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Wang S, Li F, Luan Z, Li L, Xi S, Du Z, Zhang X. Novel SERS Probe Based on Ag Nanobean/Cu Foam for Deep-Sea Extreme Environment Biomolecule Detection. ACS Sens 2024. [PMID: 38709549 DOI: 10.1021/acssensors.4c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Here, we report on progress made in coupling advances in surface-enhanced Raman scattering (SERS) techniques with a deep-ocean deployable Raman spectrometer. Our SERS capability is provided by development of a Cu foam-loaded silver-nanobean (Ag/Cu foam) which we have successfully coupled to the tip of a Raman probe head capable of insertion into deep-sea sediments and associated fluids. Our purpose is to expand the range of molecular species which can be detected in deep-sea biogeochemical environments, and our initial targets are a series of amino acids reportedly found in pore waters of seep locations. Our work has progressed to the point of a full dock-based end-to-end test of the essential ship tether-ROV-deep-sea Raman system. We show here the initial results from this test as the essential requirement before at sea full ocean depth deployment. We describe in detail the procedures for preparing the Ag/Cu foam bean and demonstrate in our end-to-end test that this, when coupled to the spectrometer probe tip, yields a SERS signal enhancement of 1.2 × 106 for test molecules and detection of amino acids at 10-6 M levels consistent with reported levels of natural occurrence. Each nanobean unit is for single-use sensing since invasion of the sample fluid into the Ag/Cu foam matrix is not reversible. We describe techniques for bean rotation/replacement at depth to allow for multiple analyses at several locations during each ROV dive.
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Affiliation(s)
- Siyu Wang
- LaoShan Laboratory, Qingdao 266237, China
- Key Laboratory of Ocean Observation and Forecasting (LOOF), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Fei Li
- College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Zhendong Luan
- LaoShan Laboratory, Qingdao 266237, China
- Key Laboratory of Ocean Observation and Forecasting (LOOF), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Lianfu Li
- LaoShan Laboratory, Qingdao 266237, China
- Key Laboratory of Ocean Observation and Forecasting (LOOF), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Shichuan Xi
- LaoShan Laboratory, Qingdao 266237, China
- Key Laboratory of Ocean Observation and Forecasting (LOOF), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zengfeng Du
- LaoShan Laboratory, Qingdao 266237, China
- Key Laboratory of Ocean Observation and Forecasting (LOOF), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xin Zhang
- LaoShan Laboratory, Qingdao 266237, China
- Key Laboratory of Ocean Observation and Forecasting (LOOF), Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 101408, China
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Castel J, Pradillon F, Cueff V, Leger G, Daguin-Thiébaut C, Ruault S, Mary J, Hourdez S, Jollivet D, Broquet T. Genetic sex determination in three closely related hydrothermal vent gastropods, including one species with intersex individuals. J Evol Biol 2024:voae051. [PMID: 38699972 DOI: 10.1093/jeb/voae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Indexed: 05/05/2024]
Abstract
Molluscs have undergone many transitions between separate sexes and hermaphroditism, which is of interest for studying the evolution of sex determination and differentiation. Here we combined multi-locus genotypes obtained from RAD sequencing with anatomical observations of the gonads for three deep-sea hydrothermal vent gastropods of the genus Alviniconcha living in the southwest Pacific. We found that all three species (A. boucheti, A. strummeri, and A. kojimai) share the same male-heterogametic XY sex determination system, but that the gonads of XX A. kojimai individuals are invaded by a variable proportion of male reproductive tissue. The identification of Y-specific RAD loci (found only in A. boucheti) and the phylogenetic analysis of three sex-linked loci shared by all species suggested that X-Y recombination has evolved differently within each species. This situation of three species showing variation in gonadal development around a common sex determination system provides new insights into the reproductive mode of poorly known deep-sea species and opens up an opportunity to study the evolution of recombination suppression on sex chromosomes and its association with mixed or transitory sexual systems.
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Affiliation(s)
- J Castel
- UMR 7144 AD2M CNRS-Sorbonne Université, Station Biologique de Roscoff, Place Georges Tessier, 29680 Roscoff, France
| | - F Pradillon
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds , F-29280 Plouzané, France
| | - V Cueff
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds , F-29280 Plouzané, France
| | - G Leger
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds , F-29280 Plouzané, France
| | - C Daguin-Thiébaut
- UMR 7144 AD2M CNRS-Sorbonne Université, Station Biologique de Roscoff, Place Georges Tessier, 29680 Roscoff, France
| | - S Ruault
- UMR 7144 AD2M CNRS-Sorbonne Université, Station Biologique de Roscoff, Place Georges Tessier, 29680 Roscoff, France
| | - J Mary
- UMR 7144 AD2M CNRS-Sorbonne Université, Station Biologique de Roscoff, Place Georges Tessier, 29680 Roscoff, France
| | - S Hourdez
- UMR 8222 LECOB CNRS-Sorbonne Université, Observatoire Océanologique de Banyuls, 1 Avenue Pierre Fabre, 66650 Banyuls-sur-Mer, France
| | - D Jollivet
- UMR 7144 AD2M CNRS-Sorbonne Université, Station Biologique de Roscoff, Place Georges Tessier, 29680 Roscoff, France
| | - T Broquet
- UMR 7144 AD2M CNRS-Sorbonne Université, Station Biologique de Roscoff, Place Georges Tessier, 29680 Roscoff, France
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Park B, Cho B, Cho J, Kim T. Microplastic Contamination of a Benthic Ecosystem in a Hydrothermal Vent. Environ Sci Technol 2024; 58:7636-7642. [PMID: 38629715 DOI: 10.1021/acs.est.4c02811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Plastic contamination is a global pervasive issue, extending from coastal areas and open oceans to polar regions and even the deep sea. Microplastic (MP) contamination in hydrothermal vents, which are known for their high biodiversity even under extreme conditions, has remained largely unexplored. Here, we present, for the first time, MP pollution in a deep-sea hydrothermal vent at one of the biodiversity hotspots─the Central Indian Ridge. Not only the environment (seawater: 2.08 ± 1.04 MPs/L, surface sediments: 0.57 ± 0.19 MP/g) but also all six major benthic species investigated were polluted by MPs. MPs mainly consisted of polypropylene, polyethylene terephthalate, and polystyrene fragments ≤100 μm and were characterized as being either transparent or white in color. Remarkably, bioaccumulation and even biomagnification of microplastics were observed in the top predators of the ecosystem, such as squat lobsters (14.25 ± 4.65 MPs/individual) and vent crabs (14.00 ± 2.16 MPs/individual), since they contained more MPs than animals at lower trophic levels (e.g., mussels and snails, 1.75-6.00 average MPs/individuals). These findings reveal MP contamination of an ecosystem in a hydrothermal vent, thereby suggesting that their accumulation and magnification can occur in top-level animals, even within remote and extreme environments.
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Affiliation(s)
- Byeongyong Park
- Program in Biomedical Science and Engineering, Inha University, Incheon 22212, Republic of Korea
- Department of Ocean Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Boongho Cho
- Program in Biomedical Science and Engineering, Inha University, Incheon 22212, Republic of Korea
- Department of Ocean Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Jaemin Cho
- Program in Biomedical Science and Engineering, Inha University, Incheon 22212, Republic of Korea
- Department of Ocean Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Taewon Kim
- Program in Biomedical Science and Engineering, Inha University, Incheon 22212, Republic of Korea
- Department of Ocean Sciences, Inha University, Incheon 22212, Republic of Korea
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Yang M, Li B, Gan Z, Dong D, Li X. A new chemosymbiotic bivalve species of the genus Acharax Dall, 1908 (Bivalvia, Solemyida, Solemyidae) from the Haima cold seep of the South China Sea. Zookeys 2024; 1198:185-192. [PMID: 38698807 PMCID: PMC11063622 DOI: 10.3897/zookeys.1198.112618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/22/2024] [Indexed: 05/05/2024] Open
Abstract
Solemyidae is an ancient group of protobranch bivalves that typically inhabit unusual environments, such as deep-sea chemosynthetic environments, and are symbiotic with chemoautotrophic and gill-hosted bacteria. In May 2018, a living solemyid bivalve was collected using a remotely operated vehicle at a depth of 1,390 m from the Haima cold seep in the northwestern slope of the South China Sea. Through a comprehensive taxonomic approach combining morphological observations and molecular phylogeny reconstruction of concatenated mitochondrial COI,16S rRNA and 18S rRNA gene sequences, a new species, Acharaxhaimaensissp. nov. is identified and described. The discovery of this new species contributes to the diversity of known solemyids in deep-sea chemosynthetic environments.
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Affiliation(s)
- Mei Yang
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaInstitute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Baoquan Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, ChinaYantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantaiChina
| | - Zhibin Gan
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaInstitute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Dong Dong
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaInstitute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Xinzheng Li
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, ChinaInstitute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, ChinaCenter for Ocean Mega-Science, Chinese Academy of SciencesQingdaoChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaUniversity of Chinese Academy of SciencesBeijingChina
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Zhang C, Peng Y, Liu X, Wang J, Dong X. Deep-sea microbial genetic resources: new frontiers for bioprospecting. Trends Microbiol 2024; 32:321-324. [PMID: 38290879 DOI: 10.1016/j.tim.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Deep-sea ecosystems are home to a diverse community of microorganisms. These microbes are not only fundamental to ecological processes but also a treasure trove of natural products and enzymes with significant scientific and industrial applications. This forum focuses on the vast diversity of deep-sea microbes and their potential for bioprospecting. It also discusses threats posed by climate change and deep-sea mining to deep-sea microbial genetic resources, and proposes future research directions.
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Affiliation(s)
- Chuwen Zhang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China; School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Xinyue Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Jieni Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
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Claes JM, Haddock SHD, Coubris C, Mallefet J. Systematic Distribution of Bioluminescence in Marine Animals: A Species-Level Inventory. Life (Basel) 2024; 14:432. [PMID: 38672704 PMCID: PMC11051050 DOI: 10.3390/life14040432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Bioluminescence is the production of visible light by an organism. This phenomenon is particularly widespread in marine animals, especially in the deep sea. While the luminescent status of numerous marine animals has been recently clarified thanks to advancements in deep-sea exploration technologies and phylogenetics, that of others has become more obscure due to dramatic changes in systematics (themselves triggered by molecular phylogenies). Here, we combined a comprehensive literature review with unpublished data to establish a catalogue of marine luminescent animals. Inventoried animals were identified to species level in over 97% of the cases and were associated with a score reflecting the robustness of their luminescence record. While luminescence capability has been established in 695 genera of marine animals, luminescence reports from 99 additional genera need further confirmation. Altogether, these luminescent and potentially luminescent genera encompass 9405 species, of which 2781 are luminescent, 136 are potentially luminescent (e.g., suggested luminescence in those species needs further confirmation), 99 are non-luminescent, and 6389 have an unknown luminescent status. Comparative analyses reveal new insights into the occurrence of luminescence among marine animal groups and highlight promising research areas. This work will provide a solid foundation for future studies related to the field of marine bioluminescence.
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Affiliation(s)
- Julien M. Claes
- Marine Biology Laboratory, Earth and Life Institute, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium; (C.C.); (J.M.)
| | - Steven H. D. Haddock
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA
| | - Constance Coubris
- Marine Biology Laboratory, Earth and Life Institute, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium; (C.C.); (J.M.)
| | - Jérôme Mallefet
- Marine Biology Laboratory, Earth and Life Institute, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium; (C.C.); (J.M.)
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Hu X, Ma Z, Gong Z, Zhao F, Guo S, Zhang D, Jiang Y. A Highly Sensitive Deep-Sea Hydrodynamic Pressure Sensor Inspired by Fish Lateral Line. Biomimetics (Basel) 2024; 9:190. [PMID: 38534875 DOI: 10.3390/biomimetics9030190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
Hydrodynamic pressure sensors offer an auxiliary approach for ocean exploration by unmanned underwater vehicles (UUVs). However, existing hydrodynamic pressure sensors often lack the ability to monitor subtle hydrodynamic stimuli in deep-sea environments. In this study, we present the development of a deep-sea hydrodynamic pressure sensor (DSHPS) capable of operating over a wide range of water depths while maintaining exceptional hydrodynamic sensing performance. The DSHPS device was systematically optimized by considering factors such as piezoelectric polyvinylidene fluoride-trifluoroethylene/barium titanate [P(VDF-TrFE)/BTO] nanofibers, electrode configurations, sensing element dimensions, integrated circuits, and packaging strategies. The optimized DSHPS exhibited a remarkable pressure gradient response, achieving a minimum pressure difference detection capability of approximately 0.11 Pa. Additionally, the DSHPS demonstrated outstanding performance in the spatial positioning of dipole sources, which was elucidated through theoretical charge modeling and fluid-structure interaction (FSI) simulations. Furthermore, the integration of a high Young's modulus packaging strategy inspired by fish skull morphology ensured reliable sensing capabilities of the DSHPS even at depths of 1000 m in the deep sea. The DSHPS also exhibited consistent and reproducible positioning performance for subtle hydrodynamic stimulus sources across this wide range of water depths. We envision that the development of the DSHPS not only enhances our understanding of the evolutionary aspects of deep-sea canal lateral lines but also paves the way for the advancement of artificial hydrodynamic pressure sensors.
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Affiliation(s)
- Xiaohe Hu
- School of Mechanical, Electronic and Control Engineering, Beijing Jiaotong University, Beijing 100044, China
| | - Zhiqiang Ma
- School of Mechanical Engineering and Automation, Beihang University, Beijing 100191, China
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China
| | - Zheng Gong
- School of Mechanical Engineering and Automation, Beihang University, Beijing 100191, China
| | - Fuqun Zhao
- School of Mechanical, Electronic and Control Engineering, Beijing Jiaotong University, Beijing 100044, China
| | - Sheng Guo
- School of Mechanical, Electronic and Control Engineering, Beijing Jiaotong University, Beijing 100044, China
| | - Deyuan Zhang
- School of Mechanical Engineering and Automation, Beihang University, Beijing 100191, China
| | - Yonggang Jiang
- School of Mechanical Engineering and Automation, Beihang University, Beijing 100191, China
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Uniacke-Lowe S, Stanton C, Hill C, Ross P. Planococcus notacanthi sp. nov., isolated from the skin of a deep-sea snub-nosed spiny eel. Int J Syst Evol Microbiol 2024; 74. [PMID: 38512752 DOI: 10.1099/ijsem.0.006298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024] Open
Abstract
A novel bacterial strain, APC 4016T, was previously isolated from the skin of a snub-nosed spiny eel, Notacanthus chemnitzii, from a depth of 1000 m in the northern Atlantic Ocean. Cells were aerobic, cocci, motile, Gram-positive to Gram-variable staining, and gave rise to orange-pigmented colonies. Growth occurred at 4-40 °C (optimum, 25-28 °C), pH 5.5-12 (optimum, pH 7-7.5), and 0-12 % (w/v) NaCl (optimum, 1 %). 16S rRNA gene phylogenetic analysis confirmed that strain APC 4016T belonged to the genus Planococcus and was most closely related to Planococcus okeanokoites IFO 12536T (98.98 % 16S similarity). However, digital DNA-DNA hybridization and average nucleotide identity values between these two strains were low, at 20.1 and 83.8 %, respectively. Major (>10 %) cellular fatty acids of strain APC 4016T were iso-C14 : 0, anteiso-C15 : 0 and C16 : 1-ω-Alc. The predominant respiratory quinones were menaquinones 5, 6, 7 and 8. The major cellular polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine, and three unknown lipids were also present. The draft genome sequence is 3.6 Mb with a G+C content of 45.25 mol%. This strain was previously shown to have antimicrobial activity and to encode bacteriocin and secondary metabolite biosynthetic gene clusters. Based on the phylogenetic analysis and its distinct phenotypic characteristics, strain APC 4016T is deemed to represent a novel species of the genus Planococcus, and for which the name Planococcus notacanthi sp. nov. is proposed. The type strain of this species is APC 4016T (=DSM 115753T=NCIMB 15463T).
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Affiliation(s)
- Shona Uniacke-Lowe
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
- Teagasc Food Research Centre, Fermoy, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, Cork, Ireland
- Teagasc Food Research Centre, Fermoy, Ireland
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
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Hirayama H, Takaki Y, Abe M, Miyazaki M, Uematsu K, Matsui Y, Takai K. Methylomarinovum tepidoasis sp. nov., a moderately thermophilic methanotroph of the family Methylothermaceae isolated from a deep-sea hydrothermal field. Int J Syst Evol Microbiol 2024; 74:006288. [PMID: 38478579 PMCID: PMC10950024 DOI: 10.1099/ijsem.0.006288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/24/2024] [Indexed: 03/21/2024] Open
Abstract
A novel aerobic methanotrophic bacterium, designated as strain IN45T, was isolated from in situ colonisation systems deployed at the Iheya North deep-sea hydrothermal field in the mid-Okinawa Trough. IN45T was a moderately thermophilic obligate methanotroph that grew only on methane or methanol at temperatures between 25 and 56 °C (optimum 45-50 °C). It was an oval-shaped, Gram-reaction-negative, motile bacterium with a single polar flagellum and an intracytoplasmic membrane system. It required 1.5-4.0 % (w/v) NaCl (optimum 2-3 %) for growth. The major phospholipid fatty acids were C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8. The 16S rRNA gene sequence comparison revealed 99.1 % sequence identity with Methylomarinovum caldicuralii IT-9T, the only species of the genus Methylomarinovum with a validly published name within the family Methylothermaceae. The complete genome sequence of IN45T consisted of a 2.42-Mbp chromosome (DNA G+C content, 64.1 mol%) and a 20.5-kbp plasmid. The genome encodes genes for particulate methane monooxygenase and two types of methanol dehydrogenase (mxaFI and xoxF). Genes involved in the ribulose monophosphate pathway for carbon assimilation are encoded, but the transaldolase gene was not found. The genome indicated that IN45T performs partial denitrification of nitrate to N2O, and its occurrence was indirectly confirmed by N2O production in cultures grown with nitrate. Genomic relatedness indices between the complete genome sequences of IN45T and M. caldicuralii IT-9T, such as digital DNA-DNA hybridisation (51.2 %), average nucleotide identity (92.94 %) and average amino acid identity (93.21 %), indicated that these two methanotrophs should be separated at the species level. On the basis of these results, strain IN45T represents a novel species, for which we propose the name Methylomarinovum tepidoasis sp. nov. with IN45T (=JCM 35101T =DSM 113422T) as the type strain.
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Affiliation(s)
- Hisako Hirayama
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Yoshihiro Takaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Mariko Abe
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Masayuki Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | | | - Yohei Matsui
- Research Institute for Global Change (RIGC), JAMSTEC, Yokosuka, Kanagawa, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
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10
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Huang X, Wang Y, Li G, Shao Z, Xia J, Qin JJ, Wang W. Secondary metabolites from the deep-sea derived fungus Aspergillus terreus MCCC M28183. Front Microbiol 2024; 15:1361550. [PMID: 38419626 PMCID: PMC10899347 DOI: 10.3389/fmicb.2024.1361550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024] Open
Abstract
Aspergillus fungi are renowned for producing a diverse range of natural products with promising biological activities. These include lovastatin, itaconic acid, terrin, and geodin, known for their cholesterol-regulating, anti-inflammatory, antitumor, and antibiotic properties. In our current study, we isolated three dimeric nitrophenyl trans-epoxyamides (1-3), along with fifteen known compounds (4-18), from the culture of Aspergillus terreus MCCC M28183, a deep-sea-derived fungus. The structures of compounds 1-3 were elucidated using a combination of NMR, MS, NMR calculation, and ECD calculation. Compound 1 exhibited moderate inhibitory activity against human gastric cancer cells MKN28, while compound 7 showed similar activity against MGC803 cells, with both showing IC50 values below 10 μM. Furthermore, compound 16 exhibited moderate potency against Vibrio parahaemolyticus ATCC 17802, with a minimum inhibitory concentration (MIC) value of 7.8 μg/mL. This promising research suggests potential avenues for developing new pharmaceuticals, particularly in targeting specific cancer cell lines and combating bacterial infections, leveraging the unique properties of these Aspergillus-derived compounds.
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Affiliation(s)
- Xiaomei Huang
- Department of Marine Biology, Xiamen Key Laboratory of Intelligent Fishery, Xiamen Ocean Vocational College, Xiamen, China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Yichao Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Guangyu Li
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Jinmei Xia
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Jiang-Jiang Qin
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
| | - Weiyi Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
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11
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Sun X, Jiang H, Zhang S. Diversities and interactions of phages and bacteria in deep-sea sediments as revealed by metagenomics. Front Microbiol 2024; 14:1337146. [PMID: 38260883 PMCID: PMC10801174 DOI: 10.3389/fmicb.2023.1337146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Phages are found virtually everywhere, even in extreme environments, and are extremely diverse both in their virion structures and in their genomic content. They are thought to shape the taxonomic and functional composition of microbial communities as well as their stability. A number of studies on laboratory culture and viral metagenomic research provide deeper insights into the abundance, diversity, distribution, and interaction with hosts of phages across a wide range of ecosystems. Although most of these studies focus on easily accessible samples, such as soils, lakes, and shallow oceans, little is known about bathypelagic phages. In this study, through analyzing the 16S rRNA sequencing and viral metagenomic sequencing data of 25 samples collected from five different bathypelagic ecosystems, we detected a high diversity of bacteria and phages, particularly in the cold seep and hydrothermal vent ecosystems, which have stable chemical energy. The relative abundance of phages in these ecosystems was higher than in other three abyssal ecosystems. The low phage/host ratios obtained from host prediction were different from shallow ecosystems and indicated the prevalence of prophages, suggesting the complexity of phage-bacteria interactions in abyssal ecosystems. In the correlation analysis, we revealed several phages-bacteria interaction networks of potential ecological relevance. Our study contributes to a better understanding of the interactions between bathypelagic bacteria and their phages.
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Affiliation(s)
| | | | - Siyuan Zhang
- School of Marine Sciences, Ningbo University, Ningbo, China
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12
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Zhao HW, Yi Y, Li JQ, Wang JH. Two new mohangic acid derivatives from the deep-sea bacteria Alcanivorax dieselolei BC-5. Nat Prod Res 2024; 38:206-210. [PMID: 35975783 DOI: 10.1080/14786419.2022.2112578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 10/15/2022]
Abstract
Mohangic acids are a class of p-aminoacetophenonic acids that contain a conjugated triene or diene moiety. Herein, this paper reports two new mohangic acids E and F (1-2) together with a known compound mohangic acid A (3), which were isolated from the deep-sea sediment-derived bacteria Alcanivorax dieselolei BC-5. The structures of 1 and 2 were established by HRESIMS, 1 D and 2 D NMR, and IR spectroscopy.
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Affiliation(s)
- Hao-Wen Zhao
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, China
| | - Yan Yi
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, China
| | - Jia-Qi Li
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, China
| | - Jin-Hui Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, China
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13
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Hampel JJ, Moseley RD, Hamdan LJ. Microbiomes respond predictably to built habitats on the seafloor. Mol Ecol 2023; 32:6686-6695. [PMID: 35567341 DOI: 10.1111/mec.16504] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 04/14/2022] [Accepted: 05/05/2022] [Indexed: 11/26/2022]
Abstract
The seafloor contains complex ecosystems where habitat heterogeneity influences biodiversity. Natural biological and geological features including vents, seeps and reefs create habitats that select for distinct populations of micro- and macrofauna. While largely studied for macrobiological diversity, built habitats may also select distinct microbiomes. Built habitat density on the seafloor is increasing with ocean sprawl expanding in the continental shelf and slope, potentially having widespread effects on benthic communities. This study addresses one type of built habitat, shipwrecks, on microbiomes in surrounding sediment. Using deep-sea sediment samples (762 total) from the Gulf of Mexico, we report elevated diversity and a predictable core microbiome around nine shipwrecks. We show the sphere of influence of built habitats extends up to 300 m onto the seafloor. Supervised learning made predictions of sample proximity to structures based on frequency of taxa. Strongest predictions occurred in sediments nearest and furthest from sites for archaea and mid-transect for bacteria. The response of archaea to built habitats was consistent across sites, while bacteria showed greater between site variability. The archaeal core shipwreck microbiome was enriched in taxa (e.g., Bathyarchaeia, Lokiarchaeia, Thermoplasmata) not present in the surrounding seafloor. Shipwrecks shaped microbiomes in expected ways, providing insight on how built habitats impact microbiome biodiversity in the Anthropocene.
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Affiliation(s)
- Justyna J Hampel
- School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, Mississippi, USA
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Rachel D Moseley
- School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, Mississippi, USA
| | - Leila J Hamdan
- School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, Mississippi, USA
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14
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Liu N, Jiang T, Cui WP, Qi XQ, Li XG, Lu Y, Wu LF, Zhang WJ. The TorRS two component system regulates expression of TMAO reductase in response to high hydrostatic pressure in Vibrio fluvialis. Front Microbiol 2023; 14:1291578. [PMID: 38029070 PMCID: PMC10662104 DOI: 10.3389/fmicb.2023.1291578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
High hydrostatic pressure (HHP) regulated gene expression is one of the most commonly adopted strategies for microbial adaptation to the deep-sea environments. Previously we showed that the HHP-inducible trimethylamine N-oxide (TMAO) reductase improves the pressure tolerance of deep-sea strain Vibrio fluvialis QY27. Here, we investigated the molecular mechanism of HHP-responsive regulation of TMAO reductase TorA. By constructing torR and torS deletion mutants, we demonstrated that the two-component regulator TorR and sensor TorS are responsible for the HHP-responsive regulation of torA. Unlike known HHP-responsive regulatory system, the abundance of torR and torS was not affected by HHP. Complementation of the ΔtorS mutant with TorS altered at conserved phosphorylation sites revealed that the three sites were indispensable for substrate-induced regulation, but only the histidine located in the alternative transmitter domain was involved in pressure-responsive regulation. Taken together, we demonstrated that the induction of TMAO reductase by HHP is mediated through the TorRS system and proposed a bifurcation of signal transduction in pressure-responsive regulation from the substrate-induction. This work provides novel knowledge of the pressure regulated gene expression and will promote the understanding of the microbial adaptation to the deep-sea HHP environment.
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Affiliation(s)
- Na Liu
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ting Jiang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Peng Cui
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Qing Qi
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Institution of Deep-sea Life Sciences, IDSSE-BGI, Sanya, China
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CAS, Sanya, China
| | - Xue-Gong Li
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Institution of Deep-sea Life Sciences, IDSSE-BGI, Sanya, China
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CAS, Sanya, China
| | - Yuan Lu
- College of Information Science & Engineering, Ocean University of China, Qingdao, China
| | - Long-Fei Wu
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CAS, Sanya, China
- Aix Marseille University, CNRS, LCB, Marseille, France
| | - Wei-Jia Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Institution of Deep-sea Life Sciences, IDSSE-BGI, Sanya, China
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CAS, Sanya, China
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15
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Claassens L, Phillips B, Ebert DA, Delaney D, Henning B, Nestor V, Ililau A, Giddens J. First records of the Pacific sleeper shark Somniosus cf. pacificus in the western tropical Pacific. J Fish Biol 2023; 103:1214-1220. [PMID: 37340632 DOI: 10.1111/jfb.15487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/19/2023] [Indexed: 06/22/2023]
Abstract
Technological advances have enabled the expansion of ocean exploration to include the deep ocean, providing new species observations. Here, the authors present two new observations, captured by deep-sea cameras, of the sleeper shark Somniosus cf. pacificus from the Solomon Islands and Palau. This presents the first observation of S. cf. pacificus in the western Pacific tropics and extends its range about 2000 nautical miles south. The observations presented here provide much-needed information on the range of this species which can help guide future management and conservation actions.
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Affiliation(s)
- Louw Claassens
- Palau International Coral Reef Center, Koror, Palau
- Department of Zoology & Entomology, Rhodes University, Grahamstown, South Africa
| | - Brennan Phillips
- University of Rhode Island, Department of Ocean Engineering, Narragansett, Rhode Island, USA
| | - David A Ebert
- Pacific Shark Research Center, Moss Landing Marine Laboratories, Moss Landing, California, USA
- South African Institute for Aquatic Biodiversity, Grahamstown, South Africa
- Department of Ichthyology, California Academy of Sciences, San Francisco, California, USA
| | - Denley Delaney
- National Geographic Society, Exploration Technology Lab, Washington, District of Columbia, USA
| | - Brad Henning
- National Geographic Society, Exploration Technology Lab, Washington, District of Columbia, USA
| | | | | | - Jonatha Giddens
- National Geographic Society, Exploration Technology Lab, Washington, District of Columbia, USA
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16
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Law STS, Yu Y, Nong W, So WL, Li Y, Swale T, Ferrier DEK, Qiu J, Qian P, Hui JHL. The genome of the deep-sea anemone Actinernus sp. contains a mega-array of ANTP-class homeobox genes. Proc Biol Sci 2023; 290:20231563. [PMID: 37876192 PMCID: PMC10598428 DOI: 10.1098/rspb.2023.1563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
Members of the phylum Cnidaria include sea anemones, corals and jellyfish, and have successfully colonized both marine and freshwater habitats throughout the world. The understanding of how cnidarians adapt to extreme environments such as the dark, high-pressure deep-sea habitat has been hindered by the lack of genomic information. Here, we report the first chromosome-level deep-sea cnidarian genome, of the anemone Actinernus sp., which was 1.39 Gbp in length and contained 44 970 gene models including 14 806 tRNA genes and 30 164 protein-coding genes. Analyses of homeobox genes revealed the longest chromosome hosts a mega-array of Hox cluster, HoxL, NK cluster and NKL homeobox genes; until now, such an array has only been hypothesized to have existed in ancient ancestral genomes. In addition to this striking arrangement of homeobox genes, analyses of microRNAs revealed cnidarian-specific complements that are distinctive for nested clades of these animals, presumably reflecting the progressive evolution of the gene regulatory networks in which they are embedded. Also, compared with other sea anemones, circadian rhythm genes were lost in Actinernus sp., which likely reflects adaptation to living in the dark. This high-quality genome of a deep-sea cnidarian thus reveals some of the likely molecular adaptations of this ecologically important group of metazoans to the extreme deep-sea environment. It also deepens our understanding of the evolution of genome content and organization of animals in general and cnidarians in particular, specifically from the viewpoint of key developmental control genes like the homeobox-encoding genes, where we find an array of genes that until now has only been hypothesized to have existed in the ancient ancestor that pre-dated both the cnidarians and bilaterians.
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Affiliation(s)
- Sean Tsz Sum Law
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Yifei Yu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Wai Lok So
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Yiqian Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Thomas Swale
- Dovetail Genomics, LLC, Scotts Valley, CA 95066, USA
| | - David E. K. Ferrier
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St. Andrews, St. Andrews, UK
| | - Jianwen Qiu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China
- Department of Biology, Hong Kong Baptist University, Hong Kong, People's Republic of China
| | - Peiyuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Jerome Ho Lam Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
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17
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Zhang Y, Xie CL, Wang Y, He XW, Xie MM, Li Y, Zhang K, Zou ZB, Yang LH, Xu R, Yang XW. Penidihydrocitrinins A-C: New Polyketides from the Deep-Sea-Derived Penicillium citrinum W17 and Their Anti-Inflammatory and Anti-Osteoporotic Bioactivities. Mar Drugs 2023; 21:538. [PMID: 37888473 PMCID: PMC10608093 DOI: 10.3390/md21100538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Three new polyketides (penidihydrocitrinins A-C, 1-3) and fourteen known compounds (4-17) were isolated from the deep-sea-derived Penicillium citrinum W17. Their structures were elucidated by comprehensive analyses of 1D and 2D NMR, HRESIMS, and ECD calculations. Compounds 1-17 were evaluated for their anti-inflammatory and anti-osteoporotic bioactivities. All isolates exhibited significant inhibitory effects on LPS-stimulated nitric oxide production in murine brain microglial BV-2 cells in a dose-response manner. Notably, compound 14 displayed the strongest effect with the IC50 value of 4.7 µM. Additionally, compounds 6, 7, and 8 significantly enhanced osteoblast mineralization, which was comparable to that of the positive control, purmorphamine. Furthermore, these three compounds also suppressed osteoclastogenesis in a dose-dependent manner under the concentrations of 2.5 μM, 5.0 μM, and 10 μM.
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Affiliation(s)
- Yong Zhang
- Key Laboratory of Marine Genetic Resources, Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Y.Z.); (C.-L.X.); (Y.W.); (X.-W.H.); (M.-M.X.); (Y.L.); (K.Z.); (Z.-B.Z.)
| | - Chun-Lan Xie
- Key Laboratory of Marine Genetic Resources, Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Y.Z.); (C.-L.X.); (Y.W.); (X.-W.H.); (M.-M.X.); (Y.L.); (K.Z.); (Z.-B.Z.)
- School of Medicine, Xiamen University, South Xiangan Road, Xiamen 361005, China
| | - Yuan Wang
- Key Laboratory of Marine Genetic Resources, Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Y.Z.); (C.-L.X.); (Y.W.); (X.-W.H.); (M.-M.X.); (Y.L.); (K.Z.); (Z.-B.Z.)
| | - Xi-Wen He
- Key Laboratory of Marine Genetic Resources, Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Y.Z.); (C.-L.X.); (Y.W.); (X.-W.H.); (M.-M.X.); (Y.L.); (K.Z.); (Z.-B.Z.)
| | - Ming-Min Xie
- Key Laboratory of Marine Genetic Resources, Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Y.Z.); (C.-L.X.); (Y.W.); (X.-W.H.); (M.-M.X.); (Y.L.); (K.Z.); (Z.-B.Z.)
| | - You Li
- Key Laboratory of Marine Genetic Resources, Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Y.Z.); (C.-L.X.); (Y.W.); (X.-W.H.); (M.-M.X.); (Y.L.); (K.Z.); (Z.-B.Z.)
| | - Kai Zhang
- Key Laboratory of Marine Genetic Resources, Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Y.Z.); (C.-L.X.); (Y.W.); (X.-W.H.); (M.-M.X.); (Y.L.); (K.Z.); (Z.-B.Z.)
| | - Zheng-Biao Zou
- Key Laboratory of Marine Genetic Resources, Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Y.Z.); (C.-L.X.); (Y.W.); (X.-W.H.); (M.-M.X.); (Y.L.); (K.Z.); (Z.-B.Z.)
| | - Long-He Yang
- Key Laboratory of Marine Genetic Resources, Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Y.Z.); (C.-L.X.); (Y.W.); (X.-W.H.); (M.-M.X.); (Y.L.); (K.Z.); (Z.-B.Z.)
| | - Ren Xu
- School of Medicine, Xiamen University, South Xiangan Road, Xiamen 361005, China
| | - Xian-Wen Yang
- Key Laboratory of Marine Genetic Resources, Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Y.Z.); (C.-L.X.); (Y.W.); (X.-W.H.); (M.-M.X.); (Y.L.); (K.Z.); (Z.-B.Z.)
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18
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Li AQ, Zhang C, Li DH, Qi XQ, Meng L, Wu LF, Li XG, Zhang WJ. Parasedimentitalea psychrophila sp. nov., a psychrophilic bacterium isolated from deep-sea sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37755238 DOI: 10.1099/ijsem.0.006046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
A novel bacterium, strain QS115T, was isolated from deep-sea sediment collected from the South China Sea at a depth of 1151 m. Phylogenetic analyses based on 16S rRNA gene sequences indicated that QS115T was most closely related to Parasedimentitalea marina W43T, with similarity of 98.21 %. Strain QS115T shared 82.39 % average nucleotide identity, 26.3 % digital DNA-DNA hybridization and 85.32 % average amino acid identity with P. marina W43T. Cells of strain QS115T were Gram-stain-negative, rod-shaped and grew optimally at 10 °C, pH 7.5 and 2 % (w/v) NaCl. The principal fatty acids were summed feature 8 (C18 : 1 ω7c/ω6c), the major respiratory quinone was ubiquinone-10 and predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, glycophospholipid, phosphatidylglycerol and phosphatidylcholine. Polyphasic analyses of physiological and phenotypic characteristics and genomic studies suggested that strain QS115T represents a novel species of the genus Parasedimentitalea, for which the name Parasedimentitalea psychrophila sp. nov. is proposed (type strain QS115T=MCCC 1K04395T=JCM 34219T).
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Affiliation(s)
- An-Qi Li
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Chan Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, PR China
- Present address: Guangdong VTR BioTech Co., Ltd, Zhuhai, Guangdong, PR China
| | - Deng-Hui Li
- BGI Research, Qingdao, PR China
- Institution of Deep-sea Life Sciences, IDSSE-BGI, Sanya, Hainan, PR China
| | - Xiao-Qing Qi
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, PR China
- Present address: Hainan Research Academy of Environmental Sciences, Sanya, Hainan, PR China
| | - Liang Meng
- BGI Research, Qingdao, PR China
- Institution of Deep-sea Life Sciences, IDSSE-BGI, Sanya, Hainan, PR China
| | - Long-Fei Wu
- Aix Marseille Univ, CNRS, LCB, IMM, IM2B, Marseille, France
| | - Xue-Gong Li
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, PR China
- Institution of Deep-sea Life Sciences, IDSSE-BGI, Sanya, Hainan, PR China
| | - Wei-Jia Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, PR China
- Institution of Deep-sea Life Sciences, IDSSE-BGI, Sanya, Hainan, PR China
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19
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Röthig T, Trevathan-Tackett SM, Voolstra CR, Ross C, Chaffron S, Durack PJ, Warmuth LM, Sweet M. Human-induced salinity changes impact marine organisms and ecosystems. Glob Chang Biol 2023; 29:4731-4749. [PMID: 37435759 DOI: 10.1111/gcb.16859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/06/2023] [Accepted: 06/11/2023] [Indexed: 07/13/2023]
Abstract
Climate change is fundamentally altering marine and coastal ecosystems on a global scale. While the effects of ocean warming and acidification on ecology and ecosystem functions and services are being comprehensively researched, less attention is directed toward understanding the impacts of human-driven ocean salinity changes. The global water cycle operates through water fluxes expressed as precipitation, evaporation, and freshwater runoff from land. Changes to these in turn modulate ocean salinity and shape the marine and coastal environment by affecting ocean currents, stratification, oxygen saturation, and sea level rise. Besides the direct impact on ocean physical processes, salinity changes impact ocean biological functions with the ecophysiological consequences are being poorly understood. This is surprising as salinity changes may impact diversity, ecosystem and habitat structure loss, and community shifts including trophic cascades. Climate model future projections (of end of the century salinity changes) indicate magnitudes that lead to modification of open ocean plankton community structure and habitat suitability of coral reef communities. Such salinity changes are also capable of affecting the diversity and metabolic capacity of coastal microorganisms and impairing the photosynthetic capacity of (coastal and open ocean) phytoplankton, macroalgae, and seagrass, with downstream ramifications on global biogeochemical cycling. The scarcity of comprehensive salinity data in dynamic coastal regions warrants additional attention. Such datasets are crucial to quantify salinity-based ecosystem function relationships and project such changes that ultimately link into carbon sequestration and freshwater as well as food availability to human populations around the globe. It is critical to integrate vigorous high-quality salinity data with interacting key environmental parameters (e.g., temperature, nutrients, oxygen) for a comprehensive understanding of anthropogenically induced marine changes and its impact on human health and the global economy.
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Affiliation(s)
- Till Röthig
- Department of Biology, University of Konstanz, Konstanz, Germany
- Branch of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Aquatic Research Facility, Nature-Based Solutions Research Centre, University of Derby, Derby, UK
| | - Stacey M Trevathan-Tackett
- School of Life and Environmental Science, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
- Deakin Marine Research and Innovation Centre, Deakin University, Geelong, Victoria, Australia
| | | | - Cliff Ross
- Department of Biology, University of North Florida, Jacksonville, Florida, USA
| | - Samuel Chaffron
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, F-75016, Paris, France
| | - Paul J Durack
- Program for Climate Model Diagnosis and Intercomparison, Lawrence Livermore National Laboratory, Livermore, California, USA
| | | | - Michael Sweet
- Aquatic Research Facility, Nature-Based Solutions Research Centre, University of Derby, Derby, UK
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Zhu X, Wang L, Lai Q, Wang J, Huang J, Li G, Zeng L, Xia J, Shao Z. Pseudophaeobacter profundi sp. nov., isolated from the Western Pacific Ocean. Int J Syst Evol Microbiol 2023; 73. [PMID: 37768178 DOI: 10.1099/ijsem.0.006071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023] Open
Abstract
A novel Gram-stain-negative, facultatively anaerobic and heterotrophic bacterium, designated strain ZH257T, was isolated from in situ enrichment samples incubated on the seamount floor of the Western Pacific Ocean. Cells were rod-shaped, oxidase- and catalase- positive, and motile by means of polar flagella. Strain ZH257T grew at 4-37 °C (optimum, 28-32 °C), pH 6.0-9.0 (optimum, pH 7.0) and with 2.0-9.0 % (w/v) NaCl (optimum, 3.0-4.0 %). Strain ZH257T was most closely related to members of the genus Pseudophaeobacter, sharing 99.13, 98.27 and 96.89 % 16S rRNA gene sequence identities with Pseudophaeobacter flagellatus GDMCC 1.2988T, Pseudophaeobacter arcticus DSM 23566T and Pseudophaeobacter leonis DSM 25627T, respectively. The DNA G+C content was 59.2 mol%. The estimated average nucleotide identity and digital DNA-DNA hybridization values between strain ZH257T and its closely related species were 79.61-93.04 % and 23.10-50.20 %, respectively. Strain ZH257T harboured complete denitrification and nitrate assimilation pathways. Strain ZH257T contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) as major fatty acids (>5 %), and Q-10 as the major respiratory quinone. The polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and four unidentified lipids. The combined phenotypic, genotypic and chemotaxonomic data showed that strain ZH257T represents a novel species of the genus Pseudophaeobacter, for which the name Pseudophaeobacter profundi sp. nov. is proposed, with the type strain ZH257T (=MCCC M29024T=KACC 23147T).
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Affiliation(s)
- Xuying Zhu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Liping Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Jianning Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Jiamei Huang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Guangyu Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Lingyu Zeng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Jingyu Xia
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
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21
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Reading JGJ, Horton T. Mesopelagic fishes of the North-West African Upwelling from the Discovery Collections. Biodivers Data J 2023; 11:e105921. [PMID: 38318511 PMCID: PMC10840843 DOI: 10.3897/bdj.11.e105921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/03/2023] [Indexed: 02/07/2024] Open
Abstract
Background Mesopelagic fish specimens from two stations in the NW African Upwelling were identified and catalogued to produce a Darwin Core-aligned dataset. A total of 9655 individual fishes were identified, with 9017 specimens identified at least to genus level and 3124 specimens identified to species level. This dataset comprises specimens collected from the 1990 RRS Discovery (III) Cruise D195 and was used to investigate depth-related trends in diversity and community composition alongside species-specific migratory behaviour. The finalised dataset was published on OBIS through the Deep-Sea node. New information This dataset contains occurrence and abundance data for midwater fishes caught between the Mauritanian coast and Cape Verde, published for the first time. The dataset records 146 different fish taxa. Twenty-three taxa in the dataset are not present in any prior OBIS datasets that cover the area. These novel taxa are: Bathylagusandriashevi, Bolinichthysindicus, Bolinichthyssupralateralis, Cyclothoneparapallida, Dolichopteroidesbinocularis, Gigantactis indet. Gymnoscopelus stet., Howellaatlantica, Hygophumproximum, Hygophumtaaningi, Ichthyococcuspolli, Lampadenaanomala, Lampanyctuscuprarius, Lampanyctusisaacsi, Lampanyctuslineatus, Lampanyctusmacdonaldi, Lampanyctusnobilis, Lestidiopsmirabilis, Loweinarara, Macroparalepisbrevis, Melamphaesmicrops and Melanonusgracilis. An anglerfish specimen belonging to Linophrynidae was also found, the first in the leftvent family to be logged in the area on OBIS; however, the specimen was too damaged to identify beyond this level.
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Affiliation(s)
- Jethro George Jack Reading
- University of Southampton, Southampton, United KingdomUniversity of SouthamptonSouthamptonUnited Kingdom
| | - Tammy Horton
- National Oceanography Centre, Southampton, United KingdomNational Oceanography CentreSouthamptonUnited Kingdom
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22
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Uniacke-Lowe S, Collins FWJ, Hill C, Ross RP. Bioactivity Screening and Genomic Analysis Reveals Deep-Sea Fish Microbiome Isolates as Sources of Novel Antimicrobials. Mar Drugs 2023; 21:444. [PMID: 37623725 PMCID: PMC10456417 DOI: 10.3390/md21080444] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/10/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
With the increase in antimicrobial resistance and the subsequent demand for novel therapeutics, the deep-sea fish microbiome can be a relatively untapped source of antimicrobials, including bacteriocins. Previously, bacterial isolates were recovered from the gut of deep-sea fish sampled from the Atlantic Ocean.In this study, we used in vitro methods to screen a subset of these isolates for antimicrobial activity, and subsequently mined genomic DNA from isolates of interest for bacteriocin and other antimicrobial metabolite genes. We observed antimicrobial activity against foodborne pathogens, including Staphylococcus aureus, Listeria monocytogenes, Enterococcus faecalis and Micrococcus luteus. In total, 147 candidate biosynthetic gene clusters were identified in the genomic sequences, including 35 bacteriocin/RiPP-like clusters. Other bioactive metabolite genes detected included non-ribosomal peptide synthases (NRPS), polyketide synthases (PKS; Types 1 and 3), beta-lactones and terpenes. Moreover, four unique bacteriocin gene clusters were annotated and shown to encode novel peptides: a class IIc bacteriocin, two class IId bacteriocins and a class I lanthipeptide (LanM subgroup). Our dual in vitro and in silico approach allowed for a more comprehensive understanding of the bacteriocinogenic potential of these deep-sea isolates and an insight into the antimicrobial molecules that they may produce.
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Affiliation(s)
- Shona Uniacke-Lowe
- Department of Microbiology, University College Cork, T12 K8AF Cork, Ireland
- APC Microbiome Ireland, T12 K8AF Cork, Ireland
- Teagasc Food Research Centre, P61 C996 Fermoy, Ireland
| | | | - Colin Hill
- Department of Microbiology, University College Cork, T12 K8AF Cork, Ireland
- APC Microbiome Ireland, T12 K8AF Cork, Ireland
| | - R Paul Ross
- Department of Microbiology, University College Cork, T12 K8AF Cork, Ireland
- APC Microbiome Ireland, T12 K8AF Cork, Ireland
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23
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Perez M, Aroh O, Sun Y, Lan Y, Juniper SK, Young CR, Angers B, Qian PY. Third-Generation Sequencing Reveals the Adaptive Role of the Epigenome in Three Deep-Sea Polychaetes. Mol Biol Evol 2023; 40:msad172. [PMID: 37494294 PMCID: PMC10414810 DOI: 10.1093/molbev/msad172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/16/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023] Open
Abstract
The roles of DNA methylation in invertebrates are poorly characterized, and critical data are missing for the phylum Annelida. We fill this knowledge gap by conducting the first genome-wide survey of DNA methylation in the deep-sea polychaetes dominant in deep-sea vents and seeps: Paraescarpia echinospica, Ridgeia piscesae, and Paralvinella palmiformis. DNA methylation calls were inferred from Oxford Nanopore sequencing after assembling high-quality genomes of these animals. The genomes of these worms encode all the key enzymes of the DNA methylation metabolism and possess a mosaic methylome similar to that of other invertebrates. Transcriptomic data of these polychaetes support the hypotheses that gene body methylation strengthens the expression of housekeeping genes and that promoter methylation acts as a silencing mechanism but not the hypothesis that DNA methylation suppresses the activity of transposable elements. The conserved epigenetic profiles of genes responsible for maintaining homeostasis under extreme hydrostatic pressure suggest DNA methylation plays an important adaptive role in these worms.
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Affiliation(s)
- Maeva Perez
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, China
- Department of Biological Sciences, Université de Montréal, Montréal, Canada
| | - Oluchi Aroh
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Yanan Sun
- Laboratory of Marine Organism Taxonomy and Phylogeny, Chinese Academy of Sciences, Institute of Oceanology, Qingdao, China
| | - Yi Lan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, China
| | - Stanley Kim Juniper
- School of Earth and Ocean Sciences, University of Victoria, Victoria, Canada
| | | | - Bernard Angers
- Department of Biological Sciences, Université de Montréal, Montréal, Canada
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, China
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24
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Dong Y, Jin E, Wang R, Bao Y, Li H. New Olimycins from a Cold-Seep-Derived Streptomyces olivaceus. Chem Biodivers 2023; 20:e202300689. [PMID: 37354440 DOI: 10.1002/cbdv.202300689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
Cold-seeps are areas of the ocean floor in which hydrogen sulfide and methane are released into the open water. The cold-seep microbes are an emerging source of novel bioactive natural products. Four new ansa-ring opened linear ansamycin analogues, named olimycins E-H (1-4) were isolated from the cold-seep-derived Streptomyces olivaceus OUCLQ19-3. The planar and stereochemical structures of the isolated compounds were elucidated based on extensive MS and NMR spectroscopic analyses together with ECD calculations.
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Affiliation(s)
- Yun Dong
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Enjing Jin
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Runyi Wang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Yilei Bao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Huayue Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
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25
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Gallo S, Nania G, Caruso V, Zicarelli G, Leonetti FL, Giglio G, Fedele G, Romano C, Bottaro M, Mangoni O, Scannella D, Vitale S, Falsone F, Sardo G, Geraci ML, Neri A, Marsili L, Mancusi C, Barca D, Sperone E. Bioaccumulation of Trace Elements in the Muscle of the Blackmouth Catshark Galeus melastomus from Mediterranean Waters. Biology (Basel) 2023; 12:951. [PMID: 37508382 PMCID: PMC10376227 DOI: 10.3390/biology12070951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023]
Abstract
Environmental pollution, particularly in the marine environment, has become a significant concern due to the increasing presence of pollutants and their adverse effects on ecosystems and human health. This study focuses on the bioaccumulation of trace elements in the muscle tissue of the blackmouth catshark (Galeus melastomus) from different areas in the Mediterranean Sea. Trace elements are of interest due to their persistence, toxicity, and potential for bioaccumulation. This research aims to assess the distribution and accumulation of trace elements in the muscle tissue of G. melastomus and investigate their potential impact on the deep-sea environment of the Mediterranean. The focused areas include the Ligurian Sea, the northern and central Tyrrhenian Sea, the southern Tyrrhenian Sea, the Ionian Sea, the Pantelleria Waters, and the Gela Waters. Samples were collected following established protocols, and trace element analysis was conducted using inductively coupled plasma mass spectrometry. The study provides data on the concentrations of 17 trace elements, namely aluminum, arsenic, cadmium, cobalt, copper, manganese, molybdenum, nickel, zinc, selenium, strontium, lead, chromium, iron, barium, bismuth, and uranium. The findings contribute to a better understanding of trace element bioaccumulation patterns in elasmobranch species, specifically G. melastomus, and highlight the potential risks associated with chemical contamination in the Mediterranean Sea. This research emphasizes the importance of studying the impacts of pollutants on marine organisms, particularly those occupying key ecological roles, like sharks, to support effective conservation and management strategies.
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Affiliation(s)
- Samira Gallo
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Via P. Bucci, 87036 Rende, Italy
| | - Gianluca Nania
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Via P. Bucci, 87036 Rende, Italy
| | - Valentina Caruso
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Via P. Bucci, 87036 Rende, Italy
| | - Giorgia Zicarelli
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Francesco Luigi Leonetti
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Via P. Bucci, 87036 Rende, Italy
- Department of Integrative Marine Ecology, Genoa Marine Centre, Anton Dohrn Zoological Station, 16126 Genoa, Italy
| | - Gianni Giglio
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Via P. Bucci, 87036 Rende, Italy
| | - Giorgio Fedele
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Via P. Bucci, 87036 Rende, Italy
| | - Chiara Romano
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Via P. Bucci, 87036 Rende, Italy
| | - Massimiliano Bottaro
- Department of Integrative Marine Ecology, Genoa Marine Centre, Anton Dohrn Zoological Station, 16126 Genoa, Italy
| | - Olga Mangoni
- Department of Biology, University of Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, 80134 Naples, Italy
| | - Danilo Scannella
- Institute for Biological Resources and Marine Biotechnology (IRBIM), National Research Council CNR, Via Luigi Vaccara 61, 91026 Mazara del Vallo, Italy
| | - Sergio Vitale
- Institute for Biological Resources and Marine Biotechnology (IRBIM), National Research Council CNR, Via Luigi Vaccara 61, 91026 Mazara del Vallo, Italy
| | - Fabio Falsone
- Institute for Biological Resources and Marine Biotechnology (IRBIM), National Research Council CNR, Via Luigi Vaccara 61, 91026 Mazara del Vallo, Italy
| | - Giacomo Sardo
- Institute for Biological Resources and Marine Biotechnology (IRBIM), National Research Council CNR, Via Luigi Vaccara 61, 91026 Mazara del Vallo, Italy
| | - Michele Luca Geraci
- Institute for Biological Resources and Marine Biotechnology (IRBIM), National Research Council CNR, Via Luigi Vaccara 61, 91026 Mazara del Vallo, Italy
- Marine Biology and Fisheries Laboratory of Fano, Department of Biological, Geological and Environmental Sciences, University of Bologna, Viale Adriatico 1/n, 61032 Fano, Italy
| | - Alessandra Neri
- Department of Environment, Earth and Physical Sciences, Siena University, Via Mattioli 4, 53100 Siena, Italy
- Consorzio per il Centro Interuniversitario di Biologia Marina ed Ecologia Applicata "G. Bacci" (CIBM), Viale N. Sauro 4, 57128 Livorno, Italy
| | - Letizia Marsili
- Department of Environment, Earth and Physical Sciences, Siena University, Via Mattioli 4, 53100 Siena, Italy
| | - Cecilia Mancusi
- Department of Environment, Earth and Physical Sciences, Siena University, Via Mattioli 4, 53100 Siena, Italy
- Environmental Protection Agency-Tuscany Region (ARPAT), Via Marradi 114, 57126 Livorno, Italy
| | - Donatella Barca
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Via P. Bucci, 87036 Rende, Italy
| | - Emilio Sperone
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Via P. Bucci, 87036 Rende, Italy
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Liu R, Wang Y, Webster G. Editorial: Microbiology of deep-sea carbon cycling. Front Microbiol 2023; 14:1236593. [PMID: 37465022 PMCID: PMC10351976 DOI: 10.3389/fmicb.2023.1236593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 06/21/2023] [Indexed: 07/20/2023] Open
Affiliation(s)
- Rulong Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Yong Wang
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Gordon Webster
- Microbiomes, Microbes and Informatics Group, School of Biosciences, Cardiff University, Cardiff, United Kingdom
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27
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Berman GH, Johnson SB, Seid CA, Vrijenhoek RC, Rouse GW. Range extensions of Pacific bone-eating worms (Annelida, Siboglinidae, Osedax). Biodivers Data J 2023; 11:e102803. [PMID: 38327359 PMCID: PMC10848615 DOI: 10.3897/bdj.11.e102803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/16/2023] [Indexed: 02/09/2024] Open
Abstract
First described in 2004 off California, Osedax worms are now known from many of the world's oceans, ranging from 10 to over 4000 m in depth. Currently, little is known about species ranges, since most descriptions are from single localities. In this study, we used new sampling in the north-eastern Pacific and available GenBank data from off Japan and Brazil to report expanded ranges for five species: Osedaxfrankpressi, O.knutei, O.packardorum, O.roseus and O.talkovici. We also provided additional DNA sequences from previously reported localities for two species: Osedaxpriapus and O.randyi. To assess the distribution of each species, we used cytochrome c oxidase subunit I (COI) sequences to generate haplotype networks and assess connectivity amongst localities where sampling permitted. Osedaxfrankpressi, O.packardorum, O.priapus, O.roseus and O.talkovici all had one or more dominant COI haplotypes shared by individuals at multiple localities, suggesting high connectivity throughout some or all of their ranges. Low ΦST values amongst populations for O.packardorum, O.roseus and O.talkovici confirmed high levels of gene flow throughout their known ranges. High ΦST values for O.frankpressi between the eastern Pacific and the Brazilian Atlantic showed little gene flow, reflected by the haplotype network, which had distinct Pacific and Atlantic haplotype clusters. This study greatly expands the ranges and provides insights into the phylogeography for these nine species.
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Affiliation(s)
- Gabriella H. Berman
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of AmericaScripps Institution of Oceanography, University of California San DiegoLa Jolla, CAUnited States of America
| | - Shannon B. Johnson
- Monterey Bay Aquarium Research Institute, Moss Landing, United States of AmericaMonterey Bay Aquarium Research InstituteMoss LandingUnited States of America
| | - Charlotte A. Seid
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of AmericaScripps Institution of Oceanography, University of California San DiegoLa Jolla, CAUnited States of America
| | - Robert C. Vrijenhoek
- Monterey Bay Aquarium Research Institute, Moss Landing, United States of AmericaMonterey Bay Aquarium Research InstituteMoss LandingUnited States of America
| | - Greg W. Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of AmericaScripps Institution of Oceanography, University of California San DiegoLa Jolla, CAUnited States of America
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28
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Piertney SB, Wenzel M, Jamieson AJ. Large effective population size masks population genetic structure in Hirondellea amphipods within the deepest marine ecosystem, the Mariana Trench. Mol Ecol 2023; 32:2206-2218. [PMID: 36808786 DOI: 10.1111/mec.16887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/20/2023]
Abstract
The examination of genetic structure in the deep-ocean hadal zone has focused on divergence between tectonic trenches to understand how environment and geography may drive species divergence and promote endemism. There has been little attempt to examine localized genetic structure within trenches, partly because of logistical challenges associated with sampling at an appropriate scale, and the large effective population sizes of species that can be sampled adequately may mask underlying genetic structure. Here we examine genetic structure in the superabundant amphipod Hirondellea gigas in the Mariana Trench at depths of 8126-10,545 m. RAD sequencing was used to identify 3182 loci containing 43,408 single nucleotide polymorphisms (SNPs) across individuals after stringent pruning of loci to prevent paralogous multicopy genomic regions being erroneously merged. Principal components analysis of SNP genotypes resolved no genetic structure between sampling locations, consistent with a signature of panmixia. However, discriminant analysis of principal components identified divergence between all sites driven by 301 outlier SNPs in 169 loci and significantly associated with latitude and depth. Functional annotation of loci identified differences between singleton loci used in analysis and paralogous loci pruned from the data set and also between outlier and nonoutlier loci, all consistent with hypotheses explaining the role of transposable elements driving genome dynamics. This study challenges the traditional perspective that highly abundant amphipods within a trench form a single panmictic population. We discuss the findings in relation to eco-evolutionary and ontogenetic processes operating in the deep sea, and highlight key challenges associated with population genetic analysis in nonmodel systems with inherent large effective population sizes and genomes.
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Affiliation(s)
| | - Marius Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Alan J Jamieson
- Minderoo-UWA Deep-Sea Research Centre, School of Biological Sciences and Oceans Institute, The University of Western Australia, Perth, Western Australia, Australia
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29
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Pizarro L, Magalhães C, Almeida CMR, Carvalho MDF, Semedo M. Cadmium effects on net N2O production by the deep-sea isolate Shewanella loihica PV-4. FEMS Microbiol Lett 2023; 370:fnad047. [PMID: 37279908 PMCID: PMC10337742 DOI: 10.1093/femsle/fnad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/19/2023] [Accepted: 06/01/2023] [Indexed: 06/08/2023] Open
Abstract
Deep-sea mining may lead to the release of high concentrations of metals into the surrounding seabed, which can disturb important ecosystem functions provided by microbial communities. Among these, the production of N2O and its reduction to N2 is of great relevance since N2O is an important greenhouse gas. Metal impacts on net N2O production by deep-sea bacteria are, however, currently unexplored. Here, we evaluated the effects of cadmium (Cd) on net N2O production by a deep-sea isolate, Shewanella loihica PV-4. We performed a series of Cd exposure incubations in oxic conditions and determined N2O fluxes during induced anoxic conditions, as well as the relative expression of the nitrite reductase gene (nirK), preceding N2O production, and N2O reductase gene (nosZ), responsible for N2O reduction. Net N2O production by S. loihica PV-4 exposed to Cd was strongly inhibited when compared to the control treatment (no metal). Both nirK and nosZ gene expression were inhibited in reactors with Cd, but nirK inhibition was stronger, supporting the lower net N2O production observed with Cd. The Cd inhibition of net N2O production observed in this study poses the question whether other deep-sea bacteria would undergo the same effects. Future studies should address this question as well as its applicability to complex communities and other physicochemical conditions, which remain to be evaluated.
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Affiliation(s)
- Leonor Pizarro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Faculty of Biotechnology, Catholic University of Portugal, Porto 4169-005, Portugal
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Department of Biology, Faculty of Sciences (FCUP), University of Porto, Porto 4169-007, Portugal
| | - C Marisa R Almeida
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Department of Chemistry and Biochemistry, Faculty of Sciences (FCUP), University of Porto, Porto 4169-007, Portugal
| | - Maria de Fátima Carvalho
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto 4050-313, Portugal
| | - Miguel Semedo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
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Golikov AV, Ceia FR, Hoving HJT, Queirós JP, Sabirov RM, Blicher ME, Larionova AM, Walkusz W, Zakharov DV, Xavier JC. Life History of the Arctic Squid Gonatus fabricii (Cephalopoda: Oegopsida) Reconstructed by Analysis of Individual Ontogenetic Stable Isotopic Trajectories. Animals (Basel) 2022; 12. [PMID: 36552473 DOI: 10.3390/ani12243548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/17/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Cephalopods are important in Arctic marine ecosystems as predators and prey, but knowledge of their life cycles is poor. Consequently, they are under-represented in the Arctic ecosystems assessment models. One important parameter is the change in ecological role (habitat and diet) associated with individual ontogenies. Here, the life history of Gonatus fabricii, the most abundant Arctic cephalopod, is reconstructed by the analysis of individual ontogenetic trajectories of stable isotopes (δ13C and δ15N) in archival hard body structures. This approach allows the prediction of the exact mantle length (ML) and mass when the species changes its ecological role. Our results show that the life history of G. fabricii is divided into four stages, each having a distinct ecology: (1) epipelagic squid (ML < 20 mm), preying mostly on copepods; (2) epi- and occasionally mesopelagic squid (ML 20−50 mm), preying on larger crustaceans, fish, and cephalopods; (3) meso- and bathypelagic squid (ML > 50 mm), preying mainly on fish and cephalopods; and (4) non-feeding bathypelagic gelatinous females (ML > 200 mm). Existing Arctic ecosystem models do not reflect the different ecological roles of G. fabricii correctly, and the novel data provided here are a necessary baseline for Arctic ecosystem modelling and forecasting.
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Xie MM, Jiang JY, Zou ZB, Xu L, Zhang Y, Wang CF, Liu CB, Yan QX, Liu Z, Yang XW. Chemical Constituents of the Deep-Sea-Derived Fungus Cladosporium oxysporum 170103 and Their Antibacterial Effects. Chem Biodivers 2022; 19:e202200963. [PMID: 36436828 DOI: 10.1002/cbdv.202200963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/08/2022] [Indexed: 11/29/2022]
Abstract
The Cladosporium fungi, one of the largest genera of dematiaceous hyphomycetes, could produce various bioactive secondary metabolites. From the AcOEt-soluble extract of Cladosporium oxysporum 170103, three new secopatulolides (1-3) and thirteen known compounds (4-16) were obtained. Their structures were established by detailed analysis of the NMR and HR-ESI-MS data. All sixteen compounds were tested for antibacterial activity against Vibrio parahemolyticus, ergosterol (10) presented moderate effect with the minimum inhibitory concentration (MIC) of 32 μM. It can destruct the membrane integrity of Vibrio parahemolyticus to change the cell shape.
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Affiliation(s)
- Ming-Min Xie
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen, 361005, China
| | - Jia-Yang Jiang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen, 361005, China.,College of Life Sciences, Hainan University, 58 People's Avenue, Haikou, Hainan 570228, China
| | - Zheng-Biao Zou
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen, 361005, China
| | - Lin Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen, 361005, China
| | - Yong Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen, 361005, China
| | - Chao-Feng Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen, 361005, China
| | - Cheng-Bin Liu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen, 361005, China
| | - Qing-Xiang Yan
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen, 361005, China
| | - Zhu Liu
- College of Life Sciences, Hainan University, 58 People's Avenue, Haikou, Hainan 570228, China
| | - Xian-Wen Yang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen, 361005, China
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Gasbarro R, Sowers D, Margolin A, Cordes EE. Distribution and predicted climatic refugia for a reef-building cold-water coral on the southeast US margin. Glob Chang Biol 2022; 28:7108-7125. [PMID: 36054745 DOI: 10.1111/gcb.16415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/23/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Climate change is reorganizing the planet's biodiversity, necessitating proactive management of species and habitats based on spatiotemporal predictions of distributions across climate scenarios. In marine settings, climatic changes will predominantly manifest via warming, ocean acidification, deoxygenation, and changes in hydrodynamics. Lophelia pertusa, the main reef-forming coral present throughout the deep Atlantic Ocean (>200 m), is particularly sensitive to such stressors with stark reductions in suitable habitat predicted to accrue by 2100 in a business-as-usual scenario. However, with new occurrence data for this species along with higher-resolution bathymetry and climate data, it may be possible to locate further climatic refugia. Here, we synthesize new and published biogeographic, geomorphological, and climatic data to build ensemble, multi-scale habitat suitability models for L. pertusa on the continental margin of the southeast United States (SEUS). We then project these models in two timepoints (2050, 2100) and four climate change scenarios to characterize the occurrence probability of this critical cold-water coral (CWC) habitat now and in the future. Our models reveal the extent of reef habitat in the SEUS and corroborate it as the largest currently known essentially continuous CWC reef province on earth, and also predict abundance of L. pertusa to identify key areas, including those outside areas currently protected from bottom-contact fishing. Drastic reductions in L. pertusa climatic suitability index emerged primarily after 2050 and were concentrated at the shallower end (<~550 m) of the regional distribution under the Gulf Stream main axis. Our results thus suggest a depth-driven climate refuge effect where deeper, cooler reef sites experience lesser declines. The strength of this effect increases with climate scenario severity. Taken together, our study has implications for the regional and global management of this species, portending changes in the biodiversity reliant on CWC habitats and the critical ecosystem services they provide.
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Affiliation(s)
- Ryan Gasbarro
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Derek Sowers
- NOAA Office of Ocean Exploration and Research, Durham, New Hampshire, USA
| | - Alex Margolin
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Erik E Cordes
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
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Zou ZB, Zhang G, Zhou YQ, Xie CL, Xie MM, Xu L, Hao YJ, Luo LZ, Zhang XK, Yang XW, Wang JS. Chemical Constituents of the Deep-Sea-Derived Penicillium citreonigrum MCCC 3A00169 and Their Antiproliferative Effects. Mar Drugs 2022; 20:md20120736. [PMID: 36547883 PMCID: PMC9781865 DOI: 10.3390/md20120736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/14/2022] [Accepted: 11/20/2022] [Indexed: 11/27/2022] Open
Abstract
Six new citreoviridins (citreoviridins J-O, 1-6) and twenty-two known compounds (7-28) were isolated from the deep-sea-derived Penicillium citreonigrum MCCC 3A00169. The structures of the new compounds were determined by spectroscopic methods, including the HRESIMS, NMR, ECD calculations, and dimolybdenum tetraacetate-induced CD (ICD) experiments. Citreoviridins J-O (1-6) are diastereomers of 6,7-epoxycitreoviridin with different chiral centers at C-2-C-7. Pyrenocine A (7), terrein (14), and citreoviridin (20) significantly induced apoptosis for HeLa cells with IC50 values of 5.4 μM, 11.3 μM, and 0.7 μM, respectively. To be specific, pyrenocine A could induce S phase arrest, while terrein and citreoviridin could obviously induce G0-G1 phase arrest. Citreoviridin could inhibit mTOR activity in HeLa cells.
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Affiliation(s)
- Zheng-Biao Zou
- Center for Molecular Metabolism, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China
| | - Gang Zhang
- Xiamen Key Laboratory of Marine Medicinal Natural Products Resources, Xiamen Medica College, 1999 Guankouzhong Road, Xiamen 361023, China
| | - Yu-Qi Zhou
- School of Pharmaceutical Sciences, Xiamen University, South Xiangan Road, Xiamen 361102, China
| | - Chun-Lan Xie
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China
| | - Ming-Min Xie
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China
| | - Lin Xu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China
| | - You-Jia Hao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China
| | - Lian-Zhong Luo
- Xiamen Key Laboratory of Marine Medicinal Natural Products Resources, Xiamen Medica College, 1999 Guankouzhong Road, Xiamen 361023, China
| | - Xiao-Kun Zhang
- School of Pharmaceutical Sciences, Xiamen University, South Xiangan Road, Xiamen 361102, China
- Correspondence: (X.-K.Z.); (X.-W.Y.); (J.-S.W.); Tel.: +86-592-2181851 (X.-K.Z.); +86-592-2195319 (X.-W.Y.); +86-258-4315512 (J.-S.W.)
| | - Xian-Wen Yang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China
- Correspondence: (X.-K.Z.); (X.-W.Y.); (J.-S.W.); Tel.: +86-592-2181851 (X.-K.Z.); +86-592-2195319 (X.-W.Y.); +86-258-4315512 (J.-S.W.)
| | - Jun-Song Wang
- Center for Molecular Metabolism, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China
- Correspondence: (X.-K.Z.); (X.-W.Y.); (J.-S.W.); Tel.: +86-592-2181851 (X.-K.Z.); +86-592-2195319 (X.-W.Y.); +86-258-4315512 (J.-S.W.)
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Lim SJ, Thompson LR, Young CM, Gaasterland T, Goodwin KD. Dominance of Sulfurospirillum in Metagenomes Associated with the Methane Ice Worm (Sirsoe methanicola). Appl Environ Microbiol 2022; 88:e0029022. [PMID: 35867581 DOI: 10.1128/aem.00290-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Sirsoe methanicola, commonly known as the methane ice worm, is the only macrofaunal species known to inhabit the Gulf of Mexico methane hydrates. Little is known about this elusive marine polychaete that can colonize rich carbon and energy reserves. Metagenomic analysis of gut contents and worm fragments predicted diverse metabolic capabilities with the ability to utilize a range of nitrogen, sulfur, and organic carbon compounds through microbial taxa affiliated with Campylobacterales, Desulfobacterales, Enterobacterales, SAR324, Alphaproteobacteria, and Mycoplasmatales. Entomoplasmatales and Chitinivibrionales were additionally identified from extracted full-length 16S rRNA sequences, and read analysis identified 196 bacterial families. Overall, the microbial community appeared dominated by uncultured Sulfurospirillum, a taxon previously considered free-living rather than host-associated. Metagenome-assembled genomes (MAGs) classified as uncultured Sulfurospirillum predicted thiosulfate disproportionation and the reduction of tetrathionate, sulfate, sulfide/polysulfide, and nitrate. Microbial amino acid and vitamin B12 biosynthesis genes were identified in multiple MAGs, suggesting nutritional value to the host. Reads assigned to aerobic or anaerobic methanotrophic taxa were rare. IMPORTANCE Methane hydrates represent vast reserves of natural gas with roles in global carbon cycling and climate change. This study provided the first analysis of metagenomes associated with Sirsoe methanicola, the only polychaete species known to colonize methane hydrates. Previously unrecognized participation of Sulfurospirillum in a gut microbiome is provided, and the role of sulfur compound redox reactions within this community is highlighted. The comparative biology of S. methanicola is of general interest given research into the adverse effects of sulfide production in human gut microbiomes. In addition, taxonomic assignments are provided for nearly 200 bacterial families, expanding our knowledge of microbiomes in the deep sea.
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Li Y, Altamia MA, Shipway JR, Brugler MR, Bernardino AF, de Brito TL, Lin Z, da Silva Oliveira FA, Sumida P, Smith CR, Trindade-Silva A, Halanych KM, Distel DL. Contrasting modes of mitochondrial genome evolution in sister taxa of wood-eating marine bivalves (Teredinidae and Xylophagaidae). Genome Biol Evol 2022; 14:evac089. [PMID: 35714221 PMCID: PMC9226539 DOI: 10.1093/gbe/evac089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/19/2022] [Accepted: 06/05/2022] [Indexed: 11/14/2022] Open
Abstract
The bivalve families Teredinidae and Xylophagaidae include voracious consumers of wood in shallow and deep-water marine environments, respectively. The taxa are sister clades whose members consume wood as food with the aid of intracellular cellulolytic endosymbionts housed in their gills. This combination of adaptations is found in no other group of animals and was likely present in the common ancestor of both families. Despite these commonalities, the two families have followed dramatically different evolutionary paths with respect to anatomy, life history and distribution. Here we present 42 new mitochondrial genome sequences from Teredinidae and Xylophagaidae and show that distinct trajectories have also occurred in the evolution and organization of their mitochondrial genomes. Teredinidae display significantly greater rates of amino acid substitution but absolute conservation of protein-coding gene order, whereas Xylophagaidae display significantly less amino acid change but have undergone numerous and diverse changes in genome organization since their divergence from a common ancestor. As with many bivalves, these mitochondrial genomes encode two ribosomal RNAs, 12 protein coding genes, and 22 tRNAs; atp8 was not detected. We further show that their phylogeny, as inferred from amino acid sequences of 12 concatenated mitochondrial protein-coding genes, is largely congruent with those inferred from their nuclear genomes based on 18S and 28S ribosomal RNA sequences. Our results provide a robust phylogenetic framework to explore the tempo and mode of mitochondrial genome evolution and offer directions for future phylogenetic and taxonomic studies of wood-boring bivalves.
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Affiliation(s)
- Yuanning Li
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Marvin A Altamia
- Ocean Genome Legacy Center, Department of Marine and Environmental Science, Northeastern University, Nahant, Massachusetts 01908, USA
| | - J Reuben Shipway
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, United Kingdom
| | - Mercer R Brugler
- Department of Natural Sciences, University of South Carolina Beaufort, 801 Carteret Street, Beaufort, South Carolina 29902, USA
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024, USA
| | | | - Thaís Lima de Brito
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Ceará, Brazil
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA
| | | | - Paulo Sumida
- Departamento de Oceanografia Biológica, Instituto Oceanográfico da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Craig R Smith
- Department of Oceanography, University of Hawai’i at Mãnoa, Hawaii, USA
| | - Amaro Trindade-Silva
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Ceará, Brazil
| | - Kenneth M Halanych
- Center for Marine Science, University of North Carolina Wilmington, North Carolina, USA
| | - Daniel L Distel
- Ocean Genome Legacy Center, Department of Marine and Environmental Science, Northeastern University, Nahant, Massachusetts 01908, USA
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Wang YJ, Sun L. A Type Ib Crustin from Deep-Sea Shrimp Possesses Antimicrobial and Immunomodulatory Activity. Int J Mol Sci 2022; 23:6444. [PMID: 35742887 DOI: 10.3390/ijms23126444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022] Open
Abstract
Crustins are small antimicrobial proteins produced by crustaceans. Of the many reported crustins, very few are from deep sea environments. Crustins are categorized into several types. Recently, the Type I crustin has been further classified into three subtypes, one of which is Type Ib, whose function is unknown. Here, we studied the function of a Type Ib crustin (designated Crus2) identified from a deep-sea crustacean. Crus2 has a whey acidic protein (WAP) domain and a long C-terminal region (named P58). Recombinant Crus2 bound to peptidoglycan (PGN), lipoteichoic acid (LTA), and lipopolysaccharide (LPS), and killed Gram-positive and Gram-negative bacteria by permeabilizing the bacterial cytomembrane. Consistently, Crus2 dramatically attenuated the inflammatory response induced by LPS and LTA. Disruption of the disulfide bonds in the WAP domain abolished the bactericidal ability of Crus2, but had no effect on the bacterial binding ability of Crus2. Deletion of the C-terminal P58 region moderately affected the antimicrobial activity of Crus2 against some bacteria. P58 as a synthesized peptide could bind bacteria and inhibit the bactericidal activity of Crus2. Taken together, these results revealed different roles played by the WAP domain and the P58 region in Type Ib crustin, and provided new insights into the antimicrobial and immunomodulatory functions of crustins.
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Perez M, Breusing C, Angers B, Beinart RA, Won YJ, Young CR. Divergent paths in the evolutionary history of maternally transmitted clam symbionts. Proc Biol Sci 2022; 289:20212137. [PMID: 35259985 PMCID: PMC8905170 DOI: 10.1098/rspb.2021.2137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Vertical transmission of bacterial endosymbionts is accompanied by virtually irreversible gene loss that results in a progressive reduction in genome size. While the evolutionary processes of genome reduction have been well described in some terrestrial symbioses, they are less understood in marine systems where vertical transmission is rarely observed. The association between deep-sea vesicomyid clams and chemosynthetic Gammaproteobacteria is one example of maternally inherited symbioses in the ocean. Here, we assessed the contributions of drift, recombination and selection to genome evolution in two extant vesicomyid symbiont clades by comparing 15 representative symbiont genomes (1.017-1.586 Mb) to those of closely related bacteria and the hosts' mitochondria. Our analyses suggest that drift is a significant force driving genome evolution in vesicomyid symbionts, though selection and interspecific recombination appear to be critical for maintaining symbiont functional integrity and creating divergent patterns of gene conservation. Notably, the two symbiont clades possess putative functional differences in sulfide physiology, anaerobic respiration and dependency on environmental vitamin B12, which probably reflect adaptations to different ecological habitats available to each symbiont group. Overall, these results contribute to our understanding of the eco-evolutionary processes shaping reductive genome evolution in vertically transmitted symbioses.
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Affiliation(s)
- Maëva Perez
- Department of Biological Sciences, Université de Montréal, Montreal, Canada
| | - Corinna Breusing
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Bernard Angers
- Department of Biological Sciences, Université de Montréal, Montreal, Canada
| | - Roxanne A Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Yong-Jin Won
- Division of EcoScience, Ewha Womans University, Seoul, South Korea
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Taenzer L, Grabb K, Kapit J, Pardis W, Wankel SD, Hansel CM. Development of a Deep-Sea Submersible Chemiluminescent Analyzer for Sensing Short-Lived Reactive Chemicals. Sensors (Basel) 2022; 22:1709. [PMID: 35270854 PMCID: PMC8914954 DOI: 10.3390/s22051709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/17/2022] [Accepted: 02/19/2022] [Indexed: 06/14/2023]
Abstract
Based on knowledge of their production pathways, and limited discrete observations, a variety of short-lived chemical species are inferred to play active roles in chemical cycling in the sea. In some cases, these species may exert a disproportionate impact on marine biogeochemical cycles, affecting the redox state of metal and carbon, and influencing the interaction between organisms and their environment. One such short-lived chemical is superoxide, a reactive oxygen species (ROS), which undergoes a wide range of environmentally important reactions. Yet, due to its fleeting existence which precludes traditional shipboard analyses, superoxide concentrations have never been characterized in the deep sea. To this end, we have developed a submersible oceanic chemiluminescent analyzer of reactive intermediate species (SOLARIS) to enable continuous measurements of superoxide at depth. Fluidic pumps on SOLARIS combine seawater for analysis with reagents in a spiral mixing cell, initiating a chemiluminescent reaction that is monitored by a photomultiplier tube. The superoxide in seawater is then related to the quantity of light produced. Initial field deployments of SOLARIS have revealed high-resolution trends in superoxide throughout the water column. SOLARIS presents the opportunity to constrain the distributions of superoxide, and any number of chemiluminescent species in previously unexplored environments.
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Affiliation(s)
- Lina Taenzer
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, MA 02543, USA; (L.T.); (K.G.); (S.D.W.)
- Massachusetts Institute of Technology, Earth, Atmospheric and Planetary Sciences, Cambridge, MA 02139, USA
| | - Kalina Grabb
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, MA 02543, USA; (L.T.); (K.G.); (S.D.W.)
- Massachusetts Institute of Technology, Earth, Atmospheric and Planetary Sciences, Cambridge, MA 02139, USA
| | - Jason Kapit
- Woods Hole Oceanographic Institution, Applied Ocean Physics and Engineering, Woods Hole, MA 02543, USA; (J.K.); (W.P.)
| | - William Pardis
- Woods Hole Oceanographic Institution, Applied Ocean Physics and Engineering, Woods Hole, MA 02543, USA; (J.K.); (W.P.)
| | - Scott D. Wankel
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, MA 02543, USA; (L.T.); (K.G.); (S.D.W.)
| | - Colleen M. Hansel
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, MA 02543, USA; (L.T.); (K.G.); (S.D.W.)
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Afoullouss S, Sanchez AR, Jennings LK, Kee Y, Allcock AL, Thomas OP. Unveiling the Chemical Diversity of the Deep-Sea Sponge Characella pachastrelloides. Mar Drugs 2022; 20:md20010052. [PMID: 35049906 PMCID: PMC8779493 DOI: 10.3390/md20010052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/29/2021] [Accepted: 12/31/2021] [Indexed: 02/01/2023] Open
Abstract
Sponges are at the forefront of marine natural product research. In the deep sea, extreme conditions have driven secondary metabolite pathway evolution such that we might expect deep-sea sponges to yield a broad range of unique natural products. Here, we investigate the chemodiversity of a deep-sea tetractinellid sponge, Characella pachastrelloides, collected from ~800 m depth in Irish waters. First, we analyzed the MS/MS data obtained from fractions of this sponge on the GNPS public online platform to guide our exploration of its chemodiversity. Novel glycolipopeptides named characellides were previously isolated from the sponge and herein cyanocobalamin, a manufactured form of vitamin B12, not previously found in nature, was isolated in a large amount. We also identified several poecillastrins from the molecular network, a class of polyketide known to exhibit cytotoxicity. Light sensitivity prevented the isolation and characterization of these polyketides, but their presence was confirmed by characteristic NMR and MS signals. Finally, we isolated the new betaine 6-methylhercynine, which contains a unique methylation at C-2 of the imidazole ring. This compound showed potent cytotoxicity towards against HeLa (cervical cancer) cells.
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Affiliation(s)
- Sam Afoullouss
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91TK33 Galway, Ireland; (S.A.); (L.K.J.)
- School of Natural Sciences and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91TK33 Galway, Ireland;
| | - Anthony R. Sanchez
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 E. Fowler Ave., Tampa, FL 33620, USA; (A.R.S.); (Y.K.)
| | - Laurence K. Jennings
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91TK33 Galway, Ireland; (S.A.); (L.K.J.)
| | - Younghoon Kee
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 E. Fowler Ave., Tampa, FL 33620, USA; (A.R.S.); (Y.K.)
| | - A. Louise Allcock
- School of Natural Sciences and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91TK33 Galway, Ireland;
| | - Olivier P. Thomas
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91TK33 Galway, Ireland; (S.A.); (L.K.J.)
- Correspondence:
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Svetashev VI. Investigation of Deep-Sea Ecosystems Using Marker Fatty Acids: Sources of Essential Polyunsaturated Fatty Acids in Abyssal Megafauna. Mar Drugs 2021; 20:md20010017. [PMID: 35049873 PMCID: PMC8779288 DOI: 10.3390/md20010017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 11/16/2022] Open
Abstract
Abyssal seafloor ecosystems cover more than 50% of the Earth's surface. Being formed by mainly heterotrophic organisms, they depend on the flux of particulate organic matter (POM) photosynthetically produced in the surface layer of the ocean. As dead phytoplankton sinks from the euphotic to the abyssal zone, the trophic value of POM and the concentration of essential polyunsaturated fatty acids (PUFA) decrease. This results in pronounced food periodicity and limitations for bottom dwellers. Deep-sea invertebrate seston eaters and surface deposit feeders consume the sinking POM. Other invertebrates utilize different food items that have undergone a trophic upgrade, with PUFA synthesized from saturated and monounsaturated FA. Foraminifera and nematodes can synthesize arachidonic acid (AA), eicosapentaenoic acid (EPA), while some barophylic bacteria produce EPA and/or docosahexaenoic acid. FA analysis of deep-sea invertebrates has shown high levels of PUFA including, in particular, arachidonic acid, bacterial FA, and a vast number of new and uncommon fatty acids such as 21:4(n-7), 22:4(n-8), 23:4(n-9), and 22:5(n-5) characteristic of foraminifera. We suppose that bacteria growing on detritus having a low trophic value provide the first trophic upgrading of organic matter for foraminifera and nematodes. In turn, these metazoans perform the second-stage upgrading for megafauna invertebrates. Deep-sea megafauna, including major members of Echinodermata, Mollusca, and Polychaeta display FA markers characteristic of bacteria, foraminifera, and nematodes and reveal new markers in the food chain.
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Affiliation(s)
- Vasily I Svetashev
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 17 Palchevskogo Str., Vladivostok 690041, Russia
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Li XG, Lin J, Bai SJ, Dai J, Jiao ZX, Tang HZ, Qi XQ, Zhang WJ, Liu M, Xu JS, Wu LF. Crassaminicella thermophila sp. nov., a moderately thermophilic bacterium isolated from a deep-sea hydrothermal vent chimney and emended description of the genus Crassaminicella. Int J Syst Evol Microbiol 2021; 71. [PMID: 34825884 DOI: 10.1099/ijsem.0.005112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel moderately thermophilic, anaerobic, heterotrophic bacterium (strain SY095T) was isolated from a hydrothermal vent chimney located on the Southwest Indian Ridge at a depth of 2730 m. Cells were Gram-stain-positive, motile, straight to slightly curved rods forming terminal endospores. SY095T was grown at 45-60 °C (optimum 50-55 °C), pH 6.0-7.5 (optimum 7.0), and in a salinity of 1-4.5 % (w/v) NaCl (optimum 2.5 %). Substrates utilized by SY095T included fructose, glucose, maltose, N-acetyl glucosamine and tryptone. Casamino acid and amino acids (glutamate, glutamine, lysine, methionine, serine and histidine) were also utilized. The main end products from glucose fermentation were acetate, H2 and CO2. Elemental sulphur, sulphate, thiosulphate, sulphite, fumarate, nitrate, nitrite and Fe(III) were not used as terminal electron acceptors. The predominant cellular fatty acids were C14 : 0 (60.5%) and C16 : 0 (7.6 %). The main polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified phospholipids and two unidentified aminophospholipids. No respiratory quinones were detected. The chromosomal DNA G+C content was 30.8 mol%. The results of phylogenetic analysis of the 16S rRNA gene sequences indicated that SY095T was closely related to Crassaminicella profunda Ra1766HT (95.8 % 16S rRNA gene sequence identity). SY095T exhibited 78.1 % average nucleotide identity (ANI) to C. profunda Ra1766HT. The in silico DNA-DNA hybridization (DDH) value indicated that SY095T shared 22.7 % DNA relatedness with C. profunda Ra1766HT. On the basis of its phenotypic, genotypic and phylogenetic characteristics, SY095T is suggested to represent a novel species of the genus Crassaminicella, for which the name Crassaminicella thermophila sp. nov. is proposed. The type strain is SY095T (=JCM 34213=MCCC 1K04191). An emended description of the genus Crassaminicella is also proposed.
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Affiliation(s)
- Xue-Gong Li
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS- Sanya.,CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,Institution of Deep-sea Life Sciences, IDSSE-BGI, Hainan Deep-sea Technology Laboratory, Sanya, Hainan, PR China
| | - Jin Lin
- Hainan Tropical Ocean University, Sanya, PR China
| | - Shi-Jie Bai
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,Laboratory of Marine Viruses and Molecular Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
| | - Jie Dai
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Ze-Xi Jiao
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Hong-Zhi Tang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Xiao-Qing Qi
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS- Sanya.,CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
| | - Wei-Jia Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS- Sanya.,CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,Institution of Deep-sea Life Sciences, IDSSE-BGI, Hainan Deep-sea Technology Laboratory, Sanya, Hainan, PR China
| | - Min Liu
- Hainan Tropical Ocean University, Sanya, PR China
| | - Jian-Sheng Xu
- Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing, PR China
| | - Long-Fei Wu
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS- Sanya.,Aix Marseille Univ, CNRS, LCB, IMM, IM2B, Marseille, France
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Hu HQ, Li YH, Fan ZW, Yan WL, He ZH, Zhong TH, Gai YB, Yang XW. Anti-HIV Compounds from the Deep-Sea-Derived Fungus Chaetomium globosum. Chem Biodivers 2021; 19:e202100804. [PMID: 34799976 DOI: 10.1002/cbdv.202100804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/19/2021] [Indexed: 11/11/2022]
Abstract
Chemical investigation on the deep-sea-derived fungus Chaetomium globosum led to the isolation of nine compounds. By extensive analyses of the 1D and 2D NMR as well as HR-ESI-MS spectra, their structures were elucidated as xylariol A (1), 1,3-dihydro-4,5,6-trihydroxy-7-methylisobenzofuran (2), epicoccone B (3), epicoccolide B (4), chaetoglobosin G (5), chaetoglobosin Fex (6), cochliodone A (7), cochliodone B (8), and chaetoviridin A (9), assorting as four phenolics (1-4), two cytochalosans (5-6), and three azaplilones (7-9). Compounds 1-3 were firstly reported from C. globosum. Under the concentrations of 20 μg/mL, 1, 2, and 3 exhibited potent in vitro anti-HIV activity with the inhibition rates of 70 %, 75 %, and 88 %, respectively.
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Affiliation(s)
- Hong-Qiang Hu
- The Emergency Department, Army 73rd Group Military Hospital, Chenggong Hospital, Xiamen University), Xiamen, 361003, China
| | - Yan-Hui Li
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, China.,Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen, 361005, China
| | - Zuo-Wang Fan
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen, 361005, China
| | - Wei-Li Yan
- The Emergency Department, Army 73rd Group Military Hospital, Chenggong Hospital, Xiamen University), Xiamen, 361003, China
| | - Zhi-Hui He
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen, 361005, China
| | - Tian-Hua Zhong
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen, 361005, China
| | - Ying-Bao Gai
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen, 361005, China
| | - Xian-Wen Yang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen, 361005, China
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Tomasino MP, Aparício M, Ribeiro I, Santos F, Caetano M, Almeida CMR, de Fátima Carvalho M, Mucha AP. Diversity and Hydrocarbon-Degrading Potential of Deep-Sea Microbial Community from the Mid-Atlantic Ridge, South of the Azores (North Atlantic Ocean). Microorganisms 2021; 9:microorganisms9112389. [PMID: 34835516 PMCID: PMC8620031 DOI: 10.3390/microorganisms9112389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/13/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022] Open
Abstract
Deep-sea sediments (DSS) are one of the largest biotopes on Earth and host a surprisingly diverse microbial community. The harsh conditions of this cold environment lower the rate of natural attenuation, allowing the petroleum pollutants to persist for a long time in deep marine sediments raising problematic environmental concerns. The present work aims to contribute to the study of DSS microbial resources as biotechnological tools for bioremediation of petroleum hydrocarbon polluted environments. Four deep-sea sediment samples were collected in the Mid-Atlantic Ridge, south of the Azores (North Atlantic Ocean). Their autochthonous microbial diversity was investigated by 16S rRNA metabarcoding analysis. In addition, a total of 26 deep-sea bacteria strains with the ability to utilize crude oil as their sole carbon and energy source were isolated from the DSS samples. Eight of them were selected for a novel hydrocarbonoclastic-bacterial consortium and their potential to degrade petroleum hydrocarbons was tested in a bioremediation experiment. Bioaugmentation treatments (with inoculum pre-grown either in sodium acetate or petroleum) showed an increase in degradation of the hydrocarbons comparatively to natural attenuation. Our results provide new insights into deep-ocean oil spill bioremediation by applying DSS hydrocarbon-degrading consortium in lab-scale microcosm to simulate an oil spill in natural seawater.
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Affiliation(s)
- Maria Paola Tomasino
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal; (M.A.); (I.R.); (F.S.); (M.C.); (C.M.R.A.); (M.d.F.C.); (A.P.M.)
- Correspondence:
| | - Mariana Aparício
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal; (M.A.); (I.R.); (F.S.); (M.C.); (C.M.R.A.); (M.d.F.C.); (A.P.M.)
| | - Inês Ribeiro
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal; (M.A.); (I.R.); (F.S.); (M.C.); (C.M.R.A.); (M.d.F.C.); (A.P.M.)
| | - Filipa Santos
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal; (M.A.); (I.R.); (F.S.); (M.C.); (C.M.R.A.); (M.d.F.C.); (A.P.M.)
| | - Miguel Caetano
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal; (M.A.); (I.R.); (F.S.); (M.C.); (C.M.R.A.); (M.d.F.C.); (A.P.M.)
- Instituto Português do Mar e da Atmosfera, I.P. Avenida de Brasília, 1449-006 Lisboa, Portugal
| | - C. Marisa R. Almeida
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal; (M.A.); (I.R.); (F.S.); (M.C.); (C.M.R.A.); (M.d.F.C.); (A.P.M.)
| | - Maria de Fátima Carvalho
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal; (M.A.); (I.R.); (F.S.); (M.C.); (C.M.R.A.); (M.d.F.C.); (A.P.M.)
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Ana P. Mucha
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal; (M.A.); (I.R.); (F.S.); (M.C.); (C.M.R.A.); (M.d.F.C.); (A.P.M.)
- Faculty of Sciences, University of Porto, Rua do Campo Alegre 790, 4150-171 Porto, Portugal
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He ZH, Wu J, Xu L, Hu MY, Xie MM, Hao YJ, Li SJ, Shao ZZ, Yang XW. Chemical Constituents of the Deep-Sea-Derived Penicillium solitum. Mar Drugs 2021; 19:580. [PMID: 34677479 PMCID: PMC8540044 DOI: 10.3390/md19100580] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/07/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022] Open
Abstract
A systematic chemical investigation of the deep-sea-derived fungus Penicillium solitum MCCC 3A00215 resulted in the isolation of one novel polyketide (1), two new alkaloids (2 and 3), and 22 known (4-25) compounds. The structures of the new compounds were established mainly on the basis of exhaustive analysis of 1D and 2D NMR data. Viridicatol (13) displayed moderate anti-tumor activities against PANC-1, Hela, and A549 cells with IC50 values of around 20 μM. Moreover, 13 displayed potent in vitro anti-food allergic activity with an IC50 value of 13 μM, compared to that of 92 μM for the positive control, loratadine, while indole-3-acetic acid methyl ester (9) and penicopeptide A (10) showed moderate effects (IC50 = 50 and 58 μM, respectively).
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Affiliation(s)
- Zhi-Hui He
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Z.-H.H.); (L.X.); (M.-Y.H.); (M.-M.X.); (Y.-J.H.); (S.-J.L.); (Z.-Z.S.)
| | - Jia Wu
- Yanjing Medical College, Capital Medical University, 4 Dadong Road, Beijing 101300, China;
| | - Lin Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Z.-H.H.); (L.X.); (M.-Y.H.); (M.-M.X.); (Y.-J.H.); (S.-J.L.); (Z.-Z.S.)
| | - Man-Yi Hu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Z.-H.H.); (L.X.); (M.-Y.H.); (M.-M.X.); (Y.-J.H.); (S.-J.L.); (Z.-Z.S.)
| | - Ming-Ming Xie
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Z.-H.H.); (L.X.); (M.-Y.H.); (M.-M.X.); (Y.-J.H.); (S.-J.L.); (Z.-Z.S.)
| | - You-Jia Hao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Z.-H.H.); (L.X.); (M.-Y.H.); (M.-M.X.); (Y.-J.H.); (S.-J.L.); (Z.-Z.S.)
| | - Shu-Jin Li
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Z.-H.H.); (L.X.); (M.-Y.H.); (M.-M.X.); (Y.-J.H.); (S.-J.L.); (Z.-Z.S.)
| | - Zong-Ze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Z.-H.H.); (L.X.); (M.-Y.H.); (M.-M.X.); (Y.-J.H.); (S.-J.L.); (Z.-Z.S.)
| | - Xian-Wen Yang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen 361005, China; (Z.-H.H.); (L.X.); (M.-Y.H.); (M.-M.X.); (Y.-J.H.); (S.-J.L.); (Z.-Z.S.)
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Li XG, Tang HZ, Zhang WJ, Qi XQ, Qu ZG, Xu J, Wu LF. Thermococcus aciditolerans sp. nov., a piezotolerant, hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent chimney in the Southwest Indian Ridge. Int J Syst Evol Microbiol 2021; 71. [PMID: 34343062 DOI: 10.1099/ijsem.0.004934] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A hyperthermophilic, strictly anaerobic archaeon, designated strain SY113T, was isolated from a deep-sea hydrothermal vent chimney on the Southwest Indian Ridge at a water depth of 2770 m. Enrichment and isolation of strain SY113T were performed at 85 °C at 0.1 MPa. Cells of strain SY113T were irregular motile cocci with peritrichous flagella and generally 0.8-2.4 µm in diameter. Growth was observed at temperatures between 50 and 90 °C (optimum at 85 °C) and under hydrostatic pressures of 0.1-60 MPa (optimum, 27 MPa). Cells of SY113T grew at pH 4.0-9.0 (optimum, pH 5.5) and a NaCl concentration of 0.5-5.5 % (w/v; optimum concentration, 3.0 % NaCl). Strain SY113T was an anaerobic chemoorganoheterotroph and grew on complex proteinaceous substrates such as yeast extract and tryptone, as well as on maltose and starch. Elemental sulphur stimulated growth, but not obligatory for its growth. The G+C content of the genomic DNA was 55.0 mol%. Phylogenetic analysis of the 16S rRNA sequence of strain SY113T showed that the novel isolate belonged to the genus Thermococcus. On the basis of physiological characteristics, average nucleotide identity values and in silico DNA-DNA hybridization results, we propose a novel species, named Thermococcus aciditolerans sp. nov. The type strain is SY113T (=MCCC 1K04190T=JCM 39083T).
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Affiliation(s)
- Xue-Gong Li
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS- Sanya, PR China.,CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
| | - Hong-Zhi Tang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Wei-Jia Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS- Sanya, PR China.,CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
| | - Xiao-Qing Qi
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China.,International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS- Sanya, PR China.,CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
| | - Zhi-Guo Qu
- Laboratory of Deep-sea Information Technology, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Long-Fei Wu
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS- Sanya, PR China.,Aix Marseille Univ, CNRS, LCB, IMM, IM2B, Marseille, France
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Wang W, Wang J, Yan R, Zeng R, Zuo Y, Wang D, Qu W. Expression and Characterization of a Novel Cold-Adapted and Stable β-Agarase Gene agaW1540 from the Deep-Sea Bacterium Shewanella sp. WPAGA9. Mar Drugs 2021; 19:md19080431. [PMID: 34436270 PMCID: PMC8398281 DOI: 10.3390/md19080431] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 12/27/2022] Open
Abstract
The neoagaro-oligosaccharides, degraded from agarose by agarases, are important natural substances with many bioactivities. In this study, a novel agarase gene, agaW1540, from the genome of a deep-sea bacterium Shewanella sp. WPAGA9, was expressed, and the recombinant AgaW1540 (rAgaW1540) displayed the maximum activity under the optimal pH and temperature of 7.0 and 35 °C, respectively. rAgaW1540 retained 85.4% of its maximum activity at 0 °C and retained more than 92% of its maximum activity at the temperature range of 20-40 °C and the pH range of 4.0-9.0, respectively, indicating its extensive working temperature and pH values. The activity of rAgaW1540 was dramatically suppressed by Cu2+ and Zn2+, whereas Fe2+ displayed an intensification of enzymatic activity. The Km and Vmax of rAgaW1540 for agarose degradation were 15.7 mg/mL and 23.4 U/mg, respectively. rAgaW1540 retained 94.7%, 97.9%, and 42.4% of its maximum activity after incubation at 20 °C, 25 °C, and 30 °C for 60 min, respectively. Thin-layer chromatography and ion chromatography analyses verified that rAgaW1540 is an endo-acting β-agarase that degrades agarose into neoagarotetraose and neoagarohexaose as the main products. The wide variety of working conditions and stable activity at room temperatures make rAgaW1540an appropriate bio-tool for further industrial production of neoagaro-oligosaccharides.
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Affiliation(s)
- Wenxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China; (W.W.); (J.W.); (Y.Z.); (D.W.)
| | - Jianxin Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China; (W.W.); (J.W.); (Y.Z.); (D.W.)
| | - Ruihua Yan
- Technical Innovation Center for Utilization of Marine Biological Resources, Ministry of Natural Resources, Xiamen 361000, China; (R.Y.); (R.Z.)
| | - Runying Zeng
- Technical Innovation Center for Utilization of Marine Biological Resources, Ministry of Natural Resources, Xiamen 361000, China; (R.Y.); (R.Z.)
| | - Yaqiang Zuo
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China; (W.W.); (J.W.); (Y.Z.); (D.W.)
| | - Dingquan Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China; (W.W.); (J.W.); (Y.Z.); (D.W.)
| | - Wu Qu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316000, China; (W.W.); (J.W.); (Y.Z.); (D.W.)
- Correspondence:
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Abstract
The deep sea comprises more than 90% of the ocean; therefore, understanding the controlling factors of biodiversity in the deep sea is of great importance for predicting future changes in the functioning of the ocean system. Consensus has recently been increasing on two plausible factors that have often been discussed as the drivers of deep-sea species richness in the contexts of the species-energy and physiological tolerance hypotheses: (i) seafloor particulate organic carbon (POC) derived from primary production in the euphotic zone and (ii) temperature. Nonetheless, factors that drive deep-sea biodiversity are still actively debated potentially owing to a mirage of correlations (sign and magnitude are generally time dependent), which are often found in nonlinear, complex ecological systems, making the characterization of causalities difficult. Here, we tested the causal influences of POC flux and temperature on species richness using long-term palaeoecological datasets derived from sediment core samples and convergent cross mapping, a numerical method for characterizing causal relationships in complex systems. The results showed that temperature, but not POC flux, influenced species richness over 103-104-year time scales. The temperature-richness relationship in the deep sea suggests that human-induced future climate change may, under some conditions, affect deep-sea ecosystems through deep-water circulation changes rather than surface productivity changes.
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Affiliation(s)
- Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Moriaki Yasuhara
- Division of Ecology and Biodiversity, School of Biological Sciences, Swire Institute of Marine Science, and State Key Laboratory of Marine Pollution, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto 606-8501, Japan.,Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan
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48
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O'Hara TD, Thuy B, Hugall AF. Relict from the Jurassic: new family of brittle-stars from a New Caledonian seamount. Proc Biol Sci 2021; 288:20210684. [PMID: 34130505 DOI: 10.1098/rspb.2021.0684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The deep-seafloor in the tropical Indo-Pacific harbours a rich and diverse benthic fauna with numerous palaeoendemics. Here, we describe a new species, genus and family of brittle-star (Ophiuroidea) from a single eight-armed specimen collected from a depth between 360 and 560 m on Banc Durand, a seamount east of New Caledonia. Leveraging a robust, fossil-calibrated (265 kbp DNA) phylogeny for the Ophiuroidea, we estimate the new lineage diverged from other ophiacanthid families in the Late Triassic or Jurassic (median = 187-178 Myr, 95% CI = 215-143 Myr), a period of elevated diversification for this group. We further report very similar microfossil remains from Early Jurassic (180 Myr) sediments of Normandy, France. The discovery of a new ancient lineage in the relatively well-known Ophiuroidea indicates the importance of ongoing taxonomic research in the deep-sea, an environment increasingly threatened by human activities.
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Affiliation(s)
- Timothy D O'Hara
- Department of Sciences, Museums Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
| | - Ben Thuy
- Department of Palaeontology, Natural History Museum of Luxembourg, 24 Rue Münster, 2160 Luxembourg, Luxembourg
| | - Andrew F Hugall
- Department of Sciences, Museums Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
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49
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Wei W, Wang L, Fang J, Liu R. Population structure, activity potential and ecotype partitioning of Pseudoalteromonas along the vertical water column of the New Britain Trench. FEMS Microbiol Lett 2021; 368:6308368. [PMID: 34160584 DOI: 10.1093/femsle/fnab078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/21/2021] [Indexed: 11/14/2022] Open
Abstract
Microbial degradation of organic matter along the vertical profile of the water column is a major process driving the carbon cycle in the ocean. Pseudoalteromonas has been identified as a dominant genus in pelagic marine environments worldwide, playing important roles in the remineralization of organic carbon. However, the current understanding of Pseudoalteromonas was mainly based on shallow water populations or cultivated species. This study analyzed for the first time the structure, activity potential and ecotypes differentiation of Pseudoalteromonas in the water column of the New Britain Trench (NBT) down to 6000 m. Analysis on diversities of the 16S rRNA gene and their transcripts showed that Pseudoalteromonas was greatly enriched in deep-sea waters and showed high activity potentials. The deep-sea Pseudoalteromonas were significantly different from their shallow-water counterparts, suggesting an obvious ecotype division along with the vertical profile. Phylogenetic analysis on the 16S rRNA gene and hsp60 gene of 219 Pseudoalteromonas strains isolated from different depths further showed that the vertical ecotype division could even occur at the strain level, which might be a result of long-term adaptation to environmental conditions at different depths. The discovered depth-specific strains provide valuable models for further studies on adaptation, evolution and functions of the deep-sea Pseudoalteromonas.
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Affiliation(s)
- Wenxia Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai,201306, China.,National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, 201306, China
| | - Li Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai,201306, China.,National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, 201306, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai,201306, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao,266000, China.,Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813, USA
| | - Rulong Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai,201306, China.,National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, 201306, China
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50
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Ning D, Li Z, Liang G, Wang Q, Zou W, Gong Y, Hou J. Design and Performance Study for Electrothermally Deep-Sea Drive Microunits Using a Paraffin Phase Change Material. Micromachines (Basel) 2021; 12:415. [PMID: 33918774 DOI: 10.3390/mi12040415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 11/17/2022]
Abstract
Considering the further exploration of the ocean, the requirements for deep-sea operation equipment have increased. Many problems existing in the widely used deep-sea hydraulic system have become increasingly prominent. Compared with the traditional deep-sea hydraulic system, actuators using a paraffin phase change material (PCM) have incomparable advantages, including lightweight structure, low energy consumption, high adaptability to the deep sea, and good biocompatibility. Thus, a deep-sea drive microunit (DDM) based on paraffin PCM is proposed in this paper. The device adopts a flexible shell, adapting to the high-pressure environment of the deep-sea based on the principle of pressure compensation. The device realizes the output of displacement and force through the electrothermal drive, which can be used as actuator or power source of other underwater operation equipment. The microunit successfully completes the functional verification experiments in air, shallow water, and hydrostatic pressure of 110 MPa. In accordance with experimental results, a reasonable control curve is fitted, highlighting its potential application in deep-sea micro electro mechanical systems, especially in underwater soft robot.
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