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Zhou J, Dong L. Structural insights linking H-bridging of archaeal GDGTs to high temperature. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:174120. [PMID: 38901598 DOI: 10.1016/j.scitotenv.2024.174120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/07/2024] [Accepted: 06/16/2024] [Indexed: 06/22/2024]
Abstract
Isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs), characteristic membrane lipids of archaea, are widely used in ecological and geochemical studies, especially for paleoenvironmental reconstruction. Glycerol monoalkyl glycerol tetraethers (GMGTs, also known as H-GDGTs), a unique variant of GDGTs, have covalent bonds linking the two alkyl chains. Despite some studies suggesting a link between GMGTs and high temperatures, the reliability and mechanisms remain unclear. Using molecular dynamics simulations, we elucidated the mechanism connecting GMGTs to high temperatures. Our findings show that H-bridging linkages reduce the distance between alkyl chains, leading to thicker and denser membranes with lower fluidity and permeability. The diffusion coefficient of GMGTs decreased by approximately 35 % compared to GDGTs, indicating their role as a archaeal high-temperature adaptation. This study provides a mechanistic basis for using archaeal GMGTs in geochemical studies and enhances confidence in their use for paleotemperature reconstruction.
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Affiliation(s)
- Jiaming Zhou
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education; and School of Oceanography, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Liang Dong
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education; and School of Oceanography, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China.
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2
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Garcia AA, Chadwick GL, Liu XL, Welander PV. Identification of two archaeal GDGT lipid-modifying proteins reveals diverse microbes capable of GMGT biosynthesis and modification. Proc Natl Acad Sci U S A 2024; 121:e2318761121. [PMID: 38885389 PMCID: PMC11214058 DOI: 10.1073/pnas.2318761121] [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: 10/26/2023] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
Archaea produce unique membrane-spanning lipids (MSLs), termed glycerol dialkyl glycerol tetraethers (GDGTs), which aid in adaptive responses to various environmental challenges. GDGTs can be modified through cyclization, cross-linking, methylation, hydroxylation, and desaturation, resulting in structurally distinct GDGT lipids. Here, we report the identification of radical SAM proteins responsible for two of these modifications-a glycerol monoalkyl glycerol tetraether (GMGT) synthase (Gms), responsible for covalently cross-linking the two hydrocarbon tails of a GDGT to produce GMGTs, and a GMGT methylase (Gmm), capable of methylating the core hydrocarbon tail. Heterologous expression of Gms proteins from various archaea in Thermococcus kodakarensis results in the production of GMGTs in two isomeric forms. Further, coexpression of Gms and Gmm produces mono- and dimethylated GMGTs and minor amounts of trimethylated GMGTs with only trace GDGT methylation. Phylogenetic analyses reveal the presence of Gms homologs in diverse archaeal genomes spanning all four archaeal superphyla and in multiple bacterial phyla with the genetic potential to synthesize fatty acid-based MSLs, demonstrating that GMGT production may be more widespread than previously appreciated. We demonstrate GMGT production in three Gms-encoding archaea, identifying an increase in GMGTs in response to elevated temperature in two Archaeoglobus species and the production of GMGTs with up to six rings in Vulcanisaeta distributa. The occurrence of such highly cyclized GMGTs has been limited to environmental samples and their detection in culture demonstrates the utility of combining genetic, bioinformatic, and lipid analyses to identify producers of distinct archaeal membrane lipids.
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Affiliation(s)
- Andy A. Garcia
- Department of Earth System Science, Stanford University, Stanford, CA94305
| | - Grayson L. Chadwick
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Xiao-Lei Liu
- Department of Geology and Geophysics, University of Oklahoma, Norman, OK73019
| | - Paula V. Welander
- Department of Earth System Science, Stanford University, Stanford, CA94305
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Pu X, Wang Y, Wang X, Sang X, Jiang M, Qi D, Zhao X, Chen R, Li J, Liu X, Liu Z, Yang J. Lipids Extracted from Mycobacterial Membrane and Enveloped PLGA Nanoparticles for Encapsulating Antibacterial Drugs Elicit Synergistic Antimicrobial Response against Mycobacteria. Mol Pharm 2024; 21:2238-2249. [PMID: 38622497 DOI: 10.1021/acs.molpharmaceut.3c01001] [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] [Indexed: 04/17/2024]
Abstract
Tuberculosis (TB) is a chronic disease caused byMycobacterium tuberculosis (Mtb), which shows a long treatment cycle often leads to drug resistance, making treatment more difficult. Immunogens present in the pathogen's cell membrane can stimulate endogenous immune responses. Therefore, an effective lipid-based vaccine or drug delivery vehicle formulated from the pathogen's cell membrane can improve treatment outcomes. Herein, we extracted and characterized lipids fromMycobacterium smegmatis, and the extracts contained lipids belonging to numerous lipid classes and compounds typically found associated with mycobacteria. The extracted lipids were used to formulate biomimetic lipid reconstituted nanoparticles (LrNs) and LrNs-coated poly(lactic-co-glycolic acid) nanoparticles (PLGA-LrNs). Physiochemical characterization and results of morphology suggested that PLGA-LrNs exhibited enhanced stability compared with LrNs. And both of these two types of nanoparticles inhibited the growth of M. smegmatis. After loading different drugs, PLGA-LrNs containing berberine or coptisine strongly and synergistically prevented the growth of M. smegmatis. Altogether, the bacterial membrane lipids we extracted with antibacterial activity can be used as nanocarrier coating for synergistic antibacterial treatment of M. smegmatis─an alternative model of Mtb, which is expected as a novel therapeutic system for TB treatment.
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Affiliation(s)
- Xueyu Pu
- Tianjin Key Laboratory of Chinese Medicine Pharmacology. Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Yuanyuan Wang
- Tianjin Key Laboratory of Chinese Medicine Pharmacology. Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Xi Wang
- Tianjin Key Laboratory of Chinese Medicine Pharmacology. Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Xiaoqing Sang
- Tianjin Key Laboratory of Chinese Medicine Pharmacology. Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Miaomiao Jiang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - DaWei Qi
- Medcity Research Laboratory, University of Turku, Tykistokatu 6, FI-20520 Turku, Finland
| | - Xin Zhao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
- Infectious Disease Drug Discovery Institute, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Rong Chen
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
- Infectious Disease Drug Discovery Institute, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Jianwei Li
- Medcity Research Laboratory, University of Turku, Tykistokatu 6, FI-20520 Turku, Finland
| | - Xiang Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
- Infectious Disease Drug Discovery Institute, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Zhidong Liu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jian Yang
- Tianjin Key Laboratory of Chinese Medicine Pharmacology. Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
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Yang W, Liu X, Yu S, Liu J, Jiang L, Lu X, Liu Y, Zhang J, Li X, Zhang S. The maize ATP-binding cassette (ABC) transporter ZmMRPA6 confers cold and salt stress tolerance in plants. PLANT CELL REPORTS 2023; 43:13. [PMID: 38135780 DOI: 10.1007/s00299-023-03094-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/10/2023] [Indexed: 12/24/2023]
Abstract
KEY MESSAGE ZmMRPA6 was cloned and characterized as the first ATP-binding cassette (ABC) transporter in maize to be proven to participate in cold and salt tolerance. Homologous genes AtABCC4 and AtABCC14 of ZmMRPA6 also responded to salt stress. ATP-binding cassette (ABC) proteins are major transmembrane transporters that play significant roles in plant development against various abiotic stresses. However, available information regarding stress-related ABC genes in maize is minimal. In this study, a maize ABC transporter gene, ZmMRPA6, was identified through genome-wide association analysis (GWAS) for cold tolerance in maize seeds germination and functionally characterized. During germination and seedling stages, the zmmrpa6 mutant exhibited enhanced resistance to cold or salt stress. Mutated of ZmMRPA6 did not affect the expression of downstream response genes related cold or salt response at the transcriptional level. Mass spectrometry analysis revealed that most of the differential proteins between zmmrpa6 and wild-type plants were involved in response to stress process including oxidative reduction, hydrolase activity, small molecule metabolism, and photosynthesis process. Meanwhile, the plants which lack the ZmMRPA6 homologous genes AtABCC4 or AtABCC14 were sensitive to salt stress in Arabidopsis. These results indicated that ZmMRPA6 and its homologous genes play a conserved role in cold and salt stress, and functional differentiation occurs in monocotyledonous and dicotyledonous plants. In summary, these findings dramatically improved our understanding of the function of ABC transporters resistance to abiotic stresses in plants.
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Affiliation(s)
- Wei Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiao Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Shaowei Yu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Jisheng Liu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, 250200, Shandong, China
| | - Lijun Jiang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, 250200, Shandong, China
| | - Yinggao Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Jiedao Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
| | - Shuxin Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
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Rempfert KR, Kraus EA, Nothaft DB, Dildar N, Spear JR, Sepúlveda J, Templeton AS. Intact polar lipidome and membrane adaptations of microbial communities inhabiting serpentinite-hosted fluids. Front Microbiol 2023; 14:1198786. [PMID: 38029177 PMCID: PMC10667739 DOI: 10.3389/fmicb.2023.1198786] [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: 04/02/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023] Open
Abstract
The generation of hydrogen and reduced carbon compounds during serpentinization provides sustained energy for microorganisms on Earth, and possibly on other extraterrestrial bodies (e.g., Mars, icy satellites). However, the geochemical conditions that arise from water-rock reaction also challenge the known limits of microbial physiology, such as hyperalkaline pH, limited electron acceptors and inorganic carbon. Because cell membranes act as a primary barrier between a cell and its environment, lipids are a vital component in microbial acclimation to challenging physicochemical conditions. To probe the diversity of cell membrane lipids produced in serpentinizing settings and identify membrane adaptations to this environment, we conducted the first comprehensive intact polar lipid (IPL) biomarker survey of microbial communities inhabiting the subsurface at a terrestrial site of serpentinization. We used an expansive, custom environmental lipid database that expands the application of targeted and untargeted lipodomics in the study of microbial and biogeochemical processes. IPLs extracted from serpentinite-hosted fluid communities were comprised of >90% isoprenoidal and non-isoprenoidal diether glycolipids likely produced by archaeal methanogens and sulfate-reducing bacteria. Phospholipids only constituted ~1% of the intact polar lipidome. In addition to abundant diether glycolipids, betaine and trimethylated-ornithine aminolipids and glycosphingolipids were also detected, indicating pervasive membrane modifications in response to phosphate limitation. The carbon oxidation state of IPL backbones was positively correlated with the reduction potential of fluids, which may signify an energy conservation strategy for lipid synthesis. Together, these data suggest microorganisms inhabiting serpentinites possess a unique combination of membrane adaptations that allow for their survival in polyextreme environments. The persistence of IPLs in fluids beyond the presence of their source organisms, as indicated by 16S rRNA genes and transcripts, is promising for the detection of extinct life in serpentinizing settings through lipid biomarker signatures. These data contribute new insights into the complexity of lipid structures generated in actively serpentinizing environments and provide valuable context to aid in the reconstruction of past microbial activity from fossil lipid records of terrestrial serpentinites and the search for biosignatures elsewhere in our solar system.
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Affiliation(s)
- Kaitlin R. Rempfert
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - Emily A. Kraus
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Daniel B. Nothaft
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - Nadia Dildar
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
- Department of Quantitative Biosciences and Engineering, Colorado School of Mines, Golden, CO, United States
| | - Julio Sepúlveda
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - Alexis S. Templeton
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
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6
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Bai X, Ya R, Tang X, Cai M. Role and interaction of bacterial sphingolipids in human health. Front Microbiol 2023; 14:1289819. [PMID: 37937219 PMCID: PMC10626005 DOI: 10.3389/fmicb.2023.1289819] [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: 09/06/2023] [Accepted: 10/09/2023] [Indexed: 11/09/2023] Open
Abstract
Sphingolipids, present in both higher animals and prokaryotes, involving in cell differentiation, pathogenesis and apoptosis in human physiological health. With increasing attention on the gut microbiome and its impact on wellbeing, there is a renewed focus on exploring bacterial sphingolipids. This review aims to consolidate the current understanding of bacterial sphingolipids and their impact on host health. Compared to mammalian sphingolipids, bacterial sphingolipids are characterized by odd chain lengths due to the presence of branched alkyl chains. Additionally, intestinal microbial sphingolipids can migrate from the gut to various host organs, affecting the immune system and metabolism. Furthermore, the intricate interplay between dietary sphingolipids and the gut microbiota is explored, shedding light on their complex relationship. Despite limited knowledge in this area, this review aims to raise awareness about the importance of bacterial sphingolipids and further our understanding of more uncharacterized bacterial sphingolipids and their significant role in maintaining host health.
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Affiliation(s)
- Xiaoye Bai
- School of Medicine, Sun Yat-sen University, Shenzhen, China
- Shenzhen Bay Laboratory, Institute of Chemical Biology, Shenzhen, China
| | - Ru Ya
- Inner Mongolia Academy of Science and Technology, Hohhot, China
| | - Xiaoyu Tang
- Shenzhen Bay Laboratory, Institute of Chemical Biology, Shenzhen, China
| | - Mingwei Cai
- Shenzhen Bay Laboratory, Institute of Chemical Biology, Shenzhen, China
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7
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Li Y, Ji T, Torre M, Shao R, Zheng Y, Wang D, Li X, Liu A, Zhang W, Deng X, Yan R, Kohane DS. Aromatized liposomes for sustained drug delivery. Nat Commun 2023; 14:6659. [PMID: 37863880 PMCID: PMC10589217 DOI: 10.1038/s41467-023-41946-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 09/25/2023] [Indexed: 10/22/2023] Open
Abstract
Insufficient drug loading and leakage of payload remain major challenges in designing liposome-based drug delivery systems. These phenomena can limit duration of effect and cause toxicity. Targeting the rate-limiting step in drug release from liposomes, we modify (aromatized) them to have aromatic groups within their lipid bilayers. Aromatized liposomes are designed with synthetic phospholipids with aromatic groups covalently conjugated onto acyl chains. The optimized aromatized liposome increases drug loading and significantly decreases the burst release of a broad range of payloads (small molecules and macromolecules, different degrees of hydrophilicity) and extends their duration of release. Aromatized liposomes encapsulating the anesthetic tetrodotoxin (TTX) achieve markedly prolonged effect and decreased toxicity in an application where liposomes are used clinically: local anesthesia, even though TTX is a hydrophilic small molecule which is typically difficult to encapsulate. Aromatization of lipid bilayers can improve the performance of liposomal drug delivery systems.
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Affiliation(s)
- Yang Li
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA, 02115, US
| | - Tianjiao Ji
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA, 02115, US
| | - Matthew Torre
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, US
| | - Rachelle Shao
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA, 02115, US
| | - Yueqin Zheng
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA, 02115, US
| | - Dali Wang
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA, 02115, US
| | - Xiyu Li
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA, 02115, US
| | - Andong Liu
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA, 02115, US
| | - Wei Zhang
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA, 02115, US
| | - Xiaoran Deng
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA, 02115, US
| | - Ran Yan
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA, 02115, US
| | - Daniel S Kohane
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA, 02115, US.
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8
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Couvillion SP, Danczak RE, Naylor D, Smith ML, Stratton KG, Paurus VL, Bloodsworth KJ, Farris Y, Schmidt DJ, Richardson RE, Bramer LM, Fansler SJ, Nakayasu ES, McDermott JE, Metz TO, Lipton MS, Jansson JK, Hofmockel KS. Rapid remodeling of the soil lipidome in response to a drying-rewetting event. MICROBIOME 2023; 11:34. [PMID: 36849975 PMCID: PMC9969633 DOI: 10.1186/s40168-022-01427-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 11/15/2022] [Indexed: 06/18/2023]
Abstract
BACKGROUND Microbiomes contribute to multiple ecosystem services by transforming organic matter in the soil. Extreme shifts in the environment, such as drying-rewetting cycles during drought, can impact the microbial metabolism of organic matter by altering microbial physiology and function. These physiological responses are mediated in part by lipids that are responsible for regulating interactions between cells and the environment. Despite this critical role in regulating the microbial response to stress, little is known about microbial lipids and metabolites in the soil or how they influence phenotypes that are expressed under drying-rewetting cycles. To address this knowledge gap, we conducted a soil incubation experiment to simulate soil drying during a summer drought of an arid grassland, then measured the response of the soil lipidome and metabolome during the first 3 h after wet-up. RESULTS Reduced nutrient access during soil drying incurred a replacement of membrane phospholipids, resulting in a diminished abundance of multiple phosphorus-rich membrane lipids. The hot and dry conditions increased the prevalence of sphingolipids and lipids containing long-chain polyunsaturated fatty acids, both of which are associated with heat and osmotic stress-mitigating properties in fungi. This novel finding suggests that lipids commonly present in eukaryotes such as fungi may play a significant role in supporting community resilience displayed by arid land soil microbiomes during drought. As early as 10 min after rewetting dry soil, distinct changes were observed in several lipids that had bacterial signatures including a rapid increase in the abundance of glycerophospholipids with saturated and short fatty acid chains, prototypical of bacterial membrane lipids. Polar metabolites including disaccharides, nucleic acids, organic acids, inositols, and amino acids also increased in abundance upon rewetting. This rapid metabolic reactivation and growth after rewetting coincided with an increase in the relative abundance of firmicutes, suggesting that members of this phylum were positively impacted by rewetting. CONCLUSIONS Our study revealed specific changes in lipids and metabolites that are indicative of stress adaptation, substrate use, and cellular recovery during soil drying and subsequent rewetting. The drought-induced nutrient limitation was reflected in the lipidome and polar metabolome, both of which rapidly shifted (within hours) upon rewet. Reduced nutrient access in dry soil caused the replacement of glycerophospholipids with phosphorus-free lipids and impeded resource-expensive osmolyte accumulation. Elevated levels of ceramides and lipids with long-chain polyunsaturated fatty acids in dry soil suggest that lipids likely play an important role in the drought tolerance of microbial taxa capable of synthesizing these lipids. An increasing abundance of bacterial glycerophospholipids and triacylglycerols with fatty acids typical of bacteria and polar metabolites suggest a metabolic recovery in representative bacteria once the environmental conditions are conducive for growth. These results underscore the importance of the soil lipidome as a robust indicator of microbial community responses, especially at the short time scales of cell-environment reactions. Video Abstract.
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Affiliation(s)
- Sneha P Couvillion
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert E Danczak
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Dan Naylor
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Montana L Smith
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kelly G Stratton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Vanessa L Paurus
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kent J Bloodsworth
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuliya Farris
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Darren J Schmidt
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Rachel E Richardson
- National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lisa M Bramer
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sarah J Fansler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ernesto S Nakayasu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jason E McDermott
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Thomas O Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mary S Lipton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
- Department of Agronomy, Iowa State University, Ames, IA, USA.
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9
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Le Moine Bauer S, Lu GS, Goulaouic S, Puzenat V, Schouw A, Barreyre T, Pawlowsky-Glahn V, Egozcue JJ, Martelat JE, Escartin J, Amend JP, Nomikou P, Vlasopoulos O, Polymenakou P, Jørgensen SL. Structure and metabolic potential of the prokaryotic communities from the hydrothermal system of Paleochori Bay, Milos, Greece. Front Microbiol 2023; 13:1060168. [PMID: 36687571 PMCID: PMC9852839 DOI: 10.3389/fmicb.2022.1060168] [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: 10/02/2022] [Accepted: 12/01/2022] [Indexed: 01/09/2023] Open
Abstract
Introduction Shallow hydrothermal systems share many characteristics with their deep-sea counterparts, but their accessibility facilitates their study. One of the most studied shallow hydrothermal vent fields lies at Paleochori Bay off the coast of Milos in the Aegean Sea (Greece). It has been studied through extensive mapping and its physical and chemical processes have been characterized over the past decades. However, a thorough description of the microbial communities inhabiting the bay is still missing. Methods We present the first in-depth characterization of the prokaryotic communities of Paleochori Bay by sampling eight different seafloor types that are distributed along the entire gradient of hydrothermal influence. We used deep sequencing of the 16S rRNA marker gene and complemented the analysis with qPCR quantification of the 16S rRNA gene and several functional genes to gain insights into the metabolic potential of the communities. Results We found that the microbiome of the bay is strongly influenced by the hydrothermal venting, with a succession of various groups dominating the sediments from the coldest to the warmest zones. Prokaryotic diversity and abundance decrease with increasing temperature, and thermophilic archaea overtake the community. Discussion Relevant geochemical cycles of the Bay are discussed. This study expands our limited understanding of subsurface microbial communities in acidic shallow-sea hydrothermal systems and the contribution of their microbial activity to biogeochemical cycling.
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Affiliation(s)
- Sven Le Moine Bauer
- Center for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway,*Correspondence: Sven Le Moine Bauer,
| | - Guang-Sin Lu
- Cooperative Institute for Climate, Ocean and Ecosystem Studies, University of Washington, Seattle, WA, United States,NOAA Pacific Marine Environmental Laboratory, Seattle, WA, United States
| | - Steven Goulaouic
- Center for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
| | - Valentine Puzenat
- Institut de Physique du Globe de Paris, CNRS, Université Paris Cité, Paris, France
| | - Anders Schouw
- Center for Deep Sea Research, Department of Biology, University of Bergen, Bergen, Norway
| | - Thibaut Barreyre
- Center for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
| | - Vera Pawlowsky-Glahn
- Department of Computer Science, Applied Mathematics and Statistics, University of Girona, Girona, Spain
| | - Juan José Egozcue
- Department of Civil and Environmental Engineering, University Politécnica de Cataluña, Barcelona, Spain
| | - Jean-Emmanuel Martelat
- Université de Lyon, UCBL, ENSL, CNRS, Laboratoire de Géologie LGL-TPE, Villeurbanne, France
| | - Javier Escartin
- Laboratoire de Géologie (CNRS UMR8538), Ecole Normale Supérieure de Paris, PSL University, Paris, France
| | - Jan P. Amend
- Departments of Earth Sciences and Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Paraskevi Nomikou
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Othonas Vlasopoulos
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Paraskevi Polymenakou
- Institute of Marine Biology Biotechnology and Aquaculture, Hellenic Center for Marine Research, Heraklion, Greece
| | - Steffen Leth Jørgensen
- Center for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
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10
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Ortiz J, Oliva A, Teruel JA, Aranda FJ, Ortiz A. Effect of pH and temperature on the aggregation behaviour of dirhamnolipid biosurfactant. An experimental and molecular dynamics study. J Colloid Interface Sci 2021; 597:160-170. [PMID: 33872875 DOI: 10.1016/j.jcis.2021.03.177] [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: 11/30/2020] [Revised: 03/26/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022]
Abstract
HYPOTHESIS Pseudomonas aeruginosa dirhamnolipid (diRL) has been shown to form aggregates of different size and structure, under various conditions. Due to the presence of a carboxyl group in the molecule, it is expected that pH would strongly affect this aggregation behaviour. In addition, preliminary observations of temperature-induced changes in the states of aggregation of diRL supported the need of further investigation. EXPERIMENTS A systematic experimental study, using differential scanning calorimetry (DSC), small-angle Xray diffraction (SAXD), and Fourier-transform infrared spectroscopy (FTIR), has been carried out to characterize pH and temperature driven changes in the aggregation behavior of diRL biosurfactant. Molecular dynamics (MD) simulations, supported by the experimental results, allowed depicting molecular details on formation of diRL membranes and other aggregated structures under various physicochemical conditions. FINDINGS DiRL could adopt fairly organized multilayered structures (membranes) at low pH and temperature, which became highly disordered upon increasing either of these parameters. The effect of pH on the gauche/all-trans conformer ratio of the diRL acyl chains was not of significance, whereas temperature-induced effects were observed. For the first time it is described that diRL underwent an endothermic thermotropic transition with Tc = 34 °C as observed by DSC, at pH 4.5 (protonated diRL), but not at pH 7.4 (unprotonated diRL). FTIR confirmed these findings, showing a significant additional disordering of the all-trans acyl chains upon increasing temperature around that same value in the protonated form, an effect not observed for the dissociated form of the biosurfactant. In addition, at pH 7.4, changing temperature did not modify the hydration state of the polar moiety of diRL, whereas at pH 4.5 a significant decrease in the hydration state around 34 °C took place. SAXD data showed that protonated diRL formed multilayered structures at 20 °C, which converted into poorly correlated layers at 50 °C. MD simulations supported these findings, showing that the membrane-like structures formed by protonated diRL at 20 °C became unstable at higher temperatures, tending to form other structures, which could be micelles or other type of layered structures, whereas the negatively charged form of diRL organized in micelle-type aggregates in the whole range of temperature under study.
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Affiliation(s)
- Julia Ortiz
- Departamento de Bioquímica y Biología Molecular-A, Facultad de Veterinaria, Universidad de Murcia, Campus de Espinardo, E-30100 Murcia, Spain
| | - Alfonso Oliva
- Departamento de Bioquímica y Biología Molecular-A, Facultad de Veterinaria, Universidad de Murcia, Campus de Espinardo, E-30100 Murcia, Spain
| | - José A Teruel
- Departamento de Bioquímica y Biología Molecular-A, Facultad de Veterinaria, Universidad de Murcia, Campus de Espinardo, E-30100 Murcia, Spain
| | - Francisco J Aranda
- Departamento de Bioquímica y Biología Molecular-A, Facultad de Veterinaria, Universidad de Murcia, Campus de Espinardo, E-30100 Murcia, Spain
| | - Antonio Ortiz
- Departamento de Bioquímica y Biología Molecular-A, Facultad de Veterinaria, Universidad de Murcia, Campus de Espinardo, E-30100 Murcia, Spain.
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11
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Cobban A, Zhang Y, Zhou A, Weber Y, Elling FJ, Pearson A, Leavitt WD. Multiple environmental parameters impact lipid cyclization in Sulfolobus acidocaldarius. Environ Microbiol 2021; 22:4046-4056. [PMID: 32783317 DOI: 10.1111/1462-2920.15194] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/09/2020] [Indexed: 01/19/2023]
Abstract
Adaptation of lipid membrane composition is an important component of archaeal homeostatic response. Historically, the number of cyclopentyl and cyclohexyl rings in the glycerol dibiphytanyl glycerol tetraether (GDGT) Archaeal lipids has been linked to variation in environmental temperature. However, recent work with GDGT-making archaea highlight the roles of other factors, such as pH or energy availability, in influencing the degree of GDGT cyclization. To better understand the role of multiple variables in a consistent experimental framework and organism, we cultivated the model Crenarchaeon Sulfolobus acidocaldarius DSM639 at different combinations of temperature, pH, oxygen flux, or agitation speed. We quantified responses in growth rate, biomass yield, and core lipid compositions, specifically the degree of core GDGT cyclization. The degree of GDGT cyclization correlated with growth rate under most conditions. The results suggest the degree of cyclization in archaeal lipids records a universal response to energy availability at the cellular level, both in thermoacidophiles, and in other recent findings in the mesoneutrophilic Thaumarchaea. Although we isolated the effects of key individual parameters, there remains a need for multi-factor experiments (e.g., pH + temperature + redox) in order to more robustly establish a framework to better understand homeostatic membrane responses.
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Affiliation(s)
- Alec Cobban
- Department of Earth Sciences, Dartmouth College, Hanover, NH, 03755, USA.,Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Yujiao Zhang
- Department of Earth Sciences, Dartmouth College, Hanover, NH, 03755, USA.,State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Alice Zhou
- Department of Earth Sciences, Dartmouth College, Hanover, NH, 03755, USA.,Department of Earth Science, University of Michigan, Ann Arbor, MI, USA
| | - Yuki Weber
- Department of Earth & Planetary Sciences, Harvard University, Cambridge, MA, 02138, USA.,Greenlight Biosciences Inc., Medford, MA, USA
| | - Felix J Elling
- Department of Earth & Planetary Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Ann Pearson
- Department of Earth & Planetary Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, 03755, USA.,Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA.,Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA
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12
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Dahuja A, Kumar RR, Sakhare A, Watts A, Singh B, Goswami S, Sachdev A, Praveen S. Role of ATP-binding cassette transporters in maintaining plant homeostasis under abiotic and biotic stresses. PHYSIOLOGIA PLANTARUM 2021; 171:785-801. [PMID: 33280130 DOI: 10.1111/ppl.13302] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 05/20/2023]
Abstract
The ATP-binding cassette (ABC) transporters belong to a large protein family predominantly present in diverse species. ABC transporters are driven by ATP hydrolysis and can act as exporters as well as importers. These proteins are localized in the membranes of chloroplasts, mitochondria, peroxisomes and vacuoles. ABC proteins are involved in regulating diverse biological processes in plants, such as growth, development, uptake of nutrients, tolerance to biotic and abiotic stresses, tolerance to metal toxicity, stomatal closure, shape and size of grains, protection of pollens, transport of phytohormones, etc. In mitochondria and chloroplast, the iron metabolism and its transport across the membrane are mediated by ABC transporters. Tonoplast-localized ABC transporters are involved in internal detoxification of metal ion; thus protecting against the DNA impairment and maintaining cell growth. ABC transporters are involved in the transport of secondary metabolites inside the cells. Microorganisms also engage a large number of ABC transporters to import and expel substrates decisive for their pathogenesis. ABC transporters also suppress the seed embryonic growth until favorable conditions come. This review aims at giving insights on ABC transporters, their evolution, structure, functions and roles in different biological processes for helping the terrestrial plants to survive under adverse environmental conditions. These specialized plant membrane transporters ensure a sustainable economic yield and high-quality products, especially under unfavorable conditions of growth. These transporters can be suitably manipulated to develop 'Plants for the Future'.
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Affiliation(s)
- Anil Dahuja
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, India
| | - Ranjeet R Kumar
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, India
| | - Akshay Sakhare
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, India
| | - Archana Watts
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, India
| | - Bhupinder Singh
- Centre for Environment Science and Climate Resilient Agriculture (CESCRA), Indian Agricultural Research Institute, New Delhi, India
| | - Suneha Goswami
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, India
| | - Archana Sachdev
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, India
| | - Shelly Praveen
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, India
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13
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Fabri JHTM, de Sá NP, Malavazi I, Del Poeta M. The dynamics and role of sphingolipids in eukaryotic organisms upon thermal adaptation. Prog Lipid Res 2020; 80:101063. [PMID: 32888959 DOI: 10.1016/j.plipres.2020.101063] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/18/2020] [Accepted: 08/27/2020] [Indexed: 01/09/2023]
Abstract
All living beings have an optimal temperature for growth and survival. With the advancement of global warming, the search for understanding adaptive processes to climate changes has gained prominence. In this context, all living beings monitor the external temperature and develop adaptive responses to thermal variations. These responses ultimately change the functioning of the cell and affect the most diverse structures and processes. One of the first structures to detect thermal variations is the plasma membrane, whose constitution allows triggering of intracellular signals that assist in the response to temperature stress. Although studies on this topic have been conducted, the underlying mechanisms of recognizing thermal changes and modifying cellular functioning to adapt to this condition are not fully understood. Recently, many reports have indicated the participation of sphingolipids (SLs), major components of the plasma membrane, in the regulation of the thermal stress response. SLs can structurally reinforce the membrane or/and send signals intracellularly to control numerous cellular processes, such as apoptosis, cytoskeleton polarization, cell cycle arresting and fungal virulence. In this review, we discuss how SLs synthesis changes during both heat and cold stresses, focusing on fungi, plants, animals and human cells. The role of lysophospholipids is also discussed.
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Affiliation(s)
- João Henrique Tadini Marilhano Fabri
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA; Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Nivea Pereira de Sá
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Maurizio Del Poeta
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA; Division of Infectious Diseases, School of Medicine, Stony Brook University, Stony Brook, New York, USA; Veterans Administration Medical Center, Northport, New York, USA.
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14
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Tourte M, Schaeffer P, Grossi V, Oger PM. Functionalized Membrane Domains: An Ancestral Feature of Archaea? Front Microbiol 2020; 11:526. [PMID: 32296409 PMCID: PMC7137397 DOI: 10.3389/fmicb.2020.00526] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/11/2020] [Indexed: 01/06/2023] Open
Abstract
Bacteria and Eukarya organize their plasma membrane spatially into domains of distinct functions. Due to the uniqueness of their lipids, membrane functionalization in Archaea remains a debated area. A novel membrane ultrastructure predicts that monolayer and bilayer domains would be laterally segregated in the hyperthermophilic archaeon Thermococcus barophilus. With very different physico-chemical parameters of the mono- and bilayer, each domain type would thus allow the docking of different membrane proteins and express different biological functions in the membrane. To estimate the ubiquity of this putative membrane ultrastructure in and out of the order Thermococcales, we re-analyzed the core lipid composition of all the Thermococcales type species and collected all the literature data available for isolated archaea. We show that all species of Thermococcales synthesize a mixture of diether bilayer forming and tetraether monolayer forming lipids, in various ratio from 10 to 80% diether in Pyrococcus horikoshii and Thermococcus gorgonarius, respectively. Since the domain formation prediction rests only on the coexistence of di- and tetraether lipids, we show that all Thermococcales have the ability for domain formation, i.e., differential functionalization of their membrane. Extrapolating this view to the whole Archaea domain, we show that almost all archaea also have the ability to synthesize di- and tetraether lipids, which supports the view that functionalized membrane domains may be shared between all Archaea. Hence domain formation and membrane compartmentalization may have predated the separation of the three domains of life and be essential for the cell cycle.
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Affiliation(s)
- Maxime Tourte
- Université de Lyon, INSA Lyon, CNRS, MAP UMR 5240, Villeurbanne, France
| | - Philippe Schaeffer
- Université de Strasbourg-CNRS, UMR 7177, Laboratoire de Biogéochimie Moléculaire, Strasbourg, France
| | - Vincent Grossi
- Université de Lyon, ENS Lyon, CNRS, Laboratoire de Géologie de Lyon, UMR 5276, Villeurbanne, France
| | - Phil M. Oger
- Université de Lyon, INSA Lyon, CNRS, MAP UMR 5240, Villeurbanne, France
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15
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Boyer GM, Schubotz F, Summons RE, Woods J, Shock EL. Carbon Oxidation State in Microbial Polar Lipids Suggests Adaptation to Hot Spring Temperature and Redox Gradients. Front Microbiol 2020; 11:229. [PMID: 32153529 PMCID: PMC7044123 DOI: 10.3389/fmicb.2020.00229] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 01/31/2020] [Indexed: 12/18/2022] Open
Abstract
The influence of oxidation-reduction (redox) potential on the expression of biomolecules is a topic of ongoing exploration in geobiology. In this study, we investigate the novel possibility that structures and compositions of lipids produced by microbial communities are sensitive to environmental redox conditions. We extracted lipids from microbial biomass collected along the thermal and redox gradients of four alkaline hot springs in Yellowstone National Park (YNP) and investigated patterns in the average oxidation state of carbon (ZC), a metric calculated from the chemical formulae of lipid structures. Carbon in intact polar lipids (IPLs) and their alkyl chains becomes more oxidized (higher ZC) with increasing distance from each of the four hot spring sources. This coincides with decreased water temperature and increased concentrations of oxidized inorganic solutes, such as dissolved oxygen, sulfate, and nitrate. Carbon in IPLs is most reduced (lowest ZC) in the hot, reduced conditions upstream, with abundance-weighted ZC values between −1.68 and −1.56. These values increase gradually downstream to around −1.36 to −1.33 in microbial communities living between 29.0 and 38.1°C. This near-linear increase in ZC can be attributed to a shift from ether-linked to ester-linked alkyl chains, a decrease in average aliphatic carbons per chain (nC), an increase in average degree of unsaturation per chain (nUnsat), and increased cyclization in tetraether lipids. The ZC of lipid headgroups and backbones did not change significantly downstream. Expression of lipids with relatively reduced carbon under reduced conditions and oxidized lipids under oxidized conditions may indicate microbial adaptation across environmental gradients in temperature and electron donor/acceptor supply.
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Affiliation(s)
- Grayson M Boyer
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, United States
| | - Florence Schubotz
- MARUM and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jade Woods
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Everett L Shock
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, United States.,School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
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16
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Zhou A, Weber Y, Chiu BK, Elling FJ, Cobban AB, Pearson A, Leavitt WD. Energy flux controls tetraether lipid cyclization in Sulfolobus acidocaldarius. Environ Microbiol 2019; 22:343-353. [PMID: 31696620 DOI: 10.1111/1462-2920.14851] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/16/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022]
Abstract
Microorganisms regulate the composition of their membranes in response to environmental cues. Many Archaea maintain the fluidity and permeability of their membranes by adjusting the number of cyclic moieties within the cores of their glycerol dibiphytanyl glycerol tetraether (GDGT) lipids. Cyclized GDGTs increase membrane packing and stability, which has been shown to help cells survive shifts in temperature and pH. However, the extent of this cyclization also varies with growth phase and electron acceptor or donor limitation. These observations indicate a relationship between energy metabolism and membrane composition. Here we show that the average degree of GDGT cyclization increases with doubling time in continuous cultures of the thermoacidophile Sulfolobus acidocaldarius (DSM 639). This is consistent with the behavior of a mesoneutrophile, Nitrosopumilus maritimus SCM1. Together, these results demonstrate that archaeal GDGT distributions can shift in response to electron donor flux and energy availability, independent of pH or temperature. Paleoenvironmental reconstructions based on GDGTs thus capture the energy available to microbes, which encompasses fluctuations in temperature and pH, as well as electron donor and acceptor availability. The ability of Archaea to adjust membrane composition and packing may be an important strategy that enables survival during episodes of energy stress.
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Affiliation(s)
- Alice Zhou
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, 03755, USA
| | - Yuki Weber
- Department of Earth & Planetary Sciences, Harvard University, Cambridge, Massachusetts, 02318, USA
| | - Beverly K Chiu
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, 03755, USA
| | - Felix J Elling
- Department of Earth & Planetary Sciences, Harvard University, Cambridge, Massachusetts, 02318, USA
| | - Alec B Cobban
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, 03755, USA
| | - Ann Pearson
- Department of Earth & Planetary Sciences, Harvard University, Cambridge, Massachusetts, 02318, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, 03755, USA.,Department of Chemistry, Dartmouth College, Hanover, New Hampshire, 03755, USA.,Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, 03755, USA
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17
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Chaves Torres L, Kaur G, Melbourne LA, Pancost RD. Selective chemical degradation of silica sinters of the Taupo Volcanic Zone (New Zealand). Implications for early Earth and Astrobiology. GEOBIOLOGY 2019; 17:449-464. [PMID: 31020785 DOI: 10.1111/gbi.12340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 02/26/2019] [Accepted: 03/21/2019] [Indexed: 06/09/2023]
Abstract
Most organic matter (OM) on Earth occurs as kerogen-like materials, that is naturally formed macromolecules insoluble with standard organic solvents. The formation of this insoluble organic matter (IOM) is a topic of much interest, especially when it limits the detection of compounds of geomicrobiological interest. For example, studies that search for biomarker evidence of life on early Earth or other planets usually use solvent-based extractions. This leaves behind a pool of OM as unexplored post-extraction residues, potentially containing diagnostic biomarkers. Since the IOM has an enhanced potential for preservation compared to soluble OM, analysing IOM-released biomarkers can also provide even deeper insights into the ecology of ancient settings, with implications for early Earth and Astrobiology investigations. Here, we analyse the prokaryotic lipid biosignature within soluble and IOM of the Taupo Volcanic Zone (TVZ) silica sinters, which are key analogues in the search for life. We apply sequential solvent extractions and a selective chemical degradation upon the post-solvent extraction residue. Moreover, we compare the IOM from TVZ sinters to analogous studies on peat and marine sediments to assess patterns in OM insolubilisation across the geosphere. Consistent with previous work, we find significant but variable proportions-1%-45% of the total prokaryotic lipids recovered-associated with IOM fractions. This occurs even in recently formed silica sinters, likely indicating inherent cell insolubility. Moreover, archaeal lipids seem more prone to insolubilisation as compared to the bacterial analogues, which might enhance their preservation and also bias overall biomarkers interpretation. These observations are similar to those observed in other settings, confirming that even in a setting where the OM derives predominantly from prokaryotic sources, patterns of IOM formation/occurrence are conserved. Differences with other settings, however, such as the occurrence of archaeol in IOM fractions, could be indicative of different mechanisms for IOM formation that merit further exploration.
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Affiliation(s)
- Lidia Chaves Torres
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
- Cabot Institute, University of Bristol, Bristol, UK
| | - Gurpreet Kaur
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
- Cabot Institute, University of Bristol, Bristol, UK
| | - Leanne A Melbourne
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
- Cabot Institute, University of Bristol, Bristol, UK
| | - Richard D Pancost
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
- Cabot Institute, University of Bristol, Bristol, UK
- School of Earth Sciences, University of Bristol, Bristol, UK
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18
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Booker AE, Hoyt DW, Meulia T, Eder E, Nicora CD, Purvine SO, Daly RA, Moore JD, Wunch K, Pfiffner SM, Lipton MS, Mouser PJ, Wrighton KC, Wilkins MJ. Deep-Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp. Appl Environ Microbiol 2019; 85:e00018-19. [PMID: 30979840 PMCID: PMC6544827 DOI: 10.1128/aem.00018-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/10/2019] [Indexed: 01/12/2023] Open
Abstract
Bacterial Halanaerobium strains become the dominant persisting microbial community member in produced fluids across geographically distinct hydraulically fractured shales. Halanaerobium is believed to be inadvertently introduced into this environment during the drilling and fracturing process and must therefore tolerate large changes in pressure, temperature, and salinity. Here, we used a Halanaerobium strain isolated from a natural gas well in the Utica Point Pleasant formation to investigate metabolic and physiological responses to growth under high-pressure subsurface conditions. Laboratory incubations confirmed the ability of Halanaerobium congolense strain WG8 to grow under pressures representative of deep shale formations (21 to 48 MPa). Under these conditions, broad metabolic and physiological shifts were identified, including higher abundances of proteins associated with the production of extracellular polymeric substances. Confocal laser scanning microscopy indicated that extracellular polymeric substance (EPS) production was associated with greater cell aggregation when biomass was cultured at high pressure. Changes in Halanaerobium central carbon metabolism under the same conditions were inferred from nuclear magnetic resonance (NMR) and gas chromatography measurements, revealing large per-cell increases in production of ethanol, acetate, and propanol and cessation of hydrogen production. These metabolic shifts were associated with carbon flux through 1,2-propanediol in response to slower fluxes of carbon through stage 3 of glycolysis. Together, these results reveal the potential for bioclogging and corrosion (via organic acid fermentation products) associated with persistent Halanaerobium growth in deep, hydraulically fractured shale ecosystems, and offer new insights into cellular mechanisms that enable these strains to dominate deep-shale microbiomes.IMPORTANCE The hydraulic fracturing of deep-shale formations for hydrocarbon recovery accounts for approximately 60% of U.S. natural gas production. Microbial activity associated with this process is generally considered deleterious due to issues associated with sulfide production, microbially induced corrosion, and bioclogging in the subsurface. Here we demonstrate that a representative Halanaerobium species, frequently the dominant microbial taxon in hydraulically fractured shales, responds to pressures characteristic of the deep subsurface by shifting its metabolism to generate more corrosive organic acids and produce more polymeric substances that cause "clumping" of biomass. While the potential for increased corrosion of steel infrastructure and clogging of pores and fractures in the subsurface may significantly impact hydrocarbon recovery, these data also offer new insights for microbial control in these ecosystems.
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Affiliation(s)
- Anne E Booker
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
| | - David W Hoyt
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tea Meulia
- College of Food, Agricultural, and Environmental Sciences, Ohio State University, Columbus, Ohio, USA
| | - Elizabeth Eder
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Rebecca A Daly
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
| | - Joseph D Moore
- DowDuPont Industrial Biosciences, Wilmington, Delaware, USA
| | - Kenneth Wunch
- DowDuPont Industrial Biosciences, Wilmington, Delaware, USA
| | - Susan M Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
| | - Mary S Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Paula J Mouser
- Department of Civil and Environmental Engineering, University of New Hampshire, Durham, New Hampshire, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
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19
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Akondi RN, Sharma S, Trexler RV, Mouser PJ, Pfiffner SM. Microbial lipid biomarkers detected in deep subsurface black shales. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2019; 21:291-307. [PMID: 30688342 DOI: 10.1039/c8em00444g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Evidence for microbes has been detected in extreme subsurface environments as deep as 2.5 km with temperatures as high as 90 °C, demonstrating that microbes can adapt and survive extreme environmental conditions. Deep subsurface shales are increasingly exploited for their energy applications, thus characterizing the prevalence and role of microbes in these ecosystems essential for understanding biogeochemical cycles and maximizing production from hydrocarbon-bearing formations. Here, we describe the distribution of bacterial ester-linked phospholipid fatty acids (PLFA) and diglyceride fatty acids (DGFA) in sidewall cores retrieved from three distinct geologic horizons collected to 2275 m below ground surface in a Marcellus Shale well, West Virginia, USA. We examined the abundance and variety of PLFA and DGFA prior to energy development within and above the Marcellus Shale Formation into the overlying Mahantango Formation of the Appalachian Basin. Lipid biomarkers in the cores suggest the presence of microbial communities comprising Gram (+), Gram (-) as well as stress indicative biomarkers. Microbial PLFA and DGFA degradation in the subsurface can be influenced by stressful environmental conditions associated with the subsurface. The PLFA concentration and variety were higher in the transition zone between the extremely low permeability Marcellus Shale Formation and the more permeable Mahantango Formation. In contrast to this distribution, more abundant and diverse DGFA membrane profiles were associated with the Mahantango Formation. The stress indicative biomarkers like the trans-membrane fatty acids, oxiranes, keto-, and dimethyl lipid fatty acids were present in all cores, potentially indicating that the bacterial communities had experienced physiological stress or nutrient deprivation during or after deposition. The DGFA profiles expressed more stress indicative biomarkers as opposed to the PLFA membrane profiles. These findings suggest the probable presence of indigenous microbial communities in the deep subsurface shale and also improves our understanding of microbial survival mechanisms in ancient deep subsurface environments.
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Affiliation(s)
- Rawlings N Akondi
- Department of Geology and Geography, West Virginia University, Morgantown, WV 26506, USA.
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Heaver SL, Johnson EL, Ley RE. Sphingolipids in host-microbial interactions. Curr Opin Microbiol 2018; 43:92-99. [PMID: 29328957 DOI: 10.1016/j.mib.2017.12.011] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/20/2017] [Accepted: 12/22/2017] [Indexed: 01/28/2023]
Abstract
Sphingolipids, a lipid class characterized by a long-chain amino alcohol backbone, serve vital structural and signaling roles in eukaryotes. Though eukaryotes produce sphingolipids, this capacity is phylogenetically highly restricted in Bacteria. Intriguingly, bacterial species commonly associated in high abundance with eukaryotic hosts include sphingolipid producers, such as the Bacteroidetes in the mammalian gut. To date, a role for bacterial sphingolipids in immune system maturation has been described, but their fate and impact in host physiology and metabolism remain to be elucidated. The structural conservation of bacterial sphingolipids with those produced by their mammalian hosts offer clues about which aspects of mammalian biology may be modulated by these intriguing lipids.
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Affiliation(s)
- Stacey L Heaver
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14580, USA
| | - Elizabeth L Johnson
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14580, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14580, USA.
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