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Liang A, Zhao W, Lv T, Zhu Z, Haotian R, Zhang J, Xie B, Yi Y, Hao Z, Sun L, Luo A. Advances in novel biosensors in biomedical applications. Talanta 2024; 280:126709. [PMID: 39151317 DOI: 10.1016/j.talanta.2024.126709] [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: 12/25/2023] [Revised: 07/09/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
Biosensors, devices capable of detecting biomolecules or bioactive substances, have recently become one of the important tools in the fields of bioanalysis and medical diagnostics. A biosensor is an analytical system composed of biosensitive elements and signal-processing elements used to detect various biological and chemical substances. Biomimetic elements are key to biosensor technology and are the components in a sensor that are responsible for identifying the target analyte. The construction methods and working principles of biosensors based on synthetic biomimetic elements, such as DNAzyme, molecular imprinted polymers and aptamers, and their updated applications in biomedical analysis are summarised. Finally, the technical bottlenecks and future development prospects for biomedical analysis are summarised and discussed.
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Affiliation(s)
- Axin Liang
- Key Laboratory of Molecular Medicine and Biotherapy, The Ministry of Industry and Information Technology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Weidong Zhao
- Key Laboratory of Molecular Medicine and Biotherapy, The Ministry of Industry and Information Technology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Tianjian Lv
- Key Laboratory of Molecular Medicine and Biotherapy, The Ministry of Industry and Information Technology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Ziyu Zhu
- Key Laboratory of Molecular Medicine and Biotherapy, The Ministry of Industry and Information Technology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Ruilin Haotian
- Key Laboratory of Molecular Medicine and Biotherapy, The Ministry of Industry and Information Technology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Jiangjiang Zhang
- Key Laboratory of Molecular Medicine and Biotherapy, The Ministry of Industry and Information Technology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Bingteng Xie
- Key Laboratory of Molecular Medicine and Biotherapy, The Ministry of Industry and Information Technology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yue Yi
- Key Laboratory of Molecular Medicine and Biotherapy, The Ministry of Industry and Information Technology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Zikai Hao
- Key Laboratory of Molecular Medicine and Biotherapy, The Ministry of Industry and Information Technology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Liquan Sun
- Key Laboratory of Molecular Medicine and Biotherapy, The Ministry of Industry and Information Technology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Aiqin Luo
- Key Laboratory of Molecular Medicine and Biotherapy, The Ministry of Industry and Information Technology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
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2
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Bonacolta AM, Visscher PT, Del Campo J, White Iii RA. The eukaryome of modern microbialites reveals distinct colonization across aquatic ecosystems. NPJ Biofilms Microbiomes 2024; 10:78. [PMID: 39227595 PMCID: PMC11372052 DOI: 10.1038/s41522-024-00547-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 08/12/2024] [Indexed: 09/05/2024] Open
Abstract
Protists are less studied for their role and diversity in ecosystems. Notably, protists have played and still play an important role in microbialites. Microbialites, or lithified microbial mats, represent the oldest evidence of fossil biofilms (~3.5 Gyr). Modern microbialites may offer a unique proxy to study the potential role of protists within a geological context. We examined protist diversity in freshwater (Kelly and Pavilion Lake in British Columbia, Canada) and marine (Highborne Cay, Bahamas) to hypersaline (Shark Bay, Australia) microbialites to decipher their geomicrobiological role. The freshwater microbialite communities were clearly distinct from their marine and hypersaline counterparts. Chlorophytes had higher numerical abundance in freshwater microbialites; whereas pennate diatoms dominated numerically in marine microbialites. Despite the differences, protists across ecosystems may have adopted similar roles and functions. We suggest a consistent biogeochemical role of protists across microbialites globally; but that salinity may shape protist composition and evolution in these ecosystems.
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Affiliation(s)
- Anthony M Bonacolta
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Pieter T Visscher
- Department of Marine Sciences and Earth Sciences, University of Connecticut, Storrs, CT, USA
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Javier Del Campo
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA.
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain.
| | - Richard Allen White Iii
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.
- North Carolina Research Center (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC, USA.
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, USA.
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3
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Ding S, Grossi V, Hopmans EC, Bale NJ, Cravo-Laureau C, Sinninghe Damsté JS. Nitrogen and sulfur for phosphorus: Lipidome adaptation of anaerobic sulfate-reducing bacteria in phosphorus-deprived conditions. Proc Natl Acad Sci U S A 2024; 121:e2400711121. [PMID: 38833476 PMCID: PMC11181052 DOI: 10.1073/pnas.2400711121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/02/2024] [Indexed: 06/06/2024] Open
Abstract
Understanding how microbial lipidomes adapt to environmental and nutrient stress is crucial for comprehending microbial survival and functionality. Certain anaerobic bacteria can synthesize glycerolipids with ether/ester bonds, yet the complexities of their lipidome remodeling under varying physicochemical and nutritional conditions remain largely unexplored. In this study, we thoroughly examined the lipidome adaptations of Desulfatibacillum alkenivorans strain PF2803T, a mesophilic anaerobic sulfate-reducing bacterium known for its high proportions of alkylglycerol ether lipids in its membrane, under various cultivation conditions including temperature, pH, salinity, and ammonium and phosphorous concentrations. Employing an extensive analytical and computational lipidomic methodology, we identified an assemblage of nearly 400 distinct lipids, including a range of glycerol ether/ester lipids with various polar head groups. Information theory-based analysis revealed that temperature fluctuations and phosphate scarcity profoundly influenced the lipidome's composition, leading to an enhanced diversity and specificity of novel lipids. Notably, phosphorous limitation led to the biosynthesis of novel glucuronosylglycerols and sulfur-containing aminolipids, termed butyramide cysteine glycerols, featuring various ether/ester bonds. This suggests a novel adaptive strategy for anaerobic heterotrophs to thrive under phosphorus-depleted conditions, characterized by a diverse array of nitrogen- and sulfur-containing polar head groups, moving beyond a reliance on conventional nonphospholipid types.
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Affiliation(s)
- Su Ding
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, TexelSZ 1797, The Netherlands
| | - Vincent Grossi
- Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement, CNRS, Université Claude Bernard Lyon 1, Villeurbanne69622, France
| | - Ellen C. Hopmans
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, TexelSZ 1797, The Netherlands
| | - Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, TexelSZ 1797, The Netherlands
| | - Cristiana Cravo-Laureau
- Institut des Sciences Analytiques et de Physico-chimie pour l’environnement et les Matériaux, Universite de Pau et des Pays de l’Adour, CNRS, Pau64000, France
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, TexelSZ 1797, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, CB3584, The Netherlands
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4
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Zhang Z, Hou D, Xu C, Wu K, You L, Cheng X, Yan X, Chen W. Accumulation and Quantitative Assessment of Terrigenous Organic Matter in Upper Oligocene to Lower Miocene Marine Source Rocks of the Qiongdongnan Basin. ACS OMEGA 2024; 9:22903-22922. [PMID: 38826535 PMCID: PMC11137699 DOI: 10.1021/acsomega.4c01777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/27/2024] [Accepted: 05/07/2024] [Indexed: 06/04/2024]
Abstract
The intense collision between marine and terrestrial agents results in the dual-source (marine and terrigenous) characteristics of marine source rocks. Our research quantitatively assessed terrestrial organic matter and revealed the crucial role of terrestrial organic materials in the organic matter enrichment of lower Miocene to upper Oligocene marine source rocks in the Qiongdognnan Basin. The quantitative assessment was achieved using partial least-squares analysis with eight biomarker parameters associated with n-alkanes, isoprenoids, bicadinanes, taraxerane, tricyclic terpanes, and gammacerane. Differential unloading of terrestrial organic materials based on sedimentary facies of the delta-marginal sea system were observed through oleanane and bicadinane contents. It should be noted that the diagnostic ratio of oleanane was excluded from the quantitative analysis due to the dual influence from differential unloading and contact with seawater of the terrestrial organic materials. Calculation results show that the terrestrial organic matter was highest in the delta front at 70%, followed by prodelta at 59% and inner shallow marine at 57%. From the late Oligocene to the early Miocene, the proportion of terrestrial organic matter in marine source rocks continuously increased, with the highest average value observed in the second member of the Sanya Formation at 69% and the lowest occurring in the third member of the Lingshui Formation at 46%. Increasing terrestrial organic material inputs and preservation driven by the East Asian summer monsoon provided first-order control of the accumulation of organic carbon in the Qiongdongnan Basin during late Oligocene to early Miocene, rather than the bioproductivity of marine algae. The redox conditions of the water column determine the enrichment extent of organic matter.
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Affiliation(s)
- Ziming Zhang
- School
of Energy Resources, China University of
Geosciences, Beijing 100083, China
- Key
Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation
Mechanism, Ministry of Education, Beijing 100083, China
- Beijing
Key Laboratory of Unconventional Natural Gas Geological Evaluation
and Development Engineering, Beijing 100083, China
| | - Dujie Hou
- School
of Energy Resources, China University of
Geosciences, Beijing 100083, China
- Key
Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation
Mechanism, Ministry of Education, Beijing 100083, China
- Beijing
Key Laboratory of Unconventional Natural Gas Geological Evaluation
and Development Engineering, Beijing 100083, China
| | - Changgui Xu
- China
National Offshore Oil Corporation, Beijing 100010, China
| | - Keqiang Wu
- China
National Offshore Oil Corporation, Hainan, Haikou 570300, China
| | - Li You
- China
National Offshore Oil Corporation, Hainan, Haikou 570300, China
| | - Xiong Cheng
- School
of Energy Resources, China University of
Geosciences, Beijing 100083, China
- Key
Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation
Mechanism, Ministry of Education, Beijing 100083, China
- Beijing
Key Laboratory of Unconventional Natural Gas Geological Evaluation
and Development Engineering, Beijing 100083, China
| | - Xiaze Yan
- School
of Energy Resources, China University of
Geosciences, Beijing 100083, China
- Key
Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation
Mechanism, Ministry of Education, Beijing 100083, China
- Beijing
Key Laboratory of Unconventional Natural Gas Geological Evaluation
and Development Engineering, Beijing 100083, China
| | - Weihe Chen
- School
of Energy Resources, China University of
Geosciences, Beijing 100083, China
- Key
Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation
Mechanism, Ministry of Education, Beijing 100083, China
- Beijing
Key Laboratory of Unconventional Natural Gas Geological Evaluation
and Development Engineering, Beijing 100083, China
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5
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Hu X, Zhao S, Li H, Pan Y, Fan Z, Lu J, Li Y, Song G, Zhang H, Liu Q, Bao M. N-alkane shape distinctive microbial patterns in Kuroshio Extension. ENVIRONMENT INTERNATIONAL 2024; 188:108757. [PMID: 38795659 DOI: 10.1016/j.envint.2024.108757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/15/2024] [Accepted: 05/15/2024] [Indexed: 05/28/2024]
Abstract
Marine microorganisms are primary drivers of the elemental cycling. The interaction between heterotrophic prokaryotes and biomarker (n-alkane) in Kuroshio Extension (KE) remains unclear. Here, we categorize KE into three characteristic areas based on ocean temperatures and nutrient conditions: Cold Water Area (CWA), Mixed Area (MA), and Warm Water Area (WWA). A total of 49 samples were collected during two-year voyage to identify the source of n-alkane and associated degrading microorganisms. Total n-alkane concentrations (Σn-Alk) in surface water (SW) spanned from 1,308 ng L-1 to 1,890 ng L-1, it was significantly higher (Tukey-Kramer test, p < 0.05) in MA than CWA and WWA. The Σn-Alk in surface sediments (SS) gradually increased from north to south, ranging from 5,982 ng g-1 to 37,857 ng g-1. Bacteria and algae were the primary sources of n-alkane in both SW and SS. Proteobacteria was the most widely distributed among three areas. The presence of Rhodobacteraceae with alkB was the primary reason affecting n-alkane concentrations in SW. The Gammaproteobacteria with alkB and alkR chiefly affected n-alkane concentrations in SS. In summary, n-alkane s serve as an energy source for particular microorganisms, shaping the unique oceanographic patterns.
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Affiliation(s)
- Xin Hu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Shanshan Zhao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Haoshuai Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Yaping Pan
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Zhongxiang Fan
- Physical Oceanography Laboratory, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Jinren Lu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Yiming Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Guodong Song
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Honghai Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Qian Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Mutai Bao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao, Shandong Province 266100, China.
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6
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Li Y, Wang Y, Guo K, Tseng KF, Zhang X, Sun W. Aza-Prilezhaev Aziridination-Enabled Multidimensional Analysis of Isomeric Lipids via High-Resolution U-Shaped Mobility Analyzer-Mass Spectrometry. Anal Chem 2024; 96:7111-7119. [PMID: 38648270 DOI: 10.1021/acs.analchem.4c00481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Unsaturated lipids constitute a significant portion of the lipidome, serving as players of multifaceted functions involving cellular signaling, membrane structure, and bioenergetics. While derivatization-assisted liquid chromatography tandem mass spectrometry (LC-MS/MS) remains the gold standard technique in lipidome, it mainly faces challenges in efficiently labeling the carbon-carbon double bond (C═C) and differentiating isomeric lipids in full dimension. This presents a need for new orthogonal methodologies. Herein, a metal- and additive-free aza-Prilezhaev aziridination (APA)-enabled ion mobility mass spectrometric method is developed for probing multiple levels of unsaturated lipid isomerization with high sensitivity. Both unsaturated polar and nonpolar lipids can be efficiently labeled in the form of N-H aziridine without significant side reactions. The signal intensity can be increased by up to 3 orders of magnitude, achieving the nM detection limit. Abundant site-specific fragmentation ions indicate C═C location and sn-position in MS/MS spectra. Better yet, a stable monoaziridination product is dominant, simplifying the spectrum for lipids with multiple double bonds. Coupled with a U-shaped mobility analyzer, identification of geometric isomers and separation of different lipid classes can be achieved. Additionally, a unique pseudo MS3 mode with UMA-QTOF MS boosts the sensitivity for generating diagnostic fragments. Overall, the current method provides a comprehensive solution for deep-profiling lipidomics, which is valuable for lipid marker discovery in disease monitoring and diagnosis.
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Affiliation(s)
- Yuling Li
- Shimadzu Research Laboratory (Shanghai) Co., Ltd., Shanghai 201206, China
| | - Yiming Wang
- Shimadzu Research Laboratory (Shanghai) Co., Ltd., Shanghai 201206, China
| | - Kang Guo
- Shimadzu Research Laboratory (Shanghai) Co., Ltd., Shanghai 201206, China
| | - Kuo-Feng Tseng
- Shimadzu Research Laboratory (Shanghai) Co., Ltd., Shanghai 201206, China
| | - Xiaoqiang Zhang
- Shimadzu Research Laboratory (Shanghai) Co., Ltd., Shanghai 201206, China
| | - Wenjian Sun
- Shimadzu Research Laboratory (Shanghai) Co., Ltd., Shanghai 201206, China
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7
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Dembitsky VM. Naturally Occurring Norsteroids and Their Design and Pharmaceutical Application. Biomedicines 2024; 12:1021. [PMID: 38790983 PMCID: PMC11117879 DOI: 10.3390/biomedicines12051021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/26/2024] Open
Abstract
The main focus of this review is to introduce readers to the fascinating class of lipid molecules known as norsteroids, exploring their distribution across various biotopes and their biological activities. The review provides an in-depth analysis of various modified steroids, including A, B, C, and D-norsteroids, each characterized by distinct structural alterations. These modifications, which range from the removal of specific methyl groups to changes in the steroid core, result in unique molecular architectures that significantly impact their biological activity and therapeutic potential. The discussion on A, B, C, and D-norsteroids sheds light on their unique configurations and how these structural modifications influence their pharmacological properties. The review also presents examples from natural sources that produce a diverse array of steroids with distinct structures, including the aforementioned A, B, C, and D-nor variants. These compounds are sourced from marine organisms like sponges, soft corals, and starfish, as well as terrestrial entities such as plants, fungi, and bacteria. The exploration of these steroids encompasses their biosynthesis, ecological significance, and potential medical applications, highlighting a crucial area of interest in pharmacology and natural product chemistry. The review emphasizes the importance of researching these steroids for drug development, particularly in addressing diseases where conventional medications are inadequate or for conditions lacking sufficient therapeutic options. Examples of norsteroid synthesis are provided to illustrate the practical applications of this research.
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Affiliation(s)
- Valery M Dembitsky
- Centre for Applied Research, Innovation and Entrepreneurship, Lethbridge College, 3000 College Drive South, Lethbridge, AB T1K 1L6, Canada
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8
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Xiao W, Xu Y, Canfield DE, Wenzhöfer F, Zhang C, Glud RN. Strong linkage between benthic oxygen uptake and bacterial tetraether lipids in deep-sea trench regions. Nat Commun 2024; 15:3439. [PMID: 38653759 DOI: 10.1038/s41467-024-47660-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
Oxygen in marine sediments regulates many key biogeochemical processes, playing a crucial role in shaping Earth's climate and benthic ecosystems. In this context, branched glycerol dialkyl glycerol tetraethers (brGDGTs), essential biomarkers in paleoenvironmental research, exhibit an as-yet-unresolved association with sediment oxygen conditions. Here, we investigated brGDGTs in sediments from three deep-sea regions (4045 to 10,100 m water depth) dominated by three respective trench systems and integrated the results with in situ oxygen microprofile data. Our results demonstrate robust correlations between diffusive oxygen uptake (DOU) obtained from microprofiles and brGDGT methylation and isomerization degrees, indicating their primary production within sediments and their strong linkage with microbial diagenetic activity. We establish a quantitative relationship between the Isomerization and Methylation index of Branched Tetraethers (IMBT) and DOU, suggesting its potential validity across deep-sea environments. Increased brGDGT methylation and isomerization likely enhance the fitness of source organisms in deep-sea habitats. Our study positions brGDGTs as a promising tool for quantifying benthic DOU in deep-sea settings, where DOU is a key metric for assessing sedimentary organic carbon degradation and microbial activity.
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Affiliation(s)
- Wenjie Xiao
- Department of Biology, HADAL & Nordcee, University of Southern Denmark, 5230, Odense M, Denmark.
- Shanghai Frontiers Research Center of the Hadal Biosphere, College of Oceanography and Ecological Science, Shanghai Ocean University, 201306, Shanghai, China.
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Yunping Xu
- Shanghai Frontiers Research Center of the Hadal Biosphere, College of Oceanography and Ecological Science, Shanghai Ocean University, 201306, Shanghai, China.
| | - Donald E Canfield
- Department of Biology, HADAL & Nordcee, University of Southern Denmark, 5230, Odense M, Denmark
- Danish Institute for Advanced Study (DIAS), University of Southern Denmark, 5230, Odense M, Denmark
| | - Frank Wenzhöfer
- Department of Biology, HADAL & Nordcee, University of Southern Denmark, 5230, Odense M, Denmark
- HGF-MPG Group for Deep Sea Ecology & Technology, Alfred Wegener Institute Helmholtz Centre for Polar- and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Celsiusstr 1, D-28359, Bremen, Germany
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, 518055, Shenzhen, China
- Shanghai Sheshan National Geophysical Observatory, 201602, Shanghai, China
| | - Ronnie N Glud
- Department of Biology, HADAL & Nordcee, University of Southern Denmark, 5230, Odense M, Denmark.
- Shanghai Frontiers Research Center of the Hadal Biosphere, College of Oceanography and Ecological Science, Shanghai Ocean University, 201306, Shanghai, China.
- Danish Institute for Advanced Study (DIAS), University of Southern Denmark, 5230, Odense M, Denmark.
- Department of Ocean and Environmental Sciences, Tokyo University of Marine Science and Technology, 26 108-8477, Tokyo, Japan.
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Buckner DK, Anderson MJ, Wisnosky S, Alvarado W, Nuevo M, Williams AJ, Ricco AJ, Anamika, Debic S, Friend L, Hoac T, Jahnke L, Radosevich L, Williams R, Wilhelm MB. Quantifying Global Origin-Diagnostic Features and Patterns in Biotic and Abiotic Acyclic Lipids for Life Detection. ASTROBIOLOGY 2024; 24:1-35. [PMID: 38150549 DOI: 10.1089/ast.2023.0012] [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: 12/29/2023]
Abstract
Lipids are a geologically robust class of organics ubiquitous to life as we know it. Lipid-like soluble organics are synthesized abiotically and have been identified in carbonaceous meteorites and on Mars. Ascertaining the origin of lipids on Mars would be a profound astrobiological achievement. We enumerate origin-diagnostic features and patterns in two acyclic lipid classes, fatty acids (i.e., carboxylic acids) and acyclic hydrocarbons, by collecting and analyzing molecular data reported in over 1500 samples from previously published studies of terrestrial and meteoritic organics. We identify 27 combined (15 for fatty acids, 12 for acyclic hydrocarbons) molecular patterns and structural features that can aid in distinguishing biotic from abiotic synthesis. Principal component analysis (PCA) demonstrates that multivariate analyses of molecular features (16 for fatty acids, 14 for acyclic hydrocarbons) can potentially indicate sample origin. Terrestrial lipids are dominated by longer straight-chain molecules (C4-C34 fatty acids, C14-C46 acyclic hydrocarbons), with predominance for specific branched and unsaturated isomers. Lipid-like meteoritic soluble organics are shorter, with random configurations. Organic solvent-extraction techniques are most commonly reported, motivating the design of our novel instrument, the Extractor for Chemical Analysis of Lipid Biomarkers in Regolith (ExCALiBR), which extracts lipids while preserving origin-diagnostic features that can indicate biogenicity.
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Affiliation(s)
- Denise K Buckner
- Department of Geological Sciences, University of Florida, Gainesville, Florida, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Morgan J Anderson
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
- Axient Corporation, Huntsville, Alabama, USA
| | - Sydney Wisnosky
- Axient Corporation, Huntsville, Alabama, USA
- Department of Biology, University of Miami, Coral Gables, Florida, USA
| | - Walter Alvarado
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
| | - Michel Nuevo
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Amy J Williams
- Department of Geological Sciences, University of Florida, Gainesville, Florida, USA
| | - Antonio J Ricco
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
- Electrical Engineering-Integrated Circuits Laboratory, Stanford University, Stanford, California, USA
| | - Anamika
- Department of Space Studies, University of North Dakota, Grand Forks, North Dakota, USA
| | - Sara Debic
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Trinh Hoac
- Axient Corporation, Huntsville, Alabama, USA
| | - Linda Jahnke
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | | | - Ross Williams
- Civil & Environmental Engineering & Earth Sciences, Notre Dame University, Notre Dame, Indiana, USA
| | - Mary Beth Wilhelm
- Space Science & Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
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10
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Brunoir T, Mulligan C, Sistiaga A, Vuu KM, Shih PM, O'Reilly SS, Summons RE, Gold DA. Common origin of sterol biosynthesis points to a feeding strategy shift in Neoproterozoic animals. Nat Commun 2023; 14:7941. [PMID: 38040676 PMCID: PMC10692144 DOI: 10.1038/s41467-023-43545-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 11/13/2023] [Indexed: 12/03/2023] Open
Abstract
Steranes preserved in sedimentary rocks serve as molecular fossils, which are thought to record the expansion of eukaryote life through the Neoproterozoic Era ( ~ 1000-541 Ma). Scientists hypothesize that ancient C27 steranes originated from cholesterol, the major sterol produced by living red algae and animals. Similarly, C28 and C29 steranes are thought to be derived from the sterols of prehistoric fungi, green algae, and other microbial eukaryotes. However, recent work on annelid worms-an advanced group of eumetazoan animals-shows that they are also capable of producing C28 and C29 sterols. In this paper, we explore the evolutionary history of the 24-C sterol methyltransferase (smt) gene in animals, which is required to make C28+ sterols. We find evidence that the smt gene was vertically inherited through animals, suggesting early eumetazoans were capable of C28+ sterol synthesis. Our molecular clock of the animal smt gene demonstrates that its diversification coincides with the rise of C28 and C29 steranes in the Neoproterozoic. This study supports the hypothesis that early eumetazoans were capable of making C28+ sterols and that many animal lineages independently abandoned its biosynthesis around the end-Neoproterozoic, coinciding with the rise of abundant eukaryotic prey.
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Affiliation(s)
- T Brunoir
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, CA, USA
| | - C Mulligan
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, CA, USA
| | - A Sistiaga
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - K M Vuu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - P M Shih
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - S S O'Reilly
- Department of Life Sciences, Atlantic Technological University, ATU Sligo, Ash Lane, Sligo, Ireland
| | - R E Summons
- Department of Earth, Atmospheric, and Planetary Sciences. Massachusetts Institute of Technology, Cambridge, MA, USA
| | - D A Gold
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, CA, USA.
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11
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Marshall B, Amritkar K, Wolfe M, Kaçar B, Landick R. Evolutionary flexibility and rigidity in the bacterial methylerythritol phosphate (MEP) pathway. Front Microbiol 2023; 14:1286626. [PMID: 38029103 PMCID: PMC10663253 DOI: 10.3389/fmicb.2023.1286626] [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: 08/31/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Terpenoids are a diverse class of compounds with wide-ranging uses including as industrial solvents, pharmaceuticals, and fragrances. Efforts to produce terpenoids sustainably by engineering microbes for fermentation are ongoing, but industrial production still largely relies on nonrenewable sources. The methylerythritol phosphate (MEP) pathway generates terpenoid precursor molecules and includes the enzyme Dxs and two iron-sulfur cluster enzymes: IspG and IspH. IspG and IspH are rate limiting-enzymes of the MEP pathway but are challenging for metabolic engineering because they require iron-sulfur cluster biogenesis and an ongoing supply of reducing equivalents to function. Therefore, identifying novel alternatives to IspG and IspH has been an on-going effort to aid in metabolic engineering of terpenoid biosynthesis. We report here an analysis of the evolutionary diversity of terpenoid biosynthesis strategies as a resource for exploration of alternative terpenoid biosynthesis pathways. Using comparative genomics, we surveyed a database of 4,400 diverse bacterial species and found that some may have evolved alternatives to the first enzyme in the pathway, Dxs making it evolutionarily flexible. In contrast, we found that IspG and IspH are evolutionarily rigid because we could not identify any species that appear to have enzymatic routes that circumvent these enzymes. The ever-growing repository of sequenced bacterial genomes has great potential to provide metabolic engineers with alternative metabolic pathway solutions. With the current state of knowledge, we found that enzymes IspG and IspH are evolutionarily indispensable which informs both metabolic engineering efforts and our understanding of the evolution of terpenoid biosynthesis pathways.
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Affiliation(s)
- Bailey Marshall
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Kaustubh Amritkar
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Michael Wolfe
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, United States
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
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12
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Malaterre C, Ten Kate IL, Baqué M, Debaille V, Grenfell JL, Javaux EJ, Khawaja N, Klenner F, Lara YJ, McMahon S, Moore K, Noack L, Patty CHL, Postberg F. Is There Such a Thing as a Biosignature? ASTROBIOLOGY 2023; 23:1213-1227. [PMID: 37962841 DOI: 10.1089/ast.2023.0042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The concept of a biosignature is widely used in astrobiology to suggest a link between some observation and a biological cause, given some context. The term itself has been defined and used in several ways in different parts of the scientific community involved in the search for past or present life on Earth and beyond. With the ongoing acceleration in the search for life in distant time and/or deep space, there is a need for clarity and accuracy in the formulation and reporting of claims. Here, we critically review the biosignature concept(s) and the associated nomenclature in light of several problems and ambiguities emphasized by recent works. One worry is that these terms and concepts may imply greater certainty than is usually justified by a rational interpretation of the data. A related worry is that terms such as "biosignature" may be inherently misleading, for example, because the divide between life and non-life-and their observable effects-is fuzzy. Another worry is that different parts of the multidisciplinary community may use non-equivalent or conflicting definitions and conceptions, leading to avoidable confusion. This review leads us to identify a number of pitfalls and to suggest how they can be circumvented. In general, we conclude that astrobiologists should exercise particular caution in deciding whether and how to use the concept of biosignature when thinking and communicating about habitability or life. Concepts and terms should be selected carefully and defined explicitly where appropriate. This would improve clarity and accuracy in the formulation of claims and subsequent technical and public communication about some of the most profound and important questions in science and society. With this objective in mind, we provide a checklist of questions that scientists and other interested parties should ask when assessing any reported detection of a "biosignature" to better understand exactly what is being claimed.
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Affiliation(s)
- Christophe Malaterre
- Département de philosophie, Chaire de recherche du Canada en philosophie des sciences de la vie, Université du Québec à Montréal (UQAM), Montréal, Québec, Canada
- Centre interuniversitaire de recherche sur la science et la technologie (CIRST), Université du Québec à Montréal (UQAM), Montréal, Québec, Canada
| | - Inge Loes Ten Kate
- Department of Earth Sciences, Utrecht University, Utrecht, the Netherlands
| | - Mickael Baqué
- Planetary Laboratories Department, Institute of Planetary Research, German Aerospace Center (DLR), Berlin, Germany
| | - Vinciane Debaille
- Laboratoire G-Time, Université libre de Bruxelles, Brussels, Belgium
| | - John Lee Grenfell
- Department of Extrasolar Planets and Atmospheres, Institute of Planetary Research, German Aerospace Center (DLR), Berlin, Germany
| | - Emmanuelle J Javaux
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Nozair Khawaja
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
| | - Fabian Klenner
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Yannick J Lara
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Sean McMahon
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
- School of GeoSciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Keavin Moore
- Department of Earth & Planetary Sciences, McGill University, Montreal, Québec, Canada
- Trottier Space Institute, McGill University, Montreal, Québec, Canada
| | - Lena Noack
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
| | - C H Lucas Patty
- Physikalisches Institut, Universität Bern, Bern, Switzerland
- Center for Space and Habitability, Universität Bern, Bern, Switzerland
| | - Frank Postberg
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
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13
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Zhang T, He W, Liang Q, Zheng F, Xiao X, Zeng Z, Zhou J, Yao W, Chen H, Zhu Y, Zhao J, Zheng Y, Zhang C. Lipidomic diversity and proxy implications of archaea from cold seep sediments of the South China Sea. Front Microbiol 2023; 14:1241958. [PMID: 37954235 PMCID: PMC10635418 DOI: 10.3389/fmicb.2023.1241958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023] Open
Abstract
Cold seeps on the continental margins are characterized by intense microbial activities that consume a large portion of methane by anaerobic methanotrophic archaea (ANME) through anaerobic oxidation of methane (AOM). Although ANMEs are known to contain unique ether lipids that may have an important function in marine carbon cycling, their full lipidomic profiles and functional distribution in particular cold-seep settings are still poorly characterized. Here, we combined the 16S rRNA gene sequencing and lipidomic approaches to analyze archaeal communities and their lipids in cold seep sediments with distinct methane supplies from the South China Sea. The archaeal community was dominated by ANME-1 in the moderate seepage area with strong methane emission. Low seepage area presented higher archaeal diversity covering Lokiarchaeia, Bathyarchaeia, and Thermoplasmata. A total of 55 core lipids (CLs) and intact polar lipids (IPLs) of archaea were identified, which included glycerol dialkyl glycerol tetraethers (GDGTs), hydroxy-GDGTs (OH-GDGTs), archaeol (AR), hydroxyarchaeol (OH-AR), and dihydroxyarchaeol (2OH-AR). Diverse polar headgroups constituted the archaeal IPLs. High concentrations of dissolved inorganic carbon (DIC) with depleted δ13CDIC and high methane index (MI) values based on both CLs (MICL) and IPLs (MIIPL) indicate that ANMEs were active in the moderate seepage area. The ANME-2 and ANME-3 clades were characterized by enhanced glycosidic and phosphoric diether lipids production, indicating their potential role in coupling carbon and phosphurus cycling in cold seep ecosystems. ANME-1, though representing a smaller proportion of total archaea than ANME-2 and ANME-3 in the low seepage area, showed a positive correlation with MIIPL, indicating a different mechanism contributing to the IPL-GDGT pool. This also suggests that MIIPL could be a sensitive index to trace AOM activities performed by ANME-1. Overall, our study expands the understanding of the archaeal lipid composition in the cold seep and improves the application of MI using intact polar lipids that potentially link to extent ANME activities.
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Affiliation(s)
- Tingting Zhang
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
- National Engineering Research Center of Gas Hydrate Exploration and Development, Guangzhou, China
- East China Sea Ecological Center, Ministry of Natural Resources, Shanghai, China
| | - Wei He
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Qianyong Liang
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
- National Engineering Research Center of Gas Hydrate Exploration and Development, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Fengfeng Zheng
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Xi Xiao
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
- National Engineering Research Center of Gas Hydrate Exploration and Development, Guangzhou, China
| | - Zhiyu Zeng
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jingzhuo Zhou
- Key Laboratory of Coal Processing and Efficient Utilization of Ministry of Education, School of Chemical Engineering and Technology, China University of Mining and Technology, Xuzhou, China
| | - Wenyong Yao
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Haodong Chen
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, China
| | - Yuanqing Zhu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
| | - Jing Zhao
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Yan Zheng
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
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14
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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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15
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Runge EA, Mansor M, Kappler A, Duda JP. Microbial biosignatures in ancient deep-sea hydrothermal sulfides. GEOBIOLOGY 2023; 21:355-377. [PMID: 36524457 DOI: 10.1111/gbi.12539] [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: 06/27/2022] [Revised: 11/03/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Deep-sea hydrothermal systems provide ideal conditions for prebiotic reactions and ancient metabolic pathways and, therefore, might have played a pivotal role in the emergence of life. To understand this role better, it is paramount to examine fundamental interactions between hydrothermal processes, non-living matter, and microbial life in deep time. However, the distribution and diversity of microbial communities in ancient deep-sea hydrothermal systems are still poorly constrained, so evolutionary, and ecological relationships remain unclear. One important reason is an insufficient understanding of the formation of diagnostic microbial biosignatures in such settings and their preservation through geological time. This contribution centers around microbial biosignatures in Precambrian deep-sea hydrothermal sulfide deposits. Intending to provide a valuable resource for scientists from across the natural sciences whose research is concerned with the origins of life, we first introduce different types of biosignatures that can be preserved over geological timescales (rock fabrics and textures, microfossils, mineral precipitates, carbonaceous matter, trace metal, and isotope geochemical signatures). We then review selected reports of biosignatures from Precambrian deep-sea hydrothermal sulfide deposits and discuss their geobiological significance. Our survey highlights that Precambrian hydrothermal sulfide deposits potentially encode valuable information on environmental conditions, the presence and nature of microbial life, and the complex interactions between fluids, micro-organisms, and minerals. It further emphasizes that the geobiological interpretation of these records is challenging and requires the concerted application of analytical and experimental methods from various fields, including geology, mineralogy, geochemistry, and microbiology. Well-orchestrated multidisciplinary studies allow us to understand the formation and preservation of microbial biosignatures in deep-sea hydrothermal sulfide systems and thus help unravel the fundamental geobiology of ancient settings. This, in turn, is critical for reconstructing life's emergence and early evolution on Earth and the search for life elsewhere in the universe.
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Affiliation(s)
- Eric Alexander Runge
- Sedimentology and Organic Geochemistry, Department of Geosciences, Tübingen University, Tübingen, Germany
| | - Muammar Mansor
- Geomicrobiology, Department of Geosciences, Tübingen University, Tübingen, Germany
| | - Andreas Kappler
- Geomicrobiology, Department of Geosciences, Tübingen University, Tübingen, Germany
- Cluster of Excellence EXC 2124, Controlling Microbes to Fight Infection, Tübingen, Germany
| | - Jan-Peter Duda
- Sedimentology and Organic Geochemistry, Department of Geosciences, Tübingen University, Tübingen, Germany
- Geobiology, Geoscience Center, Göttingen University, Göttingen, Germany
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16
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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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/25/2023] [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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17
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Peltomaa E, Asikainen H, Blomster J, Pakkanen H, Rigaud C, Salmi P, Taipale S. Phytoplankton group identification with chemotaxonomic biomarkers: In combination they do better. PHYTOCHEMISTRY 2023; 209:113624. [PMID: 36871900 DOI: 10.1016/j.phytochem.2023.113624] [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: 10/05/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Chemotaxonomic biomarkers are needed to monitor and evaluate the nutritional quality of phytoplankton communities. The biomolecules produced by different phytoplankton species do not always follow genetic phylogeny. Therefore, we analyzed fatty acids, sterols, and carotenoids from 57 freshwater phytoplankton strains to evaluate the usability of these biomolecules as chemotaxonomic biomarkers. We found 29 fatty acids, 34 sterols, and 26 carotenoids in our samples. The strains were grouped into cryptomonads, cyanobacteria, diatoms, dinoflagellates, golden algae, green algae, and raphidophytes, and the phytoplankton group explained 61%, 54%, and 89% of the variability of fatty acids, sterols, and carotenoids, respectively. Fatty acid and carotenoid profiles distinguished most phytoplankton groups, but not flawlessly. For example, fatty acids could not distinguish golden algae and cryptomonads, whereas carotenoids did not separate diatoms and golden algae. The sterol composition was heterogeneous but seemed to be useful for distinguishing different genera within a phytoplankton group. The chemotaxonomy biomarkers yielded optimal genetic phylogeny when the fatty acids, sterols, and carotenoids were used together in multivariate statistical analysis. Our results suggest that the accuracy of phytoplankton composition modeling could be enhanced by combining these three biomolecule groups.
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Affiliation(s)
- E Peltomaa
- Department of Forest Sciences, Latokartanonkaari 7, FI-00014, University of Helsinki, Finland.
| | - H Asikainen
- Department of Biological and Environmental Science, Survontie 9 C, FI-40014, University of Jyväskylä, Finland.
| | - J Blomster
- Ecosystems and Environment Research Group, Faculty of Biological and Environmental Sciences, Viikinkaari 1, FI-00014, University of Helsinki, Finland.
| | - H Pakkanen
- Department of Biological and Environmental Science, Survontie 9 C, FI-40014, University of Jyväskylä, Finland.
| | - C Rigaud
- Department of Biological and Environmental Science, Survontie 9 C, FI-40014, University of Jyväskylä, Finland.
| | - P Salmi
- Spectral Imaging Laboratory, Faculty of Information Technology, Mattilanniemi 2, FI-40014, University of Jyväskylä, Finland.
| | - S Taipale
- Department of Biological and Environmental Science, Survontie 9 C, FI-40014, University of Jyväskylä, Finland.
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18
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Taylor CW, Bowden SA. What about nitrogen? Using nitrogen as a carrier gas during the analysis of petroleum biomarkers by gas chromatography mass spectrometry. J Chromatogr A 2023; 1697:463989. [PMID: 37075497 DOI: 10.1016/j.chroma.2023.463989] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/06/2023] [Accepted: 04/11/2023] [Indexed: 04/21/2023]
Abstract
Gas chromatography mass spectrometry (GC-MS) is a commonly used method for organic geochemistry for both academic research and applications such as petroleum analysis. Gas chromatography requires a carrier gas, which needs to be both volatile and stable and in most organic geochemical applications helium or hydrogen have been used, with helium predominating for gas chromatography mass spectrometry. Helium, however, is becoming an increasingly scarce resource and is not sustainable. Hydrogen is the most commonly considered alternative carrier gas to helium but has characteristics that in certain respects make its use less practical, foremost is that hydrogen is flammable and explosive. But as hydrogen is increasingly used as a fuel, higher demand may also make its use less desirable. Here we show that nitrogen can be used for the GC-MS analysis of fossil lipid biomarkers. Using nitrogen, chromatographic separation of isomers and homologues can be achieved, but sensitivity is orders of magnitude less than for helium. It is reasonable to use nitrogen as a carrier gas in applications where low levels of detection are not needed, such as the characterization of samples of crude oil or foodstuffs, or potentially as part of a gas-mixture seeking to reduce helium-demand but maintain a level of chromatographic separation sufficient to support proxy-based characterizations of petroleum.
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Affiliation(s)
- Colin W Taylor
- Department of Geology and Geophysics, School of Geosciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom, AB24 3UE, 01224 273495.
| | - Stephen A Bowden
- Department of Geology and Geophysics, School of Geosciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom, AB24 3UE, 01224 273495
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19
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Palmitic Acid Inhibits the Growth and Metastasis of Gastric Cancer by Blocking the STAT3 Signaling Pathway. Cancers (Basel) 2023; 15:cancers15020388. [PMID: 36672337 PMCID: PMC9856364 DOI: 10.3390/cancers15020388] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 01/11/2023] Open
Abstract
Lipidomic analyses have suggested that palmitic acid (PA) is linked to gastric cancer. However, its effects and action mechanisms remain unclear. Therefore, we evaluated the effects of PA on cell proliferation, invasion, and apoptosis in human gastric cancer, as well as the role of p-STAT3 in mediating its effects. The results of the MTT and colony formation assays revealed that PA blocked gastric cancer cell proliferation in a concentration-dependent manner. The EdU-DNA assay indicated that 50 μM of PA could block gastric cell proliferation by 30.6-80.0%. The Transwell assay also confirmed the concentration dependence of PA-induced inhibitory effect on cell invasion. The flow cytometry analysis indicated that PA treatment for 18 h could induce gastric cancer cell apoptosis. The immunohistochemical staining revealed that p-STAT3 levels were higher in the gastric cancer tissues than in the control tissues. We demonstrated that PA treatment for 12 h decreased the expressions of p-STAT3, p-JAK2, N-cadherin, and vimentin, and inhibited the nuclear expression of p-STAT3 in gastric cancer cells. Finally, PA treatment (50 mg/kg) decreased gastric cancer growth (54.3%) in the xenograft models. Collectively, these findings demonstrate that PA inhibits cell proliferation and invasion and induces human gastric cancer cell apoptosis.
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20
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Razzell Hollis J, Sharma S, Abbey W, Bhartia R, Beegle L, Fries M, Hein JD, Monacelli B, Nordman AD. A Deep Ultraviolet Raman and Fluorescence Spectral Library of 51 Organic Compounds for the SHERLOC Instrument Onboard Mars 2020. ASTROBIOLOGY 2023; 23:1-23. [PMID: 36367974 PMCID: PMC9810352 DOI: 10.1089/ast.2022.0023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/01/2022] [Indexed: 06/16/2023]
Abstract
We report deep ultraviolet (DUV) Raman and Fluorescence spectra obtained on a SHERLOC (Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals) analog instrument for 51 pure organic compounds, including 5 carboxylic acids, 10 polycyclic aromatic hydrocarbons, 24 amino acids, 6 nucleobases, and 6 different grades of macromolecular carbon from humic acid to graphite. Organic mixtures were not investigated. We discuss how the DUV fluorescence and Raman spectra exhibited by different organic compounds allow for detection, classification, and identification of organics by SHERLOC. We find that 1- and 2-ring aromatic compounds produce detectable fluorescence within SHERLOC's spectral range (250-355 nm), but fluorescence spectra are not unique enough to enable easy identification of particular compounds. However, both aromatic and aliphatic compounds can be identified by their Raman spectra, with the number of Raman peaks and their positions being highly specific to chemical structure, within SHERLOC's reported spectral uncertainty of ±5 cm-1. For compounds that are not in the Library, classification is possible by comparing the general number and position of dominant Raman peaks with trends for different kinds of organic compounds.
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Affiliation(s)
- Joseph Razzell Hollis
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
| | - Sunanda Sharma
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - William Abbey
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | - Luther Beegle
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Marc Fries
- NASA Johnson Space Center, Houston, Texas, USA
| | - Jeffrey D. Hein
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Brian Monacelli
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Austin D. Nordman
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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Leblond JD, Elkins LC, Sabir K. Sterols of Amphidinium species in the Operculatum Clade: Predominance of cholesterol instead of Δ 8 (14) sterols previously considered Amphidinium-specific biomarkers. J Eukaryot Microbiol 2023; 70:e12942. [PMID: 36039683 DOI: 10.1111/jeu.12942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/17/2022] [Accepted: 08/23/2022] [Indexed: 01/13/2023]
Abstract
The dinoflagellates Amphidinium carterae and Amphidinium corpulentum have been previously characterized as having Δ8(14) -nuclear unsaturated 4α-methyl-5α-cholest-8(14)-en-3β-ol (C28:1 ) and 4α-methyl-5α-ergosta-8(14),24(28)-dien-3β-ol (amphisterol; C29:2 ) as predominant sterols, where they comprise approximately 80% of the total sterol composition. These two sterols have hence been considered as possible major sterol biomarkers for the genus. Here, we have examined the sterols of four recently identified species of Amphidinium (Amphidinium fijiense, Amphidinium magnum, Amphidinium theodori, and Amphidinium tomasii) that are closely related to Amphidinium operculatum as part of what is termed the Operculatum Clade to show that each species has its sterol composition dominated by the common dinoflagellate sterol cholesterol (cholest-5-en-3β-ol; C27:1 ), which is found in many other dinoflagellate genera, rather than Δ8(14) sterols. While the Δ8(14) sterols 4α-methyl-5α-cholest-8(14)-en-3β-ol and 4α,23,24-trimethyl-5α-cholest-8(14),22E-dien-3β-ol (C30:2 ) were present as minor sterols along with another common dinoflagellate sterol, 4α,23,24-trimethyl-5α-cholest-22E-en-3β-ol (dinosterol; C30:1 ), in some of these four species, amphisterol was not conclusively observed. From a chemotaxonomic perspective, while this does reinforce the genus Amphidinium's ability to produce Δ8(14) sterols, albeit here as minor sterols, these results demonstrate that caution should be used when considering Δ8(14) sterols, especially amphisterol, as Amphidinium-specific biomarkers within these species where cholesterol is the predominant sterol.
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Affiliation(s)
- Jeffrey D Leblond
- Ecology and Evolution Group, Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Lindsey C Elkins
- Ecology and Evolution Group, Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Kyra Sabir
- Ecology and Evolution Group, Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
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22
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Glaciers as microbial habitats: current knowledge and implication. J Microbiol 2022; 60:767-779. [DOI: 10.1007/s12275-022-2275-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 10/16/2022]
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23
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Megevand V, Carrizo D, Lezcano MÁ, Moreno-Paz M, Cabrol NA, Parro V, Sánchez-García L. Lipid Profiles From Fresh Biofilms Along a Temperature Gradient on a Hydrothermal Stream at El Tatio (Chilean Andes), as a Proxy for the Interpretation of Past and Present Biomarkers Beyond Earth. Front Microbiol 2022; 13:811904. [PMID: 35832812 PMCID: PMC9271869 DOI: 10.3389/fmicb.2022.811904] [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: 11/09/2021] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Hydrothermal systems and their deposits are primary targets in the search for fossil evidence of life beyond Earth. However, to learn how to decode fossil biomarker records in ancient hydrothermal deposits, we must first be able to interpret unambiguously modern biosignatures, their distribution patterns, and their association with physicochemical factors. Here, we investigated the molecular and isotopic profile of microbial biomarkers along a thermal gradient (from 29 to 72°C) in a hot spring (labeled Cacao) from El Tatio, a geyser field in the Chilean Andes with abundant opaline silica deposits resembling the nodular and digitate structures discovered on Mars. As a molecular forensic approach, we focused on the analysis of lipid compounds bearing recognized resistance to degradation and the potential to reconstruct the paleobiology of an environment on a broader temporal scale than other, more labile, biomolecules. By exploiting the lipid biomarkers' potential to diagnose biological sources and carbon fixation pathways, we reconstructed the microbial community structure and its ecology along the Cacao hydrothermal transect. The taxonomic adscription of the lipid biomarkers was qualitatively corroborated with DNA sequencing analysis. The forensic capacity of the lipid biomarkers to identify biosources in fresh biofilms was validated down to the genus level for Roseiflexus, Chloroflexus, and Fischerella. We identified lipid biomarkers and DNA of several new cyanobacterial species in El Tatio and reported the first detection of Fischerella biomarkers at a temperature as high as 72°C. This, together with ecological peculiarities and the proportion of clades being characterized as unclassified, illustrates the ecological singularity of El Tatio and strengthens its astrobiological relevance. The Cacao hydrothermal ecosystem was defined by a succession of microbial communities and metabolic traits associated with a high- (72°C) to low-(29°C) temperature gradient that resembled the inferred metabolic sequence events from the 16S rRNA gene universal phylogenetic tree from thermophilic to anoxygenic photosynthetic species and oxygenic phototrophs. The locally calibrated DNA-validated lipidic profile in the Cacao biofilms provided a modern (molecular and isotopic) end member to facilitate the recognition of past biosources and metabolisms from altered biomarkers records in ancient silica deposits at El Tatio analogous to Martian opaline silica structures.
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Affiliation(s)
- Valentine Megevand
- Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
- Department of Earth Sciences, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon, Lyon, France
| | | | | | | | - Nathalie A. Cabrol
- Carl Sagan Center for Research, The SETI Institute, Mountain View, CA, United States
| | - Víctor Parro
- Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
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Chirality in Organic and Mineral Systems: A Review of Reactivity and Alteration Processes Relevant to Prebiotic Chemistry and Life Detection Missions. Symmetry (Basel) 2022. [DOI: 10.3390/sym14030460] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Chirality is a central feature in the evolution of biological systems, but the reason for biology’s strong preference for specific chiralities of amino acids, sugars, and other molecules remains a controversial and unanswered question in origins of life research. Biological polymers tend toward homochiral systems, which favor the incorporation of a single enantiomer (molecules with a specific chiral configuration) over the other. There have been numerous investigations into the processes that preferentially enrich one enantiomer to understand the evolution of an early, racemic, prebiotic organic world. Chirality can also be a property of minerals; their interaction with chiral organics is important for assessing how post-depositional alteration processes could affect the stereochemical configuration of simple and complex organic molecules. In this paper, we review the properties of organic compounds and minerals as well as the physical, chemical, and geological processes that affect organic and mineral chirality during the preservation and detection of organic compounds. We provide perspectives and discussions on the reactions and analytical techniques that can be performed in the laboratory, and comment on the state of knowledge of flight-capable technologies in current and future planetary missions, with a focus on organics analysis and life detection.
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