed primarily of the class Clostridia. The primary genera detected in the incubations, Halanaerobium and Fusibacter, are known to be adapted to harsh physical and chemical conditions consistent with those that occur in the hydrofracturing environment. This study provides evidence that microorganisms in produced fluid are revivable in laboratory incubations and retained the ability to metabolize added carbon and nitrogen substrates.
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Affiliation(s)
- Yuki Morono
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Kochi, Japan.,Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Jessie R Wishart
- National Energy Technology Laboratory, United States Department of Energy, Albany, OR, United States
| | - Motoo Ito
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Kochi, Japan.,Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Akira Ijiri
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Kochi, Japan.,Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Tatsuhiko Hoshino
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Kochi, Japan.,Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Marta Torres
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| | - Circe Verba
- National Energy Technology Laboratory, United States Department of Energy, Albany, OR, United States
| | | | - Fumio Inagaki
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Kochi, Japan.,Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan.,Research and Development Center for Ocean Drilling Science, Japan Agency for Marine-Earth Science and Technology, Yokohama, Japan
| | - Frederick S Colwell
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
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18
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Varjani SJ, Gnansounou E. Microbial dynamics in petroleum oilfields and their relationship with physiological properties of petroleum oil reservoirs. BIORESOURCE TECHNOLOGY 2017; 245:1258-1265. [PMID: 28844839 DOI: 10.1016/j.biortech.2017.08.028] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/05/2017] [Accepted: 08/07/2017] [Indexed: 06/07/2023]
Abstract
Petroleum is produced by thermal decay of buried organic material over millions of years. Petroleum oilfield ecosystems represent resource of reduced carbon which favours microbial growth. Therefore, it is obvious that many microorganisms have adapted to harsh environmental conditions of these ecosystems specifically temperature, oxygen availability and pressure. Knowledge of microorganisms present in ecosystems of petroleum oil reservoirs; their physiological and biological properties help in successful exploration of petroleum. Understanding microbiology of petroleum oilfield(s) can be used to enhance oil recovery, as microorganisms in oil reservoirs produce various metabolites viz. gases, acids, solvents, biopolymers and biosurfactants. The aim of this review is to discuss characteristics of petroleum oil reservoirs. This review also provides an updated literature on microbial ecology of these extreme ecosystems including microbial origin as well as various types of microorganisms such as methanogens; iron, nitrate and sulphate reducing bacteria, and fermentative microbes present in petroleum oilfield ecosystems.
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Affiliation(s)
- Sunita J Varjani
- Gujarat Pollution Control Board, Sector-10A, Gandhinagar 382010, Gujarat, India.
| | - Edgard Gnansounou
- Bioenergy and Energy Planning Research Group (BPE), IIC, ENAC, Station 18, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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19
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Progeny production in the periplasm of Thermosipho globiformans. Extremophiles 2017; 21:805-815. [PMID: 28577249 PMCID: PMC5487896 DOI: 10.1007/s00792-017-0944-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 05/08/2017] [Indexed: 02/02/2023]
Abstract
Thermotogales are rod-shaped, Gram-negative, anaerobic, (hyper) thermophiles distinguished by an outer sheath-like toga, which comprises an outer membrane (OM) and an amorphous layer (AL). Thermosipho globiformans bacteria can transform into spheroids with multiple cells concurrently with AL disintegration during early growth; the cell is defined as the cytoplasmic membrane (CM) plus the entity surrounded by the CM. Spheroids eventually produce rapidly moving periplasmic ‘progenies’ through an unknown mechanism. Here, we used high-temperature microscopy (HTM) to directly observe spheroid generation and growth. Rod OMs abruptly inflated to form ~2 μm-diameter balloons. Concurrently, multiple globular cells emerged in the balloons, suggesting their translocation and transformation from the rod state. During spheroid growth, the cells elongated and acquired a large dish shape by possible fusion. Spheroids with dish-shaped cells further enlarged to ~12 μm in diameter. HTM and epifluorescence-microscopy results collectively indicated that the nucleoids of dish-shaped cells transformed to form a ring shape, which then distorted to form a lip shape as the spheroid enlarged. HTM showed that ‘progenies’ were produced in the spheroid periplasm. Transmission electron microscopy results suggested that the ‘progenies’ represented immature progenies lacking togas, which were acquired subsequently.
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Growth Inhibition of Sulfate-Reducing Bacteria in Produced Water from the Petroleum Industry Using Essential Oils. Molecules 2017; 22:molecules22040648. [PMID: 28422054 PMCID: PMC6153933 DOI: 10.3390/molecules22040648] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/13/2017] [Accepted: 04/15/2017] [Indexed: 11/17/2022] Open
Abstract
Strategies for the control of sulfate-reducing bacteria (SRB) in the oil industry involve the use of high concentrations of biocides, but these may induce bacterial resistance and/or be harmful to public health and the environment. Essential oils (EO) produced by plants inhibit the growth of different microorganisms and are a possible alternative for controlling SRB. We aimed to characterize the bacterial community of produced water obtained from a Brazilian petroleum facility using molecular methods, as well as to evaluate the antimicrobial activity of EO from different plants and their major components against Desulfovibrio alaskensis NCIMB 13491 and against SRB growth directly in the produced water. Denaturing gradient gel electrophoresis revealed the presence of the genera Pelobacter and Marinobacterium, Geotoga petraea, and the SRB Desulfoplanes formicivorans in our produced water samples. Sequencing of dsrA insert-containing clones confirmed the presence of sequences related to D. formicivorans. EO obtained from Citrus aurantifolia, Lippia alba LA44 and Cymbopogon citratus, as well as citral, linalool, eugenol and geraniol, greatly inhibited (minimum inhibitory concentration (MIC) = 78 µg/mL) the growth of D. alaskensis in a liquid medium. The same MIC was obtained directly in the produced water with EO from L. alba LA44 (containing 82% citral) and with pure citral. These findings may help to control detrimental bacteria in the oil industry.
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Arroua B, Ranchou-Peyruse A, Ranchou-Peyruse M, Magot M, Urios L, Grimaud R. Pleomorphochaeta caudata gen. nov., sp. nov., an anaerobic bacterium isolated from an offshore oil well, reclassification of Sphaerochaeta multiformis MO-SPC2T as Pleomorphochaeta multiformis MO-SPC2T comb. nov. as the type strain of this novel genus and emended description of the genus Sphaerochaeta. Int J Syst Evol Microbiol 2017; 67:417-424. [DOI: 10.1099/ijsem.0.001641] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Boussad Arroua
- CNRS/ Université de Pau & des Pays de l’Adour, IPREM UMR 5254, 64000, Pau, France
| | | | | | - Michel Magot
- CNRS/ Université de Pau & des Pays de l’Adour, IPREM UMR 5254, 64000, Pau, France
| | - Laurent Urios
- CNRS/ Université de Pau & des Pays de l’Adour, IPREM UMR 5254, 64000, Pau, France
| | - Régis Grimaud
- CNRS/ Université de Pau & des Pays de l’Adour, IPREM UMR 5254, 64000, Pau, France
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Jiang L, L'Haridon S, Jebbar M, Xu H, Alain K, Shao Z. Complete genome sequence and whole-genome phylogeny of Kosmotoga pacifica type strain SLHLJ1 T from an East Pacific hydrothermal sediment. Stand Genomic Sci 2017; 12:3. [PMID: 28074121 PMCID: PMC5217533 DOI: 10.1186/s40793-016-0214-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/10/2016] [Indexed: 12/02/2022] Open
Abstract
Kosmotoga pacifica strain SLHLJ1T is a thermophilic chemoorganoheterotrophic bacterium isolated from a deep-sea hydrothermal sediment. It belongs to the physiologically homogeneous Thermotogaceae family. Here, we describe the phenotypic features of K. pacifica together with its genome sequence and annotation. The chromosome has 2,169,170 bp, organized in one contig. A total of 1897 candidate protein-encoding genes and 177 RNA genes were identified. The 16S rRNA gene sequence of this strain is distantly related to sequences of some relatives classified in the same genus (K. olearia 7.02% and K. shengliensis 7.83%), with dissimilarity percentages close to the threshold generally described for genus delineation. Nevertheless, the percentage of conserved proteins (POCP), which is much higher than 50% (around 70%), together with phenotypic features of the isolates, confirm the affiliation all Kosmotoga species described so far to the same genus.
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Affiliation(s)
- Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, 361005 China ; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005 China ; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005 China
| | - Stéphane L'Haridon
- Université de Bretagne Occidentale, UMR 6197-Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), rue Dumont d'Urville, 29 280 Plouzané, France ; CNRS, UMR 6197-Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), rue Dumont d'Urville, 29 280 Plouzané, France ; Ifremer, UMR 6197-Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Brest-Iroise, BP70, 29 280 Plouzané, France
| | - Mohamed Jebbar
- Université de Bretagne Occidentale, UMR 6197-Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), rue Dumont d'Urville, 29 280 Plouzané, France ; CNRS, UMR 6197-Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), rue Dumont d'Urville, 29 280 Plouzané, France ; Ifremer, UMR 6197-Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Brest-Iroise, BP70, 29 280 Plouzané, France
| | - Hongxiu Xu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, 361005 China ; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005 China ; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005 China
| | - Karine Alain
- CNRS, UMR 6197-Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), rue Dumont d'Urville, 29 280 Plouzané, France ; Université de Bretagne Occidentale, UMR 6197-Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), rue Dumont d'Urville, 29 280 Plouzané, France ; Ifremer, UMR 6197-Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Brest-Iroise, BP70, 29 280 Plouzané, France
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, 361005 China ; State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005 China ; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005 China
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23
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Lopes JLS, Yoneda JS, Martins JM, DeMarco R, Jameson DM, Castro AM, Bossolan NRS, Wallace BA, Araujo APU. Environmental Factors Modulating the Stability and Enzymatic Activity of the Petrotoga mobilis Esterase (PmEst). PLoS One 2016; 11:e0158146. [PMID: 27351338 PMCID: PMC4924860 DOI: 10.1371/journal.pone.0158146] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/11/2016] [Indexed: 01/20/2023] Open
Abstract
Enzymes isolated from thermophilic organisms found in oil reservoirs can find applications in many fields, including the oleochemical, pharmaceutical, bioenergy, and food/dairy industries. In this study, in silico identification and recombinant production of an esterase from the extremophile bacteria Petrotoga mobilis (designated PmEst) were performed. Then biochemical, bioinformatics and structural characterizations were undertaken using a combination of synchrotron radiation circular dichroism (SRCD) and fluorescence spectroscopies to correlate PmEst stability and hydrolytic activity on different substrates. The enzyme presented a high Michaelis-Menten constant (KM 0.16 mM) and optimum activity at ~55°C for p-nitrophenyl butyrate. The secondary structure of PmEst was preserved at acid pH, but not under alkaline conditions. PmEst was unfolded at high concentrations of urea or guanidine through apparently different mechanisms. The esterase activity of PmEst was preserved in the presence of ethanol or propanol and its melting temperature increased ~8°C in the presence of these organic solvents. PmEst is a mesophilic esterase with substrate preference towards short-to medium-length acyl chains. The SRCD data of PmEst is in agreement with the prediction of an α/β protein, which leads us to assume that it displays a typical fold of esterases from this family. The increased enzyme stability in organic solvents may enable novel applications for its use in synthetic biology. Taken together, our results demonstrate features of the PmEst enzyme that indicate it may be suitable for applications in industrial processes, particularly, when the use of polar organic solvents is required.
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Affiliation(s)
- Jose L. S. Lopes
- Instituto de Física, Universidade de São Paulo, São Paulo, Brazil
| | - Juliana S. Yoneda
- Instituto de Física, Universidade de São Paulo, São Paulo, Brazil
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Julia M. Martins
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Ricardo DeMarco
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - David M. Jameson
- Department of Cell and Molecular Biology, University of Hawai’i at Manoa, Hawaii, United States of America
| | - Aline M. Castro
- Biotechnology Division, Research and Development Center, Petrobras, Brazil
| | - Nelma R. S. Bossolan
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - B. A. Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Ana P. U. Araujo
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
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Complementary Microorganisms in Highly Corrosive Biofilms from an Offshore Oil Production Facility. Appl Environ Microbiol 2016; 82:2545-2554. [PMID: 26896143 DOI: 10.1128/aem.03842-15] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/11/2016] [Indexed: 11/20/2022] Open
Abstract
Offshore oil production facilities are frequently victims of internal piping corrosion, potentially leading to human and environmental risks and significant economic losses. Microbially influenced corrosion (MIC) is believed to be an important factor in this major problem for the petroleum industry. However, knowledge of the microbial communities and metabolic processes leading to corrosion is still limited. Therefore, the microbial communities from three anaerobic biofilms recovered from the inside of a steel pipe exhibiting high corrosion rates, iron oxide deposits, and substantial amounts of sulfur, which are characteristic of MIC, were analyzed in detail. Bacterial and archaeal community structures were investigated by automated ribosomal intergenic spacer analysis, multigenic (16S rRNA and functional genes) high-throughput Illumina MiSeq sequencing, and quantitative PCR analysis. The microbial community analysis indicated that bacteria, particularly Desulfovibrio species, dominated the biofilm microbial communities. However, other bacteria, such as Pelobacter, Pseudomonas, and Geotoga, as well as various methanogenic archaea, previously detected in oil facilities were also detected. The microbial taxa and functional genes identified suggested that the biofilm communities harbored the potential for a number of different but complementary metabolic processes and that MIC in oil facilities likely involves a range of microbial metabolisms such as sulfate, iron, and elemental sulfur reduction. Furthermore, extreme corrosion leading to leakage and exposure of the biofilms to the external environment modify the microbial community structure by promoting the growth of aerobic hydrocarbon-degrading organisms.
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25
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Itoh T, Onishi M, Kato S, Iino T, Sakamoto M, Kudo T, Takashina T, Ohkuma M. Athalassotoga saccharophila gen. nov., sp. nov., isolated from an acidic terrestrial hot spring, and proposal of Mesoaciditogales ord. nov. and Mesoaciditogaceae fam. nov. in the phylum Thermotogae. Int J Syst Evol Microbiol 2016; 66:1045-1051. [DOI: 10.1099/ijsem.0.000833] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Masafumi Onishi
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
- Graduate School of Life Sciences, Toyo University, Oura, Gunma 374-0193, Japan
| | - Shingo Kato
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Takao Iino
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Mitsuo Sakamoto
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Tomonori Takashina
- Graduate School of Life Sciences, Toyo University, Oura, Gunma 374-0193, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
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26
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Zhou J, Zhou X, Li Y, Xing J. Bacterial communities in haloalkaliphilic sulfate-reducing bioreactors under different electron donors revealed by 16S rRNA MiSeq sequencing. JOURNAL OF HAZARDOUS MATERIALS 2015; 295:176-184. [PMID: 25897699 DOI: 10.1016/j.jhazmat.2015.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/17/2015] [Accepted: 04/04/2015] [Indexed: 06/04/2023]
Abstract
Biological technology used to treat flue gas is useful to replace conventional treatment, but there is sulfide inhibition. However, no sulfide toxicity effect was observed in haloalkaliphilic bioreactors. The performance of the ethanol-fed bioreactor was better than that of lactate-, glucose-, and formate-fed bioreactor, respectively. To support this result strongly, Illumina MiSeq paired-end sequencing of 16S rRNA gene was applied to investigate the bacterial communities. A total of 389,971 effective sequences were obtained and all of them were assigned to 10,220 operational taxonomic units (OTUs) at a 97% similarity. Bacterial communities in the glucose-fed bioreactor showed the greatest richness and evenness. The highest relative abundance of sulfate-reducing bacteria (SRB) was found in the ethanol-fed bioreactor, which can explain why the performance of the ethanol-fed bioreactor was the best. Different types of SRB, sulfur-oxidizing bacteria, and sulfur-reducing bacteria were detected, indicating that sulfur may be cycled among these microorganisms. Because high-throughput 16S rRNA gene paired-end sequencing has improved resolution of bacterial community analysis, many rare microorganisms were detected, such as Halanaerobium, Halothiobacillus, Desulfonatronum, Syntrophobacter, and Fusibacter. 16S rRNA gene sequencing of these bacteria would provide more functional and phylogenetic information about the bacterial communities.
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Affiliation(s)
- Jiemin Zhou
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, P.O. Box 353, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xuemei Zhou
- 101 Institute, Ministry of Civil Affairs, Beijing 100070, PR China
| | - Yuguang Li
- 101 Institute, Ministry of Civil Affairs, Beijing 100070, PR China
| | - Jianmin Xing
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, P.O. Box 353, Beijing 100190, PR China.
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27
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Kanoksilapatham W, Keawram P, Gonzalez JM, Robb FT. Isolation, characterization, and survival strategies of Thermotoga sp. strain PD524, a hyperthermophile from a hot spring in Northern Thailand. Extremophiles 2015; 19:853-61. [PMID: 26101016 DOI: 10.1007/s00792-015-0761-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/26/2015] [Indexed: 11/30/2022]
Abstract
A hyperthermophilic Thermotoga sp. strain PD524 was isolated from a hot spring in Northern Thailand. Cells were long-curved rods (0.5-0.6 × 2.5-10 μm) surrounded by a typical outer membrane toga. Strain PD524 is aero-tolerant at 4 °C but is aero-sensitive at 80 °C. A heat resistant subpopulation was observed in late-stationary phase. Cells from late-stationary phase were revealed remarkably less sensitive to 0.001 % SDS treatment than cells from exponential phase. The temperature range for growth was 70-85 °C (opt. temp. 80 °C), pH range was 6-8.5 (opt. pH 7.5-8.0), and NaCl range of 0 to <10 g/L (opt. 0.5 g/L). Glucose, sucrose, maltose, fructose, xylose, mannose, arabinose, trehalose, starch, and cellobiose were utilized as growth substrates. Growth was inhibited by S(o). Growth yield was stimulated by SO 4 (=) but not by S2O 3 (=) and NO3 (-). Analysis of 16S rRNA gene sequence (KF164213) of strain PD524 revealed closest similarity (96 %) to Thermotoga maritima MSB8(T), T. neapolitana NES(T), T. petrophila RKU-1(T), and T. naphthophila RKU-10(T).
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Affiliation(s)
- Wirojne Kanoksilapatham
- Department of Microbiology, Faculty of Science, Silpakorn University, Nakhon Pathom, 73000, Thailand,
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28
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Microbial community composition and dynamics in high-temperature biogas reactors using industrial bioethanol waste as substrate. Appl Microbiol Biotechnol 2014; 98:9095-106. [DOI: 10.1007/s00253-014-5906-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 06/19/2014] [Accepted: 06/20/2014] [Indexed: 12/31/2022]
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29
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Slobodkin AI, Slobodkina GB. Thermophilic prokaryotes from deep subterranean habitats. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714030151] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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30
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Purwasena IA, Sugai Y, Sasaki K. Petrotoga japonica sp. nov., a thermophilic, fermentative bacterium isolated from Yabase Oilfield in Japan. Arch Microbiol 2014; 196:313-21. [PMID: 24604301 DOI: 10.1007/s00203-014-0972-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 02/21/2014] [Accepted: 02/24/2014] [Indexed: 11/25/2022]
Abstract
A gram-negative, motile, fermentative, thermophilic bacterium, designated AR80(T), was isolated from a high-temperature oil reservoir in Yabase Oilfield in Akita, Japan. Cells were rod-shaped, motile by means of polar flagella, and formed circular, convex, white colonies. The strain grew at 40-65 °C (optimum 60 °C), 0.5-9 % (w/v) NaCl (optimum 0.5-1 %), pH 6-9 (optimum pH 7.5), and elemental sulfur or thiosulfate serves as terminal electron acceptor. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain AR80(T) belonged to the genus Petrotoga and shared approximately 94.5 % sequence similarity with the type species of this genus. The G + C content of genomic DNA was 32.4 mol% while the value of DNA-DNA hybridization between the closest relative species Petrotoga miotherma and AR80(T) was 58.1 %. The major cellular fatty acids of strain AR80(T) consisted of 18:1 w9c, 16:0, and 16:1 w9c. Based on genetic and phenotypic properties, strain AR80(T) was different with other identified Petrotoga species and represents as a novel species, for which the name Petrotoga japonica sp. nov. is proposed. The type strain is AR80(T) (=NBRC 108752(T) = KCTC 15103(T) = HUT 8122(T)).
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MESH Headings
- Bacterial Typing Techniques
- Base Composition
- DNA, Bacterial/genetics
- Fatty Acids/chemistry
- Fermentation
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/classification
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/genetics
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/isolation & purification
- Hot Temperature
- Japan
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Oil and Gas Fields/microbiology
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Thiosulfates/metabolism
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Affiliation(s)
- Isty Adhitya Purwasena
- School of Life Science and Technology, Bandung Institute of Technology, Ganesha 10, Bandung, West Java, 40132, Indonesia,
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31
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Microbial enhanced heavy oil recovery by the aid of inhabitant spore-forming bacteria: an insight review. ScientificWorldJournal 2014; 2014:309159. [PMID: 24550702 PMCID: PMC3914512 DOI: 10.1155/2014/309159] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 10/20/2013] [Indexed: 11/21/2022] Open
Abstract
Crude oil is the major source of energy worldwide being exploited as a source of economy, including Oman. As the price of crude oil increases and crude oil reserves collapse, exploitation of oil resources in mature reservoirs is essential for meeting future energy demands. As conventional recovery methods currently used have become less efficient for the needs, there is a continuous demand of developing a new technology which helps in the upgradation of heavy crude oil. Microbial enhanced oil recovery (MEOR) is an important tertiary oil recovery method which is cost-effective and eco-friendly technology to drive the residual oil trapped in the reservoirs. The potential of microorganisms to degrade heavy crude oil to reduce viscosity is considered to be very effective in MEOR. Earlier studies of MEOR (1950s) were based on three broad areas: injection, dispersion, and propagation of microorganisms in petroleum reservoirs; selective degradation of oil components to improve flow characteristics; and production of metabolites by microorganisms and their effects. Since thermophilic spore-forming bacteria can thrive in very extreme conditions in oil reservoirs, they are the most suitable organisms for the purpose. This paper contains the review of work done with thermophilic spore-forming bacteria by different researchers.
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32
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Members of the Order Thermotogales: From Microbiology to Hydrogen Production. MICROBIAL BIOENERGY: HYDROGEN PRODUCTION 2014. [DOI: 10.1007/978-94-017-8554-9_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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33
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Ueno Y, Kitajima Y. Suppression of Methane Gas Emissions and Analysis of the Electrode Microbial Community in a Sediment-Based Bio-Electrochemical System. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/aim.2014.45032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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34
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Kosmotoga pacifica sp. nov., a thermophilic chemoorganoheterotrophic bacterium isolated from an East Pacific hydrothermal sediment. Extremophiles 2013; 18:81-8. [DOI: 10.1007/s00792-013-0596-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/30/2013] [Indexed: 10/26/2022]
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35
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Bhandari V, Gupta RS. Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations. Antonie van Leeuwenhoek 2013; 105:143-68. [PMID: 24166034 DOI: 10.1007/s10482-013-0062-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 10/21/2013] [Indexed: 10/26/2022]
Abstract
All species from the phylum Thermotogae, class Thermotogae, are currently part of a single family, Thermotogaceae. Using genomic data from 17 Thermotogae species, detailed phylogenetic and comparative genomic analyses were carried out to understand their evolutionary relationships and identify molecular markers that are indicative of species relationships within the phylum. In the 16S rRNA gene tree and phylogenetic trees based upon two different large sets of proteins, members of the phylum Thermotogae formed a number of well-resolved clades. Character compatibility analysis on the protein sequence data also recovered a single largest clique that exhibited similar topology to the protein trees and where all nodes were supported by multiple compatible characters. Comparative genomic analyses have identified 85 molecular markers, in the form of conserved signature indels (CSIs), which are specific for different observed clades of Thermotogae at multiple phylogenetic depths. Eleven of these CSIs were specific for the phylum Thermotogae whereas nine others supported a clade comprising of the genera Thermotoga, Thermosipho and Fervidobacterium. Ten other CSIs provided evidence that the genera Thermosipho and Fervidobacterium shared a common ancestor exclusive of the other Thermotogae and four and eight CSIs in other proteins were specific for the genera Thermosipho and Fervidobacterium, respectively. Two other deep branching clades, one consisting of the genera Kosmotoga and Mesotoga and the other comprising of the genera Petrotoga and Marinitoga, were also supported by multiple CSIs. Based upon the consistent branching of the Thermotogae species using different phylogenetic approaches, and numerous identified CSIs supporting the distinctness of different clades, it is proposed that the class Thermotogae should be divided into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.). Additionally, the results of our phylogenetic/compatibility studies along with the species distribution patterns of 22 identified CSIs, provide compelling evidence that the current genus Thermotoga is comprised of two evolutionary distinct groups and that it should be divided into two genera. It is proposed that the emended genus Thermotoga should retain only the species Thermotoga maritima, Tt. neapolitana, Tt. petrophila, Tt. naphthophila, Thermotoga sp. EMP, Thermotoga sp. A7A and Thermotoga sp. RQ2 while the other Thermotoga species (viz. Tt. lettingae, Tt. thermarum, Tt. elfii, Tt. subterranean and Tt. hypogea) be transferred to a new genus, Pseudothermotoga gen. nov.
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Affiliation(s)
- Vaibhav Bhandari
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
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36
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Wentzel A, Lewin A, Cervantes FJ, Valla S, Kotlar HK. Deep Subsurface Oil Reservoirs as Poly-extreme Habitats for Microbial Life. A Current Review. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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37
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Wery N, Cambon-Bonavita MA, Lesongeur F, Barbier G. Diversity of anaerobic heterotrophic thermophiles isolated from deep-sea hydrothermal vents of the Mid-Atlantic Ridge. FEMS Microbiol Ecol 2012; 41:105-14. [PMID: 19709244 DOI: 10.1111/j.1574-6941.2002.tb00971.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Abstract During the 'MARVEL' oceanographical cruise performed in September 1997, samples were collected from the deep-sea vents of hydrothermal sites on the Mid-Atlantic Ridge. Eighty-four thermophilic and hyperthermophilic heterotrophic microorganisms were isolated using different culture media containing cellobiose, xylan, starch, lipidic or proteic substrates. These isolates were obtained in anaerobic conditions, at 65 degrees C, 85 degrees C and 95 degrees C. Fifty of them were classified using amplified ribosomal DNA restriction analysis, random amplified polymorphic DNA and 16S rDNA sequencing. The strains classified have been assigned to the archaeal order Thermococcales and to the bacterial orders Thermotogales and Clostridiales. Variations in growth temperature and carbon sources were efficient enough to generate taxonomic diversity within enrichment cultures. Presumptive new genera and new species were isolated. Two isolates were confirmed as type strains of new species of new genera recently described: Marinitoga camini and Caloranaerobacter azorensis.
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Affiliation(s)
- Nathalie Wery
- Laboratoire de Microbiologie et de Biotechnologie des Extrêmophiles, DRV-VP, IFREMER Centre de Brest, BP70, 29280 Plouzané, France
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38
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Ben Hania W, Godbane R, Postec A, Hamdi M, Ollivier B, Fardeau ML. Defluviitoga tunisiensis gen. nov., sp. nov., a thermophilic bacterium isolated from a mesothermic and anaerobic whey digester. Int J Syst Evol Microbiol 2012; 62:1377-1382. [DOI: 10.1099/ijs.0.033720-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain SulfLac1T, a thermophilic, anaerobic and slightly halophilic, rod-shaped bacterium with a sheath-like outer structure (toga), was isolated from a whey digester in Tunisia. The strain’s non-motile cells measured 3–30×1 µm and appeared singly, in pairs or as long chains. The novel strain reduced thiosulfate and elemental sulfur, but not sulfate or sulfite, into sulfide. It grew at 37–65 °C (optimum 55 °C), at pH 6.5–7.9 (optimum pH 6.9) and with 0.2–3 % (w/v) NaCl (optimum 0.5 %). The G+C content of the strain’s genomic DNA was 33.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SulfLac1T was most closely related to
Petrotoga mobilis
(91.4 % sequence similarity). Based on phenotypic, phylogenetic and chemotaxonomic evidence, strain SulfLac1T represents a novel species of a new genus within the order
Thermotogales
, for which the name Defluviitoga tunisiensis gen. nov., sp. nov. is proposed. The type strain of the type species is SulfLac1T ( = DSM 23805T = JCM 17210T).
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Affiliation(s)
- Wajdi Ben Hania
- Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis, Tunisia
- Laboratoire de Microbiologie H10, UMR 235, Aix-Marseille Univ., Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Ramzi Godbane
- Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis, Tunisia
- Laboratoire de Microbiologie H10, UMR 235, Aix-Marseille Univ., Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Anne Postec
- Laboratoire de Microbiologie H10, UMR 235, Aix-Marseille Univ., Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Moktar Hamdi
- Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Appliquées et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis, Tunisia
| | - Bernard Ollivier
- Laboratoire de Microbiologie H10, UMR 235, Aix-Marseille Univ., Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Marie-Laure Fardeau
- Laboratoire de Microbiologie H10, UMR 235, Aix-Marseille Univ., Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
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Dahle H, Hannisdal B, Steinsbu BO, Ommedal H, Einen J, Jensen S, Larsen O, Ovreås L, Norland S. Evolution of temperature optimum in Thermotogaceae and the prediction of trait values of uncultured organisms. Extremophiles 2011; 15:509-16. [PMID: 21638056 PMCID: PMC3119804 DOI: 10.1007/s00792-011-0381-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 05/20/2011] [Indexed: 11/28/2022]
Abstract
Quantitative characterization of the mode and rate of phenotypic evolution is rarely applied to prokaryotes. Here, we present an analysis of temperature optimum (Topt) evolution in the thermophilic family Thermotogaceae, which has a large number of cultured representatives. We use log-rate-interval analysis to show that Topt evolution in Thermotogaceae is consistent with a Brownian motion (BM) evolutionary model. The properties of the BM model are used to a establish confidence intervals on the unknown phenotypic trait value of an uncultured organism, given its distance to a close relative with known trait value. Cross-validation by bootstrapping indicates that the predictions are robust.
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Affiliation(s)
- Håkon Dahle
- Centre for Geobiology, University of Bergen, Allegaten, Norway.
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40
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Nunoura T, Hirai M, Imachi H, Miyazaki M, Makita H, Hirayama H, Furushima Y, Yamamoto H, Takai K. Kosmotoga arenicorallina sp. nov. a thermophilic and obligately anaerobic heterotroph isolated from a shallow hydrothermal system occurring within a coral reef, southern part of the Yaeyama Archipelago, Japan, reclassification of Thermococcoides shengliensis as Kosmotoga shengliensis comb. nov., and emended description of the genus Kosmotoga. Arch Microbiol 2010; 192:811-9. [PMID: 20694719 DOI: 10.1007/s00203-010-0611-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2010] [Revised: 07/20/2010] [Accepted: 07/26/2010] [Indexed: 11/28/2022]
Abstract
A novel thermophilic and sulfur-reducing bacterium, strain S304(T), was isolated from the Taketomi submarine hot spring shallow hydrothermal field located at southern part of the Yaeyama Archipelago, Japan. The cells were non-motile short thick rods or oval cocci 1.1-2.7 μm in length and 1.1-1.9 μm in width. Strain S304(T) was an obligately anaerobic heterotroph and sulfur reduction stimulates growth. Growth was observed between 50-65°C (optimum 60°C), pH 6.2-8.0 (optimum pH 7.1), 1.0-6.0% NaCl concentration (optimum 3.0%). The fatty acid composition was C(16:0) (71.4%), C(18:0) (20.9%) and C(18:1) (7.7%). The G + C content of genomic DNA was 40.8 mol%. The 16S rRNA gene sequence analysis indicated that strain S304(T) belonged to the genus Kosmotoga. Based on physiological and phylogenetic features of a new isolate, we propose new species in the genus Kosmotoga: the type strain of Kosmotoga arenicorallina sp. nov is S304(T) (=JCM 15790(T) = DSM22549(T)). Thermococcoides shengliensis 2SM-2(T) is phylogenetically associated with Kosmotoga olearia 14.5.1(T). Based on the phylogenetic relationship between Thermococcoides shengliensis 2SM-2(T) and Kosmotoga olearia 14.5.1(T), we propose the reclassification of Thermococcoides shengliensis as Kosmotoga shengliensis comb. nov. (type strain 2SM-2(T)). In addition, an emended description of the genus Kosmotoga is proposed.
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Affiliation(s)
- Takuro Nunoura
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology, Yokosuka, Japan.
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41
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Jayasinghearachchi HS, Lal B. Oceanotoga teriensis gen. nov., sp. nov., a thermophilic bacterium isolated from offshore oil-producing wells. Int J Syst Evol Microbiol 2010; 61:554-560. [PMID: 20382783 DOI: 10.1099/ijs.0.018036-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, moderately thermophilic, chemo-organotrophic bacterium was isolated from formation fluid samples from an offshore oil-production well head at Bombay High (Western India). Cells were rod-shaped with a sheath-like outer structure ('toga'); the cells appeared singly, in pairs or in short chains. Cells grew at 25-70 °C (optimum 55-58 °C), pH 5.5-9.0 (optimum pH 7.3-7.8) and 0-12 % (w/v) NaCl (optimum 4.0-4.5 %). The isolate was able to grow on various carbohydrates or complex proteinaceous substances. The isolate reduced thiosulfate and elemental sulfur. The major end products of glucose fermentation were acetate, H₂ and CO₂. The DNA G+C content of the genomic DNA was 26.8 mol%. Phylogenetic analysis of the 16S rRNA gene placed the strain within the order Thermotogales in the bacterial domain. On the basis of 16S rRNA gene sequence comparisons and in combination with morphological and physiological characteristics, the isolate represents a novel species of new genus, for which the name Oceanotoga teriensis gen. nov., sp. nov. is proposed. The type strain of the type species is OCT74(T) (=JCM 15580(T)=LMG 24865(T)).
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Affiliation(s)
- Himali S Jayasinghearachchi
- The Energy and Resource Institute, Darbari Seth Block, Habitat Place, Lodhi Road, New Delhi - 110 003, India
| | - Banwari Lal
- The Energy and Resource Institute, Darbari Seth Block, Habitat Place, Lodhi Road, New Delhi - 110 003, India
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Thermococcoides shengliensis gen. nov., sp. nov., a new member of the order Thermotogales isolated from oil-production fluid. Int J Syst Evol Microbiol 2010; 60:932-937. [DOI: 10.1099/ijs.0.013912-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermophilic, strictly anaerobic, heterotrophic bacterium, strain 2SM-2T, was isolated from the Shengli oilfield, China. This organism was identified as a member of the order Thermotogales on the basis of its 16S rRNA gene sequence and the presence of an external membranous toga-like structure. Cells stained Gram-negative, were non-motile, appeared as irregular cocci 0.7–0.9 μm in diameter, and occurred in clusters of two to six cells, with cells located within a ballooning toga-like membrane. Its optimum temperature, pH and NaCl concentration for growth were 65 °C, 7.0 and 15 g l−1, respectively. Under the optimum growth conditions, the doubling time was approximately 105 min. Strain 2SM-2T fermented a variety of simple and complex substrates such as glucose, acetate, methanol, starch and peptone while reducing elemental sulfur, sulfate and thiosulfate. The end products identified during growth on glucose were acetate, lactate, l-alanine, H2 and CO2. The DNA G+C content of this organism was 36.4 mol%. The results of 16S rRNA gene-based sequence comparisons revealed that the strain represented a new lineage within the family Thermotogaceae of the order Thermotogales. Based on the phenotypic and phylogenetic characteristics, it is proposed that this organism represents a novel species in a new genus within the family Thermotogaceae, for which the name Thermococcoides shengliensis gen. nov., sp. nov. is proposed. The type strain is 2SM-2T (=ACCC 00496T=DSM 22460T).
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Dipippo JL, Nesbø CL, Dahle H, Doolittle WF, Birkland NK, Noll KM. Kosmotoga olearia gen. nov., sp. nov., a thermophilic, anaerobic heterotroph isolated from an oil production fluid. Int J Syst Evol Microbiol 2009; 59:2991-3000. [PMID: 19643902 DOI: 10.1099/ijs.0.008045-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermophilic, heterotrophic bacterium, strain TBF 19.5.1(T), was isolated from oil production fluid at the Troll B oil platform in the North Sea. Cells of strain TBF 19.5.1(T) were non-motile rods with a sheath-like structure, or toga. The strain was Gram-negative and grew at 20-80 degrees C (optimum 65 degrees C), pH 5.5-8.0 (optimum pH 6.8) and NaCl concentrations of 10-60 g l(-1) (optimum 25-30 g l(-1)). For a member of the order Thermotogales, the novel isolate is capable of unprecedented growth at low temperatures, with an optimal doubling time of 175 min (specific growth rate 0.24 h(-1)) and a final optical density of >1.4 when grown on pyruvate at 37 degrees C. Various carbohydrates, proteinaceous compounds and pyruvate served as growth substrates. Thiosulfate, but not elemental sulfur, enhanced growth of the isolate. Sulfate also enhanced growth, but sulfide was not produced. The strain grew in the presence of up to approximately 15 % oxygen, but only if cysteine was included in the medium. Growth of the isolate was inhibited by acetate, lactate and propionate, while butanol and malate prevented growth. The major fermentation products formed on maltose were hydrogen, carbon dioxide and acetic acid, with traces of ethanol and propionic acid. The G+C content of the genomic DNA was 42.5 mol%. Phylogenetic analyses of the 16S and 23S rRNA gene sequences as well as 29 protein-coding ORFs placed the strain within the bacterial order Thermotogales. Based on the phylogenetic analyses and the possession of a variety of physiological characteristics not previously found in any species of this order, it is proposed that the strain represents a novel species of a new genus within the family Thermotogaceae, order Thermotogales. The name Kosmotoga olearia gen. nov., sp. nov. is proposed. The type strain of Kosmotoga olearia is TBF 19.5.1(T) (=DSM 21960(T) =ATCC BAA-1733(T)).
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Affiliation(s)
- Jonathan L Dipippo
- Department of Molecular and Cell Biology, University of Connecticut, Unit 3125, 91 N. Eagleville Road, Storrs, CT 06269-3125, USA
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Abstract
In order to survive extremes of pH, temperature, salinity and pressure, organisms have been found to develop unique defences against their environment, leading to the biosynthesis of novel molecules ranging from simple osmolytes and lipids to complex secondary metabolites. This review highlights novel molecules isolated from microorganisms that either tolerate or favour extreme growth conditions.
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Affiliation(s)
- Zoe E Wilson
- Department of Chemistry, University of Auckland, 23 Symonds St, Auckland, 1010, New Zealand
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Abstract
A universal Tree of Life has been a longstanding goal of the biosciences. The most common Tree of Life, based on the small subunit rRNA gene, may or may not represent the phylogenetic history of microorganisms. The horizontal transfer of genes from one taxon to another provides a means by which each gene may tell of an independent history. When complete genomes became available, the extent to which horizontal gene transfer (HGT) has occurred became more evident. When using genomic data to study the Tree of Life, one can use any of the four broad approaches: (i) build lots of individual gene trees ("phylogenomics"), (ii) concatenate genes together for an analysis yielding one "supergene" tree, (iii) form a single tree based on the "gene content" within genomes using either orthologs or homologs, or (iv) investigate the order of genes within genomes to discern some aspects of microbial evolution. The application of whole genome tree building has suggested that there is a core tree, that such a core tree can be investigated using these varied methods, and that the results are largely similar to those of the rRNA universal Tree of Life. Some of the most interesting features of the rRNA tree, such as early diverging hyperthermophilic lineages are still uncertain, but remain a possibility. Genomic trees and geologic evidence together suggest that the vertical descent of genes and the horizontal transfer of genes between genetically similar lineages ultimately results in a core Tree of Life with at least some lineages that have phenotypic characteristics recognizable for billions of years.
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Affiliation(s)
- Christopher H House
- Department of Geosciences and Pennsylvania State Astrobiology Research Center, Pennsylvania State University, University Park, PA, USA
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Abstract
Thermophilic anaerobes are Archaea and Bacteria that grow optimally at temperatures of 50 degrees C or higher and do not require the use of O(2) as a terminal electron acceptor for growth. The prokaryotes with this type of physiology are studied for a variety of reasons, including (a) to understand how life can thrive under extreme conditions, (b) for their biotechnological potential, and (c) because anaerobic thermophiles are thought to share characteristics with the early evolutionary life forms on Earth. Over 300 species of thermophilic anaerobes have been described; most have been isolated from thermal environments, but some are from mesobiotic environments, and others are from environments with temperatures below 0 degrees C. In this overview, the authors outline the phylogenetic and physiological diversity of thermophilic anaerobes as currently known. The purpose of this overview is to convey the incredible diversity and breadth of metabolism within this subset of anaerobic microorganisms.
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Affiliation(s)
- Isaac D Wagner
- 212 Biological Sciences Building, 1000 Cedar Street, University of Georgia, Athens, GA 30602-2605, USA
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Jorge CD, Lamosa P, Santos H. Alpha-D-mannopyranosyl-(1-->2)-alpha-D-glucopyranosyl-(1-->2)-glycerate in the thermophilic bacterium Petrotoga miotherma--structure, cellular content and function. FEBS J 2007; 274:3120-7. [PMID: 17521333 DOI: 10.1111/j.1742-4658.2007.05844.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The intracellular accumulation of low molecular mass organic compounds in response to stressful conditions was investigated in the thermophilic bacterium Petrotoga miotherma, a member of the order Thermotogales. This led to the discovery of a new solute, whose structure was established as alpha-D-mannopyranosyl-(1-->2)-alpha-D-glucopyranosyl-(1-->2)-glycerate (MGG) by MMR spectroscopy and MS. Under optimum growth conditions (3% NaCl; 55 degrees C), MGG was the major solute [up to 0.6 micromol.(mg protein)(-1)]; alpha-glutamate and proline were also present but in minor amounts [below 0.08 micromol.(mg protein)(-1)]. The level of MGG increased notably with the salinity of the growth medium up to the optimum NaCl concentration. At higher NaCl concentrations, however, the level of MGG decreased, whereas the levels of proline and alpha-glutamate increased about five-fold and 10-fold, respectively. MGG plays a role during low-level osmotic adaptation of Petrotoga miotherma, whereas alpha-glutamate and, to a lesser extent, proline are used for osmoprotection under salt stress. MGG is not part of the cell strategy for coping with heat or oxidative stress. Nevertheless, MGG was an efficient protector of pig heart malate dehydrogenase against heat inactivation and freeze-drying, although mannosylglycerate was better. This is the first report on the occurrence of MGG in living systems.
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Affiliation(s)
- Carla D Jorge
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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Miranda-Tello E, Fardeau ML, Joulian C, Magot M, Thomas P, Tholozan JL, Ollivier B. Petrotoga halophila sp. nov., a thermophilic, moderately halophilic, fermentative bacterium isolated from an offshore oil well in Congo. Int J Syst Evol Microbiol 2007; 57:40-44. [PMID: 17220438 DOI: 10.1099/ijs.0.64516-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermophilic, moderately halophilic, rod-shaped bacterium, strain MET-B(T), with a sheath-like outer structure (toga) was isolated from an offshore oil-producing well in Congo, West Africa. Strain MET-B(T) was a Gram-negative bacterium with the ability to reduce elemental sulfur, but not sulfate, thiosulfate or sulfite into sulfide. The optimum growth conditions were 60 degrees C, pH 6.7-7.2 and 4-6 % NaCl. The DNA G+C content was 34.6 mol%. Strain MET-B(T) was phylogenetically related to members of the genus Petrotoga; Petrotoga miotherma, Petrotoga olearia and Petrotoga mexicana were the closest relatives, with type strains exhibiting more than 99 % identity in an analysis of small-subunit rRNA gene sequences. The values for DNA-DNA relatedness between the type strains of these three species and strain MET-B(T) were less than 42 %. As MET-B(T) was found to be genetically and physiologically different from other species of the genus Petrotoga, this strain is proposed as representing a novel species, for which the name Petrotoga halophila sp. nov. is proposed. The type strain is MET-B(T) (=DSM 16923(T)=CCUG 50214(T)).
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MESH Headings
- Bacterial Typing Techniques
- Congo
- DNA, Bacterial/analysis
- DNA, Ribosomal/analysis
- Genes, rRNA
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/classification
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/genetics
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/isolation & purification
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/physiology
- Hot Temperature
- Molecular Sequence Data
- Petroleum
- Phenotype
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sodium Chloride
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Affiliation(s)
- Elizabeth Miranda-Tello
- El Colegio de la Frontera Sur, Unidad Chetumal, Departamento de Biotecnología Ambiental, Ecología Microbiana Aplicada y Contaminación, Av. del Centenario km 5.5, Col. Calderitas, CP 77900, Chetumal, Quintana Roo, Mexico
- IRD, UMR 180, IFR-BAIM, Universités de Provence et de la Méditerranée, ESIL case 925, 163 Avenue de Luminy, F-13288 Marseille cedex 09, France
| | - Marie-Laure Fardeau
- IRD, UMR 180, IFR-BAIM, Universités de Provence et de la Méditerranée, ESIL case 925, 163 Avenue de Luminy, F-13288 Marseille cedex 09, France
| | - Catherine Joulian
- BRGM, Environment and Process Division, Biotechnology Unit, BP 36009, F-45060 Orléans, France
- IRD, UMR 180, IFR-BAIM, Universités de Provence et de la Méditerranée, ESIL case 925, 163 Avenue de Luminy, F-13288 Marseille cedex 09, France
| | - Michel Magot
- Université de Pau et des Pays de l'Adour, Laboratoire d'Ecologie Moléculaire EA3525, F-64013 Pau, France
| | - Pierre Thomas
- IRD, UMR 180, IFR-BAIM, Universités de Provence et de la Méditerranée, ESIL case 925, 163 Avenue de Luminy, F-13288 Marseille cedex 09, France
| | - Jean-Luc Tholozan
- IRD, UMR 180, IFR-BAIM, Universités de Provence et de la Méditerranée, ESIL case 925, 163 Avenue de Luminy, F-13288 Marseille cedex 09, France
| | - Bernard Ollivier
- IRD, UMR 180, IFR-BAIM, Universités de Provence et de la Méditerranée, ESIL case 925, 163 Avenue de Luminy, F-13288 Marseille cedex 09, France
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50
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Nunoura T, Oida H, Miyazaki M, Suzuki Y, Takai K, Horikoshi K. Marinitoga okinawensis sp. nov., a novel thermophilic and anaerobic heterotroph isolated from a deep-sea hydrothermal field, Southern Okinawa Trough. Int J Syst Evol Microbiol 2007; 57:467-471. [PMID: 17329770 DOI: 10.1099/ijs.0.64640-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermophilic and sulfur-reducing heterotrophic bacterium, strain TFS10-5T, was isolated from a deep-sea hydrothermal field in Yonaguni Knoll IV, Southern Okinawa Trough. Cells of strain TFS10-5T were motile rods, 1.5–5 μm in length and 0.5–0.8 μm in width. Strain TFS10-5T was an obligately anaerobic heterotroph and sulfur-reduction stimulated growth. Growth was observed between 30 and 70 °C (optimum at 55–60 °C), pH 5.0–7.4 (optimum at pH 5.5–5.8), 1.0–5.5 NaCl % (optimum at 3.0–3.5 %). The fatty acid content was C16 : 0 (71.0 %), C16 : 1 (6.0 %), C18 : 0 (21.4 %) and C18 : 1 (1.6 %). The G+C content of the genomic DNA was 28 mol%. 16S rRNA gene sequence analysis indicated that strain TFS10-5T belongs to the genus Marinitoga. Based on the physiological and phylogenetic features of the new isolate, strain TFS10-5T represents a novel species in the genus Marinitoga for which the name Marinitoga okinawensis sp. nov. is proposed. The type strain is TFS10-5T (=JCM 13303T=DSM 17373T).
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MESH Headings
- Base Composition
- DNA, Bacterial/genetics
- DNA, Ribosomal/genetics
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/classification
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/genetics
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/isolation & purification
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/metabolism
- Molecular Sequence Data
- Oceans and Seas
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Seawater/microbiology
- Sulfur-Reducing Bacteria/classification
- Sulfur-Reducing Bacteria/genetics
- Sulfur-Reducing Bacteria/isolation & purification
- Sulfur-Reducing Bacteria/metabolism
- Temperature
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Affiliation(s)
- Takuro Nunoura
- Subground Animalcule Retrieval (SUGAR) Program, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Hanako Oida
- Subground Animalcule Retrieval (SUGAR) Program, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Masayuki Miyazaki
- Subground Animalcule Retrieval (SUGAR) Program, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yohey Suzuki
- Subground Animalcule Retrieval (SUGAR) Program, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Ken Takai
- Subground Animalcule Retrieval (SUGAR) Program, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Koki Horikoshi
- Subground Animalcule Retrieval (SUGAR) Program, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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