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Ding S, von Meijenfeldt FAB, Bale NJ, Sinninghe Damsté JS, Villanueva L. Production of structurally diverse sphingolipids by anaerobic marine bacteria in the euxinic Black Sea water column. THE ISME JOURNAL 2024; 18:wrae153. [PMID: 39113610 PMCID: PMC11334938 DOI: 10.1093/ismejo/wrae153] [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: 02/26/2024] [Revised: 06/13/2024] [Accepted: 08/07/2024] [Indexed: 08/22/2024]
Abstract
Microbial lipids, used as taxonomic markers and physiological indicators, have mainly been studied through cultivation. However, this approach is limited due to the scarcity of cultures of environmental microbes, thereby restricting insights into the diversity of lipids and their ecological roles. Addressing this limitation, here we apply metalipidomics combined with metagenomics in the Black Sea, classifying and tentatively identifying 1623 lipid-like species across 18 lipid classes. We discovered over 200 novel, abundant, and structurally diverse sphingolipids in euxinic waters, including unique 1-deoxysphingolipids with long-chain fatty acids and sulfur-containing groups. Sphingolipids were thought to be rare in bacteria and their molecular and ecological functions in bacterial membranes remain elusive. However, genomic analysis focused on sphingolipid biosynthesis genes revealed that members of 38 bacterial phyla in the Black Sea can synthesize sphingolipids, representing a 4-fold increase from previously known capabilities and accounting for up to 25% of the microbial community. These sphingolipids appear to be involved in oxidative stress response, cell wall remodeling, and are associated with the metabolism of nitrogen-containing molecules. Our findings underscore the effectiveness of multi-omics approaches in exploring microbial chemical ecology.
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Affiliation(s)
- Su Ding
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797 SZ 't Horntje, Texel, The Netherlands
| | - F A Bastiaan von Meijenfeldt
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797 SZ 't Horntje, Texel, The Netherlands
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797 SZ 't Horntje, Texel, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797 SZ 't Horntje, Texel, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3584 CS Utrecht, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797 SZ 't Horntje, Texel, The Netherlands
- Department of Biology, Faculty of Sciences, Utrecht University, 3584 CS Utrecht, The Netherlands
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Pasterski MJ, Lorenz M, Ievlev AV, Wickramasinghe RC, Hanley L, Kenig F. The Determination of the Spatial Distribution of Indigenous Lipid Biomarkers in an Immature Jurassic Sediment Using Time-of-Flight-Secondary Ion Mass Spectrometry. ASTROBIOLOGY 2023; 23:936-950. [PMID: 37459147 DOI: 10.1089/ast.2022.0145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
The ability to detect and map lipids, including potential lipid biomarkers, within a sedimentary matrix using mass spectrometry (MS) imaging may be critical to determine whether potential lipids detected in samples returned from Mars are indigenous to Mars or are contaminants. Here, we use gas chromatography-mass spectrometry (GC-MS) and time-of-flight-secondary ion mass spectrometry (ToF-SIMS) datasets collected from an organic-rich, thermally immature Jurassic geologic sample to constrain MS imaging analysis of indigenous lipid biomarkers in geologic samples. GC-MS data show that the extractable fractions are dominated by C27-C30 steranes and sterenes as well as isorenieratene derivatives. ToF-SIMS spectra from organic matter-rich laminae contain a strong, spatially restricted signal for ions m/z 370.3, m/z 372.3, and m/z 386.3, which we assign to C27 sterenes, cholestane (C27), and 4- or 24-methyl steranes (C28), respectively, as well as characteristic fragment ions of isorenieratene derivatives, including m/z 133.1, m/z 171.1, and m/z 237.1. We observed individual steroid spatial heterogeneity at the scale of tens to hundreds of microns. The fine-scale heterogeneity observed implies that indigenous lipid biomarkers concentrated within specific regions may be detectable via ToF-SIMS in samples with even low amounts of organic carbon, including in samples returned from Mars.
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Affiliation(s)
- M Joseph Pasterski
- Department of Earth and Environmental Sciences, University of Illinois Chicago, Chicago, Illinois, USA
| | - Matthias Lorenz
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Anton V Ievlev
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Luke Hanley
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois, USA
| | - Fabien Kenig
- Department of Earth and Environmental Sciences, University of Illinois Chicago, Chicago, Illinois, USA
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Saito R, Wörmer L, Taubner H, Kaiho K, Takahashi S, Tian L, Ikeda M, Summons RE, Hinrichs KU. Centennial scale sequences of environmental deterioration preceded the end-Permian mass extinction. Nat Commun 2023; 14:2113. [PMID: 37059714 PMCID: PMC10104797 DOI: 10.1038/s41467-023-37717-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 03/28/2023] [Indexed: 04/16/2023] Open
Abstract
The exact drivers for the end-Permian mass extinction (EPME) remain controversial. Here we focus on a ~10,000 yr record from the marine type section at Meishan, China, preceding and covering the onset of the EPME. Analyses of polyaromatic hydrocarbons at sampling intervals representing 1.5-6.3 yr reveal recurrent pulses of wildfires in the terrestrial realm. Massive input pulses of soil-derived organic matter and clastic materials into the oceans are indicated by patterns of C2-dibenzofuran, C30 hopane and aluminum. Importantly, in the ~2,000 years preceding the main phase of the EPME, we observe a clearly defined sequence of wildfires, soil weathering, and euxinia provoked by the fertilization of the marine environment with soil-derived nutrients. Euxinia is indicated by sulfur and iron concentrations. Our study suggests that, in South China, centennial scale processes led to a collapse of the terrestrial ecosystem ~300 yr (120-480 yr; ± 2 s.d.) before the onset of the EPME and that this collapse induced euxinic conditions in the ocean, ultimately resulting in the demise of marine ecosystems.
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Affiliation(s)
- Ryosuke Saito
- MARUM - Center for Marine Environmental Sciences & Faculty of Geosciences, University of Bremen, 28359, Bremen, Germany.
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 45 Carleton Street, Cambridge, MA, 02142, USA.
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi City, 753-8512, Japan.
- Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Lars Wörmer
- MARUM - Center for Marine Environmental Sciences & Faculty of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Heidi Taubner
- MARUM - Center for Marine Environmental Sciences & Faculty of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Kunio Kaiho
- Department of Earth Science, Tohoku University, Sendai, 980-8578, Japan
| | - Satoshi Takahashi
- Department of Earth and Environmental Sciences, Graduate School of Environmental Studies, Nagoya University, Nagoya, 464-8601, Japan
| | - Li Tian
- The Key Laboratory of Biogeology and Environmental Geology and Faculty of Earth Science, China University of Geosciences Wuhan, Wuhan, 430074, China
| | - Masayuki Ikeda
- Department of Earth and Planetary Science, University of Tokyo, Bunkyo, 113-0033, Japan
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 45 Carleton Street, Cambridge, MA, 02142, USA
| | - Kai-Uwe Hinrichs
- MARUM - Center for Marine Environmental Sciences & Faculty of Geosciences, University of Bremen, 28359, Bremen, Germany
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Rasmussen KL, Stamps BW, Vanzin GF, Ulrich SM, Spear JR. Spatial and temporal dynamics at an actively silicifying hydrothermal system. Front Microbiol 2023; 14:1172798. [PMID: 37206339 PMCID: PMC10188993 DOI: 10.3389/fmicb.2023.1172798] [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: 02/23/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
Steep Cone Geyser is a unique geothermal feature in Yellowstone National Park (YNP), Wyoming, actively gushing silicon-rich fluids along outflow channels possessing living and actively silicifying microbial biomats. To assess the geomicrobial dynamics occurring temporally and spatially at Steep Cone, samples were collected at discrete locations along one of Steep Cone's outflow channels for both microbial community composition and aqueous geochemistry analysis during field campaigns in 2010, 2018, 2019, and 2020. Geochemical analysis characterized Steep Cone as an oligotrophic, surface boiling, silicious, alkaline-chloride thermal feature with consistent dissolved inorganic carbon and total sulfur concentrations down the outflow channel ranging from 4.59 ± 0.11 to 4.26 ± 0.07 mM and 189.7 ± 7.2 to 204.7 ± 3.55 μM, respectively. Furthermore, geochemistry remained relatively stable temporally with consistently detectable analytes displaying a relative standard deviation <32%. A thermal gradient decrease of ~55°C was observed from the sampled hydrothermal source to the end of the sampled outflow transect (90.34°C ± 3.38 to 35.06°C ± 7.24). The thermal gradient led to temperature-driven divergence and stratification of the microbial community along the outflow channel. The hyperthermophile Thermocrinis dominates the hydrothermal source biofilm community, and the thermophiles Meiothermus and Leptococcus dominate along the outflow before finally giving way to more diverse and even microbial communities at the end of the transect. Beyond the hydrothermal source, phototrophic taxa such as Leptococcus, Chloroflexus, and Chloracidobacterium act as primary producers for the system, supporting heterotrophic growth of taxa such as Raineya, Tepidimonas, and Meiothermus. Community dynamics illustrate large changes yearly driven by abundance shifts of the dominant taxa in the system. Results indicate Steep Cone possesses dynamic outflow microbial communities despite stable geochemistry. These findings improve our understanding of thermal geomicrobiological dynamics and inform how we can interpret the silicified rock record.
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Affiliation(s)
- Kalen L. Rasmussen
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Blake W. Stamps
- Air Force Research Laboratory, Materials and Manufacturing Directorate, Wright-Patterson Air Force Base, Dayton, OH, United States
| | - Gary F. Vanzin
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | | | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
- *Correspondence: John R. Spear,
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Feucherolles M, Frache G. MALDI Mass Spectrometry Imaging: A Potential Game-Changer in a Modern Microbiology. Cells 2022; 11:cells11233900. [PMID: 36497158 PMCID: PMC9738593 DOI: 10.3390/cells11233900] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/11/2022] Open
Abstract
Nowadays, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is routinely implemented as the reference method for the swift and straightforward identification of microorganisms. However, this method is not flawless and there is a need to upgrade the current methodology in order to free the routine lab from incubation time and shift from a culture-dependent to an even faster independent culture system. Over the last two decades, mass spectrometry imaging (MSI) gained tremendous popularity in life sciences, including microbiology, due to its ability to simultaneously detect biomolecules, as well as their spatial distribution, in complex samples. Through this literature review, we summarize the latest applications of MALDI-MSI in microbiology. In addition, we discuss the challenges and avenues of exploration for applying MSI to solve current MALDI-TOF MS limits in routine and research laboratories.
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Evans TW, Kalambokidis MJ, Jungblut AD, Millar JL, Bauersachs T, Grotheer H, Mackey TJ, Hawes I, Summons RE. Lipid Biomarkers From Microbial Mats on the McMurdo Ice Shelf, Antarctica: Signatures for Life in the Cryosphere. Front Microbiol 2022; 13:903621. [PMID: 35756013 PMCID: PMC9232131 DOI: 10.3389/fmicb.2022.903621] [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: 03/24/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Persistent cold temperatures, a paucity of nutrients, freeze-thaw cycles, and the strongly seasonal light regime make Antarctica one of Earth's least hospitable surface environments for complex life. Cyanobacteria, however, are well-adapted to such conditions and are often the dominant primary producers in Antarctic inland water environments. In particular, the network of meltwater ponds on the 'dirty ice' of the McMurdo Ice Shelf is an ecosystem with extensive cyanobacteria-dominated microbial mat accumulations. This study investigated intact polar lipids (IPLs), heterocyte glycolipids (HGs), and bacteriohopanepolyols (BHPs) in combination with 16S and 18S rRNA gene diversity in microbial mats of twelve ponds in this unique polar ecosystem. To constrain the effects of nutrient availability, temperature and freeze-thaw cycles on the lipid membrane composition, lipids were compared to stromatolite-forming cyanobacterial mats from ice-covered lakes in the McMurdo Dry Valleys as well as from (sub)tropical regions and hot springs. The 16S rRNA gene compositions of the McMurdo Ice Shelf mats confirm the dominance of Cyanobacteria and Proteobacteria while the 18S rRNA gene composition indicates the presence of Ochrophyta, Chlorophyta, Ciliophora, and other microfauna. IPL analyses revealed a predominantly bacterial community in the meltwater ponds, with archaeal lipids being barely detectable. IPLs are dominated by glycolipids and phospholipids, followed by aminolipids. The high abundance of sugar-bound lipids accords with a predominance of cyanobacterial primary producers. The phosphate-limited samples from the (sub)tropical, hot spring, and Lake Vanda sites revealed a higher abundance of aminolipids compared to those of the nitrogen-limited meltwater ponds, affirming the direct affects that N and P availability have on IPL compositions. The high abundance of polyunsaturated IPLs in the Antarctic microbial mats suggests that these lipids provide an important mechanism to maintain membrane fluidity in cold environments. High abundances of HG keto-ols and HG keto-diols, produced by heterocytous cyanobacteria, further support these findings and reveal a unique distribution compared to those from warmer climates.
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Affiliation(s)
- Thomas W. Evans
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Maria J. Kalambokidis
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Anne D. Jungblut
- Life Sciences Department, Natural History Museum, London, United Kingdom
| | - Jasmin L. Millar
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, United Kingdom
| | - Thorsten Bauersachs
- Institute of Geosciences, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Hendrik Grotheer
- Marine Geochemistry, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Tyler J. Mackey
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, Tauranga, New Zealand
| | - Roger E. Summons
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
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7
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Mass spectrometry imaging and its potential in food microbiology. Int J Food Microbiol 2022; 371:109675. [DOI: 10.1016/j.ijfoodmicro.2022.109675] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/23/2022] [Accepted: 04/04/2022] [Indexed: 11/20/2022]
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Berlanga M, Palau M, Guerrero R. Community homeostasis of coastal microbial mats from the Camargue during winter (cold) and summer (hot) seasons. Ecosphere 2022. [DOI: 10.1002/ecs2.3922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Mercedes Berlanga
- Department of Biology, Environment and Health, Section Microbiology, Faculty of Pharmacy and Food Sciences University of Barcelona Barcelona Spain
| | - Montserrat Palau
- Department of Biology, Environment and Health, Section Microbiology, Faculty of Pharmacy and Food Sciences University of Barcelona Barcelona Spain
| | - Ricardo Guerrero
- Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, Faculty of Medicine University of Barcelona Barcelona Spain
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Trimethylornithine Membrane Lipids: Discovered in Planctomycetes and Identified in Diverse Environments. Metabolites 2021; 11:metabo11010049. [PMID: 33445571 PMCID: PMC7828035 DOI: 10.3390/metabo11010049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/03/2021] [Accepted: 01/05/2021] [Indexed: 11/17/2022] Open
Abstract
Intact polar membrane lipids (IPLs) are the building blocks of all cell membranes. There is a wide range of phosphorus-free IPL structures, including amino acid containing IPLs, that can be taxonomically specific. Trimethylornithine membrane lipids (TMOs) were discovered in northern wetland Planctomycete species that were isolated and described in the last decade. The trimethylated terminal nitrogen moiety of the ornithine amino acid in the TMO structure gives the lipid a charged polar head group, similar to certain phospholipids. Since their discovery, TMOs have been identified in various other recently described northern latitude Planctomycete species, and in diverse environments including tundra soil, a boreal eutrophic lake, meso-oligotrophic lakes, and hot springs. The majority of environments or enrichment cultures in which TMOs have been observed include predominately heterotrophic microbial communities involved in the degradation of recalcitrant material and/or low oxygen methanogenic conditions at primarily northern latitudes. Other ecosystems occupied with microbial communities that possess similar metabolic pathways, such as tropical peatlands or coastal salt marshes, may include TMO producing Planctomycetes as well, further allowing these lipids to potentially be used to understand microbial community responses to environmental change in a wide range of systems. The occurrence of TMOs in hot springs indicates that these unique lipids could have broad environmental distribution with different specialized functions. Opportunities also exist to investigate the application of TMOs in microbiome studies, including forensic necrobiomes. Further environmental and microbiome lipidomics research involving TMOs will help reveal the evolution, functions, and applications of these unique membrane lipids.
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