1
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Ding S, Hamm JN, Bale NJ, Sinninghe Damsté JS, Spang A. Selective lipid recruitment by an archaeal DPANN symbiont from its host. Nat Commun 2024; 15:3405. [PMID: 38649682 PMCID: PMC11035636 DOI: 10.1038/s41467-024-47750-2] [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: 12/06/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
The symbiont Ca. Nanohaloarchaeum antarcticus is obligately dependent on its host Halorubrum lacusprofundi for lipids and other metabolites due to its lack of certain biosynthetic genes. However, it remains unclear which specific lipids or metabolites are acquired from its host, and how the host responds to infection. Here, we explored the lipidome dynamics of the Ca. Nha. antarcticus - Hrr. lacusprofundi symbiotic relationship during co-cultivation. By using a comprehensive untargeted lipidomic methodology, our study reveals that Ca. Nha. antarcticus selectively recruits 110 lipid species from its host, i.e., nearly two-thirds of the total number of host lipids. Lipid profiles of co-cultures displayed shifts in abundances of bacterioruberins and menaquinones and changes in degree of bilayer-forming glycerolipid unsaturation. This likely results in increased membrane fluidity and improved resistance to membrane disruptions, consistent with compensation for higher metabolic load and mechanical stress on host membranes when in contact with Ca. Nha. antarcticus cells. Notably, our findings differ from previous observations of other DPANN symbiont-host systems, where no differences in lipidome composition were reported. Altogether, our work emphasizes the strength of employing untargeted lipidomics approaches to provide details into the dynamics underlying a DPANN symbiont-host system.
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Affiliation(s)
- Su Ding
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands.
| | - Joshua N Hamm
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands.
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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2
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Zhu QZ, Elvert M, Meador TB, Schröder JM, Doeana KD, Becker KW, Elling FJ, Lipp JS, Heuer VB, Zabel M, Hinrichs KU. Comprehensive molecular-isotopic characterization of archaeal lipids in the Black Sea water column and underlying sediments. GEOBIOLOGY 2024; 22:e12589. [PMID: 38465505 DOI: 10.1111/gbi.12589] [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: 05/05/2023] [Revised: 01/30/2024] [Accepted: 02/19/2024] [Indexed: 03/12/2024]
Abstract
The Black Sea is a permanently anoxic, marine basin serving as model system for the deposition of organic-rich sediments in a highly stratified ocean. In such systems, archaeal lipids are widely used as paleoceanographic and biogeochemical proxies; however, the diverse planktonic and benthic sources as well as their potentially distinct diagenetic fate may complicate their application. To track the flux of archaeal lipids and to constrain their sources and turnover, we quantitatively examined the distributions and stable carbon isotopic compositions (δ13 C) of intact polar lipids (IPLs) and core lipids (CLs) from the upper oxic water column into the underlying sediments, reaching deposits from the last glacial. The distribution of IPLs responded more sensitively to the geochemical zonation than the CLs, with the latter being governed by the deposition from the chemocline. The isotopic composition of archaeal lipids indicates CLs and IPLs in the deep anoxic water column have negligible influence on the sedimentary pool. Archaeol substitutes tetraether lipids as the most abundant IPL in the deep anoxic water column and the lacustrine methanic zone. Its elevated IPL/CL ratios and negative δ13 C values indicate active methane metabolism. Sedimentary CL- and IPL-crenarchaeol were exclusively derived from the water column, as indicated by non-variable δ13 C values that are identical to those in the chemocline and by the low BIT (branched isoprenoid tetraether index). By contrast, in situ production accounts on average for 22% of the sedimentary IPL-GDGT-0 (glycerol dibiphytanyl glycerol tetraether) based on isotopic mass balance using the fermentation product lactate as an endmember for the dissolved substrate pool. Despite the structural similarity, glycosidic crenarchaeol appears to be more recalcitrant in comparison to its non-cycloalkylated counterpart GDGT-0, as indicated by its consistently higher IPL/CL ratio in sediments. The higher TEX86 , CCaT, and GDGT-2/-3 values in glacial sediments could plausibly result from selective turnover of archaeal lipids and/or an archaeal ecology shift during the transition from the glacial lacustrine to the Holocene marine setting. Our in-depth molecular-isotopic examination of archaeal core and intact polar lipids provided new constraints on the sources and fate of archaeal lipids and their applicability in paleoceanographic and biogeochemical studies.
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Affiliation(s)
- Qing-Zeng Zhu
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Travis B Meador
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Biology Centre CAS, Soil and Water Research Infrastructure, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Jan M Schröder
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Katiana D Doeana
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kevin W Becker
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Felix J Elling
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Julius S Lipp
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Verena B Heuer
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Matthias Zabel
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
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3
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Johnson MD, Sakai HD, Paul B, Nunoura T, Dalvi S, Mudaliyar M, Shepherd DC, Shimizu M, Udupa S, Ohkuma M, Kurosawa N, Ghosal D. Large attachment organelle mediates interaction between Nanobdellota archaeon YN1 and its host. THE ISME JOURNAL 2024; 18:wrae154. [PMID: 39113594 PMCID: PMC11420986 DOI: 10.1093/ismejo/wrae154] [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: 04/01/2024] [Revised: 06/25/2024] [Accepted: 08/07/2024] [Indexed: 09/25/2024]
Abstract
DPANN archaea are an enigmatic superphylum that are difficult to isolate and culture in the laboratory due to their specific culture conditions and apparent ectosymbiotic lifestyle. Here, we successfully isolated and cultivated a coculture system of a novel Nanobdellota archaeon YN1 and its host Sulfurisphaera ohwakuensis YN1HA. We characterized the coculture system by complementary methods, including metagenomics and metabolic pathway analysis, fluorescence microscopy, and high-resolution electron cryo-tomography (cryoET). We show that YN1 is deficient in essential metabolic processes and requires host resources to proliferate. CryoET imaging revealed an enormous attachment organelle present in the YN1 envelope that forms a direct interaction with the host cytoplasm, bridging the two cells. Together, our results unravel the molecular and structural basis of ectosymbiotic relationship between YN1 and YN1HA. This research broadens our understanding of DPANN biology and the versatile nature of their ectosymbiotic relationships.
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Affiliation(s)
- Matthew D Johnson
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Hiroyuki D Sakai
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Bindusmita Paul
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka 237-0061, Japan
| | - Somavally Dalvi
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Manasi Mudaliyar
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Doulin C Shepherd
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michiru Shimizu
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Shubha Udupa
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Norio Kurosawa
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
| | - Debnath Ghosal
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
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4
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Qu YN, Rao YZ, Qi YL, Li YX, Li A, Palmer M, Hedlund BP, Shu WS, Evans PN, Nie GX, Hua ZS, Li WJ. Panguiarchaeum symbiosum, a potential hyperthermophilic symbiont in the TACK superphylum. Cell Rep 2023; 42:112158. [PMID: 36827180 DOI: 10.1016/j.celrep.2023.112158] [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: 09/08/2022] [Revised: 12/27/2022] [Accepted: 02/09/2023] [Indexed: 02/24/2023] Open
Abstract
The biology of Korarchaeia remains elusive due to the lack of genome representatives. Here, we reconstruct 10 closely related metagenome-assembled genomes from hot spring habitats and place them into a single species, proposed herein as Panguiarchaeum symbiosum. Functional investigation suggests that Panguiarchaeum symbiosum is strictly anaerobic and grows exclusively in thermal habitats by fermenting peptides coupled with sulfide and hydrogen production to dispose of electrons. Due to its inability to biosynthesize archaeal membranes, amino acids, and purines, this species likely exists in a symbiotic lifestyle similar to DPANN archaea. Population metagenomics and metatranscriptomic analyses demonstrated that genes associated with amino acid/peptide uptake and cell attachment exhibited positive selection and were highly expressed, supporting the proposed proteolytic catabolism and symbiotic lifestyle. Our study sheds light on the metabolism, evolution, and potential symbiotic lifestyle of Panguiarchaeum symbiosum, which may be a unique host-dependent archaeon within the TACK superphylum.
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Affiliation(s)
- Yan-Ni Qu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yang-Zhi Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yan-Ling Qi
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Yu-Xian Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Andrew Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Paul N Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Guo-Xing Nie
- College of Fisheries, Henan Normal University, Xinxiang, China
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China.
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5
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Kato S, Ogasawara A, Itoh T, Sakai HD, Shimizu M, Yuki M, Kaneko M, Takashina T, Ohkuma M. Nanobdella aerobiophila gen. nov., sp. nov., a thermoacidophilic, obligate ectosymbiotic archaeon, and proposal of Nanobdellaceae fam. nov., Nanobdellales ord. nov. and Nanobdellia class. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A co-culture of a novel thermoacidophilic, obligate symbiotic archaeon, designated as strain MJ1T, with its specific host archaeon
Metallosphaera sedula
strain MJ1HA was obtained from a terrestrial hot spring in Japan. Strain MJ1T grew in the co-culture under aerobic conditions. Coccoid cells of strain MJ1T were 200–500 nm in diameter, and attached to the MJ1HA cells in the co-culture. The ranges and optima of the growth temperature and pH of strain MJ1T in the co-culture were 60–75 °C (optimum, 65–70 °C) and pH 1.0–4.0 (optimum, pH 2.5), respectively. Core lipids of dialkyl glycerol tetraethers (GDGT)−3 and GDGT-4 were highly abundant in MJ1T cells concentrated from the co-culture. Strain MJ1T has a small genome (0.67 Mbp) lacking genes for biosynthesis of essential biomolecules, such as nucleotides, lipids and ATP. The genomic DNA G+C content was 24.9 mol%. The 16S rRNA gene sequence of strain MJ1T was most closely related to that of the cultivated species, ‘Nanopusillus acidilobi’ strain N7A (85.8 % similarity). Based on phylogenetic and physiological characteristics, we propose the name Nanobdella aerobiophila gen. nov., sp. nov. to accommodate the strain MJ1T (=JCM 33616T=DSM 111728T). In addition, we propose the names Nanobdellaceae fam. nov., Nanobdellales ord. nov., and Nanobdellia class. nov. to accommodate the novel genus.
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Affiliation(s)
- Shingo Kato
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Ayaka Ogasawara
- Graduate School of Life Sciences, Toyo University, Oura, Gunma 374-0193, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Hiroyuki D. Sakai
- Present address: Faculty of Science and Engineering, Soka University, Tokyo 192-8577, Hachioji, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Michiru Shimizu
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masanori Kaneko
- Research Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan
| | - Tomonori Takashina
- Graduate School of Life Sciences, Toyo University, Oura, Gunma 374-0193, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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6
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Zhu QZ, Wegener G, Hinrichs KU, Elvert M. Activity of Ancillary Heterotrophic Community Members in Anaerobic Methane-Oxidizing Cultures. Front Microbiol 2022; 13:912299. [PMID: 35722308 PMCID: PMC9201399 DOI: 10.3389/fmicb.2022.912299] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria mediate the anaerobic oxidation of methane (AOM) in marine sediments. However, even sediment-free cultures contain a substantial number of additional microorganisms not directly related to AOM. To track the heterotrophic activity of these community members and their possible relationship with AOM, we amended meso- (37°C) and thermophilic (50°C) AOM cultures (dominated by ANME-1 archaea and their partner bacteria of the Seep-SRB2 clade or Candidatus Desulfofervidus auxilii) with L-leucine-3-13C (13C-leu). Various microbial lipids incorporated the labeled carbon from this amino acid, independent of the presence of methane as an energy source, specifically bacterial fatty acids, such as iso and anteiso-branched C15:0 and C17:0, as well as unsaturated C18:1ω9 and C18:1ω7. In natural methane-rich environments, these bacterial fatty acids are strongly 13C-depleted. We, therefore, suggest that those fatty acids are produced by ancillary bacteria that grow on 13C-depleted necromass or cell exudates/lysates of the AOM core communities. Candidates that likely benefit from AOM biomass are heterotrophic bacterial members of the Spirochetes and Anaerolineae—known to produce abundant branched fatty acids and present in all the AOM enrichment cultures. For archaeal lipids, we observed minor 13C-incorporation, but still suggesting some 13C-leu anabolism. Based on their relatively high abundance in the culture, the most probable archaeal candidates are Bathyarchaeota, Thermoplasmatales, and Lokiarchaeota. The identified heterotrophic bacterial and archaeal ancillary members are likely key players in organic carbon recycling in anoxic marine sediments.
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Affiliation(s)
- Qing-Zeng Zhu
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Gunter Wegener
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Faculty of Geosciences, University of Bremen, Bremen, Germany
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7
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Krause S, Gfrerer S, von Kügelgen A, Reuse C, Dombrowski N, Villanueva L, Bunk B, Spröer C, Neu TR, Kuhlicke U, Schmidt-Hohagen K, Hiller K, Bharat TAM, Rachel R, Spang A, Gescher J. The importance of biofilm formation for cultivation of a Micrarchaeon and its interactions with its Thermoplasmatales host. Nat Commun 2022; 13:1735. [PMID: 35365607 PMCID: PMC8975820 DOI: 10.1038/s41467-022-29263-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 02/28/2022] [Indexed: 01/05/2023] Open
Abstract
Micrarchaeota is a distinctive lineage assigned to the DPANN archaea, which includes poorly characterised microorganisms with reduced genomes that likely depend on interactions with hosts for growth and survival. Here, we report the enrichment of a stable co-culture of a member of the Micrarchaeota (Ca. Micrarchaeum harzensis) together with its Thermoplasmatales host (Ca. Scheffleriplasma hospitalis), as well as the isolation of the latter. We show that symbiont-host interactions depend on biofilm formation as evidenced by growth experiments, comparative transcriptomic analyses and electron microscopy. In addition, genomic, metabolomic, extracellular polymeric substances and lipid content analyses indicate that the Micrarchaeon symbiont relies on the acquisition of metabolites from its host. Our study of the cell biology and physiology of a Micrarchaeon and its host adds to our limited knowledge of archaeal symbioses. The Micrarchaeota lineage includes poorly characterized archaea with reduced genomes that likely depend on host interactions for survival. Here, the authors report a stable co-culture of a member of the Micrarchaeota and its host, and use multi-omic and physiological analyses to shed light on this symbiosis.
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Affiliation(s)
- Susanne Krause
- Department of Applied Biology, Karlsruhe, Institute of Technology (KIT), Karlsruhe, Germany
| | - Sabrina Gfrerer
- Department of Applied Biology, Karlsruhe, Institute of Technology (KIT), Karlsruhe, Germany.,Institute for Biological Interfaces, Karlsruhe, Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | - Carsten Reuse
- Bioinformatics & Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre for Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Boyke Bunk
- Leibniz Institute DSMZ, Braunschweig, Germany
| | | | - Thomas R Neu
- Helmholtz-Centre for Environmental, Research UFZ, Magdeburg, Germany
| | - Ute Kuhlicke
- Helmholtz-Centre for Environmental, Research UFZ, Magdeburg, Germany
| | - Kerstin Schmidt-Hohagen
- Bioinformatics & Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre for Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Karsten Hiller
- Bioinformatics & Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre for Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom.,Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom
| | - Reinhard Rachel
- Center for Electron Microscopy, University of Regensburg, Regensburg, Germany
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands.,Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johannes Gescher
- Department of Applied Biology, Karlsruhe, Institute of Technology (KIT), Karlsruhe, Germany. .,Institute for Biological Interfaces, Karlsruhe, Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany. .,Institute of Technical Microbiology, Technical University of Hamburg, Hamburg, Germany.
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8
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Identification of a protein responsible for the synthesis of archaeal membrane-spanning GDGT lipids. Nat Commun 2022; 13:1545. [PMID: 35318330 PMCID: PMC8941075 DOI: 10.1038/s41467-022-29264-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/07/2022] [Indexed: 01/08/2023] Open
Abstract
Glycerol dibiphytanyl glycerol tetraethers (GDGTs) are archaeal monolayer membrane lipids that can provide a competitive advantage in extreme environments. Here, we identify a radical SAM protein, tetraether synthase (Tes), that participates in the synthesis of GDGTs. Attempts to generate a tes-deleted mutant in Sulfolobus acidocaldarius were unsuccessful, suggesting that the gene is essential in this organism. Heterologous expression of tes homologues leads to production of GDGT and structurally related lipids in the methanogen Methanococcus maripaludis (which otherwise does not synthesize GDGTs and lacks a tes homolog, but produces a putative GDGT precursor, archaeol). Tes homologues are encoded in the genomes of many archaea, as well as in some bacteria, in which they might be involved in the synthesis of bacterial branched glycerol dialkyl glycerol tetraethers.
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9
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Functional compartmentalization and metabolic separation in a prokaryotic cell. Proc Natl Acad Sci U S A 2021; 118:2022114118. [PMID: 34161262 DOI: 10.1073/pnas.2022114118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The prokaryotic cell is traditionally seen as a "bag of enzymes," yet its organization is much more complex than in this simplified view. By now, various microcompartments encapsulating metabolic enzymes or pathways are known for Bacteria These microcompartments are usually small, encapsulating and concentrating only a few enzymes, thus protecting the cell from toxic intermediates or preventing unwanted side reactions. The hyperthermophilic, strictly anaerobic Crenarchaeon Ignicoccus hospitalis is an extraordinary organism possessing two membranes, an inner and an energized outer membrane. The outer membrane (termed here outer cytoplasmic membrane) harbors enzymes involved in proton gradient generation and ATP synthesis. These two membranes are separated by an intermembrane compartment, whose function is unknown. Major information processes like DNA replication, RNA synthesis, and protein biosynthesis are located inside the "cytoplasm" or central cytoplasmic compartment. Here, we show by immunogold labeling of ultrathin sections that enzymes involved in autotrophic CO2 assimilation are located in the intermembrane compartment that we name (now) a peripheric cytoplasmic compartment. This separation may protect DNA and RNA from reactive aldehydes arising in the I. hospitalis carbon metabolism. This compartmentalization of metabolic pathways and information processes is unprecedented in the prokaryotic world, representing a unique example of spatiofunctional compartmentalization in the second domain of life.
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Bayer K, Busch K, Kenchington E, Beazley L, Franzenburg S, Michels J, Hentschel U, Slaby BM. Microbial Strategies for Survival in the Glass Sponge Vazella pourtalesii. mSystems 2020; 5:e00473-20. [PMID: 32788407 PMCID: PMC7426153 DOI: 10.1128/msystems.00473-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/23/2020] [Indexed: 01/04/2023] Open
Abstract
Few studies have explored the microbiomes of glass sponges (Hexactinellida). The present study seeks to elucidate the composition of the microbiota associated with the glass sponge Vazella pourtalesii and the functional strategies of the main symbionts. We combined microscopic approaches with metagenome-guided microbial genome reconstruction and amplicon community profiling toward this goal. Microscopic imaging revealed that the host and microbial cells appeared within dense biomass patches that are presumably syncytial tissue aggregates. Based on abundances in amplicon libraries and metagenomic data, SAR324 bacteria, Crenarchaeota, Patescibacteria, and Nanoarchaeota were identified as abundant members of the V. pourtalesii microbiome; thus, their genomic potentials were analyzed in detail. A general pattern emerged in that the V. pourtalesii symbionts had very small genome sizes, in the range of 0.5 to 2.2 Mb, and low GC contents, even below those of seawater relatives. Based on functional analyses of metagenome-assembled genomes (MAGs), we propose two major microbial strategies: the "givers," namely, Crenarchaeota and SAR324, heterotrophs and facultative anaerobes, produce and partly secrete all required amino acids and vitamins. The "takers," Nanoarchaeota and Patescibacteria, are anaerobes with reduced genomes that tap into the microbial community for resources, e.g., lipids and DNA, likely using pilus-like structures. We posit that the existence of microbial cells in sponge syncytia together with the low-oxygen conditions in the seawater environment are factors that shape the unique compositional and functional properties of the microbial community associated with V. pourtalesii IMPORTANCE We investigated the microbial community of V. pourtalesii that forms globally unique, monospecific sponge grounds under low-oxygen conditions on the Scotian Shelf, where it plays a key role in its vulnerable ecosystem. The microbial community was found to be concentrated within biomass patches and is dominated by small cells (<1 μm). MAG analyses showed consistently small genome sizes and low GC contents, which is unusual compared to known sponge symbionts. These properties, as well as the (facultatively) anaerobic metabolism and a high degree of interdependence between the dominant symbionts regarding amino acid and vitamin synthesis, are likely adaptations to the unique conditions within the syncytial tissue of their hexactinellid host and the low-oxygen environment.
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Affiliation(s)
- Kristina Bayer
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Kiel, Germany
| | - Kathrin Busch
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Kiel, Germany
| | - Ellen Kenchington
- Department of Fisheries and Oceans, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada
| | - Lindsay Beazley
- Department of Fisheries and Oceans, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada
| | - Sören Franzenburg
- Institute for Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Jan Michels
- Functional Morphology and Biomechanics, Institute of Zoology, Kiel University, Kiel, Germany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Kiel, Germany
- Kiel University, Kiel, Germany
| | - Beate M Slaby
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Symbioses, Kiel, Germany
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11
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Dombrowski N, Williams TA, Sun J, Woodcroft BJ, Lee JH, Minh BQ, Rinke C, Spang A. Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution. Nat Commun 2020; 11:3939. [PMID: 32770105 PMCID: PMC7414124 DOI: 10.1038/s41467-020-17408-w] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/25/2020] [Indexed: 01/08/2023] Open
Abstract
The recently discovered DPANN archaea are a potentially deep-branching, monophyletic radiation of organisms with small cells and genomes. However, the monophyly and early emergence of the various DPANN clades and their role in life's evolution are debated. Here, we reconstructed and analysed genomes of an uncharacterized archaeal phylum (Candidatus Undinarchaeota), revealing that its members have small genomes and, while potentially being able to conserve energy through fermentation, likely depend on partner organisms for the acquisition of certain metabolites. Our phylogenomic analyses robustly place Undinarchaeota as an independent lineage between two highly supported 'DPANN' clans. Further, our analyses suggest that DPANN have exchanged core genes with their hosts, adding to the difficulty of placing DPANN in the tree of life. This pattern can be sufficiently dominant to allow identifying known symbiont-host clades based on routes of gene transfer. Together, our work provides insights into the origins and evolution of DPANN and their hosts.
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Affiliation(s)
- Nina Dombrowski
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB, Den Burg, The Netherlands
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Jiarui Sun
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Benjamin J Woodcroft
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jun-Hoe Lee
- Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden
| | - Bui Quang Minh
- Research School of Computer Science and Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB, Den Burg, The Netherlands.
- Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden.
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12
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Pacheco AR, Segrè D. A multidimensional perspective on microbial interactions. FEMS Microbiol Lett 2020; 366:5513995. [PMID: 31187139 PMCID: PMC6610204 DOI: 10.1093/femsle/fnz125] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/10/2019] [Indexed: 12/16/2022] Open
Abstract
Beyond being simply positive or negative, beneficial or inhibitory, microbial interactions can involve a diverse set of mechanisms, dependencies and dynamical properties. These more nuanced features have been described in great detail for some specific types of interactions, (e.g. pairwise metabolic cross-feeding, quorum sensing or antibiotic killing), often with the use of quantitative measurements and insight derived from modeling. With a growing understanding of the composition and dynamics of complex microbial communities for human health and other applications, we face the challenge of integrating information about these different interactions into comprehensive quantitative frameworks. Here, we review the literature on a wide set of microbial interactions, and explore the potential value of a formal categorization based on multidimensional vectors of attributes. We propose that such an encoding can facilitate systematic, direct comparisons of interaction mechanisms and dependencies, and we discuss the relevance of an atlas of interactions for future modeling and rational design efforts.
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Affiliation(s)
- Alan R Pacheco
- Graduate Program in Bioinformatics and Biological Design Center, Boston University, 24 Cummington Mall, Boston, MA, 02215, USA
| | - Daniel Segrè
- Graduate Program in Bioinformatics and Biological Design Center, Boston University, 24 Cummington Mall, Boston, MA, 02215, USA.,Department of Biomedical Engineering, Department of Biology and Department of Physics, Boston University, 24 Cummington Mall, Boston, MA, 02215, USA
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13
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Tourte M, Kuentz V, Schaeffer P, Grossi V, Cario A, Oger PM. Novel Intact Polar and Core Lipid Compositions in the Pyrococcus Model Species, P. furiosus and P. yayanosii, Reveal the Largest Lipid Diversity Amongst Thermococcales. Biomolecules 2020; 10:biom10060830. [PMID: 32485936 PMCID: PMC7356043 DOI: 10.3390/biom10060830] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/19/2020] [Accepted: 05/25/2020] [Indexed: 01/15/2023] Open
Abstract
Elucidating the lipidome of Archaea is essential to understand their tolerance to extreme environmental conditions. Previous characterizations of the lipid composition of Pyrococcus species, a model genus of hyperthermophilic archaea belonging to the Thermococcales order, led to conflicting results, which hindered the comprehension of their membrane structure and the putative adaptive role of their lipids. In an effort to clarify the lipid composition data of the Pyrococcus genus, we thoroughly investigated the distribution of both the core lipids (CL) and intact polar lipids (IPL) of the model Pyrococcus furiosus and, for the first time, of Pyrococcus yayanosii, the sole obligate piezophilic hyperthermophilic archaeon known to date. We showed a low diversity of IPL in the lipid extract of P. furiosus, which nonetheless allowed the first report of phosphatidyl inositol-based glycerol mono- and trialkyl glycerol tetraethers. With up to 13 different CL structures identified, the acid methanolysis of Pyrococcus furiosus revealed an unprecedented CL diversity and showed strong discrepancies with the IPL compositions reported here and in previous studies. By contrast, P. yayanosii displayed fewer CL structures but a much wider variety of polar heads. Our results showed severe inconsistencies between IPL and CL relative abundances. Such differences highlight the diversity and complexity of the Pyrococcus plasma membrane composition and demonstrate that a large part of its lipids remains uncharacterized. Reassessing the lipid composition of model archaea should lead to a better understanding of the structural diversity of their lipidome and of their physiological and adaptive functions.
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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;
| | - Vanessa Kuentz
- Univ Strasbourg, CNRS, UMR 7177 Strasbourg, France; (V.K.); (P.S.)
| | | | - Vincent Grossi
- Univ Lyon, Univ Lyon 1, ENSL, CNRS, LGL-TPE, F-69622 Villeurbanne, France;
| | - Anais Cario
- Univ Lyon, INSA Lyon, CNRS, UMR 5240, F-69621 Villeurbanne, France;
- Univ Lyon, Univ Lyon 1, ENSL, CNRS, LGL-TPE, F-69622 Villeurbanne, France;
| | - Philippe M. Oger
- Univ Lyon, INSA Lyon, CNRS, UMR 5240, F-69621 Villeurbanne, France;
- Correspondence: ; Tel.: +33-04-72-43-36-01
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14
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020. [PMID: 31900730 DOI: 10.1007/s00709-019-01442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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15
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020; 257:621-753. [PMID: 31900730 PMCID: PMC7203096 DOI: 10.1007/s00709-019-01442-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/19/2019] [Indexed: 05/02/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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16
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Probst AJ, Elling FJ, Castelle CJ, Zhu Q, Elvert M, Birarda G, Holman HYN, Lane KR, Ladd B, Ryan MC, Woyke T, Hinrichs KU, Banfield JF. Lipid analysis of CO 2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria. ISME JOURNAL 2020; 14:1547-1560. [PMID: 32203118 PMCID: PMC7242380 DOI: 10.1038/s41396-020-0624-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/05/2020] [Accepted: 02/25/2020] [Indexed: 11/09/2022]
Abstract
Sediment-hosted CO2-rich aquifers deep below the Colorado Plateau (USA) contain a remarkable diversity of uncultivated microorganisms, including Candidate Phyla Radiation (CPR) bacteria that are putative symbionts unable to synthesize membrane lipids. The origin of organic carbon in these ecosystems is unknown and the source of CPR membrane lipids remains elusive. We collected cells from deep groundwater brought to the surface by eruptions of Crystal Geyser, sequenced the community, and analyzed the whole community lipidome over time. Characteristic stable carbon isotopic compositions of microbial lipids suggest that bacterial and archaeal CO2 fixation ongoing in the deep subsurface provides organic carbon for the complex communities that reside there. Coupled lipidomic-metagenomic analysis indicates that CPR bacteria lack complete lipid biosynthesis pathways but still possess regular lipid membranes. These lipids may therefore originate from other community members, which also adapt to high in situ pressure by increasing fatty acid unsaturation. An unusually high abundance of lysolipids attributed to CPR bacteria may represent an adaptation to membrane curvature stress induced by their small cell sizes. Our findings provide new insights into the carbon cycle in the deep subsurface and suggest the redistribution of lipids into putative symbionts within this community.
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Affiliation(s)
- Alexander J Probst
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA. .,Institute for Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, Essen, Germany.
| | - Felix J Elling
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany. .,Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, 02138, USA.
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Qingzeng Zhu
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Giovanni Birarda
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163,5 Basovizza, 34149, Trieste, Italy.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hoi-Ying N Holman
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katherine R Lane
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA
| | - Bethany Ladd
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada.,Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - M Cathryn Ryan
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, MA, USA
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA.
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17
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Sollai M, Villanueva L, Hopmans EC, Keil RG, Sinninghe Damsté JS. Archaeal Sources of Intact Membrane Lipid Biomarkers in the Oxygen Deficient Zone of the Eastern Tropical South Pacific. Front Microbiol 2019; 10:765. [PMID: 31031734 PMCID: PMC6470261 DOI: 10.3389/fmicb.2019.00765] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 03/26/2019] [Indexed: 11/13/2022] Open
Abstract
Archaea are ubiquitous in the modern ocean where they are involved in the carbon and nitrogen biogeochemical cycles. However, the majority of Archaea remain uncultured. Archaeal specific membrane intact polar lipids (IPLs) are biomarkers of the presence and abundance of living cells. They comprise archaeol and glycerol dibiphytanyl glycerol tetraethers (GDGTs) attached to various polar headgroups. However, little is known of the IPLs of uncultured marine Archaea, complicating their use as biomarkers. Here, we analyzed suspended particulate matter (SPM) obtained in high depth resolution from a coastal and open ocean site in the eastern tropical South Pacific (ETSP) oxygen deficient zone (ODZ) with the aim of determining possible biological sources of archaeal IPL by comparing their composition by Ultra High Pressure Liquid Chromatography coupled to high resolution mass spectrometry with the archaeal diversity by 16S rRNA gene amplicon sequencing and their abundance by quantitative PCR. Thaumarchaeotal Marine Group I (MGI) closely related to Ca. Nitrosopelagicus and Nitrosopumilus dominated the oxic surface and upper ODZ water together with Marine Euryarchaeota Group II (MGII). High relative abundance of hexose phosphohexose- (HPH) crenarchaeol, the specific biomarker for living Thaumarchaeota, and HPH-GDGT-0, dihexose- (DH) GDGT-3 and -4 were detected in these water masses. Within the ODZ, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaea) of the Woesearchaeota DHVE-6 group and Marine Euryarchaeota Group III (MGIII) were present together with a higher proportion of archaeol-based IPLs, which were likely made by MGIII, since DPANN archaea are supposedly unable to synthesize their own IPLs and possibly have a symbiotic or parasitic partnership with MGIII. Finally, in deep suboxic/oxic waters a different MGI population occurred with HPH-GDGT-1, -2 and DH-GDGT-0 and -crenarchaeol, indicating that here MGI synthesize membranes with IPLs in a different relative abundance which could be attributed to the different detected population or to an environmental adaptation. Our study sheds light on the complex archaeal community of one of the most prominent ODZs and on the IPL biomarkers they potentially synthesize.
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Affiliation(s)
- Martina Sollai
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, Netherlands
| | - Laura Villanueva
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, Netherlands
| | - Ellen C Hopmans
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, Netherlands
| | - Richard G Keil
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Jaap S Sinninghe Damsté
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, Netherlands.,Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
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18
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Purification of a Crenarchaeal ATP Synthase in the Light of the Unique Bioenergetics of Ignicoccus Species. J Bacteriol 2019; 201:JB.00510-18. [PMID: 30642991 DOI: 10.1128/jb.00510-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/08/2019] [Indexed: 11/20/2022] Open
Abstract
In this study, the ATP synthase of Ignicoccus hospitalis was purified, characterized, and structurally compared to the respective enzymes of the other Ignicoccus species, to shed light on energy conservation in this unique group of archaea. The crenarchaeal genus Ignicoccus comprises three described species, i.e., I. hospitalis and Ignicoccus islandicus from hot marine sediments near Iceland and Ignicoccus pacificus from a hydrothermal vent system in the Pacific Ocean. This genus is unique among all archaea due to the unusual cell envelope, consisting of two membranes that enclose a large intermembrane compartment (IMC). I. hospitalis is the best studied member of this genus, mainly because it is the only known host for the potentially parasitic archaeon Nanoarchaeum equitans I. hospitalis grows chemolithoautotrophically, and its sole energy-yielding reaction is the reduction of elemental sulfur with molecular hydrogen, forming large amounts of hydrogen sulfide. This reaction generates an electrochemical gradient, which is used by the ATP synthase, located in the outer cellular membrane, to generate ATP inside the IMC. The genome of I. hospitalis encodes nine subunits of an A-type ATP synthase, which we could identify in the purified complex. Although the maximal in vitro activity of the I. hospitalis enzyme was measured around pH 6, the optimal stability of the A1AO complex seemed to be at pH 9. Interestingly, the soluble A1 subcomplexes of the different Ignicoccus species exhibited significant differences in their apparent molecular masses in native electrophoresis, although their behaviors in gel filtration and chromatography-mass spectrometry were very similar.IMPORTANCE The Crenarchaeota represent one of the major phyla within the Archaea domain. This study describes the successful purification of a crenarchaeal ATP synthase. To date, all information about A-type ATP synthases is from euryarchaeal enzymes. The fact that it has not been possible to purify this enzyme complex from a member of the Crenarchaeota until now points to significant differences in stability, possibly caused by structural alterations. Furthermore, the study subject I. hospitalis has a particular importance among crenarchaeotes, since it is the only known host of N. equitans The energy metabolism in this system is still poorly understood, and our results can help elucidate the unique relationship between these two microbes.
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19
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Dombrowski N, Lee JH, Williams TA, Offre P, Spang A. Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. FEMS Microbiol Lett 2019; 366:5281434. [PMID: 30629179 PMCID: PMC6349945 DOI: 10.1093/femsle/fnz008] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/07/2019] [Indexed: 12/16/2022] Open
Abstract
Archaea-a primary domain of life besides Bacteria-have for a long time been regarded as peculiar organisms that play marginal roles in biogeochemical cycles. However, this picture changed with the discovery of a large diversity of archaea in non-extreme environments enabled by the use of cultivation-independent methods. These approaches have allowed the reconstruction of genomes of uncultivated microorganisms and revealed that archaea are diverse and broadly distributed in the biosphere and seemingly include a large diversity of putative symbiotic organisms, most of which belong to the tentative archaeal superphylum referred to as DPANN. This archaeal group encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, many members of DPANN may be obligately dependent on symbiotic interactions with other organisms and may even include novel parasites. In this contribution, we review the current knowledge of the gene repertoires and lifestyles of members of this group and discuss their placement in the tree of life, which is the basis for our understanding of the deep microbial roots and the role of symbiosis in the evolution of life on Earth.
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Affiliation(s)
- Nina Dombrowski
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA
| | - Jun-Hoe Lee
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, P.O. Box 596, Husargatan 3, SE-75123 Uppsala, Sweden
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, Bristol BS8 1TQ, UK
| | - Pierre Offre
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands
| | - Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, P.O. Box 596, Husargatan 3, SE-75123 Uppsala, Sweden
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20
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D'Souza G, Shitut S, Preussger D, Yousif G, Waschina S, Kost C. Ecology and evolution of metabolic cross-feeding interactions in bacteria. Nat Prod Rep 2018; 35:455-488. [PMID: 29799048 DOI: 10.1039/c8np00009c] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Literature covered: early 2000s to late 2017Bacteria frequently exchange metabolites with other micro- and macro-organisms. In these often obligate cross-feeding interactions, primary metabolites such as vitamins, amino acids, nucleotides, or growth factors are exchanged. The widespread distribution of this type of metabolic interactions, however, is at odds with evolutionary theory: why should an organism invest costly resources to benefit other individuals rather than using these metabolites to maximize its own fitness? Recent empirical work has shown that bacterial genotypes can significantly benefit from trading metabolites with other bacteria relative to cells not engaging in such interactions. Here, we will provide a comprehensive overview over the ecological factors and evolutionary mechanisms that have been identified to explain the evolution and maintenance of metabolic mutualisms among microorganisms. Furthermore, we will highlight general principles that underlie the adaptive evolution of interconnected microbial metabolic networks as well as the evolutionary consequences that result for cells living in such communities.
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Affiliation(s)
- Glen D'Souza
- Department of Environmental Systems Sciences, ETH-Zürich, Zürich, Switzerland
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21
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Carr SA, Schubotz F, Dunbar RB, Mills CT, Dias R, Summons RE, Mandernack KW. Acetoclastic Methanosaeta are dominant methanogens in organic-rich Antarctic marine sediments. ISME JOURNAL 2017; 12:330-342. [PMID: 29039843 PMCID: PMC5776447 DOI: 10.1038/ismej.2017.150] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 06/16/2017] [Accepted: 06/24/2017] [Indexed: 01/11/2023]
Abstract
Despite accounting for the majority of sedimentary methane, the physiology and relative abundance of subsurface methanogens remain poorly understood. We combined intact polar lipid and metagenome techniques to better constrain the presence and functions of methanogens within the highly reducing, organic-rich sediments of Antarctica's Adélie Basin. The assembly of metagenomic sequence data identified phylogenic and functional marker genes of methanogens and generated the first Methanosaeta sp. genome from a deep subsurface sedimentary environment. Based on structural and isotopic measurements, glycerol dialkyl glycerol tetraethers with diglycosyl phosphatidylglycerol head groups were classified as biomarkers for active methanogens. The stable carbon isotope (δ13C) values of these biomarkers and the Methanosaeta partial genome suggest that these organisms are acetoclastic methanogens and represent a relatively small (0.2%) but active population. Metagenomic and lipid analyses suggest that Thaumarchaeota and heterotrophic bacteria co-exist with Methanosaeta and together contribute to increasing concentrations and δ13C values of dissolved inorganic carbon with depth. This study presents the first functional insights of deep subsurface Methanosaeta organisms and highlights their role in methane production and overall carbon cycling within sedimentary environments.
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Affiliation(s)
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Robert B Dunbar
- Department of Environmental Earth Systems Science, Stanford University, Stanford, CA, USA
| | | | - Robert Dias
- US Geological Survey, Denver Federal Center, Denver, CO, USA
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kevin W Mandernack
- Department of Earth Sciences, Indiana University - Purdue University Indianapolis, Indianapolis, IN, USA
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22
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Heimerl T, Flechsler J, Pickl C, Heinz V, Salecker B, Zweck J, Wanner G, Geimer S, Samson RY, Bell SD, Huber H, Wirth R, Wurch L, Podar M, Rachel R. A Complex Endomembrane System in the Archaeon Ignicoccus hospitalis Tapped by Nanoarchaeum equitans. Front Microbiol 2017; 8:1072. [PMID: 28659892 PMCID: PMC5468417 DOI: 10.3389/fmicb.2017.01072] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/29/2017] [Indexed: 11/25/2022] Open
Abstract
Based on serial sectioning, focused ion beam scanning electron microscopy (FIB/SEM), and electron tomography, we depict in detail the highly unusual anatomy of the marine hyperthermophilic crenarchaeon, Ignicoccus hospitalis. Our data support a complex and dynamic endomembrane system consisting of cytoplasmic protrusions, and with secretory function. Moreover, we reveal that the cytoplasm of the putative archaeal ectoparasite Nanoarchaeum equitans can get in direct contact with this endomembrane system, complementing and explaining recent proteomic, transcriptomic and metabolomic data on this inter-archaeal relationship. In addition, we identified a matrix of filamentous structures and/or tethers in the voluminous inter-membrane compartment (IMC) of I. hospitalis, which might be responsible for membrane dynamics. Overall, this unusual cellular compartmentalization, ultrastructure and dynamics in an archaeon that belongs to the recently proposed TACK superphylum prompts speculation that the eukaryotic endomembrane system might originate from Archaea.
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Affiliation(s)
- Thomas Heimerl
- LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Philipps University of MarburgMarburg, Germany
| | | | - Carolin Pickl
- Plant Development and Electron Microscopy, Biocenter LMUMunich, Germany
| | - Veronika Heinz
- Center for Electron Microscopy, University of RegensburgRegensburg, Germany
| | - Benjamin Salecker
- Center for Electron Microscopy, University of RegensburgRegensburg, Germany
| | - Josef Zweck
- Institute of Experimental and Applied Physics, University of RegensburgRegensburg, Germany
| | - Gerhard Wanner
- Plant Development and Electron Microscopy, Biocenter LMUMunich, Germany
| | - Stefan Geimer
- Cell Biology and Electron Microscopy, University of BayreuthBayreuth, Germany
| | - Rachel Y. Samson
- Molecular and Cellular Biochemistry Department, Indiana UniversityBloomington, IN, United States
| | - Stephen D. Bell
- Molecular and Cellular Biochemistry Department, Indiana UniversityBloomington, IN, United States
| | - Harald Huber
- Microbiology Department, University of RegensburgRegensburg, Germany
| | - Reinhard Wirth
- Microbiology Department, University of RegensburgRegensburg, Germany
| | - Louie Wurch
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States
- Microbiology Department, University of TennesseeKnoxville, TN, United States
| | - Mircea Podar
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States
- Microbiology Department, University of TennesseeKnoxville, TN, United States
| | - Reinhard Rachel
- Center for Electron Microscopy, University of RegensburgRegensburg, Germany
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23
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Yokobori SI, Nakajima Y, Akanuma S, Yamagishi A. Birth of Archaeal Cells: Molecular Phylogenetic Analyses of G1P Dehydrogenase, G3P Dehydrogenases, and Glycerol Kinase Suggest Derived Features of Archaeal Membranes Having G1P Polar Lipids. ARCHAEA (VANCOUVER, B.C.) 2016; 2016:1802675. [PMID: 27774041 PMCID: PMC5059525 DOI: 10.1155/2016/1802675] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/08/2016] [Indexed: 01/25/2023]
Abstract
Bacteria and Eukarya have cell membranes with sn-glycerol-3-phosphate (G3P), whereas archaeal membranes contain sn-glycerol-1-phosphate (G1P). Determining the time at which cells with either G3P-lipid membranes or G1P-lipid membranes appeared is important for understanding the early evolution of terrestrial life. To clarify this issue, we reconstructed molecular phylogenetic trees of G1PDH (G1P dehydrogenase; EgsA/AraM) which is responsible for G1P synthesis and G3PDHs (G3P dehydrogenase; GpsA and GlpA/GlpD) and glycerol kinase (GlpK) which is responsible for G3P synthesis. Together with the distribution of these protein-encoding genes among archaeal and bacterial groups, our phylogenetic analyses suggested that GlpA/GlpD in the Commonote (the last universal common ancestor of all extant life with a cellular form, Commonote commonote) acquired EgsA (G1PDH) from the archaeal common ancestor (Commonote archaea) and acquired GpsA and GlpK from a bacterial common ancestor (Commonote bacteria). In our scenario based on this study, the Commonote probably possessed a G3P-lipid membrane synthesized enzymatically, after which the archaeal lineage acquired G1PDH followed by the replacement of a G3P-lipid membrane with a G1P-lipid membrane.
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Affiliation(s)
- Shin-ichi Yokobori
- Laboratory of Extremophiles, Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yoshiki Nakajima
- Laboratory of Extremophiles, Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama 359-1192, Japan
| | - Akihiko Yamagishi
- Laboratory of Extremophiles, Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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24
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Parey K, Fielding AJ, Sörgel M, Rachel R, Huber H, Ziegler C, Rajendran C. In meso
crystal structure of a novel membrane-associated octaheme cytochrome c
from the Crenarchaeon Ignicoccus hospitalis. FEBS J 2016; 283:3807-3820. [DOI: 10.1111/febs.13870] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/17/2016] [Accepted: 08/31/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Kristian Parey
- Department of Structural Biology; Max Planck Institute of Biophysics; Frankfurt am Main Germany
| | - Alistair J. Fielding
- School of Chemistry and the Photon Science Institute; University of Manchester; UK
| | - Matthias Sörgel
- Biogeochemistry Department; Max Planck Institute for Chemistry; Mainz Germany
| | - Reinhard Rachel
- Department of Microbiology; University of Regensburg; Germany
| | - Harald Huber
- Department of Microbiology; University of Regensburg; Germany
| | | | - Chitra Rajendran
- Department of Structural Biology; University of Regensburg; Germany
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25
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Villanueva L, Schouten S, Damsté JSS. Phylogenomic analysis of lipid biosynthetic genes of Archaea shed light on the ‘lipid divide’. Environ Microbiol 2016; 19:54-69. [DOI: 10.1111/1462-2920.13361] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/22/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryNIOZ, Royal Netherlands Institute for Sea Research, and Utrecht UniversityP.O. Box 591790AB Den Burg Texel The Netherlands
| | - Stefan Schouten
- Department of Marine Microbiology and BiogeochemistryNIOZ, Royal Netherlands Institute for Sea Research, and Utrecht UniversityP.O. Box 591790AB Den Burg Texel The Netherlands
- Faculty of GeosciencesUtrecht UniversityP.O. Box 80.021Utrecht3508 TA The Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryNIOZ, Royal Netherlands Institute for Sea Research, and Utrecht UniversityP.O. Box 591790AB Den Burg Texel The Netherlands
- Faculty of GeosciencesUtrecht UniversityP.O. Box 80.021Utrecht3508 TA The Netherlands
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26
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The Proteome and Lipidome of Thermococcus kodakarensis across the Stationary Phase. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:5938289. [PMID: 27274708 PMCID: PMC4870337 DOI: 10.1155/2016/5938289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/07/2016] [Indexed: 12/25/2022]
Abstract
The majority of cells in nature probably exist in a stationary-phase-like state, due to nutrient limitation in most environments. Studies on bacteria and yeast reveal morphological and physiological changes throughout the stationary phase, which lead to an increased ability to survive prolonged nutrient limitation. However, there is little information on archaeal stationary phase responses. We investigated protein- and lipid-level changes in Thermococcus kodakarensis with extended time in the stationary phase. Adaptations to time in stationary phase included increased proportion of membrane lipids with a tetraether backbone, synthesis of proteins that ensure translational fidelity, specific regulation of ABC transporters (upregulation of some, downregulation of others), and upregulation of proteins involved in coenzyme production. Given that the biological mechanism of tetraether synthesis is unknown, we also considered whether any of the protein-level changes in T. kodakarensis might shed light on the production of tetraether lipids across the same period. A putative carbon-nitrogen hydrolase, a TldE (a protease in Escherichia coli) homologue, and a membrane bound hydrogenase complex subunit were candidates for possible involvement in tetraether-related reactions, while upregulation of adenosylcobalamin synthesis proteins might lend support to a possible radical mechanism as a trigger for tetraether synthesis.
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27
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Elling FJ, Becker KW, Könneke M, Schröder JM, Kellermann MY, Thomm M, Hinrichs KU. Respiratory quinones in Archaea: phylogenetic distribution and application as biomarkers in the marine environment. Environ Microbiol 2015; 18:692-707. [PMID: 26472620 DOI: 10.1111/1462-2920.13086] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 07/28/2015] [Accepted: 10/10/2015] [Indexed: 11/30/2022]
Abstract
The distribution of respiratory quinone electron carriers among cultivated organisms provides clues on both the taxonomy of their producers and the redox processes these are mediating. Our study of the quinone inventories of 25 archaeal species belonging to the phyla Eury-, Cren- and Thaumarchaeota facilitates their use as chemotaxonomic markers for ecologically important archaeal clades. Saturated and monounsaturated menaquinones with six isoprenoid units forming the alkyl chain may serve as chemotaxonomic markers for Thaumarchaeota. Other diagnostic biomarkers are thiophene-bearing quinones for Sulfolobales and methanophenazines as functional quinone analogues of the Methanosarcinales. The ubiquity of saturated menaquinones in the Archaea in comparison to Bacteria suggests that these compounds may represent an ancestral and diagnostic feature of the Archaea. Overlap between quinone compositions of distinct thermophilic and halophilic archaea and bacteria may indicate lateral gene transfer. The biomarker potential of thaumarchaeal quinones was exemplarily demonstrated on a water column profile of the Black Sea. Both, thaumarchaeal quinones and membrane lipids showed similar distributions with maxima at the chemocline. Quinone distributions indicate that Thaumarchaeota dominate respiratory activity at a narrow interval in the chemocline, while they contribute only 9% to the microbial biomass at this depth, as determined by membrane lipid analysis.
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Affiliation(s)
- Felix J Elling
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Kevin W Becker
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Martin Könneke
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Jan M Schröder
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Matthias Y Kellermann
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Michael Thomm
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, 93053, Regensburg, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, 28359, Bremen, Germany
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28
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Mohanty S, Jobichen C, Chichili VPR, Velázquez-Campoy A, Low BC, Hogue CWV, Sivaraman J. Structural Basis for a Unique ATP Synthase Core Complex from Nanoarcheaum equitans. J Biol Chem 2015; 290:27280-27296. [PMID: 26370083 DOI: 10.1074/jbc.m115.677492] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Indexed: 11/06/2022] Open
Abstract
ATP synthesis is a critical and universal life process carried out by ATP synthases. Whereas eukaryotic and prokaryotic ATP synthases are well characterized, archaeal ATP synthases are relatively poorly understood. The hyperthermophilic archaeal parasite, Nanoarcheaum equitans, lacks several subunits of the ATP synthase and is suspected to be energetically dependent on its host, Ignicoccus hospitalis. This suggests that this ATP synthase might be a rudimentary machine. Here, we report the crystal structures and biophysical studies of the regulatory subunit, NeqB, the apo-NeqAB, and NeqAB in complex with nucleotides, ADP, and adenylyl-imidodiphosphate (non-hydrolysable analog of ATP). NeqB is ∼20 amino acids shorter at its C terminus than its homologs, but this does not impede its binding with NeqA to form the complex. The heterodimeric NeqAB complex assumes a closed, rigid conformation irrespective of nucleotide binding; this differs from its homologs, which require conformational changes for catalytic activity. Thus, although N. equitans possesses an ATP synthase core A3B3 hexameric complex, it might not function as a bona fide ATP synthase.
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Affiliation(s)
- Soumya Mohanty
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Chacko Jobichen
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | | | - Adrián Velázquez-Campoy
- the Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint-Unit Institute of Physical Chemistry "Rocasolano (IQFR)-Spanish National Research Council (CSIC)-BIFI, and Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza and Fundacion ARAID, Government of Aragon, 50018 Zaragoza, Spain
| | - Boon Chuan Low
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore,; Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore.
| | - Christopher W V Hogue
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore,; Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - J Sivaraman
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore,.
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29
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Hamerly T, Tripet BP, Tigges M, Giannone RJ, Wurch L, Hettich RL, Podar M, Copié V, Bothner B. Untargeted metabolomics studies employing NMR and LC-MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis. Metabolomics 2015; 11:895-907. [PMID: 26273237 PMCID: PMC4529127 DOI: 10.1007/s11306-014-0747-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Interspecies interactions are the basis of microbial community formation and infectious diseases. Systems biology enables the construction of complex models describing such interactions, leading to a better understanding of disease states and communities. However, before interactions between complex organisms can be understood, metabolic and energetic implications of simpler real-world host-microbe systems must be worked out. To this effect, untargeted metabolomics experiments were conducted and integrated with proteomics data to characterize key molecular-level interactions between two hyperthermophilic microbial species, both of which have reduced genomes. Metabolic changes and transfer of metabolites between the archaea Ignicoccus hospitalis and Nanoarcheum equitans were investigated using integrated LC-MS and NMR metabolomics. The study of such a system is challenging, as no genetic tools are available, growth in the laboratory is challenging, and mechanisms by which they interact are unknown. Together with information about relative enzyme levels obtained from shotgun proteomics, the metabolomics data provided useful insights into metabolic pathways and cellular networks of I. hospitalis that are impacted by the presence of N. equitans, including arginine, isoleucine, and CTP biosynthesis. On the organismal level, the data indicate that N. equitans exploits metabolites generated by I. hospitalis to satisfy its own metabolic needs. This finding is based on N. equitans's consumption of a significant fraction of the metabolite pool in I. hospitalis that cannot solely be attributed to increased biomass production for N. equitans. Combining LC-MS and NMR metabolomics datasets improved coverage of the metabolome and enhanced the identification and quantitation of cellular metabolites.
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Affiliation(s)
- Timothy Hamerly
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - Brian P. Tripet
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - Michelle Tigges
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | | | - Louie Wurch
- Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996
| | | | - Mircea Podar
- Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996
| | - Valerie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717
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30
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Meador TB, Bowles M, Lazar CS, Zhu C, Teske A, Hinrichs KU. The archaeal lipidome in estuarine sediment dominated by members of the Miscellaneous Crenarchaeotal Group. Environ Microbiol 2015; 17:2441-58. [PMID: 25403417 DOI: 10.1111/1462-2920.12716] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 11/08/2014] [Indexed: 11/27/2022]
Abstract
The anoxic sediments of the White Oak River estuary comprise a distinctive sulfate-methane transition zone (SMTZ) and natural enrichment of the archaea affiliated with the Miscellaneous Crenarchaeotal Group (MCG). Archaeal biphytanes were generally depleted in (13) C, with δ(13) C values being less than -35‰, indicative of production by active sedimentary archaeal populations. Multivariate analysis of the downcore distributions of 63 lipid biomarkers identified three major groups of lipids that were enriched in the surface, SMTZ or subsurface depths. Intact polar lipids with phosphatidylglycerol headgroups and glycerol dibiphytanyl glycerol tetraethers containing one, two or three cyclopentane rings were enriched at the base of the SMTZ and likely represent the accumulated product of a small but active ANME-1 community. The recently identified butanetriol dibiphytanyl glycerol tetraethers (BDGT), which increased relatively to other lipids with depth, were correlated with the relative abundance of MCG in archaeal 16S rRNA clone libraries, and were (13) C depleted throughout the depth profile, suggesting BDGT lipids as putative biomarkers of an MCG community that may either be autotrophic or feeding on (13) C-depleted organic substrates transported by porewater.
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Affiliation(s)
- Travis B Meador
- MARUM Center for Marine Environmental Sciences, Department of Geosciences, University of Bremen, Bremen, Germany
| | - Marshall Bowles
- MARUM Center for Marine Environmental Sciences, Department of Geosciences, University of Bremen, Bremen, Germany
| | - Cassandre S Lazar
- MARUM Center for Marine Environmental Sciences, Department of Geosciences, University of Bremen, Bremen, Germany.,Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chun Zhu
- MARUM Center for Marine Environmental Sciences, Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, Department of Geosciences, University of Bremen, Bremen, Germany
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31
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Schubotz F, Hays LE, Meyer-Dombard DR, Gillespie A, Shock EL, Summons RE. Stable isotope labeling confirms mixotrophic nature of streamer biofilm communities at alkaline hot springs. Front Microbiol 2015; 6:42. [PMID: 25699032 PMCID: PMC4318418 DOI: 10.3389/fmicb.2015.00042] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 01/12/2015] [Indexed: 11/29/2022] Open
Abstract
Streamer biofilm communities (SBC) are often observed within chemosynthetic zones of Yellowstone hot spring outflow channels, where temperatures exceed those conducive to photosynthesis. Nearest the hydrothermal source (75-88°C) SBC comprise thermophilic Archaea and Bacteria, often mixed communities including Desulfurococcales and uncultured Crenarchaeota, as well as Aquificae and Thermus, each carrying diagnostic membrane lipid biomarkers. We tested the hypothesis that SBC can alternate their metabolism between autotrophy and heterotrophy depending on substrate availability. Feeding experiments were performed at two alkaline hot springs in Yellowstone National Park: Octopus Spring and "Bison Pool," using various (13)C-labeled substrates (bicarbonate, formate, acetate, and glucose) to determine the relative uptake of these different carbon sources. Highest (13)C uptake, at both sites, was from acetate into almost all bacterial fatty acids, particularly into methyl-branched C15, C17 and C19 fatty acids that are diagnostic for Thermus/Meiothermus, and some Firmicutes as well as into universally common C16:0 and C18:0 fatty acids. (13)C-glucose showed a similar, but a 10-30 times lower uptake across most fatty acids. (13)C-bicarbonate uptake, signifying the presence of autotrophic communities was only significant at "Bison Pool" and was observed predominantly in non-specific saturated C16, C18, C20, and C22 fatty acids. Incorporation of (13)C-formate occurred only at very low rates at "Bison Pool" and was almost undetectable at Octopus Spring, suggesting that formate is not an important carbon source for SBC. (13)C-uptake into archaeal lipids occurred predominantly with (13)C-acetate, suggesting also that archaeal communities at both springs have primarily heterotrophic carbon assimilation pathways. We hypothesize that these communities are energy-limited and predominantly nurtured by input of exogenous organic material, with only a small fraction being sustained by autotrophic growth.
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Affiliation(s)
- Florence Schubotz
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of TechnologyCambridge, MA, USA
| | - Lindsay E. Hays
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of TechnologyCambridge, MA, USA
| | - D'Arcy R. Meyer-Dombard
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of TechnologyCambridge, MA, USA
- Department of Earth and Environmental Sciences, University of Illinois at ChicagoChicago, IL, USA
| | - Aimee Gillespie
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of TechnologyCambridge, MA, USA
| | - Everett L. Shock
- School of Earth and Planetary Sciences, Arizona State UniversityTempe, AZ, USA
- Department of Chemistry and Biochemistry, Arizona State UniversityTempe, AZ, USA
| | - Roger E. Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of TechnologyCambridge, MA, USA
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Klingl A. S-layer and cytoplasmic membrane - exceptions from the typical archaeal cell wall with a focus on double membranes. Front Microbiol 2014; 5:624. [PMID: 25505452 PMCID: PMC4243693 DOI: 10.3389/fmicb.2014.00624] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 10/31/2014] [Indexed: 11/13/2022] Open
Abstract
The common idea of typical cell wall architecture in archaea consists of a pseudo-crystalline proteinaceous surface layer (S-layer), situated upon the cytoplasmic membrane. This is true for the majority of described archaea, hitherto. Within the crenarchaea, the S-layer often represents the only cell wall component, but there are various exceptions from this wall architecture. Beside (glycosylated) S-layers in (hyper)thermophilic cren- and euryarchaea as well as halophilic archaea, one can find a great variety of other cell wall structures like proteoglycan-like S-layers (Halobacteria), glutaminylglycan (Natronococci), methanochondroitin (Methanosarcina) or double layered cell walls with pseudomurein (Methanothermus and Methanopyrus). The presence of an outermost cellular membrane in the crenarchaeal species Ignicoccus hospitalis already gave indications for an outer membrane similar to Gram-negative bacteria. Although there is just limited data concerning their biochemistry and ultrastructure, recent studies on the euryarchaeal methanogen Methanomassiliicoccus luminyensis, cells of the ARMAN group, and the SM1 euryarchaeon delivered further examples for this exceptional cell envelope type consisting of two membranes.
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Affiliation(s)
- Andreas Klingl
- Plant Development, Department of Biology, Biocenter LMU Munich - Botany, Ludwig Maximilian University Munich Munich, Germany
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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.
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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
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Perras AK, Wanner G, Klingl A, Mora M, Auerbach AK, Heinz V, Probst AJ, Huber H, Rachel R, Meck S, Moissl-Eichinger C. Grappling archaea: ultrastructural analyses of an uncultivated, cold-loving archaeon, and its biofilm. Front Microbiol 2014; 5:397. [PMID: 25140167 PMCID: PMC4122167 DOI: 10.3389/fmicb.2014.00397] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 07/14/2014] [Indexed: 11/13/2022] Open
Abstract
Similarly to Bacteria, Archaea are microorganisms that interact with their surrounding environment in a versatile manner. To date, interactions based on cellular structure and surface appendages have mainly been documented using model systems of cultivable archaea under laboratory conditions. Here, we report on the microbial interactions and ultrastructural features of the uncultivated SM1 Euryarchaeon, which is highly dominant in its biotope. Therefore, biofilm samples taken from the Sippenauer Moor, Germany, were investigated via transmission electron microscopy (TEM; negative staining, thin-sectioning) and scanning electron microscopy (SEM) in order to elucidate the fine structures of the microbial cells and the biofilm itself. The biofilm consisted of small archaeal cocci (0.6 μm diameter), arranged in a regular pattern (1.0-2.0 μm distance from cell to cell), whereas each archaeon was connected to 6 other archaea on average. Extracellular polymeric substances (EPS) were limited to the close vicinity of the archaeal cells, and specific cell surface appendages (hami, Moissl et al., 2005) protruded beyond the EPS matrix enabling microbial interaction by cell-cell contacts among the archaea and between archaea and bacteria. All analyzed hami revealed their previously described architecture of nano-grappling hooks and barb-wire basal structures. Considering the archaeal cell walls, the SM1 Euryarchaea exhibited a double-membrane, which has rarely been reported for members of this phylogenetic domain. Based on these findings, the current generalized picture on archaeal cell walls needs to be revisited, as archaeal cell structures are more complex and sophisticated than previously assumed, particularly when looking into the uncultivated majority.
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Affiliation(s)
- Alexandra K Perras
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Gerhard Wanner
- Department of Biology I, Biozentrum Ludwig Maximilian University of Munich Planegg-Martinsried, Germany
| | - Andreas Klingl
- Department of Biology I, Biozentrum Ludwig Maximilian University of Munich Planegg-Martinsried, Germany ; Zellbiologie, Philipps-Universität Marburg Marburg, Germany ; LOEWE Research Centre for Synthetic Microbiology (Synmikro) Marbug, Germany
| | - Maximilian Mora
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Anna K Auerbach
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Veronika Heinz
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Alexander J Probst
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Harald Huber
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Reinhard Rachel
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Sandra Meck
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
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Giannone RJ, Wurch LL, Heimerl T, Martin S, Yang Z, Huber H, Rachel R, Hettich RL, Podar M. Life on the edge: functional genomic response of Ignicoccus hospitalis to the presence of Nanoarchaeum equitans. ISME JOURNAL 2014; 9:101-14. [PMID: 25012904 DOI: 10.1038/ismej.2014.112] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 05/30/2014] [Accepted: 06/05/2014] [Indexed: 12/22/2022]
Abstract
The marine hyperthermophilic crenarchaeon Ignicoccus hospitalis supports the propagation on its surface of Nanoarchaeum equitans, an evolutionarily enigmatic archaeon that resembles highly derived parasitic and symbiotic bacteria. The cellular and molecular mechanisms that enable this interarchaea relationship and the intimate physiologic consequences to I. hospitalis are unknown. Here, we used concerted proteomic and transcriptomic analyses to probe into the functional genomic response of I. hospitalis as N. equitans multiplies on its surface. The expression of over 97% of the genes was detected at mRNA level and over 80% of the predicted proteins were identified and their relative abundance measured by proteomics. These indicate that little, if any, of the host genomic information is silenced during growth in the laboratory. The primary response to N. equitans was at the membrane level, with increases in relative abundance of most protein complexes involved in energy generation as well as that of several transporters and proteins involved in cellular membrane stabilization. Similar upregulation was observed for genes and proteins involved in key metabolic steps controlling nitrogen and carbon metabolism, although the overall biosynthetic pathways were marginally impacted. Proliferation of N. equitans resulted, however, in selective downregulation of genes coding for transcription factors and replication and cell cycle control proteins as I. hospitalis shifted its physiology from its own cellular growth to that of its ectosymbiont/parasite. The combination of these multiomic approaches provided an unprecedented level of detail regarding the dynamics of this interspecies interaction, which is especially pertinent as these organisms are not genetically tractable.
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Affiliation(s)
| | - Louie L Wurch
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Thomas Heimerl
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Regensburg, Germany
| | - Stanton Martin
- 1] Oak Ridge National Laboratory, Oak Ridge, TN, USA [2] SAS Institute Inc., Cary, NC, USA
| | - Zamin Yang
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Harald Huber
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Regensburg, Germany
| | - Reinhard Rachel
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Regensburg, Germany
| | | | - Mircea Podar
- 1] Oak Ridge National Laboratory, Oak Ridge, TN, USA [2] Department of Microbiology, University of Tennessee, Knoxville, TN, USA
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General Characteristics and Important Model Organisms. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014. [DOI: 10.1128/9781555815516.ch2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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38
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39
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Peterhoff D, Beer B, Rajendran C, Kumpula EP, Kapetaniou E, Guldan H, Wierenga RK, Sterner R, Babinger P. A comprehensive analysis of the geranylgeranylglyceryl phosphate synthase enzyme family identifies novel members and reveals mechanisms of substrate specificity and quaternary structure organization. Mol Microbiol 2014; 92:885-99. [PMID: 24684232 DOI: 10.1111/mmi.12596] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2014] [Indexed: 12/13/2022]
Abstract
Geranylgeranylglyceryl phosphate synthase (GGGPS) family enzymes catalyse the formation of an ether bond between glycerol-1-phosphate and polyprenyl diphosphates. They are essential for the biosynthesis of archaeal membrane lipids, but also occur in bacterial species, albeit with unknown physiological function. It has been known that there exist two phylogenetic groups (I and II) of GGGPS family enzymes, but a comprehensive study has been missing. We therefore visualized the variability within the family by applying a sequence similarity network, and biochemically characterized 17 representative GGGPS family enzymes regarding their catalytic activities and substrate specificities. Moreover, we present the first crystal structures of group II archaeal and bacterial enzymes. Our analysis revealed that the previously uncharacterized bacterial enzymes from group II have GGGPS activity like the archaeal enzymes and differ from the bacterial group I enzymes that are heptaprenylglyceryl phosphate synthases. The length of the isoprenoid substrate is determined in group II GGGPS enzymes by 'limiter residues' that are different from those in group I enzymes, as shown by site-directed mutagenesis. Most of the group II enzymes form hexamers. We could disrupt these hexamers to stable and catalytically active dimers by mutating a single amino acid that acts as an 'aromatic anchor'.
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Affiliation(s)
- David Peterhoff
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, 93040, Germany
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40
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Meador TB, Gagen EJ, Loscar ME, Goldhammer T, Yoshinaga MY, Wendt J, Thomm M, Hinrichs KU. Thermococcus kodakarensis modulates its polar membrane lipids and elemental composition according to growth stage and phosphate availability. Front Microbiol 2014; 5:10. [PMID: 24523718 PMCID: PMC3906577 DOI: 10.3389/fmicb.2014.00010] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 01/08/2014] [Indexed: 11/24/2022] Open
Abstract
We observed significant changes in the elemental and intact polar lipid (IPL) composition of the archaeon Thermococcus kodakarensis (KOD1) in response to growth stage and phosphorus supply. Reducing the amount of organic supplements and phosphate in growth media resulted in significant decreases in cell size and cellular quotas of carbon (C), nitrogen (N), and phosphorus (P), which coincided with significant increases in cellular IPL quota and IPLs comprising multiple P atoms and hexose moieties. Relatively more cellular P was stored as IPLs in P-limited cells (2–8%) compared to control cells (<0.8%). We also identified a specific IPL biomarker containing a phosphatidyl-N-acetylhexoseamine headgroup that was relatively enriched during rapid cell division. These observations serve as empirical evidence of IPL adaptations in Archaea that will help to interpret the distribution of these biomarkers in natural systems. The reported cell quotas of C, N, and P represent the first such data for a specific archaeon and suggest that thermophiles are C-rich compared to the cell carbon-to-volume relationship reported for planktonic bacteria.
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Affiliation(s)
- Travis B Meador
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen Bremen, Germany
| | - Emma J Gagen
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Michael E Loscar
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Tobias Goldhammer
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen Bremen, Germany
| | - Marcos Y Yoshinaga
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen Bremen, Germany
| | - Jenny Wendt
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen Bremen, Germany
| | - Michael Thomm
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen Bremen, Germany
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Forterre P. The common ancestor of archaea and eukarya was not an archaeon. ARCHAEA (VANCOUVER, B.C.) 2013; 2013:372396. [PMID: 24348094 PMCID: PMC3855935 DOI: 10.1155/2013/372396] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 09/24/2013] [Indexed: 02/06/2023]
Abstract
It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the "prokaryotic" phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other.
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Affiliation(s)
- Patrick Forterre
- Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
- Université Paris-Sud, Institut de Génétique et Microbiologie, CNRS UMR 8621, 91405 Orsay Cedex, France
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Morris BEL, Henneberger R, Huber H, Moissl-Eichinger C. Microbial syntrophy: interaction for the common good. FEMS Microbiol Rev 2013; 37:384-406. [PMID: 23480449 DOI: 10.1111/1574-6976.12019] [Citation(s) in RCA: 457] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 02/25/2013] [Accepted: 02/27/2013] [Indexed: 11/30/2022] Open
Abstract
Classical definitions of syntrophy focus on a process, performed through metabolic interaction between dependent microbial partners, such as the degradation of complex organic compounds under anoxic conditions. However, examples from past and current scientific discoveries suggest that a new, simple but wider definition is necessary to cover all aspects of microbial syntrophy. We suggest the term 'obligately mutualistic metabolism', which still focuses on microbial metabolic cooperation but also includes an ecological aspect: the benefit for both partners. By the combined metabolic activity of microorganisms, endergonic reactions can become exergonic through the efficient removal of products and therefore enable a microbial community to survive with minimal energy resources. Here, we explain the principles of classical and non-classical syntrophy and illustrate the concepts with various examples. We present biochemical fundamentals that allow microorganism to survive under a range of environmental conditions and to drive important biogeochemical processes. Novel technologies have contributed to the understanding of syntrophic relationships in cultured and uncultured systems. Recent research highlights that obligately mutualistic metabolism is not limited to certain metabolic pathways nor to certain environments or microorganisms. This beneficial microbial interaction is not restricted to the transfer of reducing agents such as hydrogen or formate, but can also involve the exchange of organic, sulfurous- and nitrogenous compounds or the removal of toxic compounds.
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Affiliation(s)
- Brandon E L Morris
- Microbiology, Institute for Biology II, University of Freiburg, Freiburg, Germany
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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.
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Affiliation(s)
- Philippe M Oger
- CNRS UMR 5276, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon cedex 07, France.
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Podar M, Makarova KS, Graham DE, Wolf YI, Koonin EV, Reysenbach AL. Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park. Biol Direct 2013; 8:9. [PMID: 23607440 PMCID: PMC3655853 DOI: 10.1186/1745-6150-8-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 04/17/2013] [Indexed: 02/02/2023] Open
Abstract
Background A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. Results The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a thermal feature in Yellowstone National Park, separated by single cell isolation, and sequenced together with its putative host, a Sulfolobales archaeon. Both the new Nanoarchaeota (Nst1) and N. equitans lack most biosynthetic capabilities, and phylogenetic analysis of ribosomal RNA and protein sequences indicates that the two form a deep-branching archaeal lineage. However, the Nst1 genome is more than 20% larger, and encodes a complete gluconeogenesis pathway as well as the full complement of archaeal flagellum proteins. With a larger genome, a smaller repertoire of split protein encoding genes and no split non-contiguous tRNAs, Nst1 appears to have experienced less severe genome reduction than N. equitans. These findings imply that, rather than representing ancestral characters, the extremely compact genomes and multiple split genes of Nanoarchaeota are derived characters associated with their symbiotic or parasitic lifestyle. The inferred host of Nst1 is potentially autotrophic, with a streamlined genome and simplified central and energetic metabolism as compared to other Sulfolobales. Conclusions Comparison of the N. equitans and Nst1 genomes suggests that the marine and terrestrial lineages of Nanoarchaeota share a common ancestor that was already a symbiont of another archaeon. The two distinct Nanoarchaeota-host genomic data sets offer novel insights into the evolution of archaeal symbiosis and parasitism, enabling further studies of the cellular and molecular mechanisms of these relationships. Reviewers This article was reviewed by Patrick Forterre, Bettina Siebers (nominated by Michael Galperin) and Purification Lopez-Garcia
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Affiliation(s)
- Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
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45
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Gibson RA, van der Meer MTJ, Hopmans EC, Reysenbach AL, Schouten S, Sinninghe Damsté JS. Comparison of intact polar lipid with microbial community composition of vent deposits of the Rainbow and Lucky Strike hydrothermal fields. GEOBIOLOGY 2013; 11:72-85. [PMID: 23231657 DOI: 10.1111/gbi.12017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 10/08/2012] [Indexed: 06/01/2023]
Abstract
The intact polar lipid (IPL) composition of twelve hydrothermal vent deposits from the Rainbow (RHF) and Lucky Strike hydrothermal fields (LSHF) has been investigated in order to assess its utility as a proxy for microbial community composition associated with deep-sea hydrothermal locations. Gene-based culture-independent surveys of the microbial populations of the same vent deposits have shown that microbial populations are different in the two locations and appear to be controlled by the geochemical and geological processes that drive hydrothermal circulation. Large differences in the IPL composition between these two sites are evident. In the ultramafic-hosted RHF, mainly archaeal-IPLs were identified, including those known to be produced by hyperthermophilic Euryarchaeota. More specifically, polyglycosyl derivatives of archaeol and macrocyclic archaeol indicate the presence of hyperthermophilic methanogenic archaea in the vent deposits, which are related to members of the Methanocaldococcaceae or Methanococcaceae. In contrast, bacterial IPLs dominate IPL distributions from LSHF, suggesting that bacteria are more predominant at LSHF than at RHF. Bacterial Diacyl glycerol (DAG) IPLs containing phosphocholine, phosphoethanolamine or phosphoglycerol head groups were identified at both vent fields. In some vent deposits from LSHF ornithine lipids and IPLs containing phosphoaminopentanetetrol head groups were also observed. By comparison with previously characterized bacterial communities at the sites, it is likely the DAG-IPLs observed derive from Epsilon- and Gammaproteobacteria. Variation in the relative amounts of archaeal versus bacterial IPLs appears to indicate differences in the microbial community between vent sites. Overall, IPL distributions appear to be consistent with gene-based surveys.
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Affiliation(s)
- R A Gibson
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands.
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Phylogenomic investigation of phospholipid synthesis in archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2012; 2012:630910. [PMID: 23304072 PMCID: PMC3533463 DOI: 10.1155/2012/630910] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 09/03/2012] [Indexed: 12/22/2022]
Abstract
Archaea have idiosyncratic cell membranes usually based on phospholipids containing glycerol-1-phosphate linked by ether bonds to isoprenoid lateral chains. Since these phospholipids strongly differ from those of bacteria and eukaryotes, the origin of the archaeal membranes (and by extension, of all cellular membranes) was enigmatic and called for accurate evolutionary studies. In this paper we review some recent phylogenomic studies that have revealed a modified mevalonate pathway for the synthesis of isoprenoid precursors in archaea and suggested that this domain uses an atypical pathway of synthesis of fatty acids devoid of any acyl carrier protein, which is essential for this activity in bacteria and eukaryotes. In addition, we show new or updated phylogenetic analyses of enzymes likely responsible for the isoprenoid chain synthesis from their precursors and the phospholipid synthesis from glycerol phosphate, isoprenoids, and polar head groups. These results support that most of these enzymes can be traced back to the last archaeal common ancestor and, in many cases, even to the last common ancestor of all living organisms.
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Lin YS, Lipp JS, Elvert M, Holler T, Hinrichs KU. Assessing production of the ubiquitous archaeal diglycosyl tetraether lipids in marine subsurface sediment using intramolecular stable isotope probing. Environ Microbiol 2012; 15:1634-46. [DOI: 10.1111/j.1462-2920.2012.02888.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 08/30/2012] [Indexed: 11/27/2022]
Affiliation(s)
- Yu-Shih Lin
- Organic Geochemistry Group; Department of Geosciences and MARUM Center for Marine Environmental Sciences; University of Bremen; PO Box 330 440; D-28359; Bremen; Germany
| | - Julius S. Lipp
- Organic Geochemistry Group; Department of Geosciences and MARUM Center for Marine Environmental Sciences; University of Bremen; PO Box 330 440; D-28359; Bremen; Germany
| | - Marcus Elvert
- Organic Geochemistry Group; Department of Geosciences and MARUM Center for Marine Environmental Sciences; University of Bremen; PO Box 330 440; D-28359; Bremen; Germany
| | - Thomas Holler
- Max Planck Institute for Marine Microbiology; Bremen; Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group; Department of Geosciences and MARUM Center for Marine Environmental Sciences; University of Bremen; PO Box 330 440; D-28359; Bremen; Germany
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Godde JS. Breaking through a phylogenetic impasse: a pair of associated archaea might have played host in the endosymbiotic origin of eukaryotes. Cell Biosci 2012; 2:29. [PMID: 22913376 PMCID: PMC3490757 DOI: 10.1186/2045-3701-2-29] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 07/03/2012] [Indexed: 11/23/2022] Open
Abstract
For over a century, the origin of eukaryotes has been a topic of intense debate among scientists. Although it has become widely accepted that organelles such as the mitochondria and chloroplasts arose via endosymbiosis, the origin of the eukaryotic nucleus remains enigmatic. Numerous models for the origin of the nucleus have been proposed over the years, many of which use endosymbiosis to explain its existence. Proposals of microbes whose ancestors may have served as either a host or a guest in various endosymbiotic scenarios abound, none of which have been able to sufficiently incorporate the cell biological as well as phylogenetic data which links these organisms to the nucleus. While it is generally agreed that eukaryotic nuclei share more features in common with archaea rather than with bacteria, different studies have identified either one or the other of the two major groups of archaea as potential ancestors, leading to somewhat of a stalemate. This paper seeks to resolve this impasse by presenting evidence that not just one, but a pair of archaea might have served as host to the bacterial ancestor of the mitochondria. This pair may have consisted of ancestors of both Ignicoccus hospitalis as well as its ectosymbiont/ectoparasite ‘Nanoarchaeum equitans’.
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Affiliation(s)
- James S Godde
- Department of Biology, Monmouth College, 700 East Broadway, Monmouth, IL 61430, USA.
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The unusual cell biology of the hyperthermophilic Crenarchaeon Ignicoccus hospitalis. Antonie van Leeuwenhoek 2012; 102:203-19. [PMID: 22653377 DOI: 10.1007/s10482-012-9748-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 04/12/2012] [Indexed: 10/28/2022]
Abstract
The Crenarchaeon Ignicoccus hospitalis is an anaerobic, obligate chemolithoautotrophic hyperthermophile, growing by reduction of elemental sulfur using molecular hydrogen as electron donor. Together with Nanoarchaeum equitans it forms a unique, archaeal biocoenosis, in which I. hospitalis serves as host for N. equitans. Both organisms can be cultivated in a stable coculture which is mandatory for N. equitans but not for I. hospitalis. This strong dependence is affirmed by the fact that N. equitans obtains its lipids and amino acids from the host. I. hospitalis cells exhibit several unique features: they can adhere to surfaces by extracellular appendages ('fibers') which are not used for motility; they use a novel CO(2) fixation pathway, the dicarboxylate/4-hydroxybutyrate pathway; and they exhibit a unique cell envelope for Archaea consisting of two membranes but lacking an S-layer. These membranes form two cell compartments, a tightly packed cytoplasm surrounded by a weakly staining intermembrane compartment (IMC) with a variable width from 20 to 1,000 nm. In this IMC, many round or elongated vesicles are found which may function as carriers of lipids or proteins out of the cytoplasm. Based on immuno-EM analyses and immuno-fluorescence experiments it was demonstrated recently that the A(1)A(O) ATP synthase, the H(2):sulfur oxidoreductase complex and the acetyl-CoA synthetase (ACS) of I. hospitalis are located in its outermost membrane. Therefore, this membrane is energized and is here renamed as "outer cellular membrane" (OCM). Among all prokaryotes possessing two membranes in their cell envelope, I. hospitalis is the first organism with an energized outermost membrane and ATP synthesis outside the cytoplasm. Since DNA and ribosomes are localized in the cytoplasm, energy conservation is separated from information processing and protein biosynthesis in I. hospitalis. This raises questions concerning the function and characterization of the two membranes, the two cell compartments and of a possible ATP transfer to N. equitans.
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Weiner A, Schopf S, Wanner G, Probst A, Wirth R. Positive, Neutral and Negative Interactions in Cocultures between Pyrococcus furiosus and Different Methanogenic Archaea. Microbiol Insights 2012. [DOI: 10.4137/mbi.s8516] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The model organism Pyrococcus furiosus has recently been reported to interact with Methanopyrus kandleri in coculture, suggesting a H2 symbiosis. In the current study we further investigated this hypothesis by growing P. furiosus with four other hyperthermophilic methanogens providing evidence that the organisms did not only exert positive effects ( P. furiosus/ Methanocaldococcus villosus and P. furiosus/ Methanocaldococcus infernus) on each other, but also neutral ( P. furiosus/ Methanocaldococcus jannaschii) and even inhibitory interactions ( P. furiosus/ Methanotorris igneus) were detected suggesting interspecies relationships not only based on H2 symbiosis. Using various microscopic techniques we further analyzed the coculture with the highest positive interactions ( P. furiosus/ M. villosus) concerning its growth behavior on various surfaces, which turned out to be in stark contrast to the previous reported coculture of P. furiosus/ M. kandleri. This communication provides new insights into possible interactions of extremophilic Archaea in cocultures and again raises the question if and how hyperthermophilic Archaea communicate besides metabolic intermediates like H2.
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Affiliation(s)
- Agnes Weiner
- University of Regensburg, Institute of Microbiology and Archaea Center, Universitaetsstrasse 31; 93053 Regensburg, Germany
- University of Tübingen, Department of Geosciences, Sigwartstrasse 10; 72076 Tübingen, Germany
| | - Simone Schopf
- University of Regensburg, Institute of Microbiology and Archaea Center, Universitaetsstrasse 31; 93053 Regensburg, Germany
| | - Gerhard Wanner
- Biozentrum der LMU–-Department of Biology I; Großhadernerstrasse 4; 82152 Planegg-Martinsried, Germany
| | - Alexander Probst
- University of Regensburg, Institute of Microbiology and Archaea Center, Universitaetsstrasse 31; 93053 Regensburg, Germany
| | - Reinhard Wirth
- University of Regensburg, Institute of Microbiology and Archaea Center, Universitaetsstrasse 31; 93053 Regensburg, Germany
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