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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, Wang H, Gao W, Gan Z, Li X. The complete mitochondrial genome of the deep-sea paskentanid snail Alviniconcha marisindica (Caenogastropoda: abyssochrysoidea) from the Carlsberg Ridge. Mitochondrial DNA B Resour 2024; 9:11-14. [PMID: 38187013 PMCID: PMC10769126 DOI: 10.1080/23802359.2023.2298090] [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: 06/25/2023] [Accepted: 12/18/2023] [Indexed: 01/09/2024] Open
Abstract
Alviniconcha marisindica Okutani 2014 is a deep-sea gastropod inhabited in hydrothermal vents of the Indo-Pacific. It belongs to superfamily Abyssochrysoidea. In the present study, we report the complete mitochondrial genome of A. marisindica, which is 15,979 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes. The nucleotide composition is 29.19% of A, 38.22% of T, 16.88% of G, and 15.71% of C. The phylogenetic analysis indicates that A. marisindica and A. boucheti clustered in the Abyssochrysoidea clade with high bootstrap support. The mitochondrial genome of A. marisindica provides valuable molecular data for further research on the evolution of deep-sea gastropods.
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Affiliation(s)
- Mei Yang
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | | | - Wei Gao
- National Deep Sea Center, Qingdao, China
| | - Zhinbin Gan
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xinzheng Li
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Xu T, Chai X, Chen C, Watanabe HK, Sun J, Xiao Y, Wang Y, Chen J, Qiu JW, Qian PY. Genetic divergence and migration patterns of a galatheoid squat lobster highlight the need for deep-sea conservation. Mol Ecol 2024; 33:e17200. [PMID: 37985390 DOI: 10.1111/mec.17200] [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: 06/16/2023] [Revised: 10/06/2023] [Accepted: 10/26/2023] [Indexed: 11/22/2023]
Abstract
Information on genetic divergence and migration patterns of vent- and seep-endemic macrobenthos can help delimit biogeographical provinces and provide scientific guidelines for deep-sea conservation under the growing threats of anthropogenic disturbances. Nevertheless, related studies are still scarce, impeding the informed conservation of these hotspots of deep-sea biodiversity. To bridge this knowledge gap, we conducted a population connectivity study on the galatheoid squat lobster Shinkaia crosnieri - a deep-sea foundation species widely distributed in vent and seep ecosystems in the Northwest Pacific. With the application of an interdisciplinary methodology involving population genomics and oceanographic approaches, we unveiled two semi-isolated lineages of S. crosnieri with limited and asymmetrical gene flow potentially shaped by the geographic settings, habitat types, and ocean currents - one comprising vent populations in the Okinawa Trough, with those inhabiting the southern trough area likely serving as the source; the other being the Jiaolong (JR) seep population in the South China Sea. The latter might have recently experienced a pronounced demographic contraction and exhibited genetic introgression from the Okinawa Trough lineage, potentially mediated by the intrusion of the North Pacific Intermediate Water. We then compared the biogeographic patterns between S. crosnieri and two other representative and co-occurring vent- and seep-endemic species using published data. Based on their biogeographical subdivisions and source-sink dynamics, we highlighted the southern Okinawa Trough vents and the JR seep warrant imperative conservation efforts to sustain the deep-sea biodiversity in the Northwest Pacific.
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Affiliation(s)
- Ting Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Xia Chai
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | | | - Jin Sun
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yao Xiao
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yan Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Junlin Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jian-Wen Qiu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - 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, Hong Kong, China
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Ge Y, Ma Y, Zhou C, Zhang Z, Yin Q, Zhang X, Zhang Z, Wu B. Kueishanamides A and B from the Hydrothermal Vent Sediment Derived Streptomyces sp. WU20. Chem Biodivers 2023; 20:e202301345. [PMID: 37985414 DOI: 10.1002/cbdv.202301345] [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: 09/03/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 11/22/2023]
Abstract
Marine actinomycetes are known for their production of remarkable organic molecules, particularly those featuring polyoxygenated long-chain backbones. Determining the absolute configurations of these compounds remains a challenging task even today. In this study, we successfully established the planar structures and absolute configurations of two highly flexible amide alkaloids from Streptomyces sp. WU20: kueishanamides A (1) and B (2). These compounds possess a C13 linear backbone and each contains five stereogenic carbon centers. Our approach involved a combination of spectroscopic and computational methods, including J-based configurational analysis and VCD calculations, ensuring the unambiguous determination of their configurations. Kueishanamide A (1) and kueishanamide B (2) showed moderate antifungal activity against pathogenic fungus Crytococcus neoformans, with MIC values of 25 μg/mL each.
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Affiliation(s)
- Yichao Ge
- Ocean College, Zhejiang University, Zhoushan, 321000, China
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Yihan Ma
- Ocean College, Zhejiang University, Zhoushan, 321000, China
| | - Chengzeng Zhou
- Ocean College, Zhejiang University, Zhoushan, 321000, China
| | - Zhixuan Zhang
- School of Physical Science, Ningbo University, Ningbo, 315210, China
| | - Qizhao Yin
- Ocean College, Zhejiang University, Zhoushan, 321000, China
| | - Xiaoqin Zhang
- Zhejiang Provincial Key Laboratory of Inheritance and Innovation of She Medicine, Lishui Hospital of Traditional Chinese Medicine, Lishui, 323000, China
| | - Zunjing Zhang
- Zhejiang Provincial Key Laboratory of Inheritance and Innovation of She Medicine, Lishui Hospital of Traditional Chinese Medicine, Lishui, 323000, China
| | - Bin Wu
- Ocean College, Zhejiang University, Zhoushan, 321000, China
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Dai J, Li XG, Zhang WJ, Wu LF. Tepidibacter hydrothermalis sp. nov., a novel anaerobic bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2023; 73. [PMID: 37921840 DOI: 10.1099/ijsem.0.006151] [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: 11/04/2023] Open
Abstract
A novel anaerobic heterotrophic bacterium, designated strain SWIR-1T, was isolated from a deep-sea hydrothermal vent field sample collected from the Southwest Indian Ridge at a depth of 2700 m. Phylogenetic analysis indicated that strain SWIR-1T belongs to the genus Tepidibacter, and the most closely related species are Tepidibacter mesophilus B1T (99.1 % 16S rRNA gene sequence similarity), Tepidibacter formicigenes DV1184T (94.6 %) and Tepidibacter thalassicus SC562T (93.9 %). Strain SWIR-1T shares 77.3-87.2 % average nucleotide identity and 21.5-35.7 % digital DNA-DNA hybridization values with the three type strains of Tepidibacter species. Cells of strain SWIR-1T were Gram-stain-positive, motile, short straight rods. Endospores were observed in stationary-phase cells when grown on Thermococcales rich medium. Strain SWIR-1T grew at 15-45 °C (optimum, 30°C), at pH 5.5-8.0 (optimum, pH 7.0) and with 1.0-6.0 % (w/v) NaCl (optimum, 2.0 %). Substrates utilized by strain SWIR-1T included complex proteinaceous, chitin, starch, lactose, maltose, fructose, galactose, glucose, rhamnose, arabinose, ribose, alanine, glycine and glycerol. The major fermentation products from glucose were acetate, lactate, H2 and CO2. Elemental sulphur, sulphate, thiosulphate, sulphite, fumarate, nitrate, nitrite and FeCl3 are not used as terminal electron acceptors. The main cellular fatty acids consisted of iso-C15 : 0 (28.4 %), C15 : 1 iso F (15.4 %) and C16 : 0 (9.8 %). The major polar lipids were phospholipids and glycolipids. No respiratory quinones were detected. Genomic comparison revealed a distinctive blended gene cluster comprising hyb-tat-hyp genes, which play a crucial role in the synthesis, maturation, activation and export of NiFe-hydrogenase. Based on the phylogenetic analysis, genomic, physiologic and chemotaxonomic characteristics, strain SWIR-1T is considered to represent a novel species within the genus Tepidibacter, for which the name Tepidibacter hydrothermalis sp. nov. is proposed. The type strain is strain SWIR-1T (=DSM 113848T=MCCC 1K07078T).
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Affiliation(s)
- Jie Dai
- 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, 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
- Institution of Deep-sea Life Sciences, IDSSE-BGI, Hainan Deep-sea Technology Laboratory, 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, 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
- Institution of Deep-sea Life Sciences, IDSSE-BGI, Hainan Deep-sea Technology Laboratory, Sanya, Hainan, PR China
| | - Long-Fei Wu
- Aix Marseille Univ, CNRS, LCB, IMM, IM2B, Marseille, France
- International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS-Marseille/ CAS, Sanya, PR China
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Arcadi E, Buschi E, Rastelli E, Tangherlini M, De Luca P, Esposito V, Calogero R, Andaloro F, Romeo T, Danovaro R. Novel Insights on the Bacterial and Archaeal Diversity of the Panarea Shallow-Water Hydrothermal Vent Field. Microorganisms 2023; 11:2464. [PMID: 37894122 PMCID: PMC10608945 DOI: 10.3390/microorganisms11102464] [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: 07/28/2023] [Revised: 09/18/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Current knowledge of the microbial diversity of shallow-water hydrothermal vents is still limited. Recent evidence suggests that these peculiar and heterogeneous systems might host highly diversified microbial assemblages with novel or poorly characterized lineages. In the present work, we used 16S rRNA gene metabarcoding to provide novel insights into the diversity of the bacterial and archaeal assemblages in seawater and sediments of three shallow-water hydrothermal systems of Panarea Island (Tyrrhenian Sea). The three areas were characterized by hot, cold, or intermediate temperatures and related venting activities. Microbial biodiversity in seawater largely differed from the benthic one, both in α-diversity (i.e., richness of amplicon sequence variants-ASVs) and in prokaryotic assemblage composition. Furthermore, at the class level, the pelagic prokaryotic assemblages were very similar among sites, whereas the benthic microbial assemblages differed markedly, reflecting the distinct features of the hydrothermal activities at the three sites we investigated. Our results show that ongoing high-temperature emissions can influence prokaryotic α-diversity at the seafloor, increasing turnover (β-)diversity, and that the intermediate-temperature-venting spot that experienced a violent gas explosion 20 years ago now displays the highest benthic prokaryotic diversity. Overall, our results suggest that hydrothermal vent dynamics around Panarea Island can contribute to an increase in the local heterogeneity of physical-chemical conditions, especially at the seafloor, in turn boosting the overall microbial (γ-)diversity of this peculiar hydrothermal system.
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Affiliation(s)
- Erika Arcadi
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Contrada Porticatello, 29, 98167 Messina, Italy; (E.A.); (R.C.); (F.A.)
| | - Emanuela Buschi
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Eugenio Rastelli
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy
| | - Pasquale De Luca
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy;
| | - Valentina Esposito
- Istituto Nazionale di Oceanografia e di Geofisica Sperimentale—OGS Borgo Grotta Gigante 42/C, 34010 Sgonico, Italy;
| | - Rosario Calogero
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Contrada Porticatello, 29, 98167 Messina, Italy; (E.A.); (R.C.); (F.A.)
| | - Franco Andaloro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Contrada Porticatello, 29, 98167 Messina, Italy; (E.A.); (R.C.); (F.A.)
| | - Teresa Romeo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Via dei Mille 46, 98057 Milazzo, Italy
- National Institute for Environmental Protection and Research, Via dei Mille 46, 98057 Milazzo, Italy
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy;
- National Biodiversity Future Centre (NBFC), 90133 Palermo, Italy
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He X, Wang H, Xu T, Zhang Y, Chen C, Sun Y, Qiu JW, Zhou Y, Sun J. Genomic analysis of a scale worm provides insights into its adaptation to deep-sea hydrothermal vents. Genome Biol Evol 2023:evad125. [PMID: 37401460 DOI: 10.1093/gbe/evad125] [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: 05/09/2023] [Revised: 06/24/2023] [Accepted: 07/03/2023] [Indexed: 07/05/2023] Open
Abstract
Deep-sea polynoid scale worms endemic to hydrothermal vents have evolved an adaptive strategy to the chronic hypoxic environment, but its underlying molecular mechanisms remain elusive. Here, we assembled a chromosome-scale genome of a vent-endemic scale worm Branchipolynoe longqiensis (first annotated genome in the subclass Errantia) and annotated two shallow-water polynoid genomes aiming to elucidate the adaptive mechanisms. We present a genome-wide molecular phylogeny in Annelida and call for extensive taxonomy revision by including more genomes from key lineages. The B. longqiensis genome with a genome size of 1.86 Gb and 18 pseudo-chromosomes is larger than the genomes of two shallow-water polynoids, possibly due to the expansion of various transposable elements (TEs) and transposons. We revealed three inter-chromosomal rearrangements in B. longqiensis when compared to the other two polynoid genomes. The intron elongation and inter-chromosomal rearrangement can influence a number of biological processes, such as vesicle transport, microtubules, and transcription factors. Furthermore, the expansion of cytoskeleton-related gene families may favor the cell structure maintenance of B. longqiensis in the deep ocean. The expansion of synaptic vesicle exocytosis genes has possibly contributed to the unique complex structure of the nerve system in B. longqiensis. Finally, we uncovered an expansion of single-domain hemoglobin and an unique formation of tetra-domain hemoglobin via tandem duplications which may be related to the adaptation to a hypoxic environment.
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Affiliation(s)
- Xing He
- Institute of Evolution & Marine Biodiversity, Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China
- Laoshan Laboratory, Qingdao 266237, China
| | - Hui Wang
- Institute of Evolution & Marine Biodiversity, Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China
- Laoshan Laboratory, Qingdao 266237, China
| | - Ting Xu
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yanjie Zhang
- School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Yanan Sun
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Jian-Wen Qiu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yadong Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Jin Sun
- Institute of Evolution & Marine Biodiversity, Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China
- Laoshan Laboratory, Qingdao 266237, China
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Maltman C, Kuzyk SB, Kyndt JA, Lengyel G, Yurkov V. Shewanella metallivivens sp. nov., a deep-sea hydrothermal vent tube worm endobiont capable of dissimilatory anaerobic metalloid oxyanion reduction. Int J Syst Evol Microbiol 2023; 73. [PMID: 37477965 DOI: 10.1099/ijsem.0.005980] [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: 07/22/2023] Open
Abstract
A polyphasic taxonomic study was carried out on a Gram-stain-negative and rod-shaped strain, ER-Te-42B-LightT, isolated from the tissue of a tube worm, Riftia pachyptila, collected near a deep-sea hydrothermal vent of the Juan de Fuca Ridge in the Pacific Ocean. This bacterium was capable of performing anaerobic respiration using tellurite, tellurate, selenite and orthovanadate as terminal electron acceptors. While facultatively anaerobic, it could aerobically resist tellurite, selenite and orthovanadate up to 2000, 7000 and 10000 µg ml-1, respectively, reducing each oxide to elemental forms. Nearly complete 16S rRNA gene sequence similarity related the strain to Shewanella, with 98.8 and 98.7 % similarity to Shewanella basaltis and Shewanella algicola, respectively. The dominant fatty acids were C16 : 0 and C16 : 1. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol and MK-7 was the predominant quinone. DNA G+C content was 42.5 mol%. Computation of average nucleotide identity and digital DNA-DNA hybridization values with the closest phylogenetic neighbours of ER-Te-42B-LightT revealed genetic divergence at the species level, which was further substantiated by differences in several physiological characteristics. Based on the obtained results, this bacterium was assigned to the genus Shewanella as a new species with the name Shewanella metallivivens sp. nov., type strain ER-Te-42B-LightT (=VKM B-3580T=DSM 113370T).
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Affiliation(s)
- Chris Maltman
- Department of Biology, Slippery Rock University, Slippery Rock, Pennsylvania, USA
| | - Steven B Kuzyk
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - John A Kyndt
- College of Science and Technology, Bellevue University, Bellevue, NE, USA
| | - George Lengyel
- Department of Chemistry, Slippery Rock University, Slippery Rock, Pennsylvania, USA
| | - Vladimir Yurkov
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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Qi L, Shi M, Zhu FC, Lian CA, He LS. Genomic evidence for the first symbiotic Deferribacterota, a novel gut symbiont from the deep-sea hydrothermal vent shrimp Rimicaris kairei. Front Microbiol 2023; 14:1179935. [PMID: 37455748 PMCID: PMC10344455 DOI: 10.3389/fmicb.2023.1179935] [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: 03/05/2023] [Accepted: 06/08/2023] [Indexed: 07/18/2023] Open
Abstract
The genus Rimicaris is the dominant organism living in hydrothermal vents. However, little research has been done on the functions of their intestinal flora. Here, we investigated the potential functions of Deferribacterota, which is dominant in the intestine of Rimicaris kairei from the Central Indian Ridge. In total, six metagenome-assembled genomes (MAGs) of Deferribacterota were obtained using the metagenomic approach. The six Deferribacterota MAGs (Def-MAGs) were clustered into a new branch in the phylogenetic tree. The six Def-MAGs were further classified into three species, including one new order and two new genera, based on the results of phylogenetic analysis, relative evolutionary divergence (RED), average nucleotide identity (ANI), average amino acid identity (AAI) and DNA-DNA hybridization (DDH) values. The results of the energy metabolism study showed that these bacteria can use a variety of carbon sources, such as glycogen, sucrose, salicin, arbutin, glucose, cellobiose, and maltose. These bacteria have a type II secretion system and effector proteins that can transport some intracellular toxins to the extracellular compartment and a type V CRISPR-Cas system that can defend against various invasions. In addition, cofactors such as biotin, riboflavin, flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD) synthesized by R. kairei gut Deferribacterota may also assist their host in surviving under extreme conditions. Taken together, the potential function of Deferribacterota in the hydrothermal R. kairei gut suggests its long-term coevolution with the host.
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Affiliation(s)
- Li Qi
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mengke Shi
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fang-Chao Zhu
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Chun-Ang Lian
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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Røyseth V, Hurysz BM, Kaczorowska AK, Dorawa S, Fedøy AE, Arsın H, Serafim MSM, Myers SA, Werbowy O, Kaczorowski T, Stokke R, O’Donoghue AJ, Steen IH. Activation mechanism and activity of globupain, a thermostable C11 protease from the Arctic Mid-Ocean Ridge hydrothermal system. Front Microbiol 2023; 14:1199085. [PMID: 37405169 PMCID: PMC10315481 DOI: 10.3389/fmicb.2023.1199085] [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: 04/02/2023] [Accepted: 05/26/2023] [Indexed: 07/06/2023] Open
Abstract
Deep-sea hydrothermal vents offer unique habitats for heat tolerant enzymes with potential new enzymatic properties. Here, we present the novel C11 protease globupain, which was prospected from a metagenome-assembled genome of uncultivated Archaeoglobales sampled from the Soria Moria hydrothermal vent system located on the Arctic Mid-Ocean Ridge. Sequence comparisons against the MEROPS-MPRO database showed that globupain has the highest sequence identity to C11-like proteases present in human gut and intestinal bacteria. Successful recombinant expression in Escherichia coli of the wild-type zymogen and 13 mutant substitution variants allowed assessment of residues involved in maturation and activity of the enzyme. For activation, globupain required the addition of DTT and Ca2+. When activated, the 52kDa proenzyme was processed at K137 and K144 into a 12kDa light- and 32kDa heavy chain heterodimer. A structurally conserved H132/C185 catalytic dyad was responsible for the proteolytic activity, and the enzyme demonstrated the ability to activate in-trans. Globupain exhibited caseinolytic activity and showed a strong preference for arginine in the P1 position, with Boc-QAR-aminomethylcoumarin (AMC) as the best substrate out of a total of 17 fluorogenic AMC substrates tested. Globupain was thermostable (Tm activated enzyme = 94.51°C ± 0.09°C) with optimal activity at 75°C and pH 7.1. Characterization of globupain has expanded our knowledge of the catalytic properties and activation mechanisms of temperature tolerant marine C11 proteases. The unique combination of features such as elevated thermostability, activity at relatively low pH values, and ability to operate under high reducing conditions makes globupain a potential intriguing candidate for use in diverse industrial and biotechnology sectors.
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Affiliation(s)
- Victoria Røyseth
- Department of Biological Sciences, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Brianna M. Hurysz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United States
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms | KPD, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Sebastian Dorawa
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Anita-Elin Fedøy
- Department of Biological Sciences, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Hasan Arsın
- Department of Biological Sciences, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Mateus Sá M. Serafim
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United States
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Samuel A. Myers
- La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Olesia Werbowy
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Runar Stokke
- Department of Biological Sciences, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United States
| | - Ida Helene Steen
- Department of Biological Sciences, Center for Deep Sea Research, University of Bergen, Bergen, Norway
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Park YJ, Lim JK, Kim YJ, Yang SH, Lee HS, Kang SG, Lee JH, Yang Y, Kwon KK. Thermococcus argininiproducens sp. nov., an arginine biosynthesis archaeal species isolated from the Central Indian Ocean ridge. Int J Syst Evol Microbiol 2023; 73. [PMID: 37022754 DOI: 10.1099/ijsem.0.005760] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
A strictly anaerobic hyperthermophilic archaeon, designated strain IOH2T, was isolated from a deep-sea hydrothermal vent (Onnuri vent field) area on the Central Indian Ocean Ridge. Strain IOH2T showed high 16S rRNA gene sequence similarity to Thermococcus sibiricus MM 739T (99.42 %), Thermococcus alcaliphilus DSM 10322T (99.28 %), Thermococcus aegaeus P5T (99.21 %), Thermococcus litoralis DSM 5473T (99.13 %), 'Thermococcus bergensis' T7324T (99.13 %), Thermococcus aggregans TYT (98.92 %) and Thermococcus prieurii Bio-pl-0405IT2T (98.01 %), with all other strains showing lower than 98 % similarity. The average nucleotide identity and in silico DNA-DNA hybridization values were highest between strain IOH2T and T. sibiricus MM 739T (79.33 and 15.00 %, respectively); these values are much lower than the species delineation cut-offs. Cells of strain IOH2T were coccoid, 1.0-1.2 µm in diameter and had no flagella. Growth ranges were 60-85 °C (optimum at 80 °C), pH 4.5-8.5 (optimum at pH 6.3) and 2.0-6.0 % (optimum at 4.0 %) NaCl. Growth of strain IOH2T was enhanced by starch, glucose, maltodextrin and pyruvate as a carbon source, and elemental sulphur as an electron acceptor. Through genome analysis of strain IOH2T, arginine biosynthesis related genes were predicted, and growth of strain IOH2T without arginine was confirmed. The genome of strain IOH2T was assembled as a circular chromosome of 1 946 249 bp and predicted 2096 genes. The DNA G+C content was 39.44 mol%. Based on the results of physiological and phylogenetic analyses, Thermococcus argininiproducens sp. nov. is proposed with type strain IOH2T (=MCCC 4K00089T=KCTC 25190T).
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Affiliation(s)
- Yeong-Jun Park
- Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Jae Kyu Lim
- Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Yun Jae Kim
- Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Sung-Hyun Yang
- Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea
| | - Hyun Sook Lee
- Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Sung Gyun Kang
- Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Jung-Hyun Lee
- Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Youngik Yang
- National Marine Biodiversity Institute of Korea, Seocheon-gun, 33662, Republic of Korea
| | - Kae Kyoung Kwon
- Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon 34113, Republic of Korea
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Wang S, Jiang L, Xie S, Alain K, Wang Z, Wang J, Liu D, Shao Z. Disproportionation of Inorganic Sulfur Compounds by Mesophilic Chemolithoautotrophic Campylobacterota. mSystems 2023; 8:e0095422. [PMID: 36541763 DOI: 10.1128/msystems.00954-22] [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] [Indexed: 12/24/2022] Open
Abstract
The disproportionation of inorganic sulfur compounds could be widespread in natural habitats, and microorganisms could produce energy to support primary productivity through this catabolism. However, the microorganisms that carry this process out and the catabolic pathways at work remain relatively unstudied. Here, we investigated the bacterial diversity involved in sulfur disproportionation in hydrothermal plumes from Carlsberg Ridge in the northwestern Indian Ocean by enrichment cultures. A bacterial community analysis revealed that bacteria of the genera Sulfurimonas and Sulfurovum, belonging to the phylum Campylobacterota and previously having been characterized as chemolithoautotrophic sulfur oxidizers, were the most dominant members in six enrichment cultures. Subsequent bacterial isolation and physiological studies confirmed that five Sulfurimonas and Sulfurovum isolates could disproportionate thiosulfate and elemental sulfur. The ability to disproportionate sulfur was also demonstrated in several strains of Sulfurimonas and Sulfurovum that were isolated from hydrothermal vents or other natural environments. Dialysis membrane experiments showed that S0 disproportionation did not require the direct contact of cells with bulk sulfur. A comparative genomic analysis showed that Campylobacterota strains did not contain some genes of the Dsr and rDSR pathways (aprAB, dsrAB, dsrC, dsrMKJOP, and qmoABC) that are involved in sulfur disproportionation in some other taxa, suggesting the existence of an unrevealed catabolic pathway for sulfur disproportionation. These findings provide evidence for the catabolic versatility of these Campylobacterota genera, which are widely distributed in chemosynthetic environments, and expand our knowledge of the microbial taxa involved in this reaction of the biogeochemical sulfur cycle in hydrothermal vent environments. IMPORTANCE The phylum Campylobacterota, notably represented by the genera Sulfurimonas and Sulfurovum, is ubiquitous and predominant in deep-sea hydrothermal systems. It is well-known to be the major chemolithoautotrophic sulfur-oxidizing group in these habitats. Herein, we show that the mesophilic predominant chemolithoautotrophs of the genera Sulfurimonas and Sulfurovum could grow via sulfur disproportionation to gain energy. This is the first report of the chemolithoautotrophic disproportionation of thiosulfate and elemental sulfur within the genera Sulfurimonas and Sulfurovum, and this comes in addition to their already known role in the chemolithoautotrophic oxidation of sulfur compounds. Sulfur disproportionation via chemolithoautotrophic Campylobacterota may represent a previously unrecognized primary production process in hydrothermal vent ecosystems.
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Chen C, Watanabe HK, Gena K, Johnson SB. Anatomical shifts linked with unusual diets in deep-sea snails. Ecology 2023; 104:e3847. [PMID: 36336886 PMCID: PMC10078515 DOI: 10.1002/ecy.3847] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 02/01/2023]
Affiliation(s)
- Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | | | - Kaul Gena
- The Papua New Guinea University of Technology, Lae, Papua New Guinea
| | - Shannon B Johnson
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, California, USA
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Holden JF, Sistu H. Formate and hydrogen in hydrothermal vents and their use by extremely thermophilic methanogens and heterotrophs. Front Microbiol 2023; 14:1093018. [PMID: 36950162 PMCID: PMC10025317 DOI: 10.3389/fmicb.2023.1093018] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 11/08/2022] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
Extremely thermophilic methanogens in the Methanococci and heterotrophs in the Thermococci are common in deep-sea hydrothermal vents. All Methanococci use H2 as an electron donor, and a few species can also use formate. Most Methanococci have a coenzyme F420-reducing formate dehydrogenase. All Thermococci reduce S0 but have hydrogenases and produce H2 in the absence of S0. Some Thermococci have formate hydrogenlyase (Fhl) that reversibly converts H2 and CO2 to formate or an NAD(P)+-reducing formate dehydrogenase (Nfd). Questions remain if Methanococci or Thermococci use or produce formate in nature, why only certain species can grow on or produce formate, and what the physiological role of formate is? Formate forms abiotically in hydrothermal fluids through chemical equilibrium with primarily H2, CO2, and CO and is strongly dependent upon H2 concentration, pH, and temperature. Formate concentrations are highest in hydrothermal fluids where H2 concentrations are also high, such as in ultramafic systems where serpentinization reactions occur. In nature, Methanococci are likely to use formate as an electron donor when H2 is limiting. Thermococci with Fhl likely convert H2 and CO2 to formate when H2 concentrations become inhibitory for growth. They are unlikely to grow on formate in nature unless formate is more abundant than H2 in the environment. Nearly all Methanococci and Thermococci have a gene for at least one formate dehydrogenase catalytic subunit, which may be used to provide free formate for de novo purine biosynthesis. However, only species with a membrane-bound formate transporter can grow on or secrete formate. Interspecies H2 transfer occurs between Thermococci and Methanococci. This and putative interspecies formate transfer may support Methanococci in low H2 environments, which in turn may prevent growth inhibition of Thermococci by its own H2. Future research directions include understanding when, where, and how formate is used and produced by these organisms in nature, and how transcription of Thermococci genes encoding formate-related enzymes are regulated.
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Zhong YW, Zhou P, Cheng H, Zhou YD, Pan J, Xu L, Li M, Tao CH, Wu YH, Xu XW. Metagenomic Features Characterized with Microbial Iron Oxidoreduction and Mineral Interaction in Southwest Indian Ridge. Microbiol Spectr 2022; 10:e0061422. [PMID: 36286994 PMCID: PMC9769843 DOI: 10.1128/spectrum.00614-22] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/25/2022] [Indexed: 01/05/2023] Open
Abstract
The Southwest Indian Ridge (SWIR) is one of the typical representatives of deep-sea ultraslow-spreading ridges, and has increasingly become a hot spot of studying subsurface geological activities and deep-sea mining management. However, the understanding of microbial activities is still limited on active hydrothermal vent chimneys in SWIR. In this study, samples from an active black smoker and a diffuse vent located in the Longqi hydrothermal region were collected for deep metagenomic sequencing, which yielded approximately 290 GB clean data and 295 mid-to-high-quality metagenome-assembled genomes (MAGs). Sulfur oxidation conducted by a variety of Gammaproteobacteria, Alphaproteobacteria, and Campylobacterota was presumed to be the major energy source for chemosynthesis in Longqi hydrothermal vents. Diverse iron-related microorganisms were recovered, including iron-oxidizing Zetaproteobacteria, iron-reducing Deferrisoma, and magnetotactic bacterium. Twenty-two bacterial MAGs from 12 uncultured phyla harbored iron oxidase Cyc2 homologs and enzymes for organic carbon degradation, indicated novel chemolithoheterotrophic iron-oxidizing bacteria that affected iron biogeochemistry in hydrothermal vents. Meanwhile, potential interactions between microbial communities and chimney minerals were emphasized as enriched metabolic potential of siderophore transportation, and extracellular electron transfer functioned by multi-heme proteins was discovered. Composition of chimney minerals probably affected microbial iron metabolic potential, as pyrrhotite might provide more available iron for microbial communities. Collectively, this study provides novel insights into microbial activities and potential mineral-microorganism interactions in hydrothermal vents. IMPORTANCE Microbial activities and interactions with minerals and venting fluid in active hydrothermal vents remain unclear in the ultraslow-spreading SWIR (Southwest Indian Ridge). Understanding about how minerals influence microbial metabolism is currently limited given the obstacles in cultivating microorganisms with sulfur or iron oxidoreduction functions. Here, comprehensive descriptions on microbial composition and metabolic profile on 2 hydrothermal vents in SWIR were obtained based on cultivation-free metagenome sequencing. In particular, autotrophic sulfur oxidation supported by minerals was presumed, emphasizing the role of chimney minerals in supporting chemosynthesis. Presence of novel heterotrophic iron-oxidizing bacteria was also indicated, suggesting overlooked biogeochemical pathways directed by microorganisms that connected sulfide mineral dissolution and organic carbon degradation in hydrothermal vents. Our findings offer novel insights into microbial function and biotic interactions on minerals in ultraslow-spreading ridges.
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Affiliation(s)
- Ying-Wen Zhong
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Peng Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Hong Cheng
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Ya-Dong Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, PR China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Chun-Hui Tao
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Submarine Geosciences, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Yue-Hong Wu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Xue-Wei Xu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
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Brunner O, Chen C, Giguère T, Kawagucci S, Tunnicliffe V, Watanabe HK, Mitarai S. Species assemblage networks identify regional connectivity pathways among hydrothermal vents in the Northwest Pacific. Ecol Evol 2022; 12:e9612. [PMID: 36568865 PMCID: PMC9771708 DOI: 10.1002/ece3.9612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 08/08/2022] [Revised: 10/24/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
The distribution of species among spatially isolated habitat patches supports regional biodiversity and stability, so understanding the underlying processes and structure is a key target of conservation. Although multivariate statistics can infer the connectivity processes driving species distribution, such as dispersal and habitat suitability, they rarely explore the structure. Methods from graph theory, applied to distribution data, give insights into both connectivity pathways and processes by intuitively formatting the data as a network of habitat patches. We apply these methods to empirical data from the hydrothermal vent habitats of the Northwest Pacific. Hydrothermal vents are "oases" of biological productivity and endemicity on the seafloor that are imminently threatened by anthropogenic disturbances with unknown consequences to biodiversity. Here, we describe the structure of species assemblage networks at hydrothermal vents, how local and regional parameters affect their structure, and the implications for conservation. Two complementary networks were formed from an extensive species assemblage dataset: a similarity network of vent site nodes linked by weighted edges based on their pairwise assemblage similarity and a bipartite network of species nodes linked to vent site nodes at which they are present. Using these networks, we assessed the role of individual vent sites in maintaining network connectivity and identified biogeographic sub-regions. The three sub-regions and two outlying sites are separated by their spatial arrangement and local environmental filters. Both networks detected vent sites that play a disproportionately important role in regional pathways, while the bipartite network also identified key vent sites maintaining the distinct species assemblages of their sub-regions. These regional connectivity pathways provide insights into historical colonization routes, while sub-regional connectivity pathways are of value when selecting sites for conservation and/or estimating the multivent impacts from proposed deep-sea mining.
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Affiliation(s)
- Otis Brunner
- Okinawa Institute of Science and TechnologyOkinawaJapan
| | - Chong Chen
- X‐STAR, Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaJapan
| | - Thomas Giguère
- School of Earth & Ocean SciencesUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | - Shinsuke Kawagucci
- X‐STAR, Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaJapan,Project Team for Developing Innovative Technologies for Exploration of Deep‐Sea ResourcesJapan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaJapan
| | - Verena Tunnicliffe
- School of Earth & Ocean SciencesUniversity of VictoriaVictoriaBritish ColumbiaCanada,Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
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Twing KI, Ward LM, Kane ZK, Sanders A, Price RE, Pendleton HL, Giovannelli D, Brazelton WJ, McGlynn SE. Microbial ecology of a shallow alkaline hydrothermal vent: Strýtan Hydrothermal Field, Eyjafördur, northern Iceland. Front Microbiol 2022; 13:960335. [PMID: 36466646 PMCID: PMC9713835 DOI: 10.3389/fmicb.2022.960335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/05/2022] [Indexed: 10/20/2023] Open
Abstract
Strýtan Hydrothermal Field (SHF) is a submarine system located in Eyjafördur in northern Iceland composed of two main vents: Big Strýtan and Arnarnesstrýtan. The vents are shallow, ranging from 16 to 70 m water depth, and vent high pH (up to 10.2), moderate temperature (T max ∼70°C), anoxic, fresh fluids elevated in dissolved silica, with slightly elevated concentrations of hydrogen and methane. In contrast to other alkaline hydrothermal vents, SHF is unique because it is hosted in basalt and therefore the high pH is not created by serpentinization. While previous studies have assessed the geology and geochemistry of this site, the microbial diversity of SHF has not been explored in detail. Here we present a microbial diversity survey of the actively venting fluids and chimneys from Big Strýtan and Arnarnesstrýtan, using 16S rRNA gene amplicon sequencing. Community members from the vent fluids are mostly aerobic heterotrophic bacteria; however, within the chimneys oxic, low oxygen, and anoxic habitats could be distinguished, where taxa putatively capable of acetogenesis, sulfur-cycling, and hydrogen metabolism were observed. Very few archaea were observed in the samples. The inhabitants of SHF are more similar to terrestrial hot spring samples than other marine sites. It has been hypothesized that life on Earth (and elsewhere in the solar system) could have originated in an alkaline hydrothermal system, however all other studied alkaline submarine hydrothermal systems to date are fueled by serpentinization. SHF adds to our understandings of hydrothermal vents in relationship to microbial diversity, evolution, and possibly the origin of life.
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Affiliation(s)
- Katrina I. Twing
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - L. M. Ward
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Department of Geosciences, Smith College, Northampton, MA, United States
| | - Zachary K. Kane
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Alexa Sanders
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Roy Edward Price
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - H. Lizethe Pendleton
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
| | - Donato Giovannelli
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - William J. Brazelton
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, United States
| | - Shawn E. McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Center for Sustainable Resource Science, RIKEN, Saitama, Japan
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Chen C, Watanabe HK. A new provannid snail (Gastropoda, Abyssochrysoidea) discovered from Northwest Eifuku Volcano, Mariana Arc. Zookeys 2022; 1112:123-137. [PMID: 36760627 PMCID: PMC9848648 DOI: 10.3897/zookeys.1112.85950] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/09/2022] [Indexed: 11/12/2022] Open
Abstract
Gastropods in the family Provannidae are characteristic members of deep-sea chemosynthesis-based communities. Recently, surveys of hydrothermal vents and hydrocarbon seeps in the western Pacific have revealed a high diversity of provannids, with new discoveries continuing to be made. Here, we report and describe a further new species, Provannaexquisita sp. nov., discovered from the Northwest Eifuku volcano on the Mariana Arc. This new species is distinguished from all other described Provanna species by its exaggerated sculpture characterised by two to three sharply raised, flange-like keels on the teleoconch whorls. The status of P.exquisita sp. nov. is also supported by a molecular phylogeny reconstruction using the mitochondrial cytochrome c oxidase subunit I (COI) gene, which suggested that it is most closely related to a clade of three species described from Okinawa Trough vents including P.clathrata, P.subglabra, and P.fenestrata. Despite being one of the better-explored regions of the world in terms of hydrothermal vent biodiversity, new discoveries like P.exquisita sp. nov. continue to remind us that we are nowhere near fully documenting the species diversity in these unique ecosystems-despite the species being threatened from imminent anthropogenic impacts such as deep-sea mining.
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Affiliation(s)
- Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, JapanX-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)YokosukaJapan
| | - Hiromi Kayama Watanabe
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, JapanX-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)YokosukaJapan
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19
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Methou P, Chen C, Kayama Watanabe H, Cambon MA, Pradillon F. Reproduction in deep-sea vent shrimps is influenced by diet, with rhythms apparently unlinked to surface production. Ecol Evol 2022; 12:e9076. [PMID: 35866019 PMCID: PMC9288886 DOI: 10.1002/ece3.9076] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 06/01/2022] [Accepted: 06/08/2022] [Indexed: 11/06/2022] Open
Abstract
Variations in offspring production according to feeding strategies or food supply have been recognized in many animals from various ecosystems. Despite an unusual trophic structure based on non-photosynthetic primary production, these relationships remain largely under-studied in chemosynthetic ecosystems. Here, we use Rimicaris shrimps as a study case to explore relationships between reproduction, diets, and food supply in these environments. For that, we compared reproductive outputs of three congeneric shrimps differing by their diets. They inhabit vents located under oligotrophic waters of tropical gyres with opposed latitudes, allowing us to also examine the prevalence of phylogenetic vs environmental drivers in their reproductive rhythms. For this, we used both our original data and a compilation of published observations on the presence of ovigerous females covering various seasons over the past 35 years. We report distinct egg production trends between Rimicaris species relying solely on chemosymbiosis-R. exoculata and R. kairei-and one relying on mixotrophy, R. chacei. Besides, our data suggest a reproductive periodicity that does not correspond to seasonal variations in surface production, with substantial proportions of brooding females during the same months of the year, despite those months corresponding to either boreal winter or austral summer depending on the hemisphere. These observations contrast with the long-standing paradigm in deep-sea species for which periodic reproductive patterns have always been attributed to seasonal variations of photosynthetic production sinking from the surface. Our results suggest the presence of an intrinsic basis for biological rhythms in the deep sea, and bring to light the importance of having year-round observations in order to understand the life history of vent animals.
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Affiliation(s)
- Pierre Methou
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds Plouzané France.,X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka Japan
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka Japan
| | | | - Marie-Anne Cambon
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds Plouzané France
| | - Florence Pradillon
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds Plouzané France
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20
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Baumgartner RJ, Hu S, Van Kranendonk MJ, Verrall M. Taphonomy of microorganisms and microbial microtextures at sulfidic hydrothermal vents: A case study from the Roman Ruins black smokers, Eastern Manus Basin. Geobiology 2022; 20:479-497. [PMID: 35315208 PMCID: PMC9310909 DOI: 10.1111/gbi.12490] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 02/01/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Biological activity at deep-sea hydrothermal chimneys is driven by chemotrophic microorganisms that metabolize chemicals from the venting high-temperature fluids. Understanding taphonomy and microbial microtextures in such environments is a necessity for micropaleontological and palaeoecological research. This study examines fossilized microorganisms and related microtextures in a recent black smoker from the Roman Ruins hydrothermal vent site, Eastern Manus Basin offshore of Papua New Guinea. Whereas the center of the examined sulfide chimney is dominated by high-temperature mineralogy (chalcopyrite and dendritic sphalerite), filamentous and coccoidal biomorphs occur in an outer, warm zone of mixing between hydrothermal fluids and seawater, which is indicated by their occurrence within colloform and botryoidal pyrite of barite-pyrite coprecipitates. Both morphotypes can be interpreted as thermophilic microorganisms based on their occurrence in a high-temperature habitat. Their separate (non-commensal) occurrence hints at sensitivities to microenvironmental conditions, which is expectable for strong temperature, pH, and redox gradients at the walls of deep-sea hydrothermal chimneys. Whereas both morphotypes experienced mild thermal overprint, taphonomic differences exist: (i) spaces left by cells in filamentous fossils are predominately filled by silica, whereas inter/extracellular features (crosswalls/septae and outer sheaths) are pyritized; (ii) coccoidal fossils show both silica- and pyrite-infilled interiors, and generally better preservation of cell walls. These different manifestations presumably relate to an interplay between microenvironmental and biological factors, potentially contrasting metabolisms, and differences in cell wall chemistries of distinct bacteria and/or archaea. A further hypothesis is that the coccoidal features represent biofilm-forming organisms, whose organic matter derivates contributed to the formation of intimately associated wavy and wrinkly carbonaceous laminations that are at least locally distinguishable from the texture of the surrounding pyrite. Hence, the presented data provide evidence that microtextures of microbiota from hydrothermal systems can have a similar significance for palaeobiological research as those from sedimentary environments.
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Affiliation(s)
- Raphael J. Baumgartner
- CSIRO Mineral ResourcesAustralian Resources Research CentreKensingtonWestern AustraliaAustralia
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental SciencesThe University of New South WalesKensingtonNew South WalesAustralia
| | - Siyu Hu
- CSIRO Mineral ResourcesAustralian Resources Research CentreKensingtonWestern AustraliaAustralia
| | - Martin J. Van Kranendonk
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental SciencesThe University of New South WalesKensingtonNew South WalesAustralia
| | - Michael Verrall
- CSIRO Mineral ResourcesAustralian Resources Research CentreKensingtonWestern AustraliaAustralia
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21
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Zhang H, Chen Y, Li Y, Song Y, Ma J, Ju J. Secondary Metabolites and Biosynthetic Gene Clusters Analysis of Deep-Sea Hydrothermal Vent-Derived Streptomyces sp. SCSIO ZS0520. Mar Drugs 2022; 20:393. [PMID: 35736196 DOI: 10.3390/md20060393] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 01/27/2023] Open
Abstract
Streptomyces sp. SCSIO ZS0520 is a deep-sea hydrothermal vent-derived actinomycete. Our previous metabolism investigation showed that Streptomyces sp. SCSIO ZS0520 is a producer of cytotoxic actinopyrones. Here, another four types of secondary metabolites were identified, including six salinomycin isomers (2–7), the macrolide elaiophylin (8), the triterpene N-acetyl-aminobacteriohopanetriol (9), and the pyrone minipyrone (10). Among them, compounds 2–6 and 10 are new compounds. To understand the biosynthetic pathway of these compounds, a bioinformatic analysis of the whole genome was carried out, which identified 34 secondary metabolite biosynthetic gene clusters. Next, the biosynthetic pathways responsive to four types of products were deduced on the basis of gene function predictions and structure information. Taken together, these findings prove the metabolite potential of ZS0520 and lay the foundations to solve the remaining biosynthetic issues in four types of marine natural products.
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22
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Methou P, Hikosaka M, Chen C, Watanabe HK, Miyamoto N, Makita H, Takahashi Y, Jenkins RG. Symbiont Community Composition in Rimicaris kairei Shrimps from Indian Ocean Vents with Notes on Mineralogy. Appl Environ Microbiol 2022; 88:e0018522. [PMID: 35404070 DOI: 10.1128/aem.00185-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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] [Indexed: 11/26/2022] Open
Abstract
Hydrothermal vent ecosystems are home to a wide array of symbioses between animals and chemosynthetic microbes, among which shrimps in the genus Rimicaris is one of the most iconic. So far, studies of Rimicaris symbioses have been restricted to Atlantic species, including Rimicaris exoculata, which is totally reliant on the symbionts for nutrition, and the mixotrophic species Rimicaris chacei. Here, we expand this by investigating and characterizing the symbiosis of the Indian Ocean species Rimicaris kairei using specimens from two vent fields, Kairei and Edmond. We also aimed to evaluate the differences in mineralogy and microbial communities between two cephalothorax color morphs, black and brown, through a combination of 16S metabarcoding, scanning electron microscopy, fluorescent in situ hybridization, energy-dispersive X-ray spectroscopy, and synchrotron near-edge X-ray absorption structure analyses. Overall, our results highlight that R. kairei exhibits similar symbiont lineages to those of its Atlantic congeners, although with a few differences, such as the lack of Zetaproteobacteria. We found distinct mineralization processes behind the two color morphs that were linked to differences in the vent fluid composition, but the symbiotic community composition was surprisingly similar. In R. exoculata, such mineralogical differences have been shown to stem from disparity in the microbial communities, but our results indicate that in R. kairei this is instead due to the shift of dominant metabolisms by the same symbiotic partners. We suggest that a combination of local environmental factors and biogeographic barriers likely contribute to the differences between Atlantic and Indian Ocean Rimicaris symbioses. IMPORTANCE Hydrothermal vent shrimps in the genus Rimicaris are among the most charismatic deep-sea animals of Atlantic and Indian Oceans, often occurring on towering black smokers in dense aggregates of thousands of individuals. Although this dominance is only possible because of symbiosis, no study on the symbiosis of Indian Ocean Rimicaris species has been conducted. Here, we characterize the Rimicaris kairei symbiosis by combining molecular, microscopic, and elemental analyses, making comparisons with those of the Atlantic species possible for the first time. Although most symbiotic partners remained consistent across the two oceans, some differences were recognized in symbiont lineages, as well as in the mechanisms behind the formation of two color morphs with distinct mineralogies. Our results shed new light on relationships among mineralogy, environmental factors, and microbial communities that are useful for understanding other deep-sea symbioses in the future.
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23
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Qi L, Lian CA, Zhu FC, Shi M, He LS. Comparative Analysis of Intestinal Microflora Between Two Developmental Stages of Rimicaris kairei, a Hydrothermal Shrimp From the Central Indian Ridge. Front Microbiol 2022; 12:802888. [PMID: 35242112 PMCID: PMC8886129 DOI: 10.3389/fmicb.2021.802888] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/28/2021] [Indexed: 01/04/2023] Open
Abstract
Despite extreme physical and chemical characteristics, deep-sea hydrothermal vents provide a place for fauna survival and reproduction. The symbiotic relationship of chemotrophic microorganisms has been investigated in the gill of Rimicaris exoculata, which are endemic to the hydrothermal vents of the Mid-Atlantic Ridge. However, only a few studies have examined intestinal symbiosis. Here, we studied the intestinal fauna in juvenile and adult Rimicaris kairei, another species in the Rimicaris genus that was originally discovered at the Kairei and Edmond hydrothermal vent fields in the Central Indian Ridge. The results showed that there were significant differences between juvenile and adult gut microbiota in terms of species richness, diversity, and evenness. The values of Chao1, observed species, and ASV rarefaction curves indicated almost four times the number of species in adults compared to juveniles. In juveniles, the most abundant phylum was Deferribacterota, at 80%, while in adults, Campilobacterota was the most abundant, at 49%. Beta diversity showed that the intestinal communities of juveniles and adults were clearly classified into two clusters based on the evaluations of Bray-Curtis and weighted UniFrac distance matrices. Deferribacteraceae and Sulfurovum were the main featured bacteria contributing to the difference. Moreover, functional prediction for all of the intestinal microbiota showed that the pathways related to ansamycin synthesis, branched-chain amino acid biosynthesis, lipid metabolism, and cell motility appeared highly abundant in juveniles. However, for adults, the most abundant pathways were those of sulfur transfer, carbohydrate, and biotin metabolism. Taken together, these results indicated large differences in intestinal microbial composition and potential functions between juvenile and adult vent shrimp (R. kairei), which may be related to their physiological needs at different stages of development.
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Affiliation(s)
- Li Qi
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chun-Ang Lian
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Fang-Chao Zhu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Mengke Shi
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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24
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Yvenou S, Allioux M, Slobodkin A, Slobodkina G, Jebbar M, Alain K. Genetic Potential of Dissulfurimicrobium hydrothermale, an Obligate Sulfur-Disproportionating Thermophilic Microorganism. Microorganisms 2021; 10:60. [PMID: 35056509 DOI: 10.3390/microorganisms10010060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 12/08/2021] [Revised: 12/22/2021] [Accepted: 12/25/2021] [Indexed: 12/12/2022] Open
Abstract
The biochemical pathways of anaerobic sulfur disproportionation are only partially deciphered, and the mechanisms involved in the first step of S0-disproportionation remain unknown. Here, we present the results of sequencing and analysis of the complete genome of Dissulfurimicrobium hydrothermale strain Sh68T, one of two strains isolated to date known to grow exclusively by anaerobic disproportionation of inorganic sulfur compounds. Dissulfurimicrobium hydrothermale Sh68T is a motile, thermophilic, anaerobic, chemolithoautotrophic microorganism isolated from a hydrothermal pond at Uzon caldera, Kamchatka, Russia. It is able to produce energy and grow by disproportionation of elemental sulfur, sulfite and thiosulfate. Its genome consists of a circular chromosome of 2,025,450 base pairs, has a G + C content of 49.66% and a completion of 97.6%. Genomic data suggest that CO2 assimilation is carried out by the Wood–Ljungdhal pathway and that central anabolism involves the gluconeogenesis pathway. The genome of strain Sh68T encodes the complete gene set of the dissimilatory sulfate reduction pathway, some of which are likely to be involved in sulfur disproportionation. A short sequence protein of unknown function present in the genome of strain Sh68T is conserved in the genomes of a large panel of other S0-disproportionating bacteria and was absent from the genomes of microorganisms incapable of elemental sulfur disproportionation. We propose that this protein may be involved in the first step of elemental sulfur disproportionation, as S0 is poorly soluble and unable to cross the cytoplasmic membrane in this form.
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25
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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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van Erk MR, Krukenberg V, Bomholt Jensen P, Littmann S, de Beer D. Conspicuous Smooth and White Egg-Shaped Sulfur Structures on a Deep-Sea Hydrothermal Vent Formed by Sulfide-Oxidizing Bacteria. Microbiol Spectr 2021; 9:e0095521. [PMID: 34468192 DOI: 10.1128/Spectrum.00955-21] [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] [Indexed: 11/20/2022] Open
Abstract
Conspicuous egg-shaped, white, and smooth structures were observed at a hydrothermal vent site in the Guaymas Basin, Gulf of California. The gelatinous structures decomposed within hours after sampling. Scanning electron microscopy (SEM) and light microscopy showed that the structure consisted of filaments of less than 0.1 μm thickness, similar to those observed for "Candidatus Arcobacter sulfidicus." SEM-energy-dispersive X-ray spectroscopy (EDS) showed that the filaments were sulfur rich. According to 16S rRNA gene amplicon and fluorescence in situ hybridization (FISH) analyses, Arcobacter, a sulfide oxidizer that is known to produce filamentous elemental sulfur, was among the dominant species in the structure and was likely responsible for its formation. Arcobacter normally produces woolly snowflake like structures in opposed gradients of sulfide and oxygen. In the laboratory, we observed sulfide consumption in the anoxic zone of the structure, suggesting an anaerobic conversion. The sulfide oxidation and decomposition of the structure in the laboratory may be explained by dissolution of the sulfur filaments by reaction with sulfide under formation of polysulfides. IMPORTANCE At the deep-sea Guaymas Basin hydrothermal vent system, sulfide-rich hydrothermal fluids mix with oxygenated seawater, thereby providing a habitat for microbial sulfur oxidation. Microbial sulfur oxidation in the deep sea involves a variety of organisms and processes and can result in the excretion of elemental sulfur. Here, we report on conspicuous white and smooth gelatinous structures found on hot vents. These strange egg-shaped structures were often observed on previous occasions in the Guaymas Basin, but their composition and formation process were unknown. Our data suggest that the notable and highly ephemeral structure was likely formed by the well-known sulfide-oxidizing Arcobacter. While normally Arcobacter produces loose flocs or woolly layers, here smooth gel-like structures were found.
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Guo LL, Wang SL, Zhu FC, Xue F, He LS. Characteristics of Two Crustins from Alvinocaris longirostris in Hydrothermal Vents. Mar Drugs 2021; 19:600. [PMID: 34822471 DOI: 10.3390/md19110600] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/16/2021] [Accepted: 10/18/2021] [Indexed: 11/17/2022] Open
Abstract
Crustins are widely distributed among different crustacean groups. They are characterized by a whey acidic protein (WAP) domain, and most examined Crustins show activity against Gram-positive bacteria. This study reports two Crustins, Al-crus 3 and Al-crus 7, from hydrothermal vent shrimp, Alvinocaris longirostris. Al-crus 3 and Al-crus 7 belong to Crustin Type IIa, with a similarity of about 51% at amino acid level. Antibacterial assays showed that Al-crus 3 mainly displayed activity against Gram-positive bacteria with MIC50 values of 10–25 μM. However, Al-crus 7 not only displayed activity against Gram-positive bacteria but also against Gram-negative bacteria Imipenem-resistant Acinetobacter baumannii, in a sensitive manner. Notably, in the effective antibacterial spectrum, Methicillin-sensitive Staphylococcus aureus, Escherichia coli (ESBLs) and Imipenem-resistant A. baumannii were drug-resistant pathogens. Narrowing down the sequence to the WAP domain, Al-crusWAP 3 and Al-crusWAP 7 demonstrated antibacterial activities but were weak. Additionally, the effects on bacteria did not significantly change after they were maintained at room temperature for 48 h. This indicated that Al-crus 3 and Al-crus 7 were relatively stable and convenient for transportation. Altogether, this study reported two new Crustins with specific characteristics. In particular, Al-crus 7 inhibited Gram-negative imipenem-resistant A. baumannii.
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Shi Y, Ma Y, Wei J, Ge Y, Jiang W, He S, Wu X, Zhang X, Wu B. Comparative Metabolomics Reveals Fungal Conversion of Co-Existing Bacterial Metabolites within a Synthetic Aspergillus- Streptomyces Community. Mar Drugs 2021; 19:526. [PMID: 34564188 DOI: 10.3390/md19090526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 08/25/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/30/2022] Open
Abstract
In nature, secondary metabolites have been proven to be the essential communication media between co-occurring microorganisms and to influence their relationship with each other. In this study, we conducted a metabolomics survey of the secondary metabolites of an artificial co-culture related to a hydrothermal vent fungal–bacterial community comprising Aspergillus sclerotiorum and Streptomyces and their reciprocal relationship. The fungal strain was found to increase the secretion of notoamides and the compound cyclo(Pro-Trp) produced by the actinomycetes strain was discovered to be the responsible molecule. This led to the hypothesis that the fungi transformed cyclo(Pro-Trp) synthesized by the actinomycetes as the biosynthetic precursors of notoamides in the chemical communication. Further analysis showed Streptomyces sp. WU20 was efficient in transforming amino acids into cyclo(Pro-Trp) and adding tryptophan as well as proline into the chemical communication enhanced the induction of the notoamide accumulation. Thus, we propose that the microbial transformation during the synthetic metabolically-mediated chemical communication might be a promising means of speeding up the discovery of novel bioactive molecules. The objective of this research was to clarify the mechanism of microbial transformation for the chemical communication. Besides, this research also highlights the utility of mass spectrometry-based metabolomics as an effective tool in the direct biochemical analysis of community metabolites.
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Xu T, Wang Y, Sun J, Chen C, Watanabe HK, Chen J, Qian PY, Qiu JW. Hidden historical habitat-linked population divergence and contemporary gene flow of a deep-sea patellogastropod limpet. Mol Biol Evol 2021; 38:5640-5654. [PMID: 34534352 PMCID: PMC8662656 DOI: 10.1093/molbev/msab278] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Indexed: 01/24/2023] Open
Abstract
Hydrothermal vents and hydrocarbon seeps in the deep ocean are rare oases fueled by chemosynthesis. Biological communities inhabiting these ecosystems are often distributed in widely separated habitats, raising intriguing questions on how these organisms achieve connectivity and whether habitat types facilitate intraspecific divergence. The deep-sea patellogastropod limpet Bathyacmaea nipponica that colonizes both vents and seeps across ∼2,400 km in the Northwest Pacific is a feasible model to answer these questions. We analyzed 123 individuals from four vents and three seeps using a comprehensive method incorporating population genomics and physical ocean modeling. Genome survey sequencing and genotyping-by-sequencing resulted in 9,838 single-nucleotide polymorphisms for population genomic analyses. Genetic divergence and demographic analyses revealed four habitat-linked (i.e., three seep and one vent) genetic groups, with the vent genetic group established via the opportunistic invasion of a few limpet larvae from a nearby seep genetic group. TreeMix analysis uncovered three historical seep-to-vent migration events. ADMIXTURE and divMigrate analyses elucidated weak contemporary gene flow from a seep genetic group to the vent genetic group. Physical ocean modeling underlined the potential roles of seafloor topography and ocean currents in shaping the genetic connectivity, contemporary migration, and local hybridization of these deep-sea limpets. Our study highlighted the power of integrating genomic and oceanographic approaches in deciphering the demography and diversification of deep-sea organisms. Given the increasing anthropogenic activities (e.g., mining and gas hydrate extraction) affecting the deep ocean, our results have implications for the conservation of deep-sea biodiversity and establishment of marine protected areas.
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Affiliation(s)
- Ting Xu
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Biology and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, Hong Kong, China
| | - Yan Wang
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jin Sun
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Hiromi Kayama Watanabe
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Junlin Chen
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jian-Wen Qiu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Biology and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, Hong Kong, China
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30
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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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31
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Leonard JM, Mitchell J, Beinart RA, Delaney JA, Sanders JG, Ellis G, Goddard EA, Girguis PR, Scott KM. Cooccurring Activities of Two Autotrophic Pathways in Symbionts of the Hydrothermal Vent Tubeworm Riftia pachyptila. Appl Environ Microbiol 2021; 87:e0079421. [PMID: 34190607 DOI: 10.1128/AEM.00794-21] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genome and proteome data predict the presence of both the reductive citric acid cycle (rCAC; also called the reductive tricarboxylic acid cycle) and the Calvin-Benson-Bassham cycle (CBB) in "Candidatus Endoriftia persephonae," the autotrophic sulfur-oxidizing bacterial endosymbiont from the giant hydrothermal vent tubeworm Riftia pachyptila. We tested whether these cycles were differentially induced by sulfide supply, since the synthesis of biosynthetic intermediates by the rCAC is less energetically expensive than that by the CBB. R. pachyptila was incubated under in situ conditions in high-pressure aquaria under low (28 to 40 μmol · h-1) or high (180 to 276 μmol · h-1) rates of sulfide supply. Symbiont-bearing trophosome samples excised from R. pachyptila maintained under the two conditions were capable of similar rates of CO2 fixation. Activities of the rCAC enzyme ATP-dependent citrate lyase (ACL) and the CBB enzyme 1,3-bisphosphate carboxylase/oxygenase (RubisCO) did not differ between the two conditions, although transcript abundances for ATP-dependent citrate lyase were 4- to 5-fold higher under low-sulfide conditions. δ13C values of internal dissolved inorganic carbon (DIC) pools were varied and did not correlate with sulfide supply rate. In samples taken from freshly collected R. pachyptila, δ13C values of lipids fell between those collected for organisms using either the rCAC or the CBB exclusively. These observations are consistent with cooccurring activities of the rCAC and the CBB in this symbiosis. IMPORTANCE Previous to this study, the activities of the rCAC and CBB in R. pachyptila had largely been inferred from "omics" studies of R. pachyptila without direct assessment of in situ conditions prior to collection. In this study, R. pachyptila was maintained and monitored in high-pressure aquaria prior to measuring its CO2 fixation parameters. Results suggest that ranges in sulfide concentrations similar to those experienced in situ do not exert a strong influence on the relative activities of the rCAC and the CBB. This observation highlights the importance of further study of this symbiosis and other organisms with multiple CO2-fixing pathways, which recent genomics and biochemical studies suggest are likely to be more prevalent than anticipated.
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Liu Q, Guo J, Ye W, Cheng K, Qi F, Zheng R, Sun Z, Zhang X. Development of an Easy-to-Operate Underwater Raman System for Deep-Sea Cold Seep and Hydrothermal Vent In Situ Detection. Sensors (Basel) 2021; 21:5090. [PMID: 34372326 DOI: 10.3390/s21155090] [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: 06/15/2021] [Revised: 07/12/2021] [Accepted: 07/22/2021] [Indexed: 12/17/2022]
Abstract
As a powerful in situ detection technique, Raman spectroscopy is becoming a popular underwater investigation method, especially in deep-sea research. In this paper, an easy-to-operate underwater Raman system with a compact design and competitive sensitivity is introduced. All the components, including the optical module and the electronic module, were packaged in an L362 × Φ172 mm titanium capsule with a weight of 20 kg in the air (about 12 kg in water). By optimising the laser coupling mode and focusing lens parameters, a competitive sensitivity was achieved with the detection limit of SO42− being 0.7 mmol/L. The first sea trial was carried out with the aid of a 3000 m grade remotely operated vehicle (ROV) “FCV3000” in October 2018. Over 20,000 spectra were captured from the targets interested, including methane hydrate, clamshell in the area of cold seep, and bacterial mats around a hydrothermal vent, with a maximum depth of 1038 m. A Raman peak at 2592 cm−1 was found in the methane hydrate spectra, which revealed the presence of hydrogen sulfide in the seeping gas. In addition, we also found sulfur in the bacterial mats, confirming the involvement of micro-organisms in the sulfur cycle in the hydrothermal field. It is expected that the system can be developed as a universal deep-sea survey and detection equipment in the near future.
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Arsın H, Jasilionis A, Dahle H, Sandaa RA, Stokke R, Nordberg Karlsson E, Steen IH. Exploring Codon Adjustment Strategies towards Escherichia coli-Based Production of Viral Proteins Encoded by HTH1, a Novel Prophage of the Marine Bacterium Hypnocyclicus thermotrophus. Viruses 2021; 13:v13071215. [PMID: 34201869 PMCID: PMC8310279 DOI: 10.3390/v13071215] [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: 05/21/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 01/15/2023] Open
Abstract
Marine viral sequence space is immense and presents a promising resource for the discovery of new enzymes interesting for research and biotechnology. However, bottlenecks in the functional annotation of viral genes and soluble heterologous production of proteins hinder access to downstream characterization, subsequently impeding the discovery process. While commonly utilized for the heterologous expression of prokaryotic genes, codon adjustment approaches have not been fully explored for viral genes. Herein, the sequence-based identification of a putative prophage is reported from within the genome of Hypnocyclicus thermotrophus, a Gram-negative, moderately thermophilic bacterium isolated from the Seven Sisters hydrothermal vent field. A prophage-associated gene cluster, consisting of 46 protein coding genes, was identified and given the proposed name Hypnocyclicus thermotrophus phage H1 (HTH1). HTH1 was taxonomically assigned to the viral family Siphoviridae, by lowest common ancestor analysis of its genome and phylogeny analyses based on proteins predicted as holin and DNA polymerase. The gene neighbourhood around the HTH1 lytic cassette was found most similar to viruses infecting Gram-positive bacteria. In the HTH1 lytic cassette, an N-acetylmuramoyl-L-alanine amidase (Amidase_2) with a peptidoglycan binding motif (LysM) was identified. A total of nine genes coding for enzymes putatively related to lysis, nucleic acid modification and of unknown function were subjected to heterologous expression in Escherichia coli. Codon optimization and codon harmonization approaches were applied in parallel to compare their effects on produced proteins. Comparison of protein yields and thermostability demonstrated that codon optimization yielded higher levels of soluble protein, but codon harmonization led to proteins with higher thermostability, implying a higher folding quality. Altogether, our study suggests that both codon optimization and codon harmonization are valuable approaches for successful heterologous expression of viral genes in E. coli, but codon harmonization may be preferable in obtaining recombinant viral proteins of higher folding quality.
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Affiliation(s)
- Hasan Arsın
- Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway; (R.-A.S.); (R.S.)
- Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway;
- Correspondence: (H.A.); (I.H.S.); Tel.: +47-555-88-375 (I.H.S.)
| | - Andrius Jasilionis
- Division of Biotechnology, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (A.J.); (E.N.K.)
| | - Håkon Dahle
- Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway;
- Computational Biology Unit, University of Bergen, N-5020 Bergen, Norway
| | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway; (R.-A.S.); (R.S.)
| | - Runar Stokke
- Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway; (R.-A.S.); (R.S.)
- Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway;
| | - Eva Nordberg Karlsson
- Division of Biotechnology, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (A.J.); (E.N.K.)
| | - Ida Helene Steen
- Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway; (R.-A.S.); (R.S.)
- Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway;
- Correspondence: (H.A.); (I.H.S.); Tel.: +47-555-88-375 (I.H.S.)
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Thomas E, Anderson RE, Li V, Rogan LJ, Huber JA. Diverse Viruses in Deep-Sea Hydrothermal Vent Fluids Have Restricted Dispersal across Ocean Basins. mSystems 2021; 6:e0006821. [PMID: 34156293 DOI: 10.1128/mSystems.00068-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Indexed: 12/24/2022] Open
Abstract
In the ocean, viruses impact microbial mortality, regulate biogeochemical cycling, and alter the metabolic potential of microbial lineages. At deep-sea hydrothermal vents, abundant viruses infect a wide range of hosts among the archaea and bacteria that inhabit these dynamic habitats. However, little is known about viral diversity, host range, and biogeography across different vent ecosystems, which has important implications for how viruses manipulate microbial function and evolution. Here, we examined viral diversity, viral and host distribution, and virus-host interactions in microbial metagenomes generated from venting fluids from several vent sites within three different geochemically and geographically distinct hydrothermal systems: Piccard and Von Damm vent fields at the Mid-Cayman Rise in the Caribbean Sea, and at several vent sites within Axial Seamount in the Pacific Ocean. Analysis of viral sequences and clustered regularly interspaced short palindromic repeat (CRISPR) spacers revealed highly diverse viral assemblages and evidence of active infection. Network analysis revealed that viral host range was relatively narrow, with very few viruses infecting multiple microbial lineages. Viruses were largely endemic to individual vent sites, indicating restricted dispersal, and in some cases, viral assemblages persisted over time. Thus, we show that hydrothermal vent fluids are home to novel, diverse viral assemblages that are highly localized to specific regions and taxa. IMPORTANCE Viruses play important roles in manipulating microbial communities and their evolution in the ocean, yet not much is known about viruses in deep-sea hydrothermal vents. However, viral ecology and evolution are of particular interest in hydrothermal vent habitats because of their unique nature: previous studies have indicated that most viruses in hydrothermal vents are temperate rather than lytic, and it has been established that rates of horizontal gene transfer (HGT) are particularly high among thermophilic vent microbes, and viruses are common vectors for HGT. If viruses have broad host range or are widespread across vent sites, they have increased potential to act as gene-sharing "highways" between vent sites. By examining viral diversity, distribution, and infection networks across disparate vent sites, this study provides the opportunity to better characterize and constrain the viral impact on hydrothermal vent microbial communities. We show that viruses in hydrothermal vents are diverse and apparently active, but most have restricted host range and are not widely distributed among vent sites. Thus, the impacts of viral infection are likely to be highly localized and constrained to specific taxa in these habitats.
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Ip JCH, Xu T, Sun J, Li R, Chen C, Lan Y, Han Z, Zhang H, Wei J, Wang H, Tao J, Cai Z, Qian PY, Qiu JW. Host-Endosymbiont Genome Integration in a Deep-Sea Chemosymbiotic Clam. Mol Biol Evol 2021; 38:502-518. [PMID: 32956455 PMCID: PMC7826175 DOI: 10.1093/molbev/msaa241] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Endosymbiosis with chemosynthetic bacteria has enabled many deep-sea invertebrates to thrive at hydrothermal vents and cold seeps, but most previous studies on this mutualism have focused on the bacteria only. Vesicomyid clams dominate global deep-sea chemosynthesis-based ecosystems. They differ from most deep-sea symbiotic animals in passing their symbionts from parent to offspring, enabling intricate coevolution between the host and the symbiont. Here, we sequenced the genomes of the clam Archivesica marissinica (Bivalvia: Vesicomyidae) and its bacterial symbiont to understand the genomic/metabolic integration behind this symbiosis. At 1.52 Gb, the clam genome encodes 28 genes horizontally transferred from bacteria, a large number of pseudogenes and transposable elements whose massive expansion corresponded to the timing of the rise and subsequent divergence of symbiont-bearing vesicomyids. The genome exhibits gene family expansion in cellular processes that likely facilitate chemoautotrophy, including gas delivery to support energy and carbon production, metabolite exchange with the symbiont, and regulation of the bacteriocyte population. Contraction in cellulase genes is likely adaptive to the shift from phytoplankton-derived to bacteria-based food. It also shows contraction in bacterial recognition gene families, indicative of suppressed immune response to the endosymbiont. The gammaproteobacterium endosymbiont has a reduced genome of 1.03 Mb but retains complete pathways for sulfur oxidation, carbon fixation, and biosynthesis of 20 common amino acids, indicating the host’s high dependence on the symbiont for nutrition. Overall, the host–symbiont genomes show not only tight metabolic complementarity but also distinct signatures of coevolution allowing the vesicomyids to thrive in chemosynthesis-based ecosystems.
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Affiliation(s)
- Jack Chi-Ho Ip
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.,HKBU Institute of Research and Continuing Education, Virtual University Park, Shenzhen, China.,Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ting Xu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.,HKBU Institute of Research and Continuing Education, Virtual University Park, Shenzhen, China.,Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jin Sun
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.,Division of Life Science, Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Runsheng Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa Prefecture, Japan
| | - Yi Lan
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.,Division of Life Science, Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhuang Han
- Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Science, Sanya, Hainan, China
| | - Haibin Zhang
- Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Science, Sanya, Hainan, China
| | - Jiangong Wei
- MLR Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Hongbin Wang
- MLR Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Jun Tao
- MLR Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
| | - Pei-Yuan Qian
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.,Division of Life Science, Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.,HKBU Institute of Research and Continuing Education, Virtual University Park, Shenzhen, China.,Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
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36
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Fortunato CS, Butterfield DA, Larson B, Lawrence-Slavas N, Algar CK, Zeigler Allen L, Holden JF, Proskurowski G, Reddington E, Stewart LC, Topçuoğlu BD, Vallino JJ, Huber JA. Seafloor Incubation Experiment with Deep-Sea Hydrothermal Vent Fluid Reveals Effect of Pressure and Lag Time on Autotrophic Microbial Communities. Appl Environ Microbiol 2021; 87:e00078-21. [PMID: 33608294 DOI: 10.1128/AEM.00078-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 01/13/2021] [Accepted: 02/10/2021] [Indexed: 12/03/2022] Open
Abstract
Diverse microbial communities drive biogeochemical cycles in Earth’s ocean, yet studying these organisms and processes is often limited by technological capabilities, especially in the deep ocean. In this study, we used a novel marine microbial incubator instrument capable of in situ experimentation to investigate microbial primary producers at deep-sea hydrothermal vents. Depressurization and sample processing delays may impact the outcome of shipboard microbial incubations of samples collected from the deep sea. To address this knowledge gap, we developed a remotely operated vehicle (ROV)-powered incubator instrument to carry out and compare results from in situ and shipboard RNA stable isotope probing (RNA-SIP) experiments to identify the key chemolithoautotrophic microbes and metabolisms in diffuse, low-temperature venting fluids from Axial Seamount. All the incubations showed microbial uptake of labeled bicarbonate primarily by thermophilic autotrophic Epsilonbacteraeota that oxidized hydrogen coupled with nitrate reduction. However, the in situ seafloor incubations showed higher abundances of transcripts annotated for aerobic processes, suggesting that oxygen was lost from the hydrothermal fluid samples prior to shipboard analysis. Furthermore, transcripts for thermal stress proteins such as heat shock chaperones and proteases were significantly more abundant in the shipboard incubations, suggesting that depressurization induced thermal stress in the metabolically active microbes in these incubations. Together, the results indicate that while the autotrophic microbial communities in the shipboard and seafloor experiments behaved similarly, there were distinct differences that provide new insight into the activities of natural microbial assemblages under nearly native conditions in the ocean. IMPORTANCE Diverse microbial communities drive biogeochemical cycles in Earth’s ocean, yet studying these organisms and processes is often limited by technological capabilities, especially in the deep ocean. In this study, we used a novel marine microbial incubator instrument capable of in situ experimentation to investigate microbial primary producers at deep-sea hydrothermal vents. We carried out identical stable isotope probing experiments coupled to RNA sequencing both on the seafloor and on the ship to examine thermophilic, microbial autotrophs in venting fluids from an active submarine volcano. Our results indicate that microbial communities were significantly impacted by the effects of depressurization and sample processing delays, with shipboard microbial communities being more stressed than seafloor incubations. Differences in metabolism were also apparent and are likely linked to the chemistry of the fluid at the beginning of the experiment. Microbial experimentation in the natural habitat provides new insights into understanding microbial activities in the ocean.
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Chang Y, Fan Q, Hou J, Zhang Y, Li J. A community-supported metaproteomic pipeline for improving peptide identifications in hydrothermal vent microbiota. Brief Bioinform 2021; 22:6214661. [PMID: 33834201 DOI: 10.1093/bib/bbab052] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/23/2021] [Accepted: 02/02/2021] [Indexed: 11/12/2022] Open
Abstract
Microorganisms in deep-sea hydrothermal vents provide valuable insights into life under extreme conditions. Mass spectrometry-based proteomics has been widely used to identify protein expression and function. However, the metaproteomic studies in deep-sea microbiota have been constrained largely by the low identification rates of protein or peptide. To improve the efficiency of metaproteomics for hydrothermal vent microbiota, we firstly constructed a microbial gene database (HVentDB) based on 117 public metagenomic samples from hydrothermal vents and proposed a metaproteomic analysis strategy, which takes the advantages of not only the sample-matched metagenome, but also the metagenomic information released publicly in the community of hydrothermal vents. A two-stage false discovery rate method was followed up to control the risk of false positive. By applying our community-supported strategy to a hydrothermal vent sediment sample, about twice as many peptides were identified when compared with the ways against the sample-matched metagenome or the public reference database. In addition, more enriched and explainable taxonomic and functional profiles were detected by the HVentDB-based approach exclusively, as well as many important proteins involved in methane, amino acid, sugar, glycan metabolism and DNA repair, etc. The new metaproteomic analysis strategy will enhance our understanding of microbiota, including their lifestyles and metabolic capabilities in extreme environments. The database HVentDB is freely accessible from http://lilab.life.sjtu.edu.cn:8080/HventDB/main.html.
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Affiliation(s)
- Yafei Chang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qilian Fan
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jialin Hou
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Li
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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38
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Xie S, Wang S, Li D, Shao Z, Lai Q, Wang Y, Wei M, Han X, Jiang L. Sulfurovum indicum sp. nov., a novel hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal plume in the Northwestern Indian Ocean. Int J Syst Evol Microbiol 2021; 71. [PMID: 33734956 DOI: 10.1099/ijsem.0.004748] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 11/18/2022] Open
Abstract
A novel mesophilic, hydrogen-, and sulfur-oxidizing bacterium, designated strain ST-419T, was isolated from a deep-sea hydrothermal vent plume on the Carlsberg Ridge of the Northwestern Indian Ocean. The isolate was a Gram-staining-negative, non-motile and coccoid to oval-shaped bacterium. Growth was observed at 4-50 °C (optimum 37 °C), pH 5.0-8.6 (optimum pH 6.0) and 1.0-5.0 % (w/v) NaCl (optimum 3.0 %). ST-419T could grow chemlithoautotrophically with molecular hydrogen, sulfide, elemental sulfur and thiosulfate as energy sources. Molecular oxygen, nitrate and elemental sulfur could be used as electron acceptors. The predominant fatty acids were C16 : 1ω7c, C18 : 1ω7c and C16 : 0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The respiratory quinone was menaquinone MK-6 and the G+C content of the genomic DNA was 42.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that ST-419T represented a member of genus Sulfurovum and was most closely related to Sulfurovum riftiae 1812ET, with 97.6 % sequence similarity. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between ST-419T and S. riftiae 1812ET were 74.6 and 19.6 %, respectively. The combined genotypic and phenotypic data indicate that ST-419T represents a novel species within the genus Sulfurovum, for which the name Sulfurovum indicum sp. nov. is proposed. The type strain is ST-419T (=MCCC 1A17954T=KCTC 25164T).
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Affiliation(s)
- Shaobin Xie
- Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Shasha Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
| | - Dengfeng Li
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Zongze Shao
- Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
| | - Qiliang Lai
- Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
| | - Yejian Wang
- Key Laboratory of Submarine Geosciences & Second Institute of oceanography, Ministry of Natural Resources of PR China, Hangzhou 310012, PR China
| | - Mingcong Wei
- Ocean College, Zhejiang University, Zhoushan, 316021, PR China.,Key Laboratory of Submarine Geosciences & Second Institute of oceanography, Ministry of Natural Resources of PR China, Hangzhou 310012, PR China
| | - Xiqiu Han
- Key Laboratory of Submarine Geosciences & Second Institute of oceanography, Ministry of Natural Resources of PR China, Hangzhou 310012, PR China.,Ocean College, Zhejiang University, Zhoushan, 316021, PR China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
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Wang S, Jiang L, Hu Q, Cui L, Zhu B, Fu X, Lai Q, Shao Z, Yang S. Characterization of Sulfurimonas hydrogeniphila sp. nov., a Novel Bacterium Predominant in Deep-Sea Hydrothermal Vents and Comparative Genomic Analyses of the Genus Sulfurimonas. Front Microbiol 2021; 12:626705. [PMID: 33717015 PMCID: PMC7952632 DOI: 10.3389/fmicb.2021.626705] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 11/06/2020] [Accepted: 02/11/2021] [Indexed: 11/13/2022] Open
Abstract
Bacteria of the genus Sulfurimonas within the class Campylobacteria are predominant in global deep-sea hydrothermal environments and widespread in global oceans. However, only few bacteria of this group have been isolated, and their adaptations for these extreme environments remain poorly understood. Here, we report a novel mesophilic, hydrogen- and sulfur-oxidizing bacterium, strain NW10T, isolated from a deep-sea sulfide chimney of Northwest Indian Ocean.16S rRNA gene sequence analysis showed that strain NW10T was most closely related to the vent species Sulfurimonas paralvinellae GO25T with 95.8% similarity, but ANI and DDH values between two strains were only 19.20 and 24.70%, respectively, indicating that strain NW10 represents a novel species. Phenotypic characterization showed strain NW10T is an obligate chemolithoautotroph utilizing thiosulfate, sulfide, elemental sulfur, or molecular hydrogen as energy sources, and molecular oxygen, nitrate, or elemental sulfur as electron acceptors. Moreover, hydrogen supported a better growth than reduced sulfur compounds. During thiosulfate oxidation, the strain can produce extracellular sulfur of elemental α-S8 with an unknown mechanism. Polyphasic taxonomy results support that strain NW10T represents a novel species of the genus Sulfurimonas, and named as Sulfurimonas hydrogeniphila sp. nov. Genome analyses revealed its diverse energy metabolisms driving carbon fixation via rTCA cycling, including pathways of sulfur/hydrogen oxidation, coupled oxygen/sulfur respiration and denitrification. Comparative analysis of the 11 available genomes from Sulfurimonas species revealed that vent bacteria, compared to marine non-vent strains, possess unique genes encoding Type V Sqr, Group II, and Coo hydrogenase, and are selectively enriched in genes related to signal transduction and inorganic ion transporters. These phenotypic and genotypic features of vent Sulfurimonas may explain their thriving in hydrothermal environments and help to understand the ecological role of Sulfurimonas bacteria in hydrothermal ecosystems.
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Affiliation(s)
- Shasha Wang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Qitao Hu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Liang Cui
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
| | - Bitong Zhu
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
| | - Xiaoteng Fu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Suping Yang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
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40
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Mullineaux LS, Mills SW, Le Bris N, Beaulieu SE, Sievert SM, Dykman LN. Prolonged recovery time after eruptive disturbance of a deep-sea hydrothermal vent community. Proc Biol Sci 2020; 287:20202070. [PMID: 33352072 PMCID: PMC7779506 DOI: 10.1098/rspb.2020.2070] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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] [Indexed: 11/26/2022] Open
Abstract
Deep-sea hydrothermal vents are associated with seafloor tectonic and magmatic activity, and the communities living there are subject to disturbance. Eruptions can be frequent and catastrophic, raising questions about how these communities persist and maintain regional biodiversity. Prior studies of frequently disturbed vents have led to suggestions that faunal recovery can occur within 2–4 years. We use an unprecedented long-term (11-year) series of colonization data following a catastrophic 2006 seafloor eruption on the East Pacific Rise to show that faunal successional changes continue beyond a decade following the disturbance. Species composition at nine months post-eruption was conspicuously different than the pre-eruption ‘baseline' state, which had been characterized in 1998 (85 months after disturbance by the previous 1991 eruption). By 96 months post-eruption, species composition was approaching the pre-eruption state, but continued to change up through to the end of our measurements at 135 months, indicating that the ‘baseline' state was not a climax community. The strong variation observed in species composition across environmental gradients and successional stages highlights the importance of long-term, distributed sampling in order to understand the consequences of disturbance for maintenance of a diverse regional species pool. This perspective is critical for characterizing the resilience of vent species to both natural disturbance and human impacts such as deep-sea mining.
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Affiliation(s)
- L S Mullineaux
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - S W Mills
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - N Le Bris
- CNRS-Sorbonne Université, Benthic Ecogeochemistry Laboratory, Banyuls-sur-Mer, France
| | - S E Beaulieu
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - S M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - L N Dykman
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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Hu Q, Wang S, Lai Q, Shao Z, Jiang L. Sulfurimonas indica sp. nov., a hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a hydrothermal sulfide chimney in the Northwest Indian Ocean. Int J Syst Evol Microbiol 2020; 71. [PMID: 33263512 DOI: 10.1099/ijsem.0.004575] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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 mesophilic, hydrogen- and sulfur-oxidizing bacterium, designated strain NW8NT, was collected from a sulfide chimney at the deep-sea hydrothermal vent on the Carlsberg Ridge of the Northwest Indian Ocean. The cells were Gram-stain-negative, motile, short rods with a single polar flagellum. The temperature, pH and salinity ranges for growth of strain NW8NT were 4-40 °C (optimum, 33 °C), pH 4.5-7.5 (optimum, pH 5.5) and 340-680 mM NaCl (optimum, 510 mM). The isolate was an obligate chemolithoautotroph capable of growth using hydrogen, thiosulfate, sulfide or elemental sulphur as the sole energy source, carbon dioxide as the sole carbon source and molecular oxygen as the sole electron acceptor. The major cellular fatty acids of strain NW8NT were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The total size of its genome was 2 093 492 bp and the genomic DNA G+C content was 36.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and core genes showed that the novel isolate belonged to the genus Sulfurimonas and was most closely related to Sulfurimonas paralvinellae GO25T (97.4 % sequence identity). The average nucleotide identity and DNA-DNAhybridization values between strain NW8NT and S. paralvinellae GO25T was 77.8 and 21.1 %, respectively. Based on the phylogenetic, genomic and phenotypic data presented here, strain NW8NT represents a novel species of the genus Sulfurimonas, for which the name Sulfurimonas indica sp. nov. is proposed, with the type strain NW8NT (=MCCC 1A13988T=KTCC 15780T).
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Affiliation(s)
- Qitao Hu
- Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
| | - Shasha Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
| | - Qiliang Lai
- Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
| | - Lijing Jiang
- Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China
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McDermott JM, Sylva SP, Ono S, German CR, Seewald JS. Abiotic redox reactions in hydrothermal mixing zones: Decreased energy availability for the subsurface biosphere. Proc Natl Acad Sci U S A 2020; 117:20453-61. [PMID: 32817473 DOI: 10.1073/pnas.2003108117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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] [Indexed: 11/25/2022] Open
Abstract
Hydrothermal fluid geochemistry exerts a key control on subseafloor microbial community structure and function. However, the effects of microbial metabolic activity, thermal decomposition of biomass, and abiotic reactions on geochemistry remain unconstrained. Depletions in molecular hydrogen and enrichments in methane in submarine hydrothermal mixing zones have been interpreted to reflect the influence of an active subseafloor biosphere. In contrast, our work reveals that these chemical shifts are driven by abiotic and thermogenic processes at temperatures beyond the limit for life. These findings have critical implications for constraining the extent to which global geochemical cycles can sustain a deep biosphere, and for the global molecular hydrogen budget. Subseafloor mixing of high-temperature hot-spring fluids with cold seawater creates intermediate-temperature diffuse fluids that are replete with potential chemical energy. This energy can be harnessed by a chemosynthetic biosphere that permeates hydrothermal regions on Earth. Shifts in the abundance of redox-reactive species in diffuse fluids are often interpreted to reflect the direct influence of subseafloor microbial activity on fluid geochemical budgets. Here, we examine hydrothermal fluids venting at 44 to 149 °C at the Piccard hydrothermal field that span the canonical 122 °C limit to life, and thus provide a rare opportunity to study the transition between habitable and uninhabitable environments. In contrast with previous studies, we show that hydrocarbons are contributed by biomass pyrolysis, while abiotic sulfate (SO42−) reduction produces large depletions in H2. The latter process consumes energy that could otherwise support key metabolic strategies employed by the subseafloor biosphere. Available Gibbs free energy is reduced by 71 to 86% across the habitable temperature range for both hydrogenotrophic SO42− reduction to hydrogen sulfide (H2S) and carbon dioxide (CO2) reduction to methane (CH4). The abiotic H2 sink we identify has implications for the productivity of subseafloor microbial ecosystems and is an important process to consider within models of H2 production and consumption in young oceanic crust.
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Glenn M, Hu S, Barnes S, Torpy A, Hughes AE, MacRae CM, Webster NAS, Wilson NC, Parr J, Binns R. Investigation of the Internal Structure of a Modern Seafloor Hydrothermal Chimney With a Combination of EBSD, EPMA, and XRD. Microsc Microanal 2020; 26:793-807. [PMID: 32431264 DOI: 10.1017/s1431927620001580] [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] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Samples from the sphalerite-dominated zone of a seafloor massive sulfide chimney, the Satanic Mills Chimney of the PACMANUS hydrothermal field, have been investigated to determine the internal macrostructure and microstructure of this zone, the phases present, and the distribution of metals. A combination of electron probe microanalysis, electron backscattered diffraction, and x-ray diffraction has been used. At the macroscale, this zone of the chimney wall is heavily porous and is comprised primarily of sphalerite, enclosing minor chalcopyrite, pyrite, and wurtzite. A Pb–As sulfosalt layer of possible microbial origins is present at the outer edge of the sphalerite matrix, next to a pore. The sphalerite has grown in globules on the order of 300 μm in diameter. At the microscale, the sphalerite features a colloform texture and a duplex-type grain structure consisting of either fine-grain regions in the center surrounded by coarse-grained regions or radiating coarse grains only. Pb- and As-rich bands have been detected in the colloform sphalerite, and growth twins have been observed in both the sphalerite and chalcopyrite crystals. A qualitative description of the growth of a typical globule is given, including nucleation, crystal growth, and solute redistribution.
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Affiliation(s)
- Matthew Glenn
- Microbeam Laboratory, CSIRO Mineral Resources, Clayton, VIC, Australia
| | - Siyu Hu
- CSIRO Mineral Resources, Kensington, WA, Australia
| | | | - Aaron Torpy
- Microbeam Laboratory, CSIRO Mineral Resources, Clayton, VIC, Australia
| | - Anthony E Hughes
- Microbeam Laboratory, CSIRO Mineral Resources, Clayton, VIC, Australia
| | - Colin M MacRae
- Microbeam Laboratory, CSIRO Mineral Resources, Clayton, VIC, Australia
| | | | - Nicholas C Wilson
- Microbeam Laboratory, CSIRO Mineral Resources, Clayton, VIC, Australia
| | - Joanna Parr
- CSIRO Mineral Resources, North Ryde, NSW, Australia
| | - Ray Binns
- CSIRO Mineral Resources, North Ryde, NSW, Australia
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Sun J, Zhou Y, Chen C, Kwan YH, Sun Y, Wang X, Yang L, Zhang R, Wei T, Yang Y, Qu L, Sun C, Qian PY. Nearest vent, dearest friend: biodiversity of Tiancheng vent field reveals cross-ridge similarities in the Indian Ocean. R Soc Open Sci 2020; 7:200110. [PMID: 32269824 PMCID: PMC7137978 DOI: 10.1098/rsos.200110] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 02/27/2020] [Indexed: 05/24/2023]
Abstract
Biodiversity of hydrothermal vents in the Indian Ocean, particularly those on the Southwest Indian Ridge (SWIR), are still relatively poorly understood. The Tiancheng field on the SWIR was initially reported with only a low-temperature diffuse flow venting area, but here we report two new active areas, including a chimney emitting high-temperature vent fluids. Biological sampling in these new sites doubled the known megafauna and macrofauna richness reported from Tiancheng. Significantly, we found several iconic species, such as the scaly-foot snail and the first Alviniconcha population on the SWIR. Tiancheng shares a high proportion of taxa with vents on the Central Indian Ridge (CIR) and lacks a number of key taxa that characterize other vents investigated so far on the SWIR. Population genetics of the scaly-foot snail confirmed this, as the Tiancheng population was clustered with populations from the CIR, showing low connectivity with the Longqi field. Unlike the previously examined populations, scales of the Tiancheng scaly-foot snail were coated in zinc sulfide, although this results only from precipitation. The close connection between Tiancheng and CIR vents indicates that the dispersal barrier for vent endemic species is not the Rodriguez Triple Junction as previously suggested but the transformation faults between Tiancheng and Longqi, warranting further studies on deep currents in this area to resolve the key barrier, which has important implications for biological conservation.
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Affiliation(s)
- Jin Sun
- Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, People's Republic of China
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Yadong Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, People's Republic of China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan
| | - Yick Hang Kwan
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Yanan Sun
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Xuyang Wang
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Lei Yang
- Marine Survey Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, People's Republic of China
| | - Ruiyan Zhang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, People's Republic of China
| | - Tong Wei
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Yi Yang
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Lingyun Qu
- Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, People's Republic of China
| | - Chengjun Sun
- Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, People's Republic of China
| | - Pei-Yuan Qian
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
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45
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McAllister SM, Polson SW, Butterfield DA, Glazer BT, Sylvan JB, Chan CS. Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents. mSystems 2020; 5:e00553-19. [PMID: 32071158 PMCID: PMC7029218 DOI: 10.1128/msystems.00553-19] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [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: 09/03/2019] [Accepted: 01/22/2020] [Indexed: 01/04/2023] Open
Abstract
Zetaproteobacteria create extensive iron (Fe) oxide mats at marine hydrothermal vents, making them an ideal model for microbial Fe oxidation at circumneutral pH. Comparison of neutrophilic Fe oxidizer isolate genomes has revealed a hypothetical Fe oxidation pathway, featuring a homolog of the Fe oxidase Cyc2 from Acidithiobacillus ferrooxidans However, Cyc2 function is not well verified in neutrophilic Fe oxidizers, particularly in Fe-oxidizing environments. Toward this, we analyzed genomes and metatranscriptomes of Zetaproteobacteria, using 53 new high-quality metagenome-assembled genomes reconstructed from Fe mats at Mid-Atlantic Ridge, Mariana Backarc, and Loihi Seamount (Hawaii) hydrothermal vents. Phylogenetic analysis demonstrated conservation of Cyc2 sequences among most neutrophilic Fe oxidizers, suggesting a common function. We confirmed the widespread distribution of cyc2 and other model Fe oxidation pathway genes across all represented Zetaproteobacteria lineages. High expression of these genes was observed in diverse Zetaproteobacteria under multiple environmental conditions and in incubations. The putative Fe oxidase gene cyc2 was highly expressed in situ, often as the top expressed gene. The cyc2 gene showed increased expression in Fe(II)-amended incubations, with corresponding increases in carbon fixation and central metabolism gene expression. These results substantiate the Cyc2-based Fe oxidation pathway in neutrophiles and demonstrate its significance in marine Fe-mineralizing environments.IMPORTANCE Iron oxides are important components of our soil, water supplies, and ecosystems, as they sequester nutrients, carbon, and metals. Microorganisms can form iron oxides, but it is unclear whether this is a significant mechanism in the environment. Unlike other major microbial energy metabolisms, there is no marker gene for iron oxidation, hindering our ability to track these microbes. Here, we investigate a promising possible iron oxidation gene, cyc2, in iron-rich hydrothermal vents, where iron-oxidizing microbes dominate. We pieced together diverse Zetaproteobacteria genomes, compared these genomes, and analyzed expression of cyc2 and other hypothetical iron oxidation genes. We show that cyc2 is widespread among iron oxidizers and is highly expressed and potentially regulated, making it a good marker for the capacity for iron oxidation and potentially a marker for activity. These findings will help us understand and potentially quantify the impacts of neutrophilic iron oxidizers in a wide variety of marine and terrestrial environments.
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Affiliation(s)
- Sean M McAllister
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
| | - Shawn W Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - David A Butterfield
- Joint Institute for the Study of Atmosphere and Ocean, University of Washington, Seattle, Washington, USA
- Pacific Marine Environmental Laboratory, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Brian T Glazer
- Department of Oceanography, University of Hawai'i, Honolulu, Hawai'i, USA
| | - Jason B Sylvan
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
| | - Clara S Chan
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
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Sun S, Sha Z, Wang Y. The complete mitochondrial genomes of two vent squat lobsters, Munidopsis lauensis and M. verrilli: Novel gene arrangements and phylogenetic implications. Ecol Evol 2019; 9:12390-12407. [PMID: 31788185 PMCID: PMC6875667 DOI: 10.1002/ece3.5542] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 10/31/2018] [Revised: 01/31/2019] [Accepted: 07/19/2019] [Indexed: 12/14/2022] Open
Abstract
Hydrothermal vents are considered as one of the most extremely harsh environments on the Earth. In this study, the complete mitogenomes of hydrothermal vent squat lobsters, Munidopsis lauensis and M. verrilli, were determined through Illumina sequencing and compared with other available mitogenomes of anomurans. The mitogenomes of M. lauensis (17,483 bp) and M. verrilli (17,636 bp) are the largest among all Anomura mitogenomes, while the A+T contents of M. lauensis (62.40%) and M. verrilli (63.99%) are the lowest. The mitogenomes of M. lauensis and M. verrilli display novel gene arrangements, which might be the result of three tandem duplication-random loss (tdrl) events from the ancestral pancrustacean pattern. The mitochondrial gene orders of M. lauensis and M. verrilli shared the most similarities with S. crosnieri. The phylogenetic analyses based on both gene order data and nucleotide sequences (PCGs and rRNAs) revealed that the two species were closely related to Shinkaia crosnieri. Positive selection analysis revealed that eighteen residues in seven genes (atp8, Cytb, nad3, nad4, nad4l, nad5, and nad6) of the hydrothermal vent anomurans were positively selected sites.
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Affiliation(s)
- Shao'e Sun
- Deep Sea Research CenterInstitute of OceanologyChinese Academy of ScienceQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
| | - Zhongli Sha
- Deep Sea Research CenterInstitute of OceanologyChinese Academy of ScienceQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yanrong Wang
- Deep Sea Research CenterInstitute of OceanologyChinese Academy of ScienceQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
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47
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Zhou K, Zhang R, Sun J, Zhang W, Tian RM, Chen C, Kawagucci S, Xu Y. Potential Interactions between Clade SUP05 Sulfur-Oxidizing Bacteria and Phages in Hydrothermal Vent Sponges. Appl Environ Microbiol 2019; 85:e00992-19. [PMID: 31492669 DOI: 10.1128/AEM.00992-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/03/2019] [Indexed: 01/27/2023] Open
Abstract
In deep-sea hydrothermal vent environments, sulfur-oxidizing bacteria belonging to the clade SUP05 are crucial symbionts of invertebrate animals. Marine viruses, as the most abundant biological entities in the ocean, play essential roles in regulating the sulfur metabolism of the SUP05 bacteria. To date, vent sponge-associated SUP05 and their phages have not been well documented. The current study analyzed microbiomes of Haplosclerida sponges from hydrothermal vents in the Okinawa Trough and recovered the dominant SUP05 genome, designated VS-SUP05. Phylogenetic analysis showed that VS-SUP05 was closely related to endosymbiotic SUP05 strains from mussels living in deep-sea hydrothermal vent fields. Homology and metabolic pathway comparisons against free-living and symbiotic SUP05 strains revealed that the VS-SUP05 genome shared many features with the deep-sea mussel symbionts. Supporting a potentially symbiotic lifestyle, the VS-SUP05 genome contained genes involved in the synthesis of essential amino acids and cofactors that are desired by the host. Analysis of sponge-associated viral sequences revealed putative VS-SUP05 phages, all of which were double-stranded viruses belonging to the families Myoviridae, Siphoviridae, Podoviridae, and Microviridae Among the phage sequences, one contig contained metabolic genes (iscR, iscS, and iscU) involved in iron-sulfur cluster formation. Interestingly, genome sequence comparison revealed horizontal transfer of the iscS gene among phages, VS-SUP05, and other symbiotic SUP05 strains, indicating an interaction between marine phages and SUP05 symbionts. Overall, our findings confirm the presence of SUP05 bacteria and their phages in sponges from deep-sea vents and imply a beneficial interaction that allows adaptation of the host sponge to the hydrothermal vent environment.IMPORTANCE Chemosynthetic SUP05 bacteria dominate the microbial communities of deep-sea hydrothermal vents around the world, SUP05 bacteria utilize reduced chemical compounds in vent fluids and commonly form symbioses with invertebrate organisms. This symbiotic relationship could be key to adapting to such unique and extreme environments. Viruses are the most abundant biological entities on the planet and have been identified in hydrothermal vent environments. However, their interactions with the symbiotic microbes of the SUP05 clade, along with their role in the symbiotic system, remain unclear. Here, using metagenomic sequence-based analyses, we determined that bacteriophages may support metabolism in SUP05 bacteria and play a role in the sponge-associated symbiosis system in hydrothermal vent environments.
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Chen RW, Zhang J, He YQ, Wang KX, Li C, Long LJ. Longirhabdus pacifica gen. nov., sp. nov., isolated from a deep-sea hydrothermal sediment in the West Pacific Ocean. Int J Syst Evol Microbiol 2019; 69:3362-3367. [PMID: 31622228 DOI: 10.1099/ijsem.0.003526] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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 Gram-stain-negative bacterium, designated as SCSIO 06110T, was isolated from a deep-sea sediment of the West Pacific Ocean. Cells were 0.5-0.8 µm in width and 3.0-4.0 µm in length, spore-forming, rod-shaped with peritrichous flagella. Positive for catalase and urease, negative for oxidase and nitrate reduction. Growth occurred at 15-37 °C, pH 6-9 and 1-5 % (w/v) NaCl, with optimum growth at 28 °C, pH 7 and 3 % (w/v) NaCl. MK-7 was the only menaquinone. The strain possessed diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unidentified phospholipids. Iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0 were the major fatty acids. The novel isolate clustered with genera in the family Paenibacillaceae, but formed a separated branch with the closest relative Chengkuizengella sediminis J15A17T (91.1 % sequence similarity) when compared in a phylogenetic analysis of 16S rRNA gene sequences. The DNA G+C content of strain SCSIO 06110T was 38.5 mol%. Based on the polyphasic data presented, a new genus, Longirhabdus gen. nov., is proposed in the family Paenibacillaceae with the type species Longirhabdus pacifica sp. nov. and the type strain SCSIO 06110T (=DSM 105158T=CGMCC 1.16550T).
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Affiliation(s)
- Rou-Wen Chen
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Key Laboratory of Marine Materia Medica; RNAM Center for Marine Microbiology; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Jing Zhang
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Yuan-Qiu He
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Key Laboratory of Marine Materia Medica; RNAM Center for Marine Microbiology; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Ke-Xin Wang
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Key Laboratory of Marine Materia Medica; RNAM Center for Marine Microbiology; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Cun Li
- University of Chinese Academy of Sciences, Beijing 100049, PR China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Key Laboratory of Marine Materia Medica; RNAM Center for Marine Microbiology; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Li-Juan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology; Guangdong Key Laboratory of Marine Materia Medica; RNAM Center for Marine Microbiology; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
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49
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Beltz BS. Adaptations to extreme conditions. eLife 2019; 8:50647. [PMID: 31469073 PMCID: PMC6716961 DOI: 10.7554/elife.50647] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 08/23/2019] [Indexed: 11/13/2022] Open
Abstract
The brain architecture of shrimp living in deep-sea vents provides clues to how these organisms have adapted to extreme living.
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Affiliation(s)
- Barbara S Beltz
- Neuroscience Department, Wellesley College, Wellesley, United States
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50
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Jorquera MA, Graether SP, Maruyama F. Editorial: Bioprospecting and Biotechnology of Extremophiles. Front Bioeng Biotechnol 2019; 7:204. [PMID: 31552232 PMCID: PMC6736590 DOI: 10.3389/fbioe.2019.00204] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/09/2019] [Indexed: 11/21/2022] Open
Affiliation(s)
- Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile.,Network for Extreme Environment Research, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Fumito Maruyama
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile.,Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Hiroshima, Japan
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