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Caro-Astorga J, Meyerowitz JT, Stork DA, Nattermann U, Piszkiewicz S, Vimercati L, Schwendner P, Hocher A, Cockell C, DeBenedictis E. Polyextremophile engineering: a review of organisms that push the limits of life. Front Microbiol 2024; 15:1341701. [PMID: 38903795 PMCID: PMC11188471 DOI: 10.3389/fmicb.2024.1341701] [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: 11/20/2023] [Accepted: 05/16/2024] [Indexed: 06/22/2024] Open
Abstract
Nature exhibits an enormous diversity of organisms that thrive in extreme environments. From snow algae that reproduce at sub-zero temperatures to radiotrophic fungi that thrive in nuclear radiation at Chernobyl, extreme organisms raise many questions about the limits of life. Is there any environment where life could not "find a way"? Although many individual extremophilic organisms have been identified and studied, there remain outstanding questions about the limits of life and the extent to which extreme properties can be enhanced, combined or transferred to new organisms. In this review, we compile the current knowledge on the bioengineering of extremophile microbes. We summarize what is known about the basic mechanisms of extreme adaptations, compile synthetic biology's efforts to engineer extremophile organisms beyond what is found in nature, and highlight which adaptations can be combined. The basic science of extremophiles can be applied to engineered organisms tailored to specific biomanufacturing needs, such as growth in high temperatures or in the presence of unusual solvents.
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Affiliation(s)
| | | | - Devon A. Stork
- Pioneer Research Laboratories, San Francisco, CA, United States
| | - Una Nattermann
- Pioneer Research Laboratories, San Francisco, CA, United States
| | | | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
| | | | - Antoine Hocher
- London Institute of Medical Sciences, London, United Kingdom
| | - Charles Cockell
- UK Centre for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Erika DeBenedictis
- The Francis Crick Institute, London, United Kingdom
- Pioneer Research Laboratories, San Francisco, CA, United States
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Zhong M, Li Y, Deng L, Fang J, Yu X. Insight into the adaptation mechanisms of high hydrostatic pressure in physiology and metabolism of hadal fungi from the deepest ocean sediment. mSystems 2024; 9:e0108523. [PMID: 38117068 PMCID: PMC10804941 DOI: 10.1128/msystems.01085-23] [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: 10/17/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
High hydrostatic pressure (HHP) influences the life processes of organisms living at depth in the oceans. While filamentous fungi are one of the essential members of deep-sea microorganisms, few works have explored their piezotolerance to HHP. Here, we obtained three homogeneous Aspergillus sydowii from terrestrial, shallow, and hadal areas, respectively, to compare their pressure resistance. A set of all-around evaluation methods including determination of growth rate, metabolic activity, and microscopic staining observation was established and indicated that A. sydowii DM1 from the hadal area displayed significant piezotolerance. Global analysis of transcriptome data under elevated HHP revealed that A. sydowii DM1 proactively modulated cell membrane permeability, hyphae morphology, and septal quantities for seeking a better livelihood under mild pressure. Besides, differentially expressed genes were mainly enriched in the biosynthesis of amino acids, carbohydrate metabolism, cell process, etc., implying how the filamentous fungi respond to elevated pressure at the molecular level. We speculated that A. sydowii DM1 could acclimatize itself to HHP by adopting several strategies, including environmental response pathway HOG-MAPK, stress proteins, and cellular metabolisms.IMPORTANCEFungi play an ecological and biological function in marine environments, while the physiology of filamentous fungi under high hydrostatic pressure (HHP) is an unknown territory due to current technologies. As filamentous fungi are found in various niches, Aspergillus sp. from deep-sea inspire us to the physiological trait of eukaryotes under HHP, which can be considered as a prospective research model. Here, the evaluation methods we constructed would be universal for most filamentous fungi to assess their pressure resistance, and we found that Aspergillus sydowii DM1 from the hadal area owned better piezotolerance and the active metabolisms under HHP indicated the existence of undiscovered metabolic strategies for hadal fungi. Since pressure-related research of marine fungi has been unexpectedly neglected, our study provided an enlightening strategy for them under HHP; we believed that understanding their adaptation and ecological function in original niches will be accelerated in the perceivable future.
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Affiliation(s)
- Maosheng Zhong
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Yongqi Li
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Ludan Deng
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Xi Yu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
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Dong H, Yu L, Xu T, Liu Y, Fu J, He Y, Gao J, Wang J, Sun S, She Y, Zhang F. Cultivation and biogeochemical analyses reveal insights into biomineralization caused by piezotolerant iron-reducing bacteria from petroleum reservoirs and their application in MEOR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166465. [PMID: 37619717 DOI: 10.1016/j.scitotenv.2023.166465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/19/2023] [Accepted: 08/19/2023] [Indexed: 08/26/2023]
Abstract
Interactions between minerals and iron-reducing bacteria under in-situ pressure and temperature conditions play important roles in oil extraction, residual oil methanation, and CO2 storage in petroleum reservoirs. However, the impacts of pressure on dissimilatory iron-reducing bacteria (DIRB) are poorly understood. Herein, the interactions between clay minerals and microbes under elevated hydrostatic pressure conditions were elucidated through enrichment experiments. Bioreduction experiments were performed under hydrostatic pressures of 0.1-40 MPa. Microbial diversity analysis revealed that high pressures significantly increased microbial diversity in petroleum reservoirs, which is helpful for restoring underground ecosystems in situ. The key piezotolerant iron-reducing bacteria in the samples were Shewanella and Flaviflexus. These two genera were isolated for the first time from petroleum reservoirs and identified as piezophiles. The SEM results clearly showed mineral surface dissolution. Moreover, nanoscale secondary minerals were produced during biomineralization. XRD analysis revealed that illite, albite, and clinoptilolite were present after bioreduction. The isolates showed the capacity to inhibit hydro-swelling and prevent plugging-related damage in reservoirs.
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Affiliation(s)
- Hao Dong
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, China
| | - Li Yu
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, China
| | - Ting Xu
- College of Resources and Environment, Yangtze University, Wuhan 430010, China
| | - Yulong Liu
- Key Laboratory of Drilling and Production Engineering for Oil and Gas, Cooperative Innovation Center of Unconventional Oil and Gas, College of Petroleum Engineering, Yangtze University, Wuhan 430010, China
| | - Jian Fu
- Key Laboratory of Drilling and Production Engineering for Oil and Gas, Cooperative Innovation Center of Unconventional Oil and Gas, College of Petroleum Engineering, Yangtze University, Wuhan 430010, China
| | - Yanlong He
- College of Petroleum Engineering, Xi'an Shiyou University, Xi'an 710065, China
| | - Ji Gao
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, China
| | - Jiaqi Wang
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, China
| | - Shanshan Sun
- Key Laboratory of Drilling and Production Engineering for Oil and Gas, Cooperative Innovation Center of Unconventional Oil and Gas, College of Petroleum Engineering, Yangtze University, Wuhan 430010, China
| | - Yuehui She
- Key Laboratory of Drilling and Production Engineering for Oil and Gas, Cooperative Innovation Center of Unconventional Oil and Gas, College of Petroleum Engineering, Yangtze University, Wuhan 430010, China.
| | - Fan Zhang
- The Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, Ministry of Education, College of Energy Resources, China University of Geosciences (Beijing), Beijing 100083, China.
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Yin YR, Li XW, Long CH, Li L, Hang YY, Rao MD, Yan X, Liu QL, Sang P, Li WJ, Yang LQ. Characterization of a GH10 extremely thermophilic xylanase from the metagenome of hot spring for prebiotic production. Sci Rep 2023; 13:16053. [PMID: 37749183 PMCID: PMC10520001 DOI: 10.1038/s41598-023-42920-6] [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: 05/04/2023] [Accepted: 09/16/2023] [Indexed: 09/27/2023] Open
Abstract
A xylanase gene (named xyngmqa) was identified from the metagenomic data of the Gumingquan hot spring (92.5 °C, pH 9.2) in Tengchong City, Yunnan Province, southwest China. It showed the highest amino acid sequence identity (82.70%) to endo-1,4-beta-xylanase from Thermotoga caldifontis. A constitutive expression plasmid (denominated pSHY211) and double-layer plate (DLP) method were constructed for cloning, expression, and identification of the XynGMQA gene. The XynGMQA gene was synthesized and successfully expressed in Escherichia coli DH5α. XynGMQA exhibited optimal activity at 90 °C and pH 4.6, being thermostable by maintaining 100% of its activity after 2 h incubated at 80 °C. Interestingly, its enzyme activity was enhanced by high temperatures (70 and 80 °C) and low pH (3.0-6.0). About 150% enzyme activity was detected after incubation at 70 °C for 20 to 60 min or 80 °C for 10 to 40 min, and more than 140% enzyme activity after incubation at pH 3.0 to 6.0 for 12 h. Hydrolytic products of beechwood xylan with XynGMQA were xylooligosaccharides, including xylobiose (X2), xylotriose (X3), and xylotetraose (X4). These properties suggest that XynGMQA as an extremely thermophilic xylanase, may be exploited for biofuel and prebiotic production from lignocellulosic biomass.
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Affiliation(s)
- Yi-Rui Yin
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China.
| | - Xin-Wei Li
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China
- Key Laboratory of Bioinformatics and Computational Biology, Department of Education of Yunnan Province, Dali University, Dali, 671003, People's Republic of China
| | - Chao-Hua Long
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China
| | - Lei Li
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China
| | - Yu-Ying Hang
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China
| | - Meng-Di Rao
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China
| | - Xin Yan
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China
| | - Quan-Lin Liu
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China
| | - Peng Sang
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China
- Key Laboratory of Bioinformatics and Computational Biology, Department of Education of Yunnan Province, Dali University, Dali, 671003, People's Republic of China
| | - Wen-Jun Li
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China.
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Li-Quan Yang
- College of Agriculture and Biological Science, Dali University, Dali, 671003, People's Republic of China.
- Key Laboratory of Bioinformatics and Computational Biology, Department of Education of Yunnan Province, Dali University, Dali, 671003, People's Republic of China.
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5
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Peres FV, Paula FS, Bendia AG, Gontijo JB, de Mahiques MM, Pellizari VH. Assessment of prokaryotic communities in Southwestern Atlantic deep-sea sediments reveals prevalent methanol-oxidising Methylomirabilales. Sci Rep 2023; 13:12782. [PMID: 37550336 PMCID: PMC10406867 DOI: 10.1038/s41598-023-39415-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 07/25/2023] [Indexed: 08/09/2023] Open
Abstract
Continental slopes can play a significant contribution to marine productivity and carbon cycling. These regions can harbour distinct geological features, such as salt diapirs and pockmarks, in which their depressions may serve as natural sediment traps where different compounds can accumulate. We investigated the prokaryotic communities in surface (0-2 cm) and subsurface (18-20 or 22-24 cm) sediments from a salt diapir and pockmark field in Santos Basin, Southwest Atlantic Ocean. Metabarcoding of 16 samples revealed that surface sediments were dominated by the archaeal class Nitrososphaeria, while the bacterial class Dehalococcoidia was the most prevalent in subsurface samples. Sediment strata were found to be a significant factor explaining 27% of the variability in community composition. However, no significant difference was observed among geomorphological features. We also performed a metagenomic analysis of three surface samples and analysed the highest quality metagenome-assembled genome retrieved, which belonged to the family CSP1-5, phylum Methylomirabilota. This non-methanotrophic methylotroph contains genes encoding for methanol oxidation and Calvin Cycle pathways, along with diverse functions that may contribute to its adaptation to deep-sea habitats and to oscillating environmental conditions. By integrating metabarcoding and metagenomic approaches, we reported that CSP1-5 is prevalent in the sediment samples from Santos Basin slope, indicating the potential importance of methanol metabolism in this region. Finally, using a phylogenetic approach integrating 16S rRNA sequences assigned to Methylomirabilota in this study with those from a public database, we argued that CSP1-5 public sequences might be misclassified as Methylomirabilaceae (the methanotrophic clade) and, therefore, the role of these organisms and the methanol cycling could also be neglected in other environments.
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Affiliation(s)
- Francielli V Peres
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil
| | - Fabiana S Paula
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil.
| | - Amanda G Bendia
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil
| | - Júlia B Gontijo
- Cell and Molecular Biology Laboratory, Centre for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Michel M de Mahiques
- Department of Physical, Chemical and Geological Oceanography, Oceanographic Institute, University of São Paulo, São Paulo, Brazil
| | - Vivian H Pellizari
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça do Oceanográfico, 191, São Paulo, CEP: 05508-120, Brazil
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6
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Scheffer G, Gieg LM. The Mystery of Piezophiles: Understudied Microorganisms from the Deep, Dark Subsurface. Microorganisms 2023; 11:1629. [PMID: 37512802 PMCID: PMC10384521 DOI: 10.3390/microorganisms11071629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023] Open
Abstract
Microorganisms that can withstand high pressure within an environment are termed piezophiles. These organisms are considered extremophiles and inhabit the deep marine or terrestrial subsurface. Because these microorganisms are not easily accessed and require expensive sampling methods and laboratory instruments, advancements in this field have been limited compared to other extremophiles. This review summarizes the current knowledge on piezophiles, notably the cellular and physiological adaptations that such microorganisms possess to withstand and grow in high-pressure environments. Based on existing studies, organisms from both the deep marine and terrestrial subsurface show similar adaptations to high pressure, including increased motility, an increase of unsaturated bonds within the cell membrane lipids, upregulation of heat shock proteins, and differential gene-regulation systems. Notably, more adaptations have been identified within the deep marine subsurface organisms due to the relative paucity of studies performed on deep terrestrial subsurface environments. Nevertheless, similar adaptations have been found within piezophiles from both systems, and therefore the microbial biogeography concepts used to assess microbial dispersal and explore if similar organisms can be found throughout deep terrestrial environments are also briefly discussed.
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Affiliation(s)
- Gabrielle Scheffer
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Lisa M Gieg
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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Sexton D, Hashimi A, Beskrovnaya P, Sibanda L, Huan T, Tocheva E. The cell envelope of Thermotogae suggests a mechanism for outer membrane biogenesis. Proc Natl Acad Sci U S A 2023; 120:e2303275120. [PMID: 37094164 PMCID: PMC10160955 DOI: 10.1073/pnas.2303275120] [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: 03/03/2023] [Accepted: 03/29/2023] [Indexed: 04/26/2023] Open
Abstract
The presence of a cell membrane is one of the major structural components defining life. Recent phylogenomic analyses have supported the hypothesis that the last universal common ancestor (LUCA) was likely a diderm. Yet, the mechanisms that guided outer membrane (OM) biogenesis remain unknown. Thermotogae is an early-branching phylum with a unique OM, the toga. Here, we use cryo-electron tomography to characterize the in situ cell envelope architecture of Thermotoga maritima and show that the toga is made of extended sheaths of β-barrel trimers supporting small (~200 nm) membrane patches. Lipidomic analyses identified the same major lipid species in the inner membrane (IM) and toga, including the rare to bacteria membrane-spanning ether-bound diabolic acids (DAs). Proteomic analyses revealed that the toga was composed of multiple SLH-domain containing Ompα and novel β-barrel proteins, and homology searches detected variable conservations of these proteins across the phylum. These results highlight that, in contrast to the SlpA/OmpM superfamily of proteins, Thermotoga possess a highly diverse bipartite OM-tethering system. We discuss the implications of our findings with respect to other early-branching phyla and propose that a toga-like intermediate may have facilitated monoderm-to-diderm cell envelope transitions.
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Affiliation(s)
- Danielle L. Sexton
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver,V6T1Z3 BC, Canada
| | - Ameena Hashimi
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver,V6T1Z3 BC, Canada
| | - Polina Beskrovnaya
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver,V6T1Z3 BC, Canada
| | - Lloyd Sibanda
- Department of Chemistry, University of British Columbia, Vancouver,V6T1Z1 BC, Canada
| | - Tao Huan
- Department of Chemistry, University of British Columbia, Vancouver,V6T1Z1 BC, Canada
| | - Elitza I. Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver,V6T1Z3 BC, Canada
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Fenouil R, Pradel N, Belahbib H, Roumagnac M, Bartoli M, Ben Hania W, Denis Y, Garel M, Tamburini C, Ollivier B, Summers Z, Armougom F, Dolla A. Adaptation Strategies to High Hydrostatic Pressures in Pseudothermotoga species Revealed by Transcriptional Analyses. Microorganisms 2023; 11:microorganisms11030773. [PMID: 36985346 PMCID: PMC10057702 DOI: 10.3390/microorganisms11030773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Pseudothermotoga elfii strain DSM9442 and P. elfii subsp. lettingae strain DSM14385 are hyperthermophilic bacteria. P. elfii DSM9442 is a piezophile and was isolated from a depth of over 1600 m in an oil-producing well in Africa. P. elfii subsp. lettingae is piezotolerant and was isolated from a thermophilic bioreactor fed with methanol as the sole carbon and energy source. In this study, we analyzed both strains at the genomic and transcriptomic levels, paying particular attention to changes in response to pressure increases. Transcriptomic analyses revealed common traits of adaptation to increasing hydrostatic pressure in both strains, namely, variations in transport membrane or carbohydrate metabolism, as well as species-specific adaptations such as variations in amino acid metabolism and transport for the deep P. elfii DSM9442 strain. Notably, this work highlights the central role played by the amino acid aspartate as a key intermediate of the pressure adaptation mechanisms in the deep strain P. elfii DSM9442. Our comparative genomic and transcriptomic analysis revealed a gene cluster involved in lipid metabolism that is specific to the deep strain and that was differentially expressed at high hydrostatic pressures and might, thus, be a good candidate for a piezophilic gene marker in Pseudothermotogales.
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Affiliation(s)
- Romain Fenouil
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Nathalie Pradel
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
- Correspondence: (N.P.); (A.D.)
| | - Hassiba Belahbib
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Marie Roumagnac
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Manon Bartoli
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Wajdi Ben Hania
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Yann Denis
- Institut de Microbiologie de la Méditerranée, CNRS—Aix Marseille Université, Marseille, France
| | - Marc Garel
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Christian Tamburini
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Bernard Ollivier
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Zarath Summers
- LanzaTech, Illinois Science and Technology Park, Skokie, IL 60077, USA
| | - Fabrice Armougom
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Alain Dolla
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
- Correspondence: (N.P.); (A.D.)
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Ugwuodo CJ, Colosimo F, Adhikari J, Shen Y, Badireddy AR, Mouser PJ. Salinity and hydraulic retention time induce membrane phospholipid acyl chain remodeling in Halanaerobium congolense WG10 and mixed cultures from hydraulically fractured shale wells. Front Microbiol 2022; 13:1023575. [PMID: 36439785 PMCID: PMC9687094 DOI: 10.3389/fmicb.2022.1023575] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/17/2022] [Indexed: 12/14/2023] Open
Abstract
Bacteria remodel their plasma membrane lipidome to maintain key biophysical attributes in response to ecological disturbances. For Halanaerobium and other anaerobic halotolerant taxa that persist in hydraulically fractured deep subsurface shale reservoirs, salinity, and hydraulic retention time (HRT) are important perturbants of cell membrane structure, yet their effects remain poorly understood. Membrane-linked activities underlie in situ microbial growth kinetics and physiologies which drive biogeochemical reactions in engineered subsurface systems. Hence, we used gas chromatography-mass spectrometry (GC-MS) to investigate the effects of salinity and HRT on the phospholipid fatty acid composition of H. congolense WG10 and mixed enrichment cultures from hydraulically fractured shale wells. We also coupled acyl chain remodeling to membrane mechanics by measuring bilayer elasticity using atomic force microscopy (AFM). For these experiments, cultures were grown in a chemostat vessel operated in continuous flow mode under strict anoxia and constant stirring. Our findings show that salinity and HRT induce significant changes in membrane fatty acid chemistry of H. congolense WG10 in distinct and complementary ways. Notably, under nonoptimal salt concentrations (7% and 20% NaCl), H. congolense WG10 elevates the portion of polyunsaturated fatty acids (PUFAs) in its membrane, and this results in an apparent increase in fluidity (homeoviscous adaptation principle) and thickness. Double bond index (DBI) and mean chain length (MCL) were used as proxies for membrane fluidity and thickness, respectively. These results provide new insight into our understanding of how environmental and engineered factors might disrupt the physical and biogeochemical equilibria of fractured shale by inducing physiologically relevant changes in the membrane fatty acid chemistry of persistent microbial taxa. GRAPHICAL ABSTRACTSalinity significantly alters membrane bilayer fluidity and thickness in Halanaerobium congolense WG10.
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Affiliation(s)
- Chika Jude Ugwuodo
- Natural Resources and Earth Systems Science, University of New Hampshire, Durham, NH, United States
- Department of Civil and Environmental Engineering, University of New Hampshire, Durham, NH, United States
| | | | - Jishnu Adhikari
- Sanborn, Head and Associates, Inc., Concord, NH, United States
| | - Yuxiang Shen
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Appala Raju Badireddy
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Paula J. Mouser
- Department of Civil and Environmental Engineering, University of New Hampshire, Durham, NH, United States
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10
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Bedoya K, Niño J, Acero J, Jaimes-Prada R, Cabarcas F, Alzate JF. Metagenomic Analysis of Biocide-Treated Neotropical Oil Reservoir Water Unveils Microdiversity of Thermophile Tepidiphilus. Front Microbiol 2021; 12:741555. [PMID: 34790180 PMCID: PMC8591294 DOI: 10.3389/fmicb.2021.741555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Microorganisms are capable of colonizing extreme environments like deep biosphere and oil reservoirs. The prokaryotes diversity in exploited oil reservoirs is composed of indigenous microbial communities and artificially introduced microbes. In the present work, high throughput sequencing techniques were applied to analyze the microbial community from the injected and produced water in a neotropical hyper-thermophile oil reservoir located in the Orinoquia region of Colombia, South America. Tepidiphilus is the dominant bacteria found in both injection and produced waters. The produced water has a higher microbial richness and exhibits a Tepidiphilus microdiversity. The reservoir injected water is recycled and treated with the biocides glutaraldehyde and tetrakis-hydroxymethyl-phosphonium sulfate (THPS) to reduce microbial load. This process reduces microbial richness and selects a single Tepidiphilus genome (T. sp. UDEAICP_D1) as the dominant isolate. Thermus and Hydrogenobacter were subdominants in both water systems. Phylogenomic analysis of the injection water dominant Tepidiphilus positioned it as an independent branch outside T. succinatimandens and T. thermophilus lineage. Comparative analysis of the Tepidiphilus genomes revealed several genes that might be related to the biocide-resistant phenotype and the tolerance to the stress conditions imposed inside the oil well, like RND efflux pumps and type II toxin-antitoxin systems. Comparing the abundance of Tepidiphilus protein-coding genes in both water systems shows that the biocide selected Tepidiphilus sp. UDEAICP_D1 genome has enriched genes annotated as ABC-2 type transporter, ABC transporter, Methionine biosynthesis protein MetW, Glycosyltransferases, and two-component system NarL.
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Affiliation(s)
- Katherine Bedoya
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica - CNSG, Sede de Investigación Universitaria - SIU, Universidad de Antioquia -UdeA, Medellín, Colombia
| | - Jhorman Niño
- Centro de Innovación y Tecnología ICP, Ecopetrol S.A, Gerencia de Operaciones, Bucaramanga, Colombia
| | - Julia Acero
- Centro de Innovación y Tecnología ICP, Ecopetrol S.A, Gerencia de Operaciones, Bucaramanga, Colombia
| | - Ronald Jaimes-Prada
- Centro de Innovación y Tecnología ICP, Ecopetrol S.A, Gerencia de Operaciones, Bucaramanga, Colombia
| | - Felipe Cabarcas
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica - CNSG, Sede de Investigación Universitaria - SIU, Universidad de Antioquia -UdeA, Medellín, Colombia.,Grupo SISTEMIC, Ingeniería Electrónica, Facultad de Ingeniería, Universidad de Antioquia - UdeA, Medellín, Colombia
| | - Juan F Alzate
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica - CNSG, Sede de Investigación Universitaria - SIU, Universidad de Antioquia -UdeA, Medellín, Colombia
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