1
|
Liman GLS, Garcia AA, Fluke KA, Anderson HR, Davidson SC, Welander PV, Santangelo TJ. Tetraether archaeal lipids promote long-term survival in extreme conditions. Mol Microbiol 2024; 121:882-894. [PMID: 38372181 PMCID: PMC11096074 DOI: 10.1111/mmi.15240] [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: 08/09/2023] [Revised: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
The sole unifying feature of the incredibly diverse Archaea is their isoprenoid-based ether-linked lipid membranes. Unique lipid membrane composition, including an abundance of membrane-spanning tetraether lipids, impart resistance to extreme conditions. Many questions remain, however, regarding the synthesis and modification of tetraether lipids and how dynamic changes to archaeal lipid membrane composition support hyperthermophily. Tetraether membranes, termed glycerol dibiphytanyl glycerol tetraethers (GDGTs), are generated by tetraether synthase (Tes) by joining the tails of two bilayer lipids known as archaeol. GDGTs are often further specialized through the addition of cyclopentane rings by GDGT ring synthase (Grs). A positive correlation between relative GDGT abundance and entry into stationary phase growth has been observed, but the physiological impact of inhibiting GDGT synthesis has not previously been reported. Here, we demonstrate that the model hyperthermophile Thermococcus kodakarensis remains viable when Tes (TK2145) or Grs (TK0167) are deleted, permitting phenotypic and lipid analyses at different temperatures. The absence of cyclopentane rings in GDGTs does not impact growth in T. kodakarensis, but an overabundance of rings due to ectopic Grs expression is highly fitness negative at supra-optimal temperatures. In contrast, deletion of Tes resulted in the loss of all GDGTs, cyclization of archaeol, and loss of viability upon transition to the stationary phase in this model archaea. These results demonstrate the critical roles of highly specialized, dynamic, isoprenoid-based lipid membranes for archaeal survival at high temperatures.
Collapse
Affiliation(s)
- Geraldy Lie Stefanus Liman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Andy A. Garcia
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA
| | - Kristin A. Fluke
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO 80523, USA
| | | | - Sarah C. Davidson
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Paula V. Welander
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA
| | - Thomas J. Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO 80523, USA
| |
Collapse
|
2
|
Blum LN, Colman DR, Eloe-Fadrosh EA, Kellom M, Boyd ES, Zhaxybayeva O, Leavitt WD. Distribution and abundance of tetraether lipid cyclization genes in terrestrial hot springs reflect pH. Environ Microbiol 2023; 25:1644-1658. [PMID: 37032561 DOI: 10.1111/1462-2920.16375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/15/2023] [Indexed: 04/11/2023]
Abstract
Many Archaea produce membrane-spanning lipids that enable life in extreme environments. These isoprenoid glycerol dibiphytanyl glycerol tetraethers (GDGTs) may contain up to eight cyclopentyl and one cyclohexyl ring, where higher degrees of cyclization are associated with more acidic, hotter or energy-limited conditions. Recently, the genes encoding GDGT ring synthases, grsAB, were identified in two Sulfolobaceae; however, the distribution and abundance of grs homologs across environments inhabited by these and related organisms remain a mystery. To address this, we examined the distribution of grs homologs in relation to environmental temperature and pH, from thermal springs across Earth, where sequences derive from metagenomes, metatranscriptomes, single-cell and cultivar genomes. The abundance of grs homologs shows a strong negative correlation to pH, but a weak positive correlation to temperature. Archaeal genomes and metagenome-assembled genomes (MAGs) that carry two or more grs copies are more abundant in low pH springs. We also find grs in 12 archaeal classes, with the most representatives in Thermoproteia, followed by MAGs of the uncultured Korarchaeia, Bathyarchaeia and Hadarchaeia, while several Nitrososphaeria encodes >3 copies. Our findings highlight the key role of grs-catalysed lipid cyclization in archaeal diversification across hot and acidic environments.
Collapse
Affiliation(s)
- Laura N Blum
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | | | - Matthew Kellom
- Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire, USA
| |
Collapse
|
3
|
Chiu BK, Waldbauer J, Elling FJ, Mete ÖZ, Zhang L, Pearson A, Eggleston EM, Leavitt WD. Membrane lipid and expression responses of Saccharolobus islandicus REY15A to acid and cold stress. Front Microbiol 2023; 14:1219779. [PMID: 37649629 PMCID: PMC10465181 DOI: 10.3389/fmicb.2023.1219779] [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: 05/09/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023] Open
Abstract
Archaea adjust the number of cyclopentane rings in their glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids as a homeostatic response to environmental stressors such as temperature, pH, and energy availability shifts. However, archaeal expression patterns that correspond with changes in GDGT composition are less understood. Here we characterize the acid and cold stress responses of the thermoacidophilic crenarchaeon Saccharolobus islandicus REY15A using growth rates, core GDGT lipid profiles, transcriptomics and proteomics. We show that both stressors result in impaired growth, lower average GDGT cyclization, and differences in gene and protein expression. Transcription data revealed differential expression of the GDGT ring synthase grsB in response to both acid stress and cold stress. Although the GDGT ring synthase encoded by grsB forms highly cyclized GDGTs with ≥5 ring moieties, S. islandicus grsB upregulation under acidic pH conditions did not correspond with increased abundances of highly cyclized GDGTs. Our observations highlight the inability to predict GDGT changes from transcription data alone. Broader analysis of transcriptomic data revealed that S. islandicus differentially expresses many of the same transcripts in response to both acid and cold stress. These included upregulation of several biosynthetic pathways and downregulation of oxidative phosphorylation and motility. Transcript responses specific to either of the two stressors tested here included upregulation of genes related to proton pumping and molecular turnover in acid stress conditions and upregulation of transposases in cold stress conditions. Overall, our study provides a comprehensive understanding of the GDGT modifications and differential expression characteristic of the acid stress and cold stress responses in S. islandicus.
Collapse
Affiliation(s)
- Beverly K. Chiu
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
| | - Jacob Waldbauer
- Department of the Geophysical Sciences, The University of Chicago, Chicago, IL, United States
| | - Felix J. Elling
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
- Leibniz-Laboratory for Radiometric Dating and Isotope Research, Kiel University, Kiel, Germany
| | - Öykü Z. Mete
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Lichun Zhang
- Department of the Geophysical Sciences, The University of Chicago, Chicago, IL, United States
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Erin M. Eggleston
- Department of Biology, Middlebury College, Middlebury, VT, United States
| | - William D. Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
- Department of Chemistry, Dartmouth College, Hanover, NH, United States
| |
Collapse
|
4
|
Mohammadpour H, Cardin M, Carraro L, Fasolato L, Cardazzo B. Characterization of the archaeal community in foods: The neglected part of the food microbiota. Int J Food Microbiol 2023; 401:110275. [PMID: 37295268 DOI: 10.1016/j.ijfoodmicro.2023.110275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/30/2023] [Accepted: 05/28/2023] [Indexed: 06/12/2023]
Abstract
Despite the large number of studies conducted on archaea associated with extreme environments, the archaeal community composition in food products is still poorly known. Here, we investigated a new insight into exploring the archaeal community in several food matrices, with a particular focus on determining whether living archaea were present. A total of 71 samples of milk, cheese and its derived brine, honey, hamburger, clam, and trout were analyzed by high-throughput 16S rRNA sequencing. Archaea were detected in all the samples, ranging from 0.62 % of microbial communities in trout to 37.71 % in brine. Methanogens dominated 47.28 % of the archaeal communities, except for brine, which was dominated by halophilic taxa affiliated with the genus Haloquadratum (52.45 %). Clams were found to be a food with high richness and diversity of archaea and were targeted for culturing living archaea under different incubation time and temperature conditions. A subset of 16 communities derived from culture-dependent and culture-independent communities were assessed. Among the homogenates and living archaeal communities, the predominant taxa were distributed in the genera Nitrosopumilus (47.61 %) and Halorussus (78.78 %), respectively. A comparison of the 28 total taxa obtained by culture-dependent and culture-independent methods enabled their categorization into different groups, including detectable (8 out of 28), cultivable (8 out of 28), and detectable-cultivable (12 out of 28) taxa. Furthermore, using the culture method, the majority (14 out of 20) of living taxa grew at lower temperatures of 22 and 4 °C during long-term incubation, and few taxa (2 out of 20) were found at 37 °C during the initial days of incubation. Our results demonstrated the distribution of archaea in all analyzed food matrices, which opens new perspectives to expand our knowledge on archaea in foods and their beneficial and detrimental effects.
Collapse
Affiliation(s)
- Hooriyeh Mohammadpour
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Universit'a 16, 35020 Legnaro, Pd, Italy
| | - Marco Cardin
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Universit'a 16, 35020 Legnaro, Pd, Italy
| | - Lisa Carraro
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Universit'a 16, 35020 Legnaro, Pd, Italy
| | - Luca Fasolato
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Universit'a 16, 35020 Legnaro, Pd, Italy.
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Universit'a 16, 35020 Legnaro, Pd, Italy
| |
Collapse
|
5
|
de Kok NAW, Driessen AJM. The catalytic and structural basis of archaeal glycerophospholipid biosynthesis. Extremophiles 2022; 26:29. [PMID: 35976526 PMCID: PMC9385802 DOI: 10.1007/s00792-022-01277-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/02/2022] [Indexed: 12/03/2022]
Abstract
Archaeal glycerophospholipids are the main constituents of the cytoplasmic membrane in the archaeal domain of life and fundamentally differ in chemical composition compared to bacterial phospholipids. They consist of isoprenyl chains ether-bonded to glycerol-1-phosphate. In contrast, bacterial glycerophospholipids are composed of fatty acyl chains ester-bonded to glycerol-3-phosphate. This largely domain-distinguishing feature has been termed the “lipid-divide”. The chemical composition of archaeal membranes contributes to the ability of archaea to survive and thrive in extreme environments. However, ether-bonded glycerophospholipids are not only limited to extremophiles and found also in mesophilic archaea. Resolving the structural basis of glycerophospholipid biosynthesis is a key objective to provide insights in the early evolution of membrane formation and to deepen our understanding of the molecular basis of extremophilicity. Many of the glycerophospholipid enzymes are either integral membrane proteins or membrane-associated, and hence are intrinsically difficult to study structurally. However, in recent years, the crystal structures of several key enzymes have been solved, while unresolved enzymatic steps in the archaeal glycerophospholipid biosynthetic pathway have been clarified providing further insights in the lipid-divide and the evolution of early life.
Collapse
Affiliation(s)
- Niels A W de Kok
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands.
| |
Collapse
|
6
|
Abstract
Archaeal membrane lipids are widely used for paleotemperature reconstructions, yet these molecular fossils also bear rich information about ecology and evolution of marine ammonia-oxidizing archaea (AOA). Here we identified thermal and nonthermal behaviors of archaeal glycerol dialkyl glycerol tetraethers (GDGTs) by comparing the GDGT-based temperature index (TEX86) to the ratio of GDGTs with two and three cyclopentane rings (GDGT-2/GDGT-3). Thermal-dependent biosynthesis should increase TEX86 and decrease GDGT-2/GDGT-3 when the ambient temperature increases. This presumed temperature-dependent (PTD) trend is observed in GDGTs derived from cultures of thermophilic and mesophilic AOA. The distribution of GDGTs in suspended particulate matter (SPM) and sediments collected from above the pycnocline-shallow water samples-also follows the PTD trend. These similar GDGT distributions between AOA cultures and shallow water environmental samples reflect shallow ecotypes of marine AOA. While there are currently no cultures of deep AOA clades, GDGTs derived from deep water SPM and marine sediment samples exhibit nonthermal behavior deviating from the PTD trend. The presence of deep AOA increases the GDGT-2/GDGT-3 ratio and distorts the temperature-controlled correlation between GDGT-2/GDGT-3 and TEX86. We then used Gaussian mixture models to statistically characterize these diagnostic patterns of modern AOA ecology from paleo-GDGT records to infer the evolution of marine AOA from the Mid-Mesozoic to the present. Long-term GDGT-2/GDGT-3 trends suggest a suppression of today's deep water marine AOA during the Mesozoic-early Cenozoic greenhouse climates. Our analysis provides invaluable insights into the evolutionary timeline and the expansion of AOA niches associated with major oceanographic and climate changes.
Collapse
|
7
|
Tourte M, Schaeffer P, Grossi V, Oger PM. Membrane adaptation in the hyperthermophilic archaeon Pyrococcus furiosus relies upon a novel strategy involving glycerol monoalkyl glycerol tetraether lipids. Environ Microbiol 2022; 24:2029-2046. [PMID: 35106897 DOI: 10.1111/1462-2920.15923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 11/28/2022]
Abstract
Microbes preserve membrane functionality under fluctuating environmental conditions by modulating their membrane lipid composition. Although several studies have documented membrane adaptations in Archaea, the influence of most biotic and abiotic factors on archaeal lipid compositions remains underexplored. Here, we studied the influence of temperature, pH, salinity, the presence/absence of elemental sulfur, the carbon source, and the genetic background on the lipid core composition of the hyperthermophilic neutrophilic marine archaeon Pyrococcus furiosus. Every growth parameter tested affected the lipid core composition to some extent, the carbon source and the genetic background having the greatest influence. Surprisingly, P. furiosus appeared to only marginally rely on the two major responses implemented by Archaea, i.e., the regulation of the ratio of diether to tetraether lipids and that of the number of cyclopentane rings in tetraethers. Instead, this species increased the ratio of glycerol monoalkyl glycerol tetraethers (GMGT, aka. H-shaped tetraethers) to glycerol dialkyl glycerol tetrathers (GDGT) in response to decreasing temperature and pH and increasing salinity, thus providing for the first time evidence of adaptive functions for GMGT. Besides P. furiosus, numerous other species synthesize significant proportions of GMGT, which suggests that this unprecedented adaptive strategy might be common in Archaea. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Maxime Tourte
- Univ Lyon, Univ. Lyon 1, CNRS, UMR 5240, F-69622, Villeurbanne, France.,Univ Lyon, INSA Lyon, CNRS, UMR 5240, F-69621, Villeurbanne, France
| | | | - Vincent Grossi
- Univ Lyon, Univ. Lyon 1, CNRS, ENSL, UJM, UMR 5276 LGL-TPE, F-69622, Villeurbanne, France
| | - Philippe M Oger
- Univ Lyon, INSA Lyon, CNRS, UMR 5240, F-69621, Villeurbanne, France
| |
Collapse
|
8
|
Guha A, McGuire ML, Leriche G, Yang J, Mayer M. A single-liposome assay that enables temperature-dependent measurement of proton permeability of extremophile-inspired lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183567. [PMID: 33476579 DOI: 10.1016/j.bbamem.2021.183567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 10/22/2022]
Affiliation(s)
- Anirvan Guha
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Melissa L McGuire
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Geoffray Leriche
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States of America
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States of America
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland.
| |
Collapse
|
9
|
Ma C, Coffinet S, Lipp JS, Hinrichs KU, Zhang C. Marine Group II Euryarchaeota Contribute to the Archaeal Lipid Pool in Northwestern Pacific Ocean Surface Waters. Front Microbiol 2020; 11:1034. [PMID: 32582055 PMCID: PMC7291766 DOI: 10.3389/fmicb.2020.01034] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/27/2020] [Indexed: 12/17/2022] Open
Abstract
Planktonic archaea include predominantly Marine Group I Thaumarchaeota (MG I) and Marine Group II Euryarchaeota (MG II), which play important roles in the oceanic carbon cycle. MG I produce specific lipids called isoprenoid glycerol dibiphytanyl glycerol tetraethers (GDGTs), which are being used in the sea surface temperature proxy named TEX86. Although MG II may be the most abundant planktonic archaeal group in surface water, their lipid composition remains poorly characterized because of the lack of cultured representatives. Circumstantial evidence from previous studies of marine suspended particulate matter suggests that MG II may produce both GDGTs and archaeol-based lipids. In this study, integration of the 16S rRNA gene quantification and sequencing and lipid analysis demonstrated that MG II contributed significantly to the pool of archaeal tetraether lipids in samples collected from MG II-dominated surface waters of the Northwestern Pacific Ocean (NWPO). The archaeal lipid composition in MG II-dominated NWPO waters differed significantly from that of known MG I cultures, containing relatively more 2G-OH-, 2G- and 1G- GDGTs, especially in their acyclic form. Lipid composition in NWPO waters was also markedly different from MG I-dominated surface water samples collected in the East China Sea. GDGTs from MG II-dominated samples seemed to respond to temperature similarly to GDGTs from the MG I-dominated samples, which calls for further study using pure cultures to determine the exact impact of MG II on GDGT-based proxies.
Collapse
Affiliation(s)
- Cenling Ma
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Sarah Coffinet
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Julius S Lipp
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Bischof LF, Haurat MF, Hoffmann L, Albersmeier A, Wolf J, Neu A, Pham TK, Albaum SP, Jakobi T, Schouten S, Neumann-Schaal M, Wright PC, Kalinowski J, Siebers B, Albers SV. Early Response of Sulfolobus acidocaldarius to Nutrient Limitation. Front Microbiol 2019; 9:3201. [PMID: 30687244 PMCID: PMC6335949 DOI: 10.3389/fmicb.2018.03201] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/10/2018] [Indexed: 01/13/2023] Open
Abstract
In natural environments microorganisms encounter extreme changes in temperature, pH, osmolarities and nutrient availability. The stress response of many bacterial species has been described in detail, however, knowledge in Archaea is limited. Here, we describe the cellular response triggered by nutrient limitation in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. We measured changes in gene transcription and protein abundance upon nutrient depletion up to 4 h after initiation of nutrient depletion. Transcript levels of 1118 of 2223 protein coding genes and abundance of approximately 500 proteins with functions in almost all cellular processes were affected by nutrient depletion. Our study reveals a significant rerouting of the metabolism with respect to degradation of internal as well as extracellular-bound organic carbon and degradation of proteins. Moreover, changes in membrane lipid composition were observed in order to access alternative sources of energy and to maintain pH homeostasis. At transcript level, the cellular response to nutrient depletion in S. acidocaldarius seems to be controlled by the general transcription factors TFB2 and TFEβ. In addition, ribosome biogenesis is reduced, while an increased protein degradation is accompanied with a loss of protein quality control. This study provides first insights into the early cellular response of Sulfolobus to organic carbon and organic nitrogen depletion.
Collapse
Affiliation(s)
- Lisa F Bischof
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - M Florencia Haurat
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Lena Hoffmann
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Andreas Albersmeier
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jacqueline Wolf
- Department of Bioinformatics and Biochemistry, Braunschweig University of Technology, Braunschweig, Germany
| | - Astrid Neu
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Trong Khoa Pham
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
| | - Stefan P Albaum
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Jakobi
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Stefan Schouten
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute of Sea Research, Den Burg, Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Meina Neumann-Schaal
- Department of Bioinformatics and Biochemistry, Braunschweig University of Technology, Braunschweig, Germany
| | - Phillip C Wright
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| |
Collapse
|
12
|
Li F, Zheng F, Wang Y, Liu W, Zhang CL. Thermoplasmatales and Methanogens: Potential Association with the Crenarchaeol Production in Chinese Soils. Front Microbiol 2017; 8:1200. [PMID: 28717356 PMCID: PMC5494375 DOI: 10.3389/fmicb.2017.01200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 06/12/2017] [Indexed: 11/13/2022] Open
Abstract
Crenarchaeol is a unique isoprenoid glycerol dibiphytanyl glycerol tetraether (iGDGT) lipid, which is only identified in cultures of ammonia-oxidizing Thaumarchaeota. However, the taxonomic origins of crenarchaeol have been debated recently. The archaeal populations, other than Thaumarchaeota, may have associations with the production of crenarchaeol in ecosystems characterized by non-thaumarchaeotal microorganisms. To this end, we investigated 47 surface soils from upland and wetland soils and rice fields and another three surface sediments from river banks. The goal was to examine the archaeal community compositions in comparison with patterns of iGDGTs in four fractional forms (intact polar-, core-, monoglycosidic- and diglycosidic-lipid fractions) along gradients of environments. The DistLM analysis identified that Group I.1b Thaumarchaeota were mainly responsible for changes in crenarchaeol in the overall soil samples; however, Thermoplasmatales may also contribute to it. This is further supported by the comparison of crenarchaeol between samples characterized by methanogens, Thermoplasmatales or Group I.1b Thaumarchaeota, which suggests that the former two may contribute to the crenarchaeol pool. Last, when samples containing enhanced abundance of Thermoplasmatales and methanogens were considered, crenarchaeol was observed to correlate positively with Thermoplasmatales and archaeol, respectively. Collectively, our data suggest that the crenarchaeol production is mainly derived from Thaumarchaeota and partly associated with uncultured representatives of Thermoplasmatales and archaeol-producing methanogens in soil environments that may be in favor of their growth. Our finding supports the notion that Thaumarchaeota may not be the sole source of crenarchaeol in the natural environment, which may have implication for the evolution of lipid synthesis among different types of archaea.
Collapse
Affiliation(s)
- Fuyan Li
- Department of Ocean Science and Engineering, Southern University of Science and TechnologyShenzhen, China.,College of Life Sciences, Wuhan UniversityWuhan, China.,Division of Geological and Planetary Sciences, California Institute of Technology, PasadenaCA, United States.,State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Fengfeng Zheng
- State Key Laboratory of Marine Geology, Tongji UniversityShanghai, China
| | - Yongli Wang
- Key Laboratory of Petroleum Resources Research, Institute of Geology and Geophysics, Chinese Academy of SciencesLanzhou, China
| | - Weiguo Liu
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of SciencesXi'an, China.,School of Human Settlement and Civil Engineering, Xi'an Jiaotong UniversityXi'an, China
| | - Chuanlun L Zhang
- Department of Ocean Science and Engineering, Southern University of Science and TechnologyShenzhen, China
| |
Collapse
|
13
|
Siliakus MF, van der Oost J, Kengen SWM. Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure. Extremophiles 2017; 21:651-670. [PMID: 28508135 PMCID: PMC5487899 DOI: 10.1007/s00792-017-0939-x] [Citation(s) in RCA: 189] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 04/29/2017] [Indexed: 12/30/2022]
Abstract
The cytoplasmic membrane of a prokaryotic cell consists of a lipid bilayer or a monolayer that shields the cellular content from the environment. In addition, the membrane contains proteins that are responsible for transport of proteins and metabolites as well as for signalling and energy transduction. Maintenance of the functionality of the membrane during changing environmental conditions relies on the cell's potential to rapidly adjust the lipid composition of its membrane. Despite the fundamental chemical differences between bacterial ester lipids and archaeal ether lipids, both types are functional under a wide range of environmental conditions. We here provide an overview of archaeal and bacterial strategies of changing the lipid compositions of their membranes. Some molecular adjustments are unique for archaea or bacteria, whereas others are shared between the two domains. Strikingly, shared adjustments were predominantly observed near the growth boundaries of bacteria. Here, we demonstrate that the presence of membrane spanning ether-lipids and methyl branches shows a striking relationship with the growth boundaries of archaea and bacteria.
Collapse
Affiliation(s)
- Melvin F Siliakus
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| |
Collapse
|
14
|
Caforio A, Driessen AJM. Archaeal phospholipids: Structural properties and biosynthesis. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1325-1339. [PMID: 28007654 DOI: 10.1016/j.bbalip.2016.12.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/13/2016] [Accepted: 12/15/2016] [Indexed: 01/06/2023]
Abstract
Phospholipids are major components of the cellular membranes present in all living organisms. They typically form a lipid bilayer that embroiders the cell or cellular organelles, constitute a barrier for ions and small solutes and form a matrix that supports the function of membrane proteins. The chemical composition of the membrane phospholipids present in the two prokaryotic domains Archaea and Bacteria are vastly different. Archaeal lipids are composed of highly-methylated isoprenoid chains that are ether-linked to a glycerol-1-phosphate backbone while bacterial phospholipids consist of straight fatty acids bound by ester bonds to the enantiomeric glycerol-3-phosphate backbone. The chemical structure of the archaeal lipids and their compositional diversity ensures the required stability at extreme environmental conditions as many archaea thrive at such conditions including high or low temperature, high salinity and extreme acidic or alkaline pH values. However, not all archaea are extremophiles, and the presence of ether-linked phospholipids is a phylogenetic marker that distinguishes Archaea from other life forms. During the past decade, our understanding of the biosynthesis of archaeal lipids has progressed resulting in the characterization of the main biosynthetic steps of the pathway including the reconstitution of lipid biosynthesis in vitro. Here we describe the chemical and physical properties of archaeal lipids and membranes derived thereof, summarize the existing knowledge about the enzymology of the archaeal lipid biosynthetic pathway and discuss evolutionary theories associated with the "Lipid Divide" that resulted in the differentiation of bacterial and archaeal organisms. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
Collapse
Affiliation(s)
- Antonella Caforio
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands; The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands; The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| |
Collapse
|
15
|
Abstract
Because membranes play a central role in regulating fluxes inward and outward from the cells, maintaining the appropriate structure of the membrane is crucial to maintain cellular integrity and functions. Microbes often face contrasted and fluctuating environmental conditions, to which they need to adapt or die. Membrane adaptation is achieved by a modification of the membrane lipid composition, a strategy termed homeoviscous adaptation. Homeoviscous adaptation in archaea involves strategies similar to that observed in bacteria and eucarya, such as the regulation of lipid chain length or saturation levels, as well as strategies specific to archaea, such as the regulation of the number of cycles along the isoprenoid chains or the regulation of the ratio between mono and bipolar lipids. Although not described yet described in hyperthermophilic bacteria, it is possible that these two strategies also apply to these latter organisms.
Collapse
|
16
|
Jensen SM, Neesgaard VL, Skjoldbjerg SLN, Brandl M, Ejsing CS, Treusch AH. The Effects of Temperature and Growth Phase on the Lipidomes of Sulfolobus islandicus and Sulfolobus tokodaii. Life (Basel) 2015; 5:1539-66. [PMID: 26308060 PMCID: PMC4598652 DOI: 10.3390/life5031539] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 08/02/2015] [Accepted: 08/14/2015] [Indexed: 12/18/2022] Open
Abstract
The functionality of the plasma membrane is essential for all organisms. Adaption to high growth temperatures imposes challenges and Bacteria, Eukarya, and Archaea have developed several mechanisms to cope with these. Hyperthermophilic archaea have earlier been shown to synthesize tetraether membrane lipids with an increased number of cyclopentane moieties at higher growth temperatures. Here we used shotgun lipidomics to study this effect as well as the influence of growth phase on the lipidomes of Sulfolobus islandicus and Sulfolobus tokodaii for the first time. Both species were cultivated at three different temperatures, with samples withdrawn during lag, exponential, and stationary phases. Three abundant tetraether lipid classes and one diether lipid class were monitored. Beside the expected increase in the number of cyclopentane moieties with higher temperature in both archaea, we observed previously unreported changes in the average cyclization of the membrane lipids throughout growth. The average number of cyclopentane moieties showed a significant dip in exponential phase, an observation that might help to resolve the currently debated biosynthesis pathway of tetraether lipids.
Collapse
Affiliation(s)
- Sara Munk Jensen
- Department of Biology and Nordic Center for Earth Evolution, University of Southern Denmark, Odense 5230, Denmark.
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark.
| | - Vinnie Lund Neesgaard
- Department of Biology and Nordic Center for Earth Evolution, University of Southern Denmark, Odense 5230, Denmark.
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark.
| | - Sandra Landbo Nedergaard Skjoldbjerg
- Department of Biology and Nordic Center for Earth Evolution, University of Southern Denmark, Odense 5230, Denmark.
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark.
| | - Martin Brandl
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense 5230, Denmark.
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense 5230, Denmark.
| | - Alexander H Treusch
- Department of Biology and Nordic Center for Earth Evolution, University of Southern Denmark, Odense 5230, Denmark.
| |
Collapse
|
17
|
Microbial diversity and adaptation to high hydrostatic pressure in deep-sea hydrothermal vents prokaryotes. Extremophiles 2015; 19:721-40. [DOI: 10.1007/s00792-015-0760-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/26/2015] [Indexed: 12/15/2022]
|
18
|
Yoshinaga MY, Gagen EJ, Wörmer L, Broda NK, Meador TB, Wendt J, Thomm M, Hinrichs KU. Methanothermobacter thermautotrophicus modulates its membrane lipids in response to hydrogen and nutrient availability. Front Microbiol 2015; 6:5. [PMID: 25657645 PMCID: PMC4302986 DOI: 10.3389/fmicb.2015.00005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 01/04/2015] [Indexed: 11/13/2022] Open
Abstract
Methanothermobacter thermautotrophicus strain ΔH is a model hydrogenotrophic methanogen, for which extensive biochemical information, including the complete genome sequence, is available. Nevertheless, at the cell membrane lipid level, little is known about the responses of this archaeon to environmental stimuli. In this study, the lipid composition of M. thermautotrophicus was characterized to verify how this archaeon modulates its cell membrane components during growth phases and in response to hydrogen depletion and nutrient limitation (potassium and phosphate). As opposed to the higher abundance of phospholipids in the stationary phase of control experiments, cell membranes under nutrient, and energy stress were dominated by glycolipids that likely provided a more effective barrier against ion leakage. We also identified particular lipid regulatory mechanisms in M. thermautotrophicus, which included the accumulation of polyprenols under hydrogen-limited conditions and an increased content of sodiated adducts of lipids in nutrient-limited cells. These findings suggest that M. thermautotrophicus intensely modulates its cell membrane lipid composition to cope with energy and nutrient availability in dynamic environments.
Collapse
Affiliation(s)
- Marcos Y Yoshinaga
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences, University of Bremen Bremen, Germany
| | - Emma J Gagen
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Lars Wörmer
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences, University of Bremen Bremen, Germany
| | - Nadine K Broda
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences, University of Bremen Bremen, Germany
| | - Travis B Meador
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences, University of Bremen Bremen, Germany
| | - Jenny Wendt
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences, University of Bremen Bremen, Germany
| | - Michael Thomm
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences, University of Bremen Bremen, Germany
| |
Collapse
|
19
|
Xie W, Zhang CL, Wang J, Chen Y, Zhu Y, de la Torre JR, Dong H, Hartnett HE, Hedlund BP, Klotz MG. Distribution of ether lipids and composition of the archaeal community in terrestrial geothermal springs: impact of environmental variables. Environ Microbiol 2014; 17:1600-14. [PMID: 25142282 DOI: 10.1111/1462-2920.12595] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 08/08/2014] [Indexed: 11/26/2022]
Abstract
Archaea can respond to changes in the environment by altering the composition of their membrane lipids, for example, by modification of the abundance and composition of glycerol dialkyl glycerol tetraethers (GDGTs). Here, we investigated the abundance and proportions of polar GDGTs (P-GDGTs) and core GDGTs (C-GDGTs) sampled in different seasons from Tengchong hot springs (Yunnan, China), which encompassed a pH range of 2.5-10.1 and a temperature range of 43.7-93.6°C. The phylogenetic composition of the archaeal community (reanalysed from published work) divided the Archaea in spring sediment samples into three major groups that corresponded with spring pH: acidic, circumneutral and alkaline. Cluster analysis showed correlation between spring pH and the composition of P- and C-GDGTs and archaeal 16S rRNA genes, indicating an intimate link between resident Archaea and the distribution of P- and C-GDGTs in Tengchong hot springs. The distribution of GDGTs in Tengchong springs was also significantly affected by temperature; however, the relationship was weaker than with pH. Analysis of published datasets including samples from Tibet, Yellowstone and the US Great Basin hot springs revealed a similar relationship between pH and GDGT content. Specifically, low pH springs had higher concentrations of GDGTs with high numbers of cyclopentyl rings than neutral and alkaline springs, which is consistent with the predominance of high cyclopentyl ring-characterized Sulfolobales and Thermoplasmatales present in some of the low pH springs. Our study suggests that the resident Archaea in these hot springs are acclimated if not adapted to low pH by their genetic capacity to effect the packing density of their membranes by increasing cyclopentyl rings in GDGTs at the rank of community.
Collapse
Affiliation(s)
- Wei Xie
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China; Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Biosignatures in chimney structures and sediment from the Loki’s Castle low-temperature hydrothermal vent field at the Arctic Mid-Ocean Ridge. Extremophiles 2014; 18:545-60. [DOI: 10.1007/s00792-014-0640-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 03/02/2014] [Indexed: 11/26/2022]
|
21
|
Oger PM, Cario A. Adaptation of the membrane in Archaea. Biophys Chem 2013; 183:42-56. [PMID: 23915818 DOI: 10.1016/j.bpc.2013.06.020] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 06/25/2013] [Accepted: 06/25/2013] [Indexed: 12/11/2022]
Abstract
Microbes often face contrasted and fluctuating environmental conditions, to which they need to adapt or die. Because membranes play a central role in regulating fluxes inward and outward from the cells, maintaining the appropriate structure of the membrane is crucial to maintain cellular integrity and functions. This is achieved in bacteria and eucarya by a modification of the membrane lipid compositions, a strategy termed homeoviscous adaptation. We review here evidence for homeoviscous adaptation in Archaea, and discuss the limits of this strategy and our knowledge in this very peculiar domain of life.
Collapse
Affiliation(s)
- Philippe M Oger
- CNRS UMR 5276, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon cedex 07, France.
| | | |
Collapse
|
22
|
Jaeschke A, Jørgensen SL, Bernasconi SM, Pedersen RB, Thorseth IH, Früh-Green GL. Microbial diversity of Loki's Castle black smokers at the Arctic Mid-Ocean Ridge. GEOBIOLOGY 2012; 10:548-561. [PMID: 23006788 DOI: 10.1111/gbi.12009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 08/16/2012] [Indexed: 06/01/2023]
Abstract
Hydrothermal vent systems harbor rich microbial communities ranging from aerobic mesophiles to anaerobic hyperthermophiles. Among these, members of the archaeal domain are prevalent in microbial communities in the most extreme environments, partly because of their temperature-resistant and robust membrane lipids. In this study, we use geochemical and molecular microbiological methods to investigate the microbial diversity in black smoker chimneys from the newly discovered Loki's Castle hydrothermal vent field on the Arctic Mid-Ocean Ridge (AMOR) with vent fluid temperatures of 310-320 °C and pH of 5.5. Archaeal glycerol dialkyl glycerol tetraether lipids (GDGTs) and H-shaped GDGTs with 0-4 cyclopentane moieties were dominant in all sulfide samples and are most likely derived from both (hyper)thermophilic Euryarchaeota and Crenarchaeota. Crenarchaeol has been detected in low abundances in samples derived from the chimney exterior indicating the presence of Thaumarchaeota at lower ambient temperatures. Aquificales and members of the Epsilonproteobacteria were the dominant bacterial groups detected. Our observations based on the analysis of 16S rRNA genes and biomarker lipid analysis provide insight into microbial communities thriving within the porous sulfide structures of active and inactive deep-sea hydrothermal vents. Microbial cycling of sulfur, hydrogen, and methane by archaea in the chimney interior and bacteria in the chimney exterior may be the prevailing biogeochemical processes in this system.
Collapse
MESH Headings
- Arctic Regions
- Atlantic Ocean
- Biota
- Cluster Analysis
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Genes, rRNA
- Hot Temperature
- Hydrogen-Ion Concentration
- Hydrothermal Vents/microbiology
- Lipids/analysis
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
Collapse
Affiliation(s)
- A Jaeschke
- Department of Earth Sciences, ETH Zurich, Zurich, Switzerland.
| | | | | | | | | | | |
Collapse
|
23
|
Knappy C, Barillà D, de Blaquiere J, Morgan H, Nunn C, Suleman M, Tan C, Keely B. Structural complexity in isoprenoid glycerol dialkyl glycerol tetraether lipid cores of Sulfolobus and other archaea revealed by liquid chromatography–tandem mass spectrometry. Chem Phys Lipids 2012; 165:648-55. [DOI: 10.1016/j.chemphyslip.2012.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 06/18/2012] [Accepted: 06/28/2012] [Indexed: 11/29/2022]
|
24
|
Jacquemet A, Lemiègre L, Lambert O, Benvegnu T. How the Stereochemistry of a Central Cyclopentyl Ring Influences the Self-Assembling Properties of Archaeal Lipid Analogues: Synthesis and CryoTEM Observations. J Org Chem 2011; 76:9738-47. [DOI: 10.1021/jo201827h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alicia Jacquemet
- Ecole Nationale Supérieure
de Chimie de Rennes, CNRS, UMR 6226, Avenue
du Général Leclerc, CS 50837, 35708 Rennes Cedex 7,
France
- Université Européenne de Bretagne, France
| | - Loı̈c Lemiègre
- Ecole Nationale Supérieure
de Chimie de Rennes, CNRS, UMR 6226, Avenue
du Général Leclerc, CS 50837, 35708 Rennes Cedex 7,
France
- Université Européenne de Bretagne, France
| | - Olivier Lambert
- Chimie et Biologie des Membranes
UMR CNRS 5248 − Université Bordeaux 1-IPB, IECB, Allée Geoffroy Saint-Hilaire, 33600 Pessac,
France
| | - Thierry Benvegnu
- Ecole Nationale Supérieure
de Chimie de Rennes, CNRS, UMR 6226, Avenue
du Général Leclerc, CS 50837, 35708 Rennes Cedex 7,
France
- Université Européenne de Bretagne, France
| |
Collapse
|
25
|
Knappy CS, Nunn CEM, Morgan HW, Keely BJ. The major lipid cores of the archaeon Ignisphaera aggregans: implications for the phylogeny and biosynthesis of glycerol monoalkyl glycerol tetraether isoprenoid lipids. Extremophiles 2011; 15:517-28. [PMID: 21630026 DOI: 10.1007/s00792-011-0382-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 05/20/2011] [Indexed: 10/18/2022]
Abstract
The lipid cores from Ignisphaera aggregans, a hyperthermophilic Crenarchaeon recently isolated from New Zealand hot springs, have been profiled by liquid chromatography-tandem mass spectrometry. The distribution revealed includes relatively high proportions of monoalkyl (also known as H-shaped) tetraether cores which have previously been implicated as kingdom-specific biomarkers for the Euryarchaeota. Such high expression of monoalkyl tetraether lipids is unusual in the archaeal domain and may indicate that formation of these components is an adaptive mechanism that allows I. aggregans to regulate membrane behaviour at high temperatures. The observed dialkyl tetraether and monoalkyl tetraether lipid distributions are similar but not fully concordant, showing differences in the average number of incorporated rings. The similarity supports a biosynthetic route to the ring-containing dialkyl and monoalkyl tetraether lipids via a dialkyl tetraether core containing zero rings, or a closely related structural relative, as an intermediate. Currently, however, the precise nature of the biosynthetic route to these lipids cannot be deduced.
Collapse
|
26
|
Chong PLG. Archaebacterial bipolar tetraether lipids: Physico-chemical and membrane properties. Chem Phys Lipids 2010; 163:253-65. [PMID: 20060818 DOI: 10.1016/j.chemphyslip.2009.12.006] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 12/18/2009] [Accepted: 12/30/2009] [Indexed: 11/18/2022]
Abstract
Bipolar tetraether lipids (BTL) are abundant in archaea and can be chemically synthesized. The structures of BTL are distinctly different from the lipids found in bacteria and eukaryotes. In aqueous solution, BTL can form extraordinarily stable liposomes with different sizes, lamellarities and membrane packing densities. BTL liposomes can serve as membrane models for understanding the structure-function relationship of the plasma membrane in thermoacidophiles and can be used for technological applications. This article reviews the separation, characterization and structures of BTL as well as the physical properties and technological applications of BTL liposomes. One of the structural features of BTL is the presence of cyclopentane rings in the lipid hydrocarbon core. Archaea use the cyclopentane ring as an adaptation strategy to cope with high growth temperature. Special attention of this article is focused on how the number of cyclopentane rings varies with environmental factors and affects membrane properties.
Collapse
Affiliation(s)
- Parkson Lee-Gau Chong
- Department of Biochemistry, Temple University School of Medicine, Philadelphia, PA 19140, United States.
| |
Collapse
|
27
|
Effect of growth temperature and growth phase on the lipid composition of the archaeal membrane from Thermococcus kodakaraensis. Biosci Biotechnol Biochem 2009; 73:104-8. [PMID: 19129645 DOI: 10.1271/bbb.80520] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Archaea have unique membrane lipids typified by ether linkages of the glycerol-to-isoprenoid chains with sn-2,3 stereochemistry that runs against the naturally occurring sn-1,2 stereochemistry of the glycerophospholipids of Bacteria and Eukarya. Membrane lipids were extracted and analyzed from the hyperthermophilic archaeon, Thermococcus kodakaraensis, cultivated at various temperatures. At all growth temperatures examined, both the diphytanylglycerol diether (archaeol, C(20)) and diphytanyldiglycerol tetraether (caldarchaeol, C(40)) were identified as saturated forms, and no other lipids could be identified. The ratio of caldarchaeol to archaeol increased with increasing growth temperature, particularly at 93 degrees C. A larger amount of archaeol was detected from cells in the logarithmic phase than from those in the stationary phase at all temperatures examined. These results indicate that T. kodakaraensis modulated the membrane lipid composition depending on both the growth phase and the growth temperature, and suggest that the membrane fluidity to environmental change was maintained by altering the length of the hydrocarbon chains, and not by side-chain saturation such as double-bond hydrogenation nor by such a modification as cyclopentane ring formation.
Collapse
|
28
|
Factors controlling the distribution of archaeal tetraethers in terrestrial hot springs. Appl Environ Microbiol 2008; 74:3523-32. [PMID: 18390673 DOI: 10.1128/aem.02450-07] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glycerol dialkyl glycerol tetraethers (GDGTs) found in hot springs reflect the abundance and community structure of Archaea in these extreme environments. The relationships between GDGTs, archaeal communities, and physical or geochemical variables are underexamined to date and when reported often result in conflicting interpretations. Here, we examined profiles of GDGTs from pure cultures of Crenarchaeota and from terrestrial geothermal springs representing a wide distribution of locations, including Yellowstone National Park (United States), the Great Basin of Nevada and California (United States), Kamchatka (Russia), Tengchong thermal field (China), and Thailand. These samples had temperatures of 36.5 to 87 degrees C and pH values of 3.0 to 9.2. GDGT abundances also were determined for three soil samples adjacent to some of the hot springs. Principal component analysis identified four factors that accounted for most of the variance among nine individual GDGTs, temperature, and pH. Significant correlations were observed between pH and the GDGTs crenarchaeol and GDGT-4 (four cyclopentane rings, m/z 1,294); pH correlated positively with crenarchaeol and inversely with GDGT-4. Weaker correlations were observed between temperature and the four factors. Three of the four GDGTs used in the marine TEX(86) paleotemperature index (GDGT-1 to -3, but not crenarchaeol isomer) were associated with a single factor. No correlation was observed for GDGT-0 (acyclic caldarchaeol): it is effectively its own variable. The biosynthetic mechanisms and exact archaeal community structures leading to these relationships remain unknown. However, the data in general show promise for the continued development of GDGT lipid-based physiochemical proxies for archaeal evolution and for paleo-ecology or paleoclimate studies.
Collapse
|
29
|
Effect of growth temperature on ether lipid biochemistry in Archaeoglobus fulgidus. Extremophiles 2007; 12:271-8. [DOI: 10.1007/s00792-007-0126-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 11/19/2007] [Indexed: 10/22/2022]
|
30
|
Schouten S, Baas M, Hopmans EC, Reysenbach AL, Damsté JSS. Tetraether membrane lipids of Candidatus "Aciduliprofundum boonei", a cultivated obligate thermoacidophilic euryarchaeote from deep-sea hydrothermal vents. Extremophiles 2007; 12:119-24. [PMID: 17901915 PMCID: PMC2175526 DOI: 10.1007/s00792-007-0111-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Accepted: 08/28/2007] [Indexed: 10/27/2022]
Abstract
The lipid composition of Candidatus "Aciduliprofundum boonei", the only cultivated representative of archaea falling in the DHVE2 phylogenetic cluster, a group of microorganisms ubiquitously occurring at hydrothermal vents, was studied. The predominant core membrane lipids in this thermophilic euryarchaeote were found to be composed of glycerol dibiphytanyl glycerol tetraethers (GDGTs) containing 0-4 cyclopentyl moieties. In addition, GDGTs with an additional covalent bond between the isoprenoid hydrocarbon chains, so-called H-shaped GDGTs, were present. The latter core lipids have been rarely reported previously. Intact polar lipid analysis revealed that they predominantly consist of GDGTs with a phospho-glycerol headgroup.
Collapse
Affiliation(s)
- Stefan Schouten
- Department of Marine Biogeochemistry and Toxicology, Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, Texel, The Netherlands.
| | | | | | | | | |
Collapse
|
31
|
Schouten S, van der Meer MTJ, Hopmans EC, Rijpstra WIC, Reysenbach AL, Ward DM, Sinninghe Damsté JS. Archaeal and bacterial glycerol dialkyl glycerol tetraether lipids in hot springs of yellowstone national park. Appl Environ Microbiol 2007; 73:6181-91. [PMID: 17693566 PMCID: PMC2074994 DOI: 10.1128/aem.00630-07] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glycerol dialkyl glycerol tetraethers (GDGTs) are core membrane lipids originally thought to be produced mainly by (hyper)thermophilic archaea. Environmental screening of low-temperature environments showed, however, the abundant presence of structurally diverse GDGTs from both bacterial and archaeal sources. In this study, we examined the occurrences and distribution of GDGTs in hot spring environments in Yellowstone National Park with high temperatures (47 to 83 degrees C) and mostly neutral to alkaline pHs. GDGTs with 0 to 4 cyclopentane moieties were dominant in all samples and are likely derived from both (hyper)thermophilic Crenarchaeota and Euryarchaeota. GDGTs with 4 to 8 cyclopentane moieties, likely derived from the crenarchaeotal order Sulfolobales and the euryarchaeotal order Thermoplasmatales, are usually present in much lower abundance, consistent with the relatively high pH values of the hot springs. The relative abundances of cyclopentane-containing GDGTs did not correlate with in situ temperature and pH, suggesting that other environmental and possibly genetic factors play a role as well. Crenarchaeol, a biomarker thought to be specific for nonthermophilic group I Crenarchaeota, was also found in most hot springs, though in relatively low concentrations, i.e., <5% of total GDGTs. Its abundance did not correlate with temperature, as has been reported previously. Instead, the cooccurrence of relatively abundant nonisoprenoid GDGTs thought to be derived from soil bacteria suggests a predominantly allochthonous source for crenarchaeol in these hot spring environments. Finally, the distribution of bacterial branched GDGTs suggests that they may be derived from the geothermally heated soils surrounding the hot springs.
Collapse
Affiliation(s)
- Stefan Schouten
- Department of Marine Biogeochemistry & Toxicology, Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|