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Kong X, Chen J, Wang S, Li B, Zou R, Zhang Y. When polyethylene terephthalate microplastics meet Perfluorooctane sulfonate in thermophilic biogas upgrading system: Their effect on methanogenesis. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133626. [PMID: 38301444 DOI: 10.1016/j.jhazmat.2024.133626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/03/2024]
Abstract
Microplastics (MPs) and Perfluorooctane sulfonate (PFOS) are two hard-biodegradable pollutants widely existing in the waste streams treated by anaerobic digestion. However, their synergistic effect on methanogenic metabolism is still unknown. This study investigated the impact of polyethylene terephthalate (PET) MPs alone and co-existing with PFOS on CO2 conversion to CH4 in a thermophilic biogas upgrading system. The results showed that either PET MPs addition alone or coexisting with PFOS improved the ultimate CH4 percentage and increased CO2 utilization rate. When Fe0 was added into the reactors with PET to enhance the interspecies electron transfer, a potential defluorination was observed with a defluorination rate of 15.88 ± 1.53%. Exposure of the reactor to PFOS of 300 μg/L could change the methanogenic pathway, resulting in a newly emerged Methanomassiliicoccus with dominance of 16%. Furthermore, under the exposure of PFOS, the number of predicted genes regulating enzymes in methanogenic steps from CO2 increased. These results suggest that the co-existence of PET MPs and PFOS will not inhibit the activity of hydrotrophic methanogenes, and a portion of PFOS may be biodegraded during the methanogenesis under Fe0 regulation.
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Affiliation(s)
- Xin Kong
- College of Environmental Science and Engineering, Taiyuan University of Technology, Jinzhong 030600, PR China; Department of Environmental and Resource Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark.
| | - Junmei Chen
- College of Environmental Science and Engineering, Taiyuan University of Technology, Jinzhong 030600, PR China
| | - Song Wang
- Department of Environmental and Resource Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Biao Li
- Department of Environmental and Resource Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Rusen Zou
- Department of Environmental and Resource Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Yifeng Zhang
- Department of Environmental and Resource Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark.
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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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Borrel G, Fadhlaoui K, Ben Hania W, Gaci N, Pehau-Arnaudet G, Chaudhary PP, Vandekerckove P, Ballet N, Alric M, O’Toole PW, Fardeau ML, Ollivier B, Brugère JF. Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov. Microorganisms 2023; 11:2794. [PMID: 38004804 PMCID: PMC10673518 DOI: 10.3390/microorganisms11112794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The methanogenic strain Mx-05T was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales. It shares 86.9% 16S rRNA gene sequence identity with Methanomassiliicoccus luminyensis, the only member of this order previously isolated. The cells of Mx-05T were non-motile cocci, with a diameter range of 0.4-0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H2 as an electron donor. H2/CO2, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05T required an unknown medium factor(s) provided by Eggerthella lenta and present in rumen fluid. Mx-05T grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9-8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L-1 NaCl (optimum 0.12 mol.L-1 NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H4MPT Wood-Ljungdahl pathway, as described for other Methanomassiliicoccales members. Based on an average nucleotide identity analysis, we propose strain Mx-05T as being a novel representative of the order Methanomassiliicoccales, within the novel family Methanomethylophilaceae, for which the name Methanomethylophilus alvi gen. nov, sp. nov. is proposed. The type strain is Mx-05T (JCM 31474T).
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Affiliation(s)
- Guillaume Borrel
- Institut Pasteur, Université Paris Cité, Evolutionary Biology of the Microbial Cell, 75015 Paris, France
| | - Khaled Fadhlaoui
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
- Université Clermont Auvergne, INRA, MEDIS, 63000 Clermont-Ferrand, France
- Université Clermont Auvergne, CNRS, UMR 6023 CNRS-UCA, Laboratoire Microorganismes: Génome et Environnement LMGE, 63000 Clermont-Ferrand, France
| | - Wajdi Ben Hania
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | - Nadia Gaci
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | - Gérard Pehau-Arnaudet
- Institut Pasteur, Université Paris Cité, Ultrastructural Bioimaging, 75015 Paris, France
| | - Prem Prashant Chaudhary
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Nathalie Ballet
- Lesaffre International, Lesaffre Group, 59700 Marcq-en-Barœul, France
| | - Monique Alric
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | | | - Marie-Laure Fardeau
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
| | - Bernard Ollivier
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
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Rempfert KR, Kraus EA, Nothaft DB, Dildar N, Spear JR, Sepúlveda J, Templeton AS. Intact polar lipidome and membrane adaptations of microbial communities inhabiting serpentinite-hosted fluids. Front Microbiol 2023; 14:1198786. [PMID: 38029177 PMCID: PMC10667739 DOI: 10.3389/fmicb.2023.1198786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023] Open
Abstract
The generation of hydrogen and reduced carbon compounds during serpentinization provides sustained energy for microorganisms on Earth, and possibly on other extraterrestrial bodies (e.g., Mars, icy satellites). However, the geochemical conditions that arise from water-rock reaction also challenge the known limits of microbial physiology, such as hyperalkaline pH, limited electron acceptors and inorganic carbon. Because cell membranes act as a primary barrier between a cell and its environment, lipids are a vital component in microbial acclimation to challenging physicochemical conditions. To probe the diversity of cell membrane lipids produced in serpentinizing settings and identify membrane adaptations to this environment, we conducted the first comprehensive intact polar lipid (IPL) biomarker survey of microbial communities inhabiting the subsurface at a terrestrial site of serpentinization. We used an expansive, custom environmental lipid database that expands the application of targeted and untargeted lipodomics in the study of microbial and biogeochemical processes. IPLs extracted from serpentinite-hosted fluid communities were comprised of >90% isoprenoidal and non-isoprenoidal diether glycolipids likely produced by archaeal methanogens and sulfate-reducing bacteria. Phospholipids only constituted ~1% of the intact polar lipidome. In addition to abundant diether glycolipids, betaine and trimethylated-ornithine aminolipids and glycosphingolipids were also detected, indicating pervasive membrane modifications in response to phosphate limitation. The carbon oxidation state of IPL backbones was positively correlated with the reduction potential of fluids, which may signify an energy conservation strategy for lipid synthesis. Together, these data suggest microorganisms inhabiting serpentinites possess a unique combination of membrane adaptations that allow for their survival in polyextreme environments. The persistence of IPLs in fluids beyond the presence of their source organisms, as indicated by 16S rRNA genes and transcripts, is promising for the detection of extinct life in serpentinizing settings through lipid biomarker signatures. These data contribute new insights into the complexity of lipid structures generated in actively serpentinizing environments and provide valuable context to aid in the reconstruction of past microbial activity from fossil lipid records of terrestrial serpentinites and the search for biosignatures elsewhere in our solar system.
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Affiliation(s)
- Kaitlin R. Rempfert
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - Emily A. Kraus
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Daniel B. Nothaft
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - Nadia Dildar
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
- Department of Quantitative Biosciences and Engineering, Colorado School of Mines, Golden, CO, United States
| | - Julio Sepúlveda
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - Alexis S. Templeton
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
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5
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Khairunisa BH, Heryakusuma C, Ike K, Mukhopadhyay B, Susanti D. Evolving understanding of rumen methanogen ecophysiology. Front Microbiol 2023; 14:1296008. [PMID: 38029083 PMCID: PMC10658910 DOI: 10.3389/fmicb.2023.1296008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Production of methane by methanogenic archaea, or methanogens, in the rumen of ruminants is a thermodynamic necessity for microbial conversion of feed to volatile fatty acids, which are essential nutrients for the animals. On the other hand, methane is a greenhouse gas and its production causes energy loss for the animal. Accordingly, there are ongoing efforts toward developing effective strategies for mitigating methane emissions from ruminant livestock that require a detailed understanding of the diversity and ecophysiology of rumen methanogens. Rumen methanogens evolved from free-living autotrophic ancestors through genome streamlining involving gene loss and acquisition. The process yielded an oligotrophic lifestyle, and metabolically efficient and ecologically adapted descendants. This specialization poses serious challenges to the efforts of obtaining axenic cultures of rumen methanogens, and consequently, the information on their physiological properties remains in most part inferred from those of their non-rumen representatives. This review presents the current knowledge of rumen methanogens and their metabolic contributions to enteric methane production. It also identifies the respective critical gaps that need to be filled for aiding the efforts to mitigate methane emission from livestock operations and at the same time increasing the productivity in this critical agriculture sector.
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Affiliation(s)
| | - Christian Heryakusuma
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
| | - Kelechi Ike
- Department of Biology, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
| | - Biswarup Mukhopadhyay
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
- Virginia Tech Carilion School of Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Dwi Susanti
- Microbial Discovery Research, BiomEdit, Greenfield, IN, United States
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6
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Řezanka T, Kyselová L, Murphy DJ. Archaeal lipids. Prog Lipid Res 2023; 91:101237. [PMID: 37236370 DOI: 10.1016/j.plipres.2023.101237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023]
Abstract
The major archaeal membrane glycerolipids are distinguished from those of bacteria and eukaryotes by the contrasting stereochemistry of their glycerol backbones, and by the use of ether-linked isoprenoid-based alkyl chains rather than ester-linked fatty acyl chains for their hydrophobic moieties. These fascinating compounds play important roles in the extremophile lifestyles of many species, but are also present in the growing numbers of recently discovered mesophilic archaea. The past decade has witnessed significant advances in our understanding of archaea in general and their lipids in particular. Much of the new information has come from the ability to screen large microbial populations via environmental metagenomics, which has revolutionised our understanding of the extent of archaeal biodiversity that is coupled with a strict conservation of their membrane lipid compositions. Significant additional progress has come from new culturing and analytical techniques that are gradually enabling archaeal physiology and biochemistry to be studied in real time. These studies are beginning to shed light on the much-discussed and still-controversial process of eukaryogenesis, which probably involved both bacterial and archaeal progenitors. Puzzlingly, although eukaryotes retain many attributes of their putative archaeal ancestors, their lipid compositions only reflect their bacterial progenitors. Finally, elucidation of archaeal lipids and their metabolic pathways have revealed potentially interesting applications that have opened up new frontiers for biotechnological exploitation of these organisms. This review is concerned with the analysis, structure, function, evolution and biotechnology of archaeal lipids and their associated metabolic pathways.
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Affiliation(s)
- Tomáš Řezanka
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 00 Prague, Czech Republic
| | - Lucie Kyselová
- Research Institute of Brewing and Malting, Lípová 511, 120 44 Prague, Czech Republic
| | - Denis J Murphy
- School of Applied Sciences, University of South Wales, Pontypridd, CF37 1DL, United Kingdom.
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Finkel PL, Carrizo D, Parro V, Sánchez-García L. An Overview of Lipid Biomarkers in Terrestrial Extreme Environments with Relevance for Mars Exploration. ASTROBIOLOGY 2023; 23:563-604. [PMID: 36880883 PMCID: PMC10150655 DOI: 10.1089/ast.2022.0083] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Lipid molecules are organic compounds, insoluble in water, and based on carbon-carbon chains that form an integral part of biological cell membranes. As such, lipids are ubiquitous in life on Earth, which is why they are considered useful biomarkers for life detection in terrestrial environments. These molecules display effective membrane-forming properties even under geochemically hostile conditions that challenge most of microbial life, which grants lipids a universal biomarker character suitable for life detection beyond Earth, where a putative biological membrane would also be required. What discriminates lipids from nucleic acids or proteins is their capacity to retain diagnostic information about their biological source in their recalcitrant hydrocarbon skeletons for thousands of millions of years, which is indispensable in the field of astrobiology given the time span that the geological ages of planetary bodies encompass. This work gathers studies that have employed lipid biomarker approaches for paleoenvironmental surveys and life detection purposes in terrestrial environments with extreme conditions: hydrothermal, hyperarid, hypersaline, and highly acidic, among others; all of which are analogous to current or past conditions on Mars. Although some of the compounds discussed in this review may be abiotically synthesized, we focus on those with a biological origin, namely lipid biomarkers. Therefore, along with appropriate complementary techniques such as bulk and compound-specific stable carbon isotope analysis, this work recapitulates and reevaluates the potential of lipid biomarkers as an additional, powerful tool to interrogate whether there is life on Mars, or if there ever was.
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Affiliation(s)
- Pablo L Finkel
- Centro de Astrobiología (CAB), CSIC-INTA, Madrid, Spain
- Department of Physics and Mathematics and Department of Automatics, University of Alcalá, Madrid, Spain
| | | | - Victor Parro
- Centro de Astrobiología (CAB), CSIC-INTA, Madrid, Spain
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Waheed H, Mehmood CT, Li Y, Du Y, Xiao Y. Biofouling control potential of quorum quenching anaerobes in lab-scale anaerobic membrane bioreactors: Foulants profile and microbial dynamics. CHEMOSPHERE 2023; 315:137760. [PMID: 36610508 DOI: 10.1016/j.chemosphere.2023.137760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/19/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Indigenously isolated anaerobes encoding four quorum quenching (QQ) enzymes were applied in immobilized- and bioaugmented forms for their implications on membrane foulants, microbial taxa, and biofouling control. Two identical anaerobic membrane bioreactors (AnMBRs) with different immobilizing media, i.e. silica-alginate (AnMBR-Si) and hollow fiber-alginate (AnMBR-Hf), were sequentially operated for two conventional and three QQ based phases. The synergistic addition of QQ anaerobes in free cells and the immobilized form prolonged the membrane filtration operation by 172 ± 29% and 284 ± 12% in AnMBR-Si and AnMBR-Hf, respectively. Biocake with low surface coverage was prominent during QQ application compared to conventional phases. Despite the better control of AHLs (3OC6-, C6-, 3OC8, C8, and C10-HSL) and AI-2 at various points of QQ phases, the QQ consortium could not maintain a low concentration of signals for longer period. Therefrom, quenching of targeted signal molecules instigate the dominance of microbial species bearing non-targeted quorum sensing mechanism. The QQ significantly altered the biofilm-forming community in mixed liquor, while the members with robust signal transduction systems became dominant to counteract the QQ mechanism and were the ultimate cause of biofouling. The improved methane content in biogas and increased methanogens composition during QQ phases demonstrated the synergism of exogenous and immobilized QQ as the most viable option for long-term AnMBR operation.
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Affiliation(s)
- Hira Waheed
- Department of Civil and Environmental Engineering, Shantou University, Shantou, Guangdong, 515063, China
| | - Ch Tahir Mehmood
- Department of Chemical Engineering, Guangdong Technion - Israel Institute of Technology, Shantou, Guangdong, 515063, China
| | - Yiwei Li
- Department of Civil and Environmental Engineering, Shantou University, Shantou, Guangdong, 515063, China
| | - Ying Du
- Department of Civil and Environmental Engineering, Shantou University, Shantou, Guangdong, 515063, China
| | - Yeyuan Xiao
- Department of Civil and Environmental Engineering, Shantou University, Shantou, Guangdong, 515063, China.
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9
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de Kok NAW, Driessen AJM. The catalytic and structural basis of archaeal glycerophospholipid biosynthesis. Extremophiles 2022; 26:29. [PMID: 35976526 PMCID: PMC9385802 DOI: 10.1007/s00792-022-01277-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/02/2022] [Indexed: 12/03/2022]
Abstract
Archaeal glycerophospholipids are the main constituents of the cytoplasmic membrane in the archaeal domain of life and fundamentally differ in chemical composition compared to bacterial phospholipids. They consist of isoprenyl chains ether-bonded to glycerol-1-phosphate. In contrast, bacterial glycerophospholipids are composed of fatty acyl chains ester-bonded to glycerol-3-phosphate. This largely domain-distinguishing feature has been termed the “lipid-divide”. The chemical composition of archaeal membranes contributes to the ability of archaea to survive and thrive in extreme environments. However, ether-bonded glycerophospholipids are not only limited to extremophiles and found also in mesophilic archaea. Resolving the structural basis of glycerophospholipid biosynthesis is a key objective to provide insights in the early evolution of membrane formation and to deepen our understanding of the molecular basis of extremophilicity. Many of the glycerophospholipid enzymes are either integral membrane proteins or membrane-associated, and hence are intrinsically difficult to study structurally. However, in recent years, the crystal structures of several key enzymes have been solved, while unresolved enzymatic steps in the archaeal glycerophospholipid biosynthetic pathway have been clarified providing further insights in the lipid-divide and the evolution of early life.
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Affiliation(s)
- Niels A W de Kok
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands.
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10
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Tourte M, Coffinet S, Wörmer L, Lipp JS, Hinrichs KU, Oger PM. The Exploration of the Thermococcus barophilus Lipidome Reveals the Widest Variety of Phosphoglycolipids in Thermococcales. Front Microbiol 2022; 13:869479. [PMID: 35865931 PMCID: PMC9294538 DOI: 10.3389/fmicb.2022.869479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
One of the most distinctive characteristics of archaea is their unique lipids. While the general nature of archaeal lipids has been linked to their tolerance to extreme conditions, little is known about the diversity of lipidic structures archaea are able to synthesize, which hinders the elucidation of the physicochemical properties of their cell membrane. In an effort to widen the known lipid repertoire of the piezophilic and hyperthermophilic model archaeon Thermococcus barophilus, we comprehensively characterized its intact polar lipid (IPL), core lipid (CL), and polar head group compositions using a combination of cutting-edge liquid chromatography and mass spectrometric ionization systems. We tentatively identified 82 different IPLs based on five distinct CLs and 10 polar head group derivatives of phosphatidylhexoses, including compounds reported here for the first time, e.g., di-N-acetylhexosamine phosphatidylhexose-bearing lipids. Despite having extended the knowledge on the lipidome, our results also indicate that the majority of T. barophilus lipids remain inaccessible to current analytical procedures and that improvements in lipid extraction and analysis are still required. This expanded yet incomplete lipidome nonetheless opens new avenues for understanding the physiology, physicochemical properties, and organization of the membrane in this archaeon as well as other archaea.
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Affiliation(s)
- Maxime Tourte
- Univ. Lyon, Univ. Lyon 1, CNRS, UMR 5240, Villeurbanne, France
- Univ. Lyon, INSA Lyon, CNRS, UMR 5240, Villeurbanne, France
| | - Sarah Coffinet
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Lars Wörmer
- 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
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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11
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Kudisi D, Lu X, Zheng C, Wang Y, Cai T, Li W, Hu L, Zhang R, Zhang Y, Zhen G. Long-term performance, membrane fouling behaviors and microbial community in a hollow fiber anaerobic membrane bioreactor (HF-AnMBR) treating synthetic terephthalic acid-containing wastewater. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127458. [PMID: 34653863 DOI: 10.1016/j.jhazmat.2021.127458] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/02/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
Purified terephthalic acid (PTA) wastewater with properties of poor biodegradation and high toxicity is produced from refining and synthesis of petrochemical products. In this study, a lab-scale hollow fiber membrane bioreactor (HF-AnMBR) fed with synthetic PTA wastewater was operated over 200 days with stepwise decreased hydraulic retention time (HRT) to investigate the long-term performance, membrane fouling mechanism and microbial community evolution. Results showed that a stable chemical oxygen demand (COD) removal rate of 65.8 ± 4.1% was achieved at organic loading rate of 3.1 ± 0.3 g-COD/L-reactor/d and HRT 24 h, under which the methane production rate reached 0.33 ± 0.02 L/L-reactor/d. Further shortening HRT, however, led to the decreased COD removal efficiency and low methane bioconversion. A mild membrane fouling occurred due to the production of colloidal biopolymers and the interaction between increased colloidal substances secreted/cracked by microorganisms and membrane interface. Further 16S rRNA analysis indicated that microbial diversity and richness had changed with the variation of HRT while Methanosaeta, and Methanolinea species were always the dominant methanogens responsible for methane production. The results verify that HF-AnMBR is an alternative technology for PTA wastewater treatment along with energy harvesting, and provide a new avenue toward sustainable petrochemical wastewater management.
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Affiliation(s)
- Dilibaierkezi Kudisi
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Xueqin Lu
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Institute of Eco-Chongming (IEC), 3663 N. Zhongshan Rd., Shanghai 200062, PR China; Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai 200241, PR China.
| | - Chaoting Zheng
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Yue Wang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Teng Cai
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Wanjiang Li
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Lingtan Hu
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Ruiliang Zhang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Yizhi Zhang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Guangyin Zhen
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, 1515 North Zhongshan Rd. (No. 2), Shanghai 200092, PR China; Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, 3663 N. Zhongshan Road, Shanghai 200062, PR China.
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12
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Tourte M, Schaeffer P, Grossi V, Oger PM. Membrane adaptation in the hyperthermophilic archaeon Pyrococcus furiosus relies upon a novel strategy involving glycerol monoalkyl glycerol tetraether lipids. Environ Microbiol 2022; 24:2029-2046. [PMID: 35106897 DOI: 10.1111/1462-2920.15923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 11/28/2022]
Abstract
Microbes preserve membrane functionality under fluctuating environmental conditions by modulating their membrane lipid composition. Although several studies have documented membrane adaptations in Archaea, the influence of most biotic and abiotic factors on archaeal lipid compositions remains underexplored. Here, we studied the influence of temperature, pH, salinity, the presence/absence of elemental sulfur, the carbon source, and the genetic background on the lipid core composition of the hyperthermophilic neutrophilic marine archaeon Pyrococcus furiosus. Every growth parameter tested affected the lipid core composition to some extent, the carbon source and the genetic background having the greatest influence. Surprisingly, P. furiosus appeared to only marginally rely on the two major responses implemented by Archaea, i.e., the regulation of the ratio of diether to tetraether lipids and that of the number of cyclopentane rings in tetraethers. Instead, this species increased the ratio of glycerol monoalkyl glycerol tetraethers (GMGT, aka. H-shaped tetraethers) to glycerol dialkyl glycerol tetrathers (GDGT) in response to decreasing temperature and pH and increasing salinity, thus providing for the first time evidence of adaptive functions for GMGT. Besides P. furiosus, numerous other species synthesize significant proportions of GMGT, which suggests that this unprecedented adaptive strategy might be common in Archaea. This article is protected by copyright. All rights reserved.
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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
| | | | - Vincent Grossi
- Univ Lyon, Univ. Lyon 1, CNRS, ENSL, UJM, UMR 5276 LGL-TPE, F-69622, Villeurbanne, France
| | - Philippe M Oger
- Univ Lyon, INSA Lyon, CNRS, UMR 5240, F-69621, Villeurbanne, France
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13
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Evidence for enzymatic backbone methylation of the main membrane lipids in the archaeon Methanomassiliicoccus luminyensis. Appl Environ Microbiol 2021; 88:e0215421. [PMID: 34936840 DOI: 10.1128/aem.02154-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Butanetriol and pentanetriol dibiphytanyl glycerol tetraethers (BDGTs and PDGTs, respectively) are recently identified classes of archaeal membrane lipids that are prominent constituents in anoxic subseafloor sediments. These lipids are intriguing as they possess unusual backbones with four or five carbon atoms instead of the canonical three-carbon glycerol backbone. In this study, we examined the biosynthesis of BDGTs and PDGTs by the methanogen Methanomassiliicoccus luminyensis, the only available isolate known to produce these compounds, via stable isotope labeling with [methyl-13C] methionine followed by mass spectrometry analysis. We show that their biosynthesis proceeds from transfer(s) of the terminal methyl group of methionine to the more common archaeal membrane lipids, i.e., glycerol dibiphytanyl glycerol tetraethers (GDGTs). As this methylation targets a methylene group, a radical mechanism involving a radical S-adenosylmethionine (SAM) enzyme is probable. Over the course of the incubation, the abundance of PDGTs relative to BDGTs, expressed as backbone methylation index, increased, implying that backbone methylation may be related to the growth shift to stationary conditions, possibly due to limited energy and/or substrate availability. The increase of the backbone methylation index with increasing sediment age in a sample set from the Mediterranean Sea adds support for such a relationship. Importance Butanetriol and pentanetriol dibiphytanyl glycerol tetraethers are membrane lipids recently discovered in anoxic environments. These lipids differ from typical membrane-spanning tetraether lipids because they possess a non-glycerol backbone. The biosynthetic pathway and physiological role of these unique lipids are currently unknown. Here, we show that in the strain Methanomassiliicoccus luminyensis these lipids are the result of methyl transfer(s) from a S-adenosyl methionine (SAM) intermediate. We observed a relative increase of the doubly methylated compound, pentanetriol dibiphytanyl glycerol tetraether, in the stationary phase of M. luminyensis as well as in the subseafloor of the Mediterranean Sea and thus introduced a backbone methylation index, which could be used to further explore microbial activity in natural settings.
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14
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Law KP, He W, Tao J, Zhang C. A Novel Approach to Characterize the Lipidome of Marine Archaeon Nitrosopumilus maritimus by Ion Mobility Mass Spectrometry. Front Microbiol 2021; 12:735878. [PMID: 34925256 PMCID: PMC8674956 DOI: 10.3389/fmicb.2021.735878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Archaea are differentiated from the other two domains of life by their biomolecular characteristics. One such characteristic is the unique structure and composition of their lipids. Characterization of the whole set of lipids in a biological system (the lipidome) remains technologically challenging. This is because the lipidome is innately complex, and not all lipid species are extractable, separable, or ionizable by a single analytical method. Furthermore, lipids are structurally and chemically diverse. Many lipids are isobaric or isomeric and often indistinguishable by the measurement of mass or even their fragmentation spectra. Here we developed a novel analytical protocol based on liquid chromatography ion mobility mass spectrometry to enhance the coverage of the lipidome and characterize the conformations of archaeal lipids by their collision cross-sections (CCSs). The measurements of ion mobility revealed the gas-phase ion chemistry of representative archaeal lipids and provided further insights into their attributions to the adaptability of archaea to environmental stresses. A comprehensive characterization of the lipidome of mesophilic marine thaumarchaeon, Nitrosopumilus maritimus (strain SCM1) revealed potentially an unreported phosphate- and sulfate-containing lipid candidate by negative ionization analysis. It was the first time that experimentally derived CCS values of archaeal lipids were reported. Discrimination of crenarchaeol and its proposed stereoisomer was, however, not achieved with the resolving power of the SYNAPT G2 ion mobility system, and a high-resolution ion mobility system may be required for future work. Structural and spectral libraries of archaeal lipids were constructed in non-vendor-specific formats and are being made available to the community to promote research of Archaea by lipidomics.
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Affiliation(s)
- Kai P Law
- Southern University of Science and Technology, SUSTech Academy for Advanced Interdisciplinary Studies, Shenzhen, China.,Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Wei He
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jianchang Tao
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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15
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Cozannet M, Borrel G, Roussel E, Moalic Y, Allioux M, Sanvoisin A, Toffin L, Alain K. New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments. Microorganisms 2020; 9:E30. [PMID: 33374130 PMCID: PMC7824343 DOI: 10.3390/microorganisms9010030] [Citation(s) in RCA: 21] [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: 12/01/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Members of the archaeal order Methanomassiliicoccales are methanogens mainly associated with animal digestive tracts. However, environmental members remain poorly characterized as no representatives not associated with a host have been cultivated so far. In this study, metabarcoding screening combined with quantitative PCR analyses on a collection of diverse non-host-associated environmental samples revealed that Methanomassiliicoccales were very scarce in most terrestrial and aquatic ecosystems. Relative abundance of Methanomassiliicoccales and substrates/products of methanogenesis were monitored during incubation of environmental slurries. A sediment slurry enriched in Methanomassiliicoccales was obtained from a freshwater sample. It allowed the reconstruction of a high-quality metagenome-assembled genome (MAG) corresponding to a new candidate species, for which we propose the name of Candidatus 'Methanomassiliicoccus armoricus MXMAG1'. Comparison of the annotated genome of MXMAG1 with the published genomes and MAGs from Methanomassiliicoccales belonging to the 2 known clades ('free-living'/non-host-associated environmental clade and 'host-associated'/digestive clade) allowed us to explore the putative physiological traits of Candidatus 'M. armoricus MXMAG1'. As expected, Ca. 'Methanomassiliicoccus armoricus MXMAG1' had the genetic potential to produce methane by reduction of methyl compounds and dihydrogen oxidation. This MAG encodes for several putative physiological and stress response adaptations, including biosynthesis of trehalose (osmotic and temperature regulations), agmatine production (pH regulation), and arsenic detoxication, by reduction and excretion of arsenite, a mechanism that was only present in the 'free-living' clade. An analysis of co-occurrence networks carried out on environmental samples and slurries also showed that Methanomassiliicoccales detected in terrestrial and aquatic ecosystems were strongly associated with acetate and dihydrogen producing bacteria commonly found in digestive habitats and which have been reported to form syntrophic relationships with methanogens.
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Affiliation(s)
- Marc Cozannet
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Guillaume Borrel
- Unit Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institute Pasteur, 75015 Paris, France;
| | - Erwan Roussel
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Yann Moalic
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Maxime Allioux
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Amandine Sanvoisin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Laurent Toffin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, UMR 6197, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (M.C.); (E.R.); (Y.M.); (M.A.); (A.S.); (L.T.)
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16
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Yoshida R, Hemmi H. Construction of an artificial biosynthetic pathway for hyperextended archaeal membrane lipids in the bacterium Escherichia coli. Synth Biol (Oxf) 2020; 5:ysaa018. [PMID: 33263085 PMCID: PMC7680562 DOI: 10.1093/synbio/ysaa018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/08/2020] [Accepted: 09/16/2020] [Indexed: 11/12/2022] Open
Abstract
Archaea produce unique membrane lipids, which possess two fully saturated isoprenoid chains linked to the glycerol moiety via ether bonds. The isoprenoid chain length of archaeal membrane lipids is believed to be important for some archaea to thrive in extreme environments because the hyperthermophilic archaeon Aeropyrum pernix and some halophilic archaea synthesize extended C25,C25-archaeal diether-type membrane lipids, which have isoprenoid chains that are longer than those of typical C20,C20-diether lipids. Natural archaeal diether lipids possessing longer C30 or C35 isoprenoid chains, however, have yet to be isolated. In the present study, we attempted to synthesize such hyperextended archaeal membrane lipids. We investigated the substrate preference of the enzyme sn-2,3-(digeranylfarnesyl)glycerol-1-phosphate synthase from A. pernix, which catalyzes the transfer of the second C25 isoprenoid chain to the glycerol moiety in the biosynthetic pathway of C25,C25-archaeal membrane lipids. The enzyme was shown to accept sn-3-hexaprenylglycerol-1-phosphate, which has a C30 isoprenoid chain, as a prenyl acceptor substrate to synthesize sn-2-geranylfarnesyl-3-hexaprenylglycerol-1-phosphate, a supposed precursor for hyperextended C25,C30-archaeal membrane lipids. Furthermore, we constructed an artificial biosynthetic pathway by introducing 4 archaeal genes and 1 gene from Bacillus subtilis in the cells of Escherichia coli, which enabled the E. coli strain to produce hyperextended C25,C30-archaeal membrane lipids, which have never been reported so far.
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Affiliation(s)
- Ryo Yoshida
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 460-8601, Japan
| | - Hisashi Hemmi
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 460-8601, Japan
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17
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Abstract
Host-associated microbial communities have an important role in shaping the health and fitness of plants and animals. Most studies have focused on the bacterial, fungal or viral communities, but often the archaeal component has been neglected. The archaeal community, the so-called archaeome, is now increasingly recognized as an important component of host-associated microbiomes. It is composed of various lineages, including mainly Methanobacteriales and Methanomassiliicoccales (Euryarchaeota), as well as representatives of the Thaumarchaeota. Host-archaeome interactions have mostly been delineated from methanogenic archaea in the gastrointestinal tract, where they contribute to substantial methane production and are potentially also involved in disease-relevant processes. In this Review, we discuss the diversity and potential roles of the archaea associated with protists, plants and animals. We also present the current understanding of the archaeome in humans, the specific adaptations involved in interaction with the resident microbial community as well as with the host, and the roles of the archaeome in both health and disease.
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18
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Sandberg LM, Thaller G, Görs S, Kuhla B, Metges CC, Krattenmacher N. The relationship between methane emission and daytime-dependent fecal archaeol concentration in lactating dairy cows fed two different diets. Arch Anim Breed 2020; 63:211-218. [PMID: 32760788 PMCID: PMC7397718 DOI: 10.5194/aab-63-211-2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 05/27/2020] [Indexed: 11/11/2022] Open
Abstract
Archaeol is a cell membrane lipid of methanogenic archaea excreted in feces and is therefore a potential biomarker for individual methane emission (MEM). The aims of this study were to examine the potential of the fecal archaeol concentration (fArch) to be a proxy for MEM prediction in cows fed different diets and determine if the time of fecal collection affected the archaeol concentration. Thus, we investigated (i) the variation of the fArch concentration in spot samples of feces taken thrice within 8 h during respiration chamber measurements and (ii) the effect of two diets differing in nutrient composition and net energy content on the relationship between fArch and MEM in lactating cows. Two consecutive
respiration trials with four primiparous and six multiparous lactating
Holstein cows were performed. In the first trial (T1) at 100±3 d in milk (IM), a diet moderate in starch and fat content was fed for ad libitum intake, whereas in the second trial (T2) at 135±3 d IM, cows
received a diet lower in starch and fat. Individual MEM (g d-1) was measured
for 24 h. Fecal samples were taken at 06:30, 10:00, and 14:30 LT and analyzed for fArch using Soxhlet lipid extraction and GC–MS. Cows produced less methane (364 g CH4 d-1) during T1 and had significantly lower fArch concentrations (37.1 µg g-1 dry matter; DM) compared to T2 (392 g CH4 d-1 and 47.6 µg g-1 DM). A significant positive relationship
between fArch (µg g-1 fecal DM) and MEM, expressed on a dry matter intake (DMI) basis (g kg-1 DMI), was found (R2=0.53, n=20). Among samples collected over the day, those collected at 10:00 LT provided the best coefficient of determination for MEM (R2=0.23). In conclusion, fArch offers some potential in serving as a proxy for innovative breeding schemes to lower enteric methane when fecal samples are taken at a certain time of the day, but more data on the sources of variation of the MEM : fArch ratios are required.
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Affiliation(s)
- Lisa-Marie Sandberg
- Institute of Animal Breeding and Husbandry, Kiel University, Kiel, 24098, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Kiel University, Kiel, 24098, Germany
| | - Solvig Görs
- Institute of Nutritional Physiology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, 18196, Germany
| | - Björn Kuhla
- Institute of Nutritional Physiology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, 18196, Germany
| | - Cornelia C Metges
- Institute of Nutritional Physiology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, 18196, Germany.,Chair of Nutritional Physiology and Animal Nutrition, Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, 18059, Germany
| | - Nina Krattenmacher
- Institute of Animal Breeding and Husbandry, Kiel University, Kiel, 24098, Germany
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19
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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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20
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Becker S, Tebben J, Coffinet S, Wiltshire K, Iversen MH, Harder T, Hinrichs KU, Hehemann JH. Laminarin is a major molecule in the marine carbon cycle. Proc Natl Acad Sci U S A 2020; 117:6599-6607. [PMID: 32170018 PMCID: PMC7104365 DOI: 10.1073/pnas.1917001117] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Marine microalgae sequester as much CO2 into carbohydrates as terrestrial plants. Polymeric carbohydrates (i.e., glycans) provide carbon for heterotrophic organisms and constitute a carbon sink in the global oceans. The quantitative contributions of different algal glycans to cycling and sequestration of carbon remain unknown, partly because of the analytical challenge to quantify glycans in complex biological matrices. Here, we quantified a glycan structural type using a recently developed biocatalytic strategy, which involves laminarinase enzymes that specifically cleave the algal glycan laminarin into readily analyzable fragments. We measured laminarin along transects in the Arctic, Atlantic, and Pacific oceans and during three time series in the North Sea. These data revealed a median of 26 ± 17% laminarin within the particulate organic carbon pool. The observed correlation between chlorophyll and laminarin suggests an annual production of algal laminarin of 12 ± 8 gigatons: that is, approximately three times the annual atmospheric carbon dioxide increase by fossil fuel burning. Moreover, our data revealed that laminarin accounted for up to 50% of organic carbon in sinking diatom-containing particles, thus substantially contributing to carbon export from surface waters. Spatially and temporally variable laminarin concentrations in the sunlit ocean are driven by light availability. Collectively, these observations highlight the prominent ecological role and biogeochemical function of laminarin in oceanic carbon export and energy flow to higher trophic levels.
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Affiliation(s)
- Stefan Becker
- MARUM Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- Department of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Jan Tebben
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Sarah Coffinet
- MARUM Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
- Department of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Karen Wiltshire
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Morten Hvitfeldt Iversen
- MARUM Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
- Department of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Tilmann Harder
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
- Faculty of Biology and Chemistry, University of Bremen, 28359 Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
- Department of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Jan-Hendrik Hehemann
- MARUM Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany;
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- Department of Geosciences, University of Bremen, 28359 Bremen, Germany
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21
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Methylotrophic methanogens everywhere - physiology and ecology of novel players in global methane cycling. Biochem Soc Trans 2020; 47:1895-1907. [PMID: 31819955 DOI: 10.1042/bst20180565] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 01/14/2023]
Abstract
Research on methanogenic Archaea has experienced a revival, with many novel lineages of methanogens recently being found through cultivation and suggested via metagenomics approaches, respectively. Most of these lineages comprise Archaea (potentially) capable of methanogenesis from methylated compounds, a pathway that had previously received comparably little attention. In this review, we provide an overview of these new lineages with a focus on the Methanomassiliicoccales. These lack the Wood-Ljungdahl pathway and employ a hydrogen-dependent methylotrophic methanogenesis pathway fundamentally different from traditional methylotrophic methanogens. Several archaeal candidate lineages identified through metagenomics, such as the Ca. Verstraetearchaeota and Ca. Methanofastidiosa, encode genes for a methylotrophic methanogenesis pathway similar to the Methanomassiliicoccales. Thus, the latter are emerging as a model system for physiological, biochemical and ecological studies of hydrogen-dependent methylotrophic methanogens. Methanomassiliicoccales occur in a large variety of anoxic habitats including wetlands and animal intestinal tracts, i.e. in the major natural and anthropogenic sources of methane emissions, respectively. Especially in ruminant animals, they likely are among the major methane producers. Taken together, (hydrogen-dependent) methylotrophic methanogens are much more diverse and widespread than previously thought. Considering the role of methane as potent greenhouse gas, resolving the methanogenic nature of a broad range of putative novel methylotrophic methanogens and assessing their role in methane emitting environments are pressing issues for future research on methanogens.
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Salvador-Castell M, Tourte M, Oger PM. In Search for the Membrane Regulators of Archaea. Int J Mol Sci 2019; 20:E4434. [PMID: 31505830 PMCID: PMC6770870 DOI: 10.3390/ijms20184434] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 11/23/2022] Open
Abstract
Membrane regulators such as sterols and hopanoids play a major role in the physiological and physicochemical adaptation of the different plasmic membranes in Eukarya and Bacteria. They are key to the functionalization and the spatialization of the membrane, and therefore indispensable for the cell cycle. No archaeon has been found to be able to synthesize sterols or hopanoids to date. They also lack homologs of the genes responsible for the synthesis of these membrane regulators. Due to their divergent membrane lipid composition, the question whether archaea require membrane regulators, and if so, what is their nature, remains open. In this review, we review evidence for the existence of membrane regulators in Archaea, and propose tentative location and biological functions. It is likely that no membrane regulator is shared by all archaea, but that they may use different polyterpenes, such as carotenoids, polyprenols, quinones and apolar polyisoprenoids, in response to specific stressors or physiological needs.
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Affiliation(s)
- Marta Salvador-Castell
- Université de Lyon, CNRS, UMR 5240, F-69621 Villeurbanne, France.
- Université de Lyon, INSA de Lyon, UMR 5240, F-69621 Villeurbanne, France.
| | - Maxime Tourte
- Université de Lyon, CNRS, UMR 5240, F-69621 Villeurbanne, France.
- Université de Lyon, INSA de Lyon, UMR 5240, F-69621 Villeurbanne, France.
| | - Philippe M Oger
- Université de Lyon, CNRS, UMR 5240, F-69621 Villeurbanne, France.
- Université de Lyon, INSA de Lyon, UMR 5240, F-69621 Villeurbanne, France.
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Kröninger L, Steiniger F, Berger S, Kraus S, Welte CU, Deppenmeier U. Energy conservation in the gut microbeMethanomassiliicoccus luminyensisis based on membrane‐bound ferredoxin oxidation coupled to heterodisulfide reduction. FEBS J 2019; 286:3831-3843. [DOI: 10.1111/febs.14948] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/17/2019] [Accepted: 06/01/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Lena Kröninger
- Institute of Microbiology and Biotechnology University of Bonn Bonn Germany
| | - Fabian Steiniger
- Institute of Microbiology and Biotechnology University of Bonn Bonn Germany
| | - Stefanie Berger
- Department of Microbiology IWWR Radboud University Nijmegen The Netherlands
| | - Sebastian Kraus
- Institute of Microbiology and Biotechnology University of Bonn Bonn Germany
| | - Cornelia U. Welte
- Department of Microbiology IWWR Radboud University Nijmegen The Netherlands
| | - Uwe Deppenmeier
- Institute of Microbiology and Biotechnology University of Bonn Bonn Germany
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24
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Bale NJ, Sorokin DY, Hopmans EC, Koenen M, Rijpstra WIC, Villanueva L, Wienk H, Sinninghe Damsté JS. New Insights Into the Polar Lipid Composition of Extremely Halo(alkali)philic Euryarchaea From Hypersaline Lakes. Front Microbiol 2019; 10:377. [PMID: 30930858 PMCID: PMC6423904 DOI: 10.3389/fmicb.2019.00377] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/13/2019] [Indexed: 12/14/2022] Open
Abstract
We analyzed the polar membrane lipids of 13 strains of halo(alkali)philic euryarchaea from hypersaline lakes. Nine belong to the class Halobacteria, representing two functional groups: aerobic polysaccharide utilizers and sulfur-respiring anaerobes. The other four strains represent halo(alkali)philic methanogens from the class Methanomicrobia and a recently discovered class Methanonatronarchaeia. A wide range of polar lipids were detected across the 13 strains including dialkyl glycerol diethers (archaeols), membrane-spanning glycerol tetraethers and diether-based cardiolipins. The archaeols contained a range of core lipid structures, including combinations of C20 and C25 isoprenoidal alkyl chains, unsaturations, and hydroxy moieties. Several diether lipids were novel, including: (a) a phosphatidylglycerolhexose (PG-Gly) headgroup, (b) a N,N,N-trimethyl aminopentanetetrol (APT)-like lipid with a methoxy group in place of a hydroxy group on the pentanetetrol, (c) a series of polar lipids with a headgroup with elemental composition of either C12H25NO13S or C12H25NO16S2, and (d) novel cardiolipins containing a putative phosphatidylglycerolphosphate glycerophosphate (PGPGP) polar moiety. We found that the lipid distribution of the 13 strains could be generally separated into two groups, the methanogens (group) and the Halobacteria (class) based on the presence of specific core lipids. Within the methanogens, adaption to a high or more moderate salt concentration resulted in different ratios of glycerol dialkyl glycerol tetraethers (GDGTs) to archaeol. The methanogen Methanosalsum natronophilum AME2T had the most complex diether lipid composition of any of the 13 strains, including hydroxy archaeol and macrocyclic archaeol which we surmise is an order-specific membrane adaption. The zwitterionic headgroups APT and APT-Me were detected only in the Methanomicrobiales member Methanocalculus alkaliphilus AMF2T which also contained the highest level of unsaturated lipids. Only alkaliphilic members of the Natrialbales order contained PGPGP cardiolipins and the PG-Gly headgroup. The four analyzed neutrophilic members of the Halobacteria were characterized by the presence of sulfur-containing headgroups and glycolipids. The presence of cardiolipins with one or more i-C25 alkyl chains, generally termed extended archaeol (EXT-AR), in one of the Methanonatronarchaeia strains was unexpected as only one other order of methanogenic archaea has been reported to produce EXT-AR. We examined this further by looking into the genomic potential of various archaea to produce EXT-AR.
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Affiliation(s)
- Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Dimitry Y. Sorokin
- Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Delft, Netherlands
| | - Ellen C. Hopmans
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - W. Irene C. Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
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25
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Korzhenkov AA, Toshchakov SV, Bargiela R, Gibbard H, Ferrer M, Teplyuk AV, Jones DL, Kublanov IV, Golyshin PN, Golyshina OV. Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity. MICROBIOME 2019; 7:11. [PMID: 30691532 PMCID: PMC6350386 DOI: 10.1186/s40168-019-0623-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 01/10/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND The current view suggests that in low-temperature acidic environments, archaea are significantly less abundant than bacteria. Thus, this study of the microbiome of Parys Mountain (Anglesey, UK) sheds light on the generality of this current assumption. Parys Mountain is a historically important copper mine and its acid mine drainage (AMD) water streams are characterised by constant moderate temperatures (8-18 °C), extremely low pH (1.7) and high concentrations of soluble iron and other metal cations. RESULTS Metagenomic and SSU rRNA amplicon sequencing of DNA from Parys Mountain revealed a significant proportion of archaea affiliated with Euryarchaeota, which accounted for ca. 67% of the community. Within this phylum, potentially new clades of Thermoplasmata were overrepresented (58%), with the most predominant group being "E-plasma", alongside low-abundant Cuniculiplasmataceae, 'Ca. Micrarchaeota' and 'Terrestrial Miscellaneous Euryarchaeal Group' (TMEG) archaea, which were phylogenetically close to Methanomassilicoccales and clustered with counterparts from acidic/moderately acidic settings. In the sediment, archaea and Thermoplasmata contributed the highest numbers in V3-V4 amplicon reads, in contrast with the water body community, where Proteobacteria, Nitrospirae, Acidobacteria and Actinobacteria outnumbered archaea. Cultivation efforts revealed the abundance of archaeal sequences closely related to Cuniculiplasma divulgatum in an enrichment culture established from the filterable fraction of the water sample. Enrichment cultures with unfiltered samples showed the presence of Ferrimicrobium acidiphilum, C. divulgatum, 'Ca. Mancarchaeum acidiphilum Mia14', 'Ca. Micrarchaeota'-related and diverse minor (< 2%) bacterial metagenomic reads. CONCLUSION Contrary to expectation, our study showed a high abundance of archaea in this extremely acidic mine-impacted environment. Further, archaeal populations were dominated by one particular group, suggesting that they are functionally important. The prevalence of archaea over bacteria in these microbiomes and their spatial distribution patterns represents a novel and important advance in our understanding of acidophile ecology. We also demonstrated a procedure for the specific enrichment of cell wall-deficient members of the archaeal component of this community, although the large fraction of archaeal taxa remained unculturable. Lastly, we identified a separate clustering of globally occurring acidophilic members of TMEG that collectively belong to a distinct order within Thermoplasmata with yet unclear functional roles in the ecosystem.
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Affiliation(s)
- Aleksei A. Korzhenkov
- National Research Center “Kurchatov Institute”, Akademika Kurchatova sq., 1, Moscow, 123182 Russia
| | - Stepan V. Toshchakov
- Winogradsky Institute of Microbiology, Federal Research Center for Biotechnology, Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/2, Moscow, 117312 Russia
| | - Rafael Bargiela
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
| | - Huw Gibbard
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
| | | | - Alina V. Teplyuk
- National Research Center “Kurchatov Institute”, Akademika Kurchatova sq., 1, Moscow, 123182 Russia
| | - David L. Jones
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
- UWA School of Agriculture and Environment, University of Western Australia, Crawley, WA 6009 Australia
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Federal Research Center for Biotechnology, Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/2, Moscow, 117312 Russia
| | - Peter N. Golyshin
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
- Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
| | - Olga V. Golyshina
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
- Centre for Environmental Biotechnology, Bangor University, Deiniol Rd, Bangor, LL57 2UW UK
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26
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Sollai M, Villanueva L, Hopmans EC, Reichart G, Sinninghe Damsté JS. A combined lipidomic and 16S rRNA gene amplicon sequencing approach reveals archaeal sources of intact polar lipids in the stratified Black Sea water column. GEOBIOLOGY 2019; 17:91-109. [PMID: 30281902 PMCID: PMC6586073 DOI: 10.1111/gbi.12316] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/02/2018] [Accepted: 08/21/2018] [Indexed: 05/25/2023]
Abstract
Archaea are important players in marine biogeochemical cycles, and their membrane lipids are useful biomarkers in environmental and geobiological studies. However, many archaeal groups remain uncultured and their lipid composition unknown. Here, we aim to expand the knowledge on archaeal lipid biomarkers and determine the potential sources of those lipids in the water column of the euxinic Black Sea. The archaeal community was evaluated by 16S rRNA gene amplicon sequencing and by quantitative PCR. The archaeal intact polar lipids (IPLs) were investigated by ultra-high-pressure liquid chromatography coupled to high-resolution mass spectrometry. Our study revealed both a complex archaeal community and large changes with water depth in the IPL assemblages. In the oxic/upper suboxic waters (<105 m), the archaeal community was dominated by marine group (MG) I Thaumarchaeota, coinciding with a higher relative abundance of hexose phosphohexose crenarchaeol, a known marker for Thaumarchaeota. In the suboxic waters (80-110 m), MGI Nitrosopumilus sp. dominated and produced predominantly monohexose glycerol dibiphytanyl glycerol tetraethers (GDGTs) and hydroxy-GDGTs. Two clades of MGII Euryarchaeota were present in the oxic and upper suboxic zones in much lower abundances, preventing the detection of their specific IPLs. In the deep sulfidic waters (>110 m), archaea belonging to the DPANN Woesearchaeota, Bathyarchaeota, and ANME-1b clades dominated. Correlation analyses suggest that the IPLs GDGT-0, GDGT-1, and GDGT-2 with two phosphatidylglycerol (PG) head groups and archaeol with a PG, phosphatidylethanolamine, and phosphatidylserine head groups were produced by ANME-1b archaea. Bathyarchaeota represented 55% of the archaea in the deeper part of the euxinic zone and likely produces archaeol with phospho-dihexose and hexose-glucuronic acid head groups.
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Affiliation(s)
- Martina Sollai
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Laura Villanueva
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Ellen C. Hopmans
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Gert‐Jan Reichart
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
- Department of Earth SciencesFaculty of GeosciencesUniversity of UtrechtUtrechtThe Netherlands
| | - Jaap S. Sinninghe Damsté
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
- Department of Earth SciencesFaculty of GeosciencesUniversity of UtrechtUtrechtThe Netherlands
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Speth DR, Orphan VJ. Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales. PeerJ 2018; 6:e5614. [PMID: 30245936 PMCID: PMC6147122 DOI: 10.7717/peerj.5614] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/21/2018] [Indexed: 01/24/2023] Open
Abstract
Over the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads. We use our mcrA dataset to assess the environmental distribution of the Methanomassiliicoccales and reconstruct and analyze a draft genome belonging to the ‘Lake Pavin cluster’, an uncultivated environmental clade of the Methanomassiliicoccales. Analysis of the ‘Lake Pavin cluster’ draft genome suggests that this organism has a more restricted capacity for hydrogenotrophic methylotrophic methanogenesis than previously studied Methanomassiliicoccales, with only genes for growth on methanol present. However, the presence of the soluble subunits of methyltetrahydromethanopterin:CoM methyltransferase (mtrAH) provide hypothetical pathways for methanol fermentation, and aceticlastic methanogenesis that await experimental verification. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subset of reads needs to be assembled. It is therefore a suitable approach to extract knowledge from the many publicly available sequencing projects.
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Affiliation(s)
- Daan R Speth
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States of America
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States of America
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28
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Park J, Lee B, Shi P, Kwon H, Jeong SM, Jun H. Methanol metabolism and archaeal community changes in a bioelectrochemical anaerobic digestion sequencing batch reactor with copper-coated graphite cathode. BIORESOURCE TECHNOLOGY 2018; 259:398-406. [PMID: 29597148 DOI: 10.1016/j.biortech.2018.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/28/2018] [Accepted: 03/01/2018] [Indexed: 06/08/2023]
Abstract
In this study, the metabolism of methanol and changes in an archaeal community were examined in a bioelectrochemical anaerobic digestion sequencing batch reactor with a copper-coated graphite cathode (BEAD-SBRCu). Copper-coated graphite cathode produced methanol from food waste. The BEAD-SBRCu showed higher methanol removal and methane production than those of the anaerobic digestion (AD)-SBR. The methane production and pH of the BEAD-SBRCu were stable even under a high organic loading rate (OLR). The hydrogenotrophic methanogens increased from 32.2 to 60.0%, and the hydrogen-dependent methylotrophic methanogens increased from 19.5 to 37.7% in the bulk of BEAD-SBRCu at high OLR. Where methanol was directly injected as a single substrate into the BEAD-SBRCu, the main metabolism of methane production was hydrogenotrophic methanogenesis using carbon dioxide and hydrogen released by the oxidation of methanol on the anode through bioelectrochemical reactions.
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Affiliation(s)
- Jungyu Park
- Department of Environmental Engineering, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Beom Lee
- Department of Environmental Engineering, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Peng Shi
- Department of Environmental Engineering, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Hyejeong Kwon
- Department of Environmental Engineering, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Sang Mun Jeong
- Department of Chemical Engineering, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Hangbae Jun
- Department of Environmental Engineering, Chungbuk National University, Cheongju 361-763, Republic of Korea.
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29
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Isoprenoid Quinones Resolve the Stratification of Redox Processes in a Biogeochemical Continuum from the Photic Zone to Deep Anoxic Sediments of the Black Sea. Appl Environ Microbiol 2018. [PMID: 29523543 DOI: 10.1128/aem.02736-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The stratified water column of the Black Sea serves as a model ecosystem for studying the interactions of microorganisms with major biogeochemical cycles. Here, we provide detailed analysis of isoprenoid quinones to study microbial redox processes in the ocean. In a continuum from the photic zone through the chemocline into deep anoxic sediments of the southern Black Sea, diagnostic quinones and inorganic geochemical parameters indicate niche segregation between redox processes and corresponding shifts in microbial community composition. Quinones specific for oxygenic photosynthesis and aerobic respiration dominate oxic waters, while quinones associated with thaumarchaeal ammonia oxidation and bacterial methanotrophy, respectively, dominate a narrow interval in suboxic waters. Quinone distributions indicate highest metabolic diversity within the anoxic zone, with anoxygenic photosynthesis being a major process in its photic layer. In the dark anoxic layer, quinone profiles indicate the occurrence of bacterial sulfur and nitrogen cycling, archaeal methanogenesis, and archaeal methanotrophy. Multiple novel ubiquinone isomers, possibly originating from unidentified intra-aerobic anaerobes, occur in this zone. The respiration modes found in the anoxic zone continue into shallow subsurface sediments, but quinone abundances rapidly decrease within the upper 50 cm below the sea floor, reflecting the transition to lower energy availability. In the deep subseafloor sediments, quinone distributions and geochemical profiles indicate archaeal methanogenesis/methanotrophy and potentially bacterial fermentative metabolisms. We observed that sedimentary quinone distributions track lithology, which supports prior hypotheses that deep biosphere community composition and metabolisms are determined by environmental conditions during sediment deposition.IMPORTANCE Microorganisms play crucial roles in global biogeochemical cycles, yet we have only a fragmentary understanding of the diversity of microorganisms and their metabolisms, as the majority remains uncultured. Thus, culture-independent approaches are critical for determining microbial diversity and active metabolic processes. In order to resolve the stratification of microbial communities in the Black Sea, we comprehensively analyzed redox process-specific isoprenoid quinone biomarkers in a unique continuous record from the photic zone through the chemocline into anoxic subsurface sediments. We describe an unprecedented quinone diversity that allowed us to detect distinct biogeochemical processes, including oxygenic photosynthesis, archaeal ammonia oxidation, aerobic methanotrophy, and anoxygenic photosynthesis in defined geochemical zones.
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30
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Environmental factors shaping the archaeal community structure and ether lipid distribution in a subtropic river and estuary, China. Appl Microbiol Biotechnol 2017; 102:461-474. [PMID: 29103169 DOI: 10.1007/s00253-017-8595-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 10/18/2022]
Abstract
Archaea are widespread and abundant in aquatic and terrestrial habitats and play fundamental roles in global biogeochemical cycles. Archaeal lipids, such as isoprenoid glycerol diakyl glycerol tetraethers (iGDGTs), are important biomarkers tracing changes in archaeal community structure and biogeochemical processes in nature. However, the linkage between the archaeal populations and the GDGT distribution in the natural environment is poorly examined, which hindered the application and interpretation of GDGT-based climate or environmental proxies. We addressed this question by investigating changes in archaeal lipid composition and community structure in the context of environmental variables along the subtropical Jiulong River Watershed (JRW) and Jiulong River Estuary (JRE) in southern China. The results showed that both the archaeal cells and the polar GDGTs (P-GDGTs) in the JRW and JRE were mostly autochthonous rather than exogenous input from surrounding soils. We further found that only five (Methanobacteriales, Ca. Bathyarchaeota, Marine Benthic Groups A (MBGA), Marine Benthic Groups B (MBGB), and Marine Benthic Groups D (MBGD)) out of sixteen lineages showed significant impacts on the composition of P-GDGTs, suggesting the significant contribution of those archaea to the changes of P-GDGT compositions. Salinity and total phosphorus (TP) showed significant impact on the distribution of both genetic and P-GDGTs compositions of archaea; whereas, sand and silt contents only had significant impact on the P-GDGTs. MBGD archaea, which occur widely in marine sediments, showed positive correlations with P-TEX86 in the JRW and JRE, suggesting that uncultivated MBGD might also contribute to the variations in TEX86 signals in marine sediments. This study provided insight into the sources of P-GDGTs and the factors controlling their distributions in river-dominated continental margins, which has relevance to applications of GDGT-based proxies in paleoclimate studies.
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31
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Immunogenic properties of the human gut-associated archaeon Methanomassiliicoccus luminyensis and its susceptibility to antimicrobial peptides. PLoS One 2017; 12:e0185919. [PMID: 28982164 PMCID: PMC5628862 DOI: 10.1371/journal.pone.0185919] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/21/2017] [Indexed: 01/20/2023] Open
Abstract
The methanogenic archaeon Methanomassiliicoccus luminyensis strain B10T was isolated from human feces just a few years ago. Due to its remarkable metabolic properties, particularly the degradation of trimethylamines, this strain was supposed to be used as "Archaebiotic" during metabolic disorders of the human intestine. However, there is still no data published regarding adaptations to the natural habitat of M. luminyensis as it has been shown for the other two reported mucosa-associated methanoarchaea. This study aimed at unraveling susceptibility of M. luminyensis to antimicrobial peptides as well as its immunogenicity. By using the established microtiter plate assay adapted to the anaerobic growth requirements of methanogenic archaea, we demonstrated that M. luminyensis is highly sensitive against LL32, a derivative of human cathelicidin (MIC = 2 μM). However, the strain was highly resistant against the porcine lysin NK-2 (MIC = 10 μM) and the synthetic antilipopolysaccharide peptide (Lpep) (MIC>10 μM) and overall differed from the two other methanoarchaea, Methanobrevibacter smithii and Methanosphaera stadtmanae in respect to AMP sensitivity. Moreover, only weak immunogenic potential of M. luminyensis was demonstrated using peripheral blood mononuclear cells (PBMCs) and monocyte-derived dendritic cells (moDCs) by determining release of pro-inflammatory cytokines. Overall, our findings clearly demonstrate that the archaeal gut inhabitant M. luminyensis is susceptible to the release of human-derived antimicrobial peptides and exhibits low immunogenicity towards human immune cells in vitro-revealing characteristics of a typical commensal gut microbe.
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Elling FJ, Könneke M, Nicol GW, Stieglmeier M, Bayer B, Spieck E, de la Torre JR, Becker KW, Thomm M, Prosser JI, Herndl GJ, Schleper C, Hinrichs KU. Chemotaxonomic characterisation of the thaumarchaeal lipidome. Environ Microbiol 2017; 19:2681-2700. [PMID: 28419726 DOI: 10.1111/1462-2920.13759] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 11/28/2022]
Abstract
Thaumarchaeota are globally distributed and abundant microorganisms occurring in diverse habitats and thus represent a major source of archaeal lipids. The scope of lipids as taxonomic markers in microbial ecological studies is limited by the scarcity of comparative data on the membrane lipid composition of cultivated representatives, including the phylum Thaumarchaeota. Here, we comprehensively describe the core and intact polar lipid (IPL) inventory of ten ammonia-oxidising thaumarchaeal cultures representing all four characterized phylogenetic clades. IPLs of these thaumarchaeal strains are generally similar and consist of membrane-spanning, glycerol dibiphytanyl glycerol tetraethers with monoglycosyl, diglycosyl, phosphohexose and hexose-phosphohexose headgroups. However, the relative abundances of these IPLs and their core lipid compositions differ systematically between the phylogenetic subgroups, indicating high potential for chemotaxonomic distinction of thaumarchaeal clades. Comparative lipidomic analyses of 19 euryarchaeal and crenarchaeal strains suggested that the lipid methoxy archaeol is synthesized exclusively by Thaumarchaeota and may thus represent a diagnostic lipid biomarker for this phylum. The unprecedented diversity of the thaumarchaeal lipidome with 118 different lipids suggests that membrane lipid composition and adaptation mechanisms in Thaumarchaeota are more complex than previously thought and include unique lipids with as yet unresolved properties.
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Affiliation(s)
- Felix J Elling
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Martin Könneke
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany.,Marine Archaea Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Graeme W Nicol
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, 69134, Ecully, France
| | | | - Barbara Bayer
- Limnology and Bio-Oceanography, Center of Ecology, University of Vienna, Vienna, 1090, Austria
| | - Eva Spieck
- Biocenter Klein Flottbek, Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, 22609, Germany
| | - José R de la Torre
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Kevin W Becker
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
| | - Michael Thomm
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Regensburg, 93053, Germany
| | - James I Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - Gerhard J Herndl
- Limnology and Bio-Oceanography, Center of Ecology, University of Vienna, Vienna, 1090, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, 1790 AB Den Burg, Texel, The Netherlands
| | | | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, 28359, Germany
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López-García P, Eme L, Moreira D. Symbiosis in eukaryotic evolution. J Theor Biol 2017; 434:20-33. [PMID: 28254477 DOI: 10.1016/j.jtbi.2017.02.031] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 02/19/2017] [Accepted: 02/25/2017] [Indexed: 01/27/2023]
Abstract
Fifty years ago, Lynn Margulis, inspiring in early twentieth-century ideas that put forward a symbiotic origin for some eukaryotic organelles, proposed a unified theory for the origin of the eukaryotic cell based on symbiosis as evolutionary mechanism. Margulis was profoundly aware of the importance of symbiosis in the natural microbial world and anticipated the evolutionary significance that integrated cooperative interactions might have as mechanism to increase cellular complexity. Today, we have started fully appreciating the vast extent of microbial diversity and the importance of syntrophic metabolic cooperation in natural ecosystems, especially in sediments and microbial mats. Also, not only the symbiogenetic origin of mitochondria and chloroplasts has been clearly demonstrated, but improvement in phylogenomic methods combined with recent discoveries of archaeal lineages more closely related to eukaryotes further support the symbiogenetic origin of the eukaryotic cell. Margulis left us in legacy the idea of 'eukaryogenesis by symbiogenesis'. Although this has been largely verified, when, where, and specifically how eukaryotic cells evolved are yet unclear. Here, we shortly review current knowledge about symbiotic interactions in the microbial world and their evolutionary impact, the status of eukaryogenetic models and the current challenges and perspectives ahead to reconstruct the evolutionary path to eukaryotes.
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Affiliation(s)
- Purificación López-García
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France.
| | - Laura Eme
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada NS B3H 4R2
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France
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