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Wei ZF, Ta KW, Zhang NN, Liu SS, Meng L, Liu KQ, Cai CY, Peng XT, Shao CW. Molecular phylogenetic relationships based on mitochondrial genomes of novel deep-sea corals (Octocorallia: Alcyonacea): Insights into slow evolution and adaptation to extreme deep-sea environments. Zool Res 2024; 45:215-225. [PMID: 38247179 PMCID: PMC10839654 DOI: 10.24272/j.issn.2095-8137.2023.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/11/2023] [Indexed: 01/23/2024] Open
Abstract
A total of 10 specimens of Alcyonacea corals were collected at depths ranging from 905 m to 1 633 m by the manned submersible Shenhai Yongshi during two cruises in the South China Sea (SCS). Based on mitochondrial genomic characteristics, morphological examination, and sclerite scanning electron microscopy, the samples were categorized into four suborders (Calcaxonia, Holaxonia, Scleraxonia, and Stolonifera), and identified as 9 possible new cold-water coral species. Assessments of GC-skew dissimilarity, phylogenetic distance, and average nucleotide identity (ANI) revealed a slow evolutionary rate for the octocoral mitochondrial sequences. The nonsynonymous ( Ka) to synonymous ( Ks) substitution ratio ( Ka/ Ks) suggested that the 14 protein-coding genes (PCGs) were under purifying selection, likely due to specific deep-sea environmental pressures. Correlation analysis of the median Ka/ Ks values of five gene families and environmental factors indicated that the genes encoding cytochrome b (cyt b) and DNA mismatch repair protein ( mutS) may be influenced by environmental factors in the context of deep-sea species formation. This study highlights the slow evolutionary pace and adaptive mechanisms of deep-sea corals.
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Affiliation(s)
- Zhan-Fei Wei
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Kai-Wen Ta
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China
| | - Nan-Nan Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Shan-Shan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Liang Meng
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Kai-Qiang Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
| | - Chong-Yang Cai
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Xiao-Tong Peng
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan 572000, China. E-mail:
| | - Chang-Wei Shao
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China. E-mail:
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Schwander L, Brabender M, Mrnjavac N, Wimmer JLE, Preiner M, Martin WF. Serpentinization as the source of energy, electrons, organics, catalysts, nutrients and pH gradients for the origin of LUCA and life. Front Microbiol 2023; 14:1257597. [PMID: 37854333 PMCID: PMC10581274 DOI: 10.3389/fmicb.2023.1257597] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/04/2023] [Indexed: 10/20/2023] Open
Abstract
Serpentinization in hydrothermal vents is central to some autotrophic theories for the origin of life because it generates compartments, reductants, catalysts and gradients. During the process of serpentinization, water circulates through hydrothermal systems in the crust where it oxidizes Fe (II) in ultramafic minerals to generate Fe (III) minerals and H2. Molecular hydrogen can, in turn, serve as a freely diffusible source of electrons for the reduction of CO2 to organic compounds, provided that suitable catalysts are present. Using catalysts that are naturally synthesized in hydrothermal vents during serpentinization H2 reduces CO2 to formate, acetate, pyruvate, and methane. These compounds represent the backbone of microbial carbon and energy metabolism in acetogens and methanogens, strictly anaerobic chemolithoautotrophs that use the acetyl-CoA pathway of CO2 fixation and that inhabit serpentinizing environments today. Serpentinization generates reduced carbon, nitrogen and - as newer findings suggest - reduced phosphorous compounds that were likely conducive to the origins process. In addition, it gives rise to inorganic microcompartments and proton gradients of the right polarity and of sufficient magnitude to support chemiosmotic ATP synthesis by the rotor-stator ATP synthase. This would help to explain why the principle of chemiosmotic energy harnessing is more conserved (older) than the machinery to generate ion gradients via pumping coupled to exergonic chemical reactions, which in the case of acetogens and methanogens involve H2-dependent CO2 reduction. Serpentinizing systems exist in terrestrial and deep ocean environments. On the early Earth they were probably more abundant than today. There is evidence that serpentinization once occurred on Mars and is likely still occurring on Saturn's icy moon Enceladus, providing a perspective on serpentinization as a source of reductants, catalysts and chemical disequilibrium for life on other worlds.
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Affiliation(s)
- Loraine Schwander
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Max Brabender
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Natalia Mrnjavac
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Jessica L. E. Wimmer
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Martina Preiner
- Microcosm Earth Center, Max Planck Institute for Terrestrial Microbiology and Philipps-Universität, Marburg, Germany
| | - William F. Martin
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
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Mullis MM, Selwyn JD, Kevorkian R, Tague ED, Castro HF, Campagna SR, Lloyd KG, Reese BK. Microbial survival mechanisms within serpentinizing Mariana forearc sediments. FEMS Microbiol Ecol 2023; 99:6985003. [PMID: 36631299 DOI: 10.1093/femsec/fiad003] [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: 02/23/2022] [Revised: 12/07/2022] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
Marine deep subsurface sediment is often a microbial environment under energy-limited conditions. However, microbial life has been found to persist and even thrive in deep subsurface environments. The Mariana forearc represents an ideal location for determining how microbial life can withstand extreme conditions including pH 10-12.5 and depleted nutrients. The International Ocean Discovery Program Expedition 366 to the Mariana Convergent Margin sampled three serpentinizing seamounts located along the Mariana forearc chain with elevated concentrations of methane, hydrogen, and sulfide. Across all three seamount summits, the most abundant transcripts were for cellular maintenance such as cell wall and membrane repair, and the most abundant metabolic pathways were the Entner-Doudoroff pathway and tricarboxylic acid cycle. At flank samples, sulfur cycling involving taurine assimilation dominated the metatranscriptomes. The in situ activity of these pathways was supported by the detection of their metabolic intermediates. All samples had transcripts from all three domains of Bacteria, Archaea, and Eukarya, dominated by Burkholderiales, Deinococcales, and Pseudomonales, as well as the fungal group Opisthokonta. All samples contained transcripts for aerobic methane oxidation (pmoABC) and denitrification (nirKS). The Mariana forearc microbial communities show activity not only consistent with basic survival mechanisms, but also coupled metabolic reactions.
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Affiliation(s)
- Megan M Mullis
- Life Sciences Department, Texas A&M University - Corpus Christi, Corpus Christi, TX, United States.,Dauphin Island Sea Lab, Mobile, AL, United States
| | - Jason D Selwyn
- Life Sciences Department, Texas A&M University - Corpus Christi, Corpus Christi, TX, United States
| | - Richard Kevorkian
- Microbiology Department, University of Tennessee, Knoxville, TN, United States
| | - Eric D Tague
- Microbiology Department, University of Tennessee, Knoxville, TN, United States
| | - Hector F Castro
- Microbiology Department, University of Tennessee, Knoxville, TN, United States.,Chemistry Department, UTK Biological and Small Molecule Mass Spectrometry Core, Knoxville, TN, United States
| | - Shawn R Campagna
- Microbiology Department, University of Tennessee, Knoxville, TN, United States.,Chemistry Department, UTK Biological and Small Molecule Mass Spectrometry Core, Knoxville, TN, United States
| | - Karen G Lloyd
- Microbiology Department, University of Tennessee, Knoxville, TN, United States
| | - Brandi Kiel Reese
- Dauphin Island Sea Lab, Mobile, AL, United States.,Marine Sciences Department, University of South Alabama, Mobile, AL, United States
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Li HY, Zhao RP, Li J, Tamura Y, Spencer C, Stern RJ, Ryan JG, Xu YG. Molybdenum isotopes unmask slab dehydration and melting beneath the Mariana arc. Nat Commun 2021; 12:6015. [PMID: 34650082 PMCID: PMC8517010 DOI: 10.1038/s41467-021-26322-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 09/23/2021] [Indexed: 11/09/2022] Open
Abstract
How serpentinites in the forearc mantle and subducted lithosphere become involved in enriching the subarc mantle source of arc magmas is controversial. Here we report molybdenum isotopes for primitive submarine lavas and serpentinites from active volcanoes and serpentinite mud volcanoes in the Mariana arc. These data, in combination with radiogenic isotopes and elemental ratios, allow development of a model whereby shallow, partially serpentinized and subducted forearc mantle transfers fluid and melt from the subducted slab into the subarc mantle. These entrained forearc mantle fragments are further metasomatized by slab fluids/melts derived from the dehydration of serpentinites in the subducted lithospheric slab. Multistage breakdown of serpentinites in the subduction channel ultimately releases fluids/melts that trigger Mariana volcanic front volcanism. Serpentinites dragged down from the forearc mantle are likely exhausted at >200 km depth, after which slab-derived serpentinites are responsible for generating slab melts. How the subducted oceanic lithosphere provides fluids and melts to flux the subarc mantle source of arc magmas is controversial. Here the authors use Mo and other isotopes to show serpentinites formed in both the forearc mantle and the subducted lithosphere contribute to generating arc magmas.
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Affiliation(s)
- Hong-Yan Li
- State Key Laboratory of Isotope Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China. .,CAS Center for Excellence in Deep Earth Science, Guangzhou, 510640, China. .,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
| | - Rui-Peng Zhao
- State Key Laboratory of Isotope Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Li
- State Key Laboratory of Isotope Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.,CAS Center for Excellence in Deep Earth Science, Guangzhou, 510640, China
| | - Yoshihiko Tamura
- Research Institute for Marine Geodynamics (IMG), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan
| | - Christopher Spencer
- Department of Geological Sciences and Geological Engineering, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Robert J Stern
- Department of Geoscience, University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Jeffrey G Ryan
- School of Geosciences, University of South Florida, Tampa, FL, 33620, USA
| | - Yi-Gang Xu
- State Key Laboratory of Isotope Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.,CAS Center for Excellence in Deep Earth Science, Guangzhou, 510640, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
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Subduction hides high-pressure sources of energy that may feed the deep subsurface biosphere. Nat Commun 2020; 11:3880. [PMID: 32759942 PMCID: PMC7406650 DOI: 10.1038/s41467-020-17342-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 06/25/2020] [Indexed: 11/10/2022] Open
Abstract
Geological sources of H2 and abiotic CH4 have had a critical role in the evolution of our planet and the development of life and sustainability of the deep subsurface biosphere. Yet the origins of these sources are largely unconstrained. Hydration of mantle rocks, or serpentinization, is widely recognized to produce H2 and favour the abiotic genesis of CH4 in shallow settings. However, deeper sources of H2 and abiotic CH4 are missing from current models, which mainly invoke more oxidized fluids at convergent margins. Here we combine data from exhumed subduction zone high-pressure rocks and thermodynamic modelling to show that deep serpentinization (40–80 km) generates significant amounts of H2 and abiotic CH4, as well as H2S and NH3. Our results suggest that subduction, worldwide, hosts large sources of deep H2 and abiotic CH4, potentially providing energy to the overlying subsurface biosphere in the forearc regions of convergent margins. Geological sources of H2 and abiotic CH4 have had a critical role in the evolution of life and sustainability of the deep subsurface biosphere, yet the origins of these sources remain largely unconstrained. Here the authors show that deep serpentinization (40–80 km) during subduction generates significant amounts of H2 and abiotic CH4, potentially providing energy to the overlying subsurface biosphere.
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McCaig AM, Früh-Green GL, Kelemen P, Teagle DAH. Serpentinite in the Earth system. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20190332. [PMID: 31902338 PMCID: PMC7015303 DOI: 10.1098/rsta.2019.0332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/12/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Andrew M. McCaig
- School of Earth and Environment, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | | | - Peter Kelemen
- Lamont-Doherty Earth Observatory, Palisades, NY, USA
- Earth and Environmental Sciences, Columbia University, New York, NY, USA
| | - Damon A. H. Teagle
- Ocean and Earth Science, University of Southampton, National Oceanography Centre Southampton, European Way, Southampton SO14 3ZH, UK
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