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Wang H, Xiao H, Feng B, Lan Y, Fung CW, Zhang H, Yan G, Lian C, Zhong Z, Li J, Wang M, Wu AR, Li C, Qian PY. Single-cell RNA-seq reveals distinct metabolic "microniches" and close host-symbiont interactions in deep-sea chemosynthetic tubeworm. SCIENCE ADVANCES 2024; 10:eadn3053. [PMID: 39047091 PMCID: PMC11268408 DOI: 10.1126/sciadv.adn3053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 06/21/2024] [Indexed: 07/27/2024]
Abstract
Vestimentiferan tubeworms that thrive in deep-sea chemosynthetic ecosystems rely on a single species of sulfide-oxidizing gammaproteobacterial endosymbionts housed in a specialized symbiotic organ called trophosome as their primary carbon source. While this simple symbiosis is remarkably productive, the host-symbiont molecular interactions remain unelucidated. Here, we applied an approach for deep-sea in situ single-cell fixation in a cold-seep tubeworm, Paraescarpia echinospica. Single-cell RNA sequencing analysis and further molecular characterizations of both the trophosome and endosymbiont indicate that the tubeworm maintains two distinct metabolic "microniches" in the trophosome by controlling the availability of chemosynthetic gases and metabolites, resulting in oxygenated and hypoxic conditions. The endosymbionts in the oxygenated niche actively conduct autotrophic carbon fixation and are digested for nutrients, while those in the hypoxic niche conduct anaerobic denitrification, which helps the host remove ammonia waste. Our study provides insights into the molecular interactions between animals and their symbiotic microbes.
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Affiliation(s)
- Hao Wang
- Institute of Oceanology, Chinese Academy of Science, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Laoshan Laboratory, Qingdao, China
| | - Hongxiu Xiao
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Buhan Feng
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Yi Lan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Nansha, Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Cheuk Wang Fung
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Huan Zhang
- Institute of Oceanology, Chinese Academy of Science, Qingdao, China
| | - Guoyong Yan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Nansha, Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Chao Lian
- Institute of Oceanology, Chinese Academy of Science, Qingdao, China
| | - Zhaoshan Zhong
- Institute of Oceanology, Chinese Academy of Science, Qingdao, China
| | - Jing Li
- Institute of Oceanology, Chinese Academy of Science, Qingdao, China
| | - Minxiao Wang
- Institute of Oceanology, Chinese Academy of Science, Qingdao, China
| | - Angela Ruohao Wu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Chaolun Li
- Institute of Oceanology, Chinese Academy of Science, Qingdao, China
- South China Sea Institute of Oceanology, Chinese Academy of Science, Guanzhou, China
- University of Chinese Academy of Science, Beijing, China
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Nansha, Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
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2
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Ricci F, Greening C. Chemosynthesis: a neglected foundation of marine ecology and biogeochemistry. Trends Microbiol 2024; 32:631-639. [PMID: 38296716 DOI: 10.1016/j.tim.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/06/2023] [Accepted: 11/28/2023] [Indexed: 02/02/2024]
Abstract
Chemosynthesis is a metabolic process that transfers carbon to the biosphere using reduced compounds. It is well recognised that chemosynthesis occurs in much of the ocean, but it is often thought to be a negligible process compared to photosynthesis. Here we propose that chemosynthesis is the underlying process governing primary production in much of the ocean and suggest that it extends to a much wider range of compounds, microorganisms, and ecosystems than previously thought. In turn, this process has had a central role in controlling marine biogeochemistry, ecology, and carbon budgets across the vast realms of the ocean, from the dawn of life to contemporary times.
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Affiliation(s)
- Francesco Ricci
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia.
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Melbourne, Victoria, Australia.
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3
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Buschi E, Dell’Anno A, Tangherlini M, Candela M, Rampelli S, Turroni S, Palladino G, Esposito E, Martire ML, Musco L, Stefanni S, Munari C, Fiori J, Danovaro R, Corinaldesi C. Resistance to freezing conditions of endemic Antarctic polychaetes is enhanced by cryoprotective proteins produced by their microbiome. SCIENCE ADVANCES 2024; 10:eadk9117. [PMID: 38905343 PMCID: PMC11192080 DOI: 10.1126/sciadv.adk9117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
The microbiome plays a key role in the health of all metazoans. Whether and how the microbiome favors the adaptation processes of organisms to extreme conditions, such as those of Antarctica, which are incompatible with most metazoans, is still unknown. We investigated the microbiome of three endemic and widespread species of Antarctic polychaetes: Leitoscoloplos geminus, Aphelochaeta palmeri, and Aglaophamus trissophyllus. We report here that these invertebrates contain a stable bacterial core dominated by Meiothermus and Anoxybacillus, equipped with a versatile genetic makeup and a unique portfolio of proteins useful for coping with extremely cold conditions as revealed by pangenomic and metaproteomic analyses. The close phylosymbiosis between Meiothermus and Anoxybacillus and these Antarctic polychaetes indicates a connection with their hosts that started in the past to support holobiont adaptation to the Antarctic Ocean. The wide suite of bacterial cryoprotective proteins found in Antarctic polychaetes may be useful for the development of nature-based biotechnological applications.
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Affiliation(s)
- Emanuela Buschi
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica “Anton Dohrn,” Fano Marine Centre, Fano, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn,” Fano Marine Centre, Fano, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giorgia Palladino
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Erika Esposito
- Department of Chemistry “G. Ciamician” Alma Mater Studiorum, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
| | - Marco Lo Martire
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Luigi Musco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Sergio Stefanni
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica “Anton Dohrn,” Villa Comunale, Napoli, Italy
| | - Cristina Munari
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
| | - Jessica Fiori
- Department of Chemistry “G. Ciamician” Alma Mater Studiorum, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, Italy
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Kendlbacher V, Winter TMR, Bright M. Zoothamnium mariella sp. nov., a marine, colonial ciliate with an atypcial growth pattern, and its ectosymbiont Candidatus Fusimicrobium zoothamnicola gen. nov., sp. nov. PLoS One 2024; 19:e0300758. [PMID: 38557976 PMCID: PMC10984469 DOI: 10.1371/journal.pone.0300758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Ciliates are unicellular eukaryotes, regularly involved in symbiotic associations. Symbionts may colonize the inside of their cells as well as their surface as ectosymbionts. Here, we report on a new ciliate species, designated as Zoothamnium mariella sp. nov. (Peritrichia, Sessilida), discovered in the northern Adriatic Sea (Mediterranean Sea) in 2021. We found this ciliate species to be monospecifically associated with a new genus of ectosymbiotic bacteria, here proposed as Candidatus Fusimicrobium zoothamnicola gen. nov., sp. nov. To formally describe the new ciliate species, we investigated its morphology and sequenced its 18S rRNA gene. To demonstrate its association with a single species of bacterial ectosymbiont, we performed 16S rRNA gene sequencing, fluorescence in situ hybridization, and scanning electron microscopy. Additionally, we explored the two partners' cultivation requirements and ecology. Z. mariella sp. nov. was characterized by a colony length of up to 1 mm. A consistent number of either seven or eight long branches alternated on the stalk in close distance to each other. The colony developed three different types of zooids: microzooids ("trophic stage"), macrozooids ("telotroch stage"), and terminal zooids ("dividing stage"). Viewed from inside the cell, the microzooids' oral ciliature ran in 1 ¼ turns in a clockwise direction around the peristomial disc before entering the infundibulum, where it performed another ¾ turn. Phylogenetic analyses assigned Z. mariella sp. nov. to clade II of the family Zoothamnidae. The ectosymbiont formed a monophyletic clade within the Gammaproteobacteria along with two other ectosymbionts of peritrichous ciliates and a free-living vent bacterium. It colonized the entire surface of its ciliate host, except for the most basal stalk of large colonies, and exhibited a single, spindle-shaped morphotype. Furthermore, the two partners together appear to be generalists of temperate, oxic, marine shallow-water environments and were collectively cultivable in steady flow-through systems.
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Affiliation(s)
- Vincent Kendlbacher
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | | | - Monika Bright
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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Chen C, Jamieson JW, Tunnicliffe V. Hydrothermal vent fauna of the Galápagos Rift: updated species list with new records. MARINE BIODIVERSITY : A JOURNAL OF THE SENCKENBERG RESEARCH INSTITUTE 2024; 54:16. [PMID: 38371229 PMCID: PMC10869388 DOI: 10.1007/s12526-024-01408-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/09/2024] [Accepted: 01/18/2024] [Indexed: 02/20/2024]
Abstract
The sighting of giant bivalves and tubeworms at the Rose Garden vent field on the Galápagos Rift in 1977 marked the discovery of hydrothermal vents, a turning point for modern biology. The following decade saw a flurry of taxonomic descriptions of vent endemic species from the first vents. With the finding of high-temperature "black smokers" on the East Pacific Rise, exploration shifted away from Galápagos. A faunal list of Galápagos vents with 65 species was published in 1991, then updated to 74 species in 2006. Since then, few expeditions returned to the Galápagos Rift. Here, we revisited several Galápagos vents including recently confirmed high-temperature sites and inactive sulfide mounds. From our collecting efforts and observations, as well as revisions from the literature, we update the faunal list to 92 species including 15 new records, restricted to obvious vent associates. Accurate regional faunal lists are important for understanding the biogeography of vent fauna, and our list will also be valuable for setting management strategies.
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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 Japan
| | - John W. Jamieson
- Department of Earth Sciences, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3X5 Canada
| | - Verena Tunnicliffe
- Department of Biology and School of Earth/Ocean Sciences, University of Victoria, Victoria, British Columbia V8P 3E6 Canada
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6
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Zhou K, Zhang T, Chen XW, Xu Y, Zhang R, Qian PY. Viruses in Marine Invertebrate Holobionts: Complex Interactions Between Phages and Bacterial Symbionts. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:467-485. [PMID: 37647612 DOI: 10.1146/annurev-marine-021623-093133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Marine invertebrates are ecologically and economically important and have formed holobionts by evolving symbiotic relationships with cellular and acellular microorganisms that reside in and on their tissues. In recent decades, significant focus on symbiotic cellular microorganisms has led to the discovery of various functions and a considerable expansion of our knowledge of holobiont functions. Despite this progress, our understanding of symbiotic acellular microorganisms remains insufficient, impeding our ability to achieve a comprehensive understanding of marine holobionts. In this review, we highlight the abundant viruses, with a particular emphasis on bacteriophages; provide an overview of their diversity, especially in extensively studied sponges and corals; and examine their potential life cycles. In addition, we discuss potential phage-holobiont interactions of various invertebrates, including participating in initial bacterial colonization, maintaining symbiotic relationships, and causing or exacerbating the diseases of marine invertebrates. Despite the importance of this subject, knowledge of how viruses contribute to marine invertebrate organisms remains limited. Advancements in technology and greater attention to viruses will enhance our understanding of marine invertebrate holobionts.
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Affiliation(s)
- Kun Zhou
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China;
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Ting Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Xiao-Wei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China;
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China;
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China;
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
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7
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Betters MJ, Cordes EE. New records of Provanna (Gastropoda, Provannidae) from the Costa Rica Margin and an identification key for the genus. Zookeys 2024; 1189:1-32. [PMID: 38314107 PMCID: PMC10836654 DOI: 10.3897/zookeys.1189.109734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/20/2023] [Indexed: 02/06/2024] Open
Abstract
Consistent species identification is foundational to biological research and requires coordination among a diversity of researchers and institutions. However, such consistency may be hindered for rare organisms where specimens, identification resources, and taxonomic experts are few. This is often the case for deep-sea taxonomic groups. For example, the deep-sea gastropod genus Provanna Dall, 1918 is common at chemosynthetic sites throughout the world's oceans, yet no formal guide to these species has yet been produced. Recent exploration has recovered new specimens of Provanna from hydrocarbon seeps off the Pacific Costa Rica Margin. The current work assesses the species identity of these specimens using shell morphology, radular morphology, and genetic barcoding (mitochondrial CO1 and nuclear H3). Records of occurrence for P.laevis Warén & Ponder, 1991, P.ios Warén & Bouchet, 1986, and P.pacifica Warén & Bouchet, 1986 are herein presented from the Costa Rica Margin. A critical taxonomic review of the 29 extant species within this genus was conducted and their genetic, morphological, and biogeographical distinction assessed. In this review, genetic and morphological support was found for nearly all current species delineations except for P.glabraOkutani et al., 1992, syn. nov. and P.laevis, syn. nov., which are herein synonymized to P.laevis, and for P.ios, syn. nov. and P.goniata Warén & Bouchet, 1986, syn. nov., which are synonymized to P.ios. Finally, the first species identification key for the extant species in this genus is presented. This work clarifies the taxonomy and systematics of this deep-sea gastropod genus and contributes a novel polytomous key for use in future research.
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Affiliation(s)
- Melissa J Betters
- Department of Biology, Temple University, Philadelphia, PA, USA Temple University Philadelphia United States of America
| | - Erik E Cordes
- Department of Biology, Temple University, Philadelphia, PA, USA Temple University Philadelphia United States of America
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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] [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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Wang M, Ruan L, Liu M, Liu Z, He J, Zhang L, Wang Y, Shi H, Chen M, Yang F, Zeng R, He J, Guo C, Chen J. The genome of a vestimentiferan tubeworm (Ridgeia piscesae) provides insights into its adaptation to a deep-sea environment. BMC Genomics 2023; 24:72. [PMID: 36774470 PMCID: PMC9921365 DOI: 10.1186/s12864-023-09166-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/03/2023] [Indexed: 02/13/2023] Open
Abstract
BACKGROUND Vestimentifera (Polychaeta, Siboglinidae) is a taxon of deep-sea worm-like animals living in deep-sea hydrothermal vents, cold seeps, and organic falls. The morphology and lifespan of Ridgeia piscesae, which is the only vestimentiferan tubeworm species found in the hydrothermal vents on the Juan de Fuca Ridge, vary greatly according to endemic environment. Recent analyses have revealed the genomic basis of adaptation in three vent- and seep-dwelling vestimentiferan tubeworms. However, the evolutionary history and mechanism of adaptation in R. piscesae, a unique species in the family Siboglinidae, remain to be investigated. RESULT We assembled a draft genome of R. piscesae collected at the Cathedral vent of the Juan de Fuca Ridge. Comparative genomic analysis showed that vent-dwelling tubeworms with a higher growth rate had smaller genome sizes than seep-dwelling tubeworms that grew much slower. A strong positive correlation between repeat content and genome size but not intron size and the number of protein-coding genes was identified in these deep-sea tubeworm species. Evolutionary analysis revealed that Ridgeia pachyptila and R. piscesae, the two tubeworm species that are endemic to hydrothermal vents of the eastern Pacific, started to diverge between 28.5 and 35 million years ago. Four genes involved in cell proliferation were found to be subject to positive selection in the genome of R. piscesae. CONCLUSION Ridgeia pachyptila and R. piscesae started to diverge after the formation of the Gorda/Juan de Fuca/Explorer ridge systems and the East Pacific Rise. The high growth rates of vent-dwelling tubeworms might be derived from their small genome sizes. Cell proliferation is important for regulating the growth rate in R. piscesae.
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Affiliation(s)
- Muhua Wang
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China ,grid.12981.330000 0001 2360 039XChina-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Lingwei Ruan
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Meng Liu
- grid.410753.4Novogene Bioinformatics Institute, Beijing, 100083 China
| | - Zixuan Liu
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
| | - Jian He
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China ,grid.12981.330000 0001 2360 039XChina-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Long Zhang
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
| | - Yuanyuan Wang
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
| | - Hong Shi
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Mingliang Chen
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Feng Yang
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Runying Zeng
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Jianguo He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China. .,China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Changjun Guo
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China. .,China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Jianming Chen
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005, China. .,Fujian Key Laboratory On Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
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10
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Chou PH, Hu MY, Guh YJ, Wu GC, Yang SH, Tandon K, Shao YT, Lin LY, Chen C, Tseng KY, Wang MC, Zhang CM, Han BC, Lin CC, Tang SL, Jeng MS, Chang CF, Tseng YC. Cellular mechanisms underlying extraordinary sulfide tolerance in a crustacean holobiont from hydrothermal vents. Proc Biol Sci 2023; 290:20221973. [PMID: 36629118 PMCID: PMC9832567 DOI: 10.1098/rspb.2022.1973] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/17/2022] [Indexed: 01/12/2023] Open
Abstract
The shallow-water hydrothermal vent system of Kueishan Island has been described as one of the world's most acidic and sulfide-rich marine habitats. The only recorded metazoan species living in the direct vicinity of the vents is Xenograpsus testudinatus, a brachyuran crab endemic to marine sulfide-rich vent systems. Despite the toxicity of hydrogen sulfide, X. testudinatus occupies an ecological niche in a sulfide-rich habitat, with the underlying detoxification mechanism remaining unknown. Using laboratory and field-based experiments, we characterized the gills of X. testudinatus that are the major site of sulfide detoxification. Here sulfide is oxidized to thiosulfate or bound to hypotaurine to generate the less toxic thiotaurine. Biochemical and molecular analyses demonstrated that the accumulation of thiosulfate and hypotaurine is mediated by the sodium-independent sulfate anion transporter (SLC26A11) and taurine transporter (Taut), which are expressed in gill epithelia. Histological and metagenomic analyses of gill tissues demonstrated a distinct bacterial signature dominated by Epsilonproteobacteria. Our results suggest that thiotaurine synthesized in gills is used by sulfide-oxidizing endo-symbiotic bacteria, creating an effective sulfide-buffering system. This work identified physiological mechanisms involving host-microbe interactions that support life of a metazoan in one of the most extreme environments on our planet.
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Affiliation(s)
- Pei-Hsuan Chou
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, I-Lan County, Taiwan
| | - Marian Y. Hu
- Institute of Physiology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Ying-Jey Guh
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, I-Lan County, Taiwan
| | - Guan-Chung Wu
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans National Taiwan Ocean University, Keelung, Taiwan
| | - Shan-Hua Yang
- Institute of Fisheries Science, National Taiwan University, Taipei City, Taiwan
| | - Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, Taipei City, Taiwan
| | - Yi-Ta Shao
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
| | - Li-Yih Lin
- Department of Life Science, National Taiwan Normal University, Taipei City, Taiwan
| | - Chi Chen
- Doctoral Degree Program in Marine Biotechnology, National Taiwan Ocean University and Academia Sinica, Taipei City, Taiwan
| | - Kuang-Yu Tseng
- Department of Life Science, Tunghai University, Taichung, Taiwan
| | - Min-Chen Wang
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, I-Lan County, Taiwan
| | - Cheng-Mao Zhang
- Biodiversity Research Center, Academia Sinica, Taipei City, Taiwan
| | - Bor-Cheng Han
- School of Public Health, Taipei Medical College, Taipei, Taiwan
| | - Ching-Chun Lin
- Biomedical Translation Research Center, Academia Sinica, Taipei City, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei City, Taiwan
| | - Ming-Shiou Jeng
- Biodiversity Research Center, Academia Sinica, Taipei City, Taiwan
| | - Ching-Fong Chang
- Center of Excellence for the Oceans National Taiwan Ocean University, Keelung, Taiwan
| | - Yung-Che Tseng
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, I-Lan County, Taiwan
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11
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In situ electrosynthetic bacterial growth using electricity generated by a deep-sea hydrothermal vent. THE ISME JOURNAL 2023; 17:12-20. [PMID: 36151459 PMCID: PMC9751133 DOI: 10.1038/s41396-022-01316-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 08/28/2022] [Accepted: 09/01/2022] [Indexed: 11/08/2022]
Abstract
Electroautotrophic microorganisms have attracted great attention since they exhibit a new type of primary production. Here, in situ electrochemical cultivation was conducted using the naturally occurring electromotive forces at a deep-sea hydrothermal vent. The voltage and current generation originating from the resulting microbial activity was observed for 12 days of deployment, with fluctuation in response to tidal cycles. A novel bacterium belonging to the genus Thiomicrorhabdus dominated the microbial community specifically enriched on the cathode. Metagenomic analysis provided the draft genome of the bacterium and the gene repertoire indicated that the bacterium has the potential for thio-autotrophic growth, which is a typical physiological feature of the members of the genus, while the bacterium had a unique gene cluster encoding multi-heme cytochrome c proteins responsible for extracellular electron transfer. Herein, we propose this bacterium as a new species, specifically enriched during electricity generation, as 'Candidatus Thiomicrorhabdus electrophagus'. This finding suggests the natural occurrence of electrosynthetic microbial populations using the geoelectricity in deep-sea hydrothermal environments.
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12
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Hui M, Wang A, Cheng J, Sha Z. Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts. PeerJ 2022; 10:e13758. [PMID: 35966925 PMCID: PMC9368993 DOI: 10.7717/peerj.13758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 06/29/2022] [Indexed: 01/17/2023] Open
Abstract
Shrimps of the family Alvinocarididae, endemic species to deep sea chemosynthetic ecosystems, harbor epibiotic microbes on gills which probably play important roles in the survival of the shrimps. Among them, Alvinocaris longirostris and Shinkaicaris leurokolos occupy different ecological niches within the same hydrothermal vent in Okinawa Trough, and A. longirostris also exists in a methane seep of the South China Sea. In this study, full-length 16S rRNA sequences of the gill associated bacteria of two alvinocaridid species from different chemosynthetically ecological niches were first captured by single-molecule real-time sequencing. Totally, 120,792 optimized circular consensus sequences with ∼1,450 bp in length were obtained and clustered into 578 operational taxonomic units. Alpha diversity analysis showed seep A. longirostris had the highest species richness and evenness (average Chao1 = 213.68, Shannon = 3.39). Beta diversity analysis revealed that all samples were clearly divided into three groups, and microbial community of A. longirostris from seep and vent were more related than the other comparisons. By permutational multivariate analysis of variance, the most significant community compositional variance was detected between seep A. longirostris and vent S. leurokolos (R 2 = 0.731, P = 0.001). The taxon tags were further classified into 21 phyla, 40 classes, 89 orders, 124 families and 135 genera. Overall, the microbial communities were dominated by Campylobacteria and Gammaproteobacteria. Alphaproteobacteria, Bacteroidia, Verrucomicrobiae, Bacilli and other minor groups were also detected at lower abundance. Taxonomic groups recovered from the vent S. leurokolos samples were only dominated by Sulfurovaceae (94.06%). In comparison, gill-associated microbiota of vent A. longirostris consisted of more diverse sulfur-oxidizing bacteria, including Sulfurovaceae (69.21%), Thiotrichaceae (6.77%) and a putative novel Gammaproteobacteria group (14.37%), while in seep A. longirostris, Gammaproteobacteria un-group (44.01%) constituted the major component, following the methane-oxidizing bacteria Methylomonadaceae (19.38%), and Sulfurovaceae (18.66%). Therefore, the gill associated bacteria composition and abundance of alvinocaridid shrimps are closely related to the habitat heterogeneity and the selection of microbiota by the host. However, the interaction between these alvinocaridid shrimps and the epibiotic communities requires further study based on metagenome sequencing and fluorescence in situ hybridization.
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Affiliation(s)
- Min Hui
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Aiyang Wang
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,University of Chinese Academy of Sciences, Beijing, China
| | - Jiao Cheng
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhongli Sha
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,University of Chinese Academy of Sciences, Beijing, China
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13
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McClain CR, Bryant SR, Hanks G, Bowles MW. Extremophiles in Earth's Deep Seas: A View Toward Life in Exo-Oceans. ASTROBIOLOGY 2022; 22:1009-1028. [PMID: 35549348 DOI: 10.1089/ast.2021.0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Humanity's search for extraterrestrial life is a modern manifestation of the exploratory and curious nature that has led us through millennia of scientific discoveries. With the ongoing exploration of extraterrestrial bodies, the potential for discovery of extraterrestrial life has expanded. We may better inform this search through an understanding of how life persists and flourishes on Earth in a myriad of environmental extremes. A significant proportion of our knowledge of extremophiles on Earth comes from studies on deep ocean life. Here, we review and synthesize the range of environmental extremes observed in the deep sea, the life that persists in these extreme conditions, and the biological adaptations utilized by these remarkable life-forms. We also review confirmed and predicted extraterrestrial oceans in our solar system and propose deep-sea sites that may serve as planetary field analog environments. We show that the clever ingenuity of evolution under deep-sea conditions suggests that the plausibility of extraterrestrial life is much greater than previously thought.
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Affiliation(s)
- Craig R McClain
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - S River Bryant
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - Granger Hanks
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
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14
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Heldebrant DJ, Kothandaraman J, Dowell NM, Brickett L. Next steps for solvent-based CO 2 capture; integration of capture, conversion, and mineralisation. Chem Sci 2022; 13:6445-6456. [PMID: 35756509 PMCID: PMC9172129 DOI: 10.1039/d2sc00220e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/11/2022] [Indexed: 12/13/2022] Open
Abstract
In this perspective, we detail how solvent-based carbon capture integrated with conversion can be an important element in a net-zero emission economy. Carbon capture and utilization (CCU) is a promising approach for at-scale production of green CO2-derived fuels, chemicals and materials. The challenge is that CO2-derived materials and products have yet to reach market competitiveness because costs are significantly higher than those from conventional means. We present here the key to making CO2-derived products more efficiently and cheaper, integration of solvent-based CO2 capture and conversion. We present the fundamentals and benefits of integration within a changing energy landscape (i.e., CO2 from point source emissions transitioning to CO2 from the atmosphere), and how integration could lead to lower costs and higher efficiency, but more importantly how CO2 altered in solution can offer new reactive pathways to produce products that cannot be made today. We discuss how solvents are the key to integration, and how solvents can adapt to differing needs for capture, conversion and mineralisation in the near, intermediate and long term. We close with a brief outlook of this emerging field of study, and identify critical needs to achieve success, including establishing a green-premium for fuels, chemicals, and materials produced in this manner. In this perspective, we detail how solvent-based carbon capture integrated with conversion can be an important element in a net-zero emission economy.![]()
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Affiliation(s)
- David J Heldebrant
- Pacific Northwest National Laboratory Richland WA USA .,Washington State University Pullman WA USA
| | | | | | - Lynn Brickett
- US Department of Energy, Office of Fossil Energy USA
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15
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Malakhov VV, Rimskaya-Korsakova NN, Gantsevich MM. Structure and Origin of the Vestimentiferan Trophosome (Annelida, Siboglinidae). DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2022; 502:42-45. [PMID: 35298753 DOI: 10.1134/s0012496622010082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 06/14/2023]
Abstract
The anatomical and histological structure of the trophosome of the giant vestimentiferan Riftiapachyptila has been studied. The trophosome consists of longitudinally oriented cords. The cords of the trophosome intertwine, form diverticula and anastomose with each other. Each cord has an axial blood vessel inside, which is connected to afferent vessels on the surface of the cord by radial capillaries. Based on the data on the structure and development of the trophosome, it is suggested that the evolutionary precursor of the trophosome was a blood network connecting the ventral and dorsal vessels. The cells of the coelomic lining on the surface of the vessels grew and gave rise to the parenchymal tissue of the trophosome. At the same time, the trophosome developed from two sources, namely: due to the coelomic lining on the surface of the vessels of the intestinal plexus and due to the coelomic lining on the surface of the vessels of the circulatory plexus of the body wall.
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16
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Rafiqi AM, Polo PG, Milat NS, Durmuş ZÖ, Çolak-Al B, Alarcón ME, Çağıl FZ, Rajakumar A. Developmental Integration of Endosymbionts in Insects. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.846586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In endosymbiosis, two independently existing entities are inextricably intertwined such that they behave as a single unit. For multicellular hosts, the endosymbiont must be integrated within the host developmental genetic network to maintain the relationship. Developmental integration requires innovations in cell type, gene function, gene regulation, and metabolism. These innovations are contingent upon the existing ecological interactions and may evolve mutual interdependence. Recent studies have taken significant steps toward characterizing the proximate mechanisms underlying interdependence. However, the study of developmental integration is only in its early stages of investigation. Here, we review the literature on mutualistic endosymbiosis to explore how unicellular endosymbionts developmentally integrate into their multicellular hosts with emphasis on insects as a model. Exploration of this process will help gain a more complete understanding of endosymbiosis. This will pave the way for a better understanding of the endosymbiotic theory of evolution in the future.
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17
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Paight C, Hunter ES, Lane CE. Codependence of individuals in the Nephromyces species swarm requires heterospecific bacterial endosymbionts. Curr Biol 2022; 32:2948-2955.e4. [DOI: 10.1016/j.cub.2022.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/07/2022] [Accepted: 05/04/2022] [Indexed: 10/18/2022]
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18
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de Oliveira AL, Mitchell J, Girguis P, Bright M. Novel insights on obligate symbiont lifestyle and adaptation to chemosynthetic environment as revealed by the giant tubeworm genome. Mol Biol Evol 2021; 39:6454105. [PMID: 34893862 PMCID: PMC8789280 DOI: 10.1093/molbev/msab347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The mutualism between the giant tubeworm Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone has been extensively researched over the past 40 years. However, the lack of the host whole genome information has impeded the full comprehension of the genotype/phenotype interface in Riftia. Here we described the high-quality draft genome of Riftia, its complete mitogenome, and tissue-specific transcriptomic data. The Riftia genome presents signs of reductive evolution, with gene family contractions exceeding expansions. Expanded gene families are related to sulphur metabolism, detoxification, anti-oxidative stress, oxygen transport, immune system, and lysosomal digestion, reflecting evolutionary adaptations to the vent environment and endosymbiosis. Despite the derived body plan, the developmental gene repertoire in the gutless tubeworm is extremely conserved with the presence of a near intact and complete Hox cluster. Gene expression analyses establishes that the trophosome is a multi-functional organ marked by intracellular digestion of endosymbionts, storage of excretory products and haematopoietic functions. Overall, the plume and gonad tissues both in contact to the environment harbour highly expressed genes involved with cell cycle, programmed cell death, and immunity indicating a high cell turnover and defence mechanisms against pathogens. We posit that the innate immune system plays a more prominent role into the establishment of the symbiosis during the infection in the larval stage, rather than maintaining the symbiostasis in the trophosome. This genome bridges four decades of physiological research in Riftia, whilst simultaneously provides new insights into the development, whole organism functions and evolution in the giant tubeworm.
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Affiliation(s)
| | - Jessica Mitchell
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Peter Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Monika Bright
- Department of Functional and Evolutionary Ecology, University of Vienna, Austria
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19
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Hourdez S, Boidin-Wichlacz C, Jollivet D, Massol F, Rayol MC, Bruno R, Zeppilli D, Thomas F, Lesven L, Billon G, Duperron S, Tasiemski A. Investigation of Capitella spp. symbionts in the context of varying anthropic pressures: First occurrence of a transient advantageous epibiosis with the giant bacteria Thiomargarita sp. to survive seasonal increases of sulfides in sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149149. [PMID: 34375231 DOI: 10.1016/j.scitotenv.2021.149149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/15/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Capitella spp. is considered as an important ecological indicator of eutrophication due to its high densities in organic-rich, reduced, and sometimes polluted coastal ecosystems. We investigated whether such ability to cope with adverse ecological contexts might be a response to the microorganisms these worms are associated with. In populations from the French Atlantic coast (Roscoff, Brittany), we observed an epibiotic association covering the tegument of 20-30% specimens from an anthropized site while individuals from a reference, non-anthropized site were devoid of any visible epibionts. Using RNAseq, molecular and microscopic analyses, we described and compared the microbial communities associated with the epibiotic versus the non-epibiotic specimens at both locations. Interestingly, data showed that the epibiosis is characterized by sulfur-oxidizing bacteria among which the giant bacterium Thiomargarita sp., to date only described in deep sea habitats. Survey of Capitella combined with the geochemical analysis of their sediment revealed that epibiotic specimens are always found in muds with the highest concentration of sulfides, mostly during the summer. Concomitantly, tolerance tests demonstrated that the acquisition of epibionts increased survival against toxic level of sulfides. Overall, the present data highlight for the first time a peculiar plastic adaptation to seasonal variations of the habitat based on a transcient epibiosis allowing a coastal species to survive temporary harsher conditions.
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Affiliation(s)
- Stéphane Hourdez
- Observatoire Océanologique de Banyuls-sur-Mer, UMR 8222 CNRS-SU, avenue Pierre Fabre, 66650 Banyuls-sur-Mer, France
| | - Céline Boidin-Wichlacz
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France; Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Didier Jollivet
- Sorbonne Université, CNRS UMR 7144 'Adaptation et Diversité en Milieux Marins' (AD2M), Team 'Dynamique de la Diversité Marine' (DyDiv), Station biologique de Roscoff, Place G. Teissier, 29680 Roscoff, France
| | - François Massol
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France; Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Maria Claudia Rayol
- Centro Interdisciplinar em Energia e Ambiente - CIEnAm, Universidade Federal da Bahia, 40170-115 Salvador, BA, Brazil
| | - Renato Bruno
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France; Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Daniela Zeppilli
- IFREMER, Centre Brest, REM/EEP/LEP, ZI de la Pointe du Diable, CS10070, 29280 Plouzané, France
| | - Frédéric Thomas
- CREEC/CREES, UMR IRD-Université de Montpellier, Montpellier, France
| | - Ludovic Lesven
- Univ. Lille, CNRS, UMR 8516 - LASIRE, Laboratoire Avancé de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, F-59000 Lille, France
| | - Gabriel Billon
- Univ. Lille, CNRS, UMR 8516 - LASIRE, Laboratoire Avancé de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, F-59000 Lille, France
| | - Sébastien Duperron
- Muséum National d'Histoire Naturelle, CNRS UMR7245 Mécanismes de Communication et Adaptation des Micro-organismes, 12 rue Buffon, 75005 Paris, France
| | - Aurélie Tasiemski
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France; Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France.
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20
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Zhou K, Xu Y, Zhang R, Qian PY. Arms race in a cell: genomic, transcriptomic, and proteomic insights into intracellular phage-bacteria interplay in deep-sea snail holobionts. MICROBIOME 2021; 9:182. [PMID: 34479645 PMCID: PMC8418041 DOI: 10.1186/s40168-021-01099-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/20/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Deep-sea animals in hydrothermal vents often form endosymbioses with chemosynthetic bacteria. Endosymbionts serve essential biochemical and ecological functions, but the prokaryotic viruses (phages) that determine their fate are unknown. RESULTS We conducted metagenomic analysis of a deep-sea vent snail. We assembled four genome bins for Caudovirales phages that had developed dual endosymbiosis with sulphur-oxidising bacteria (SOB) and methane-oxidising bacteria (MOB). Clustered regularly interspaced short palindromic repeat (CRISPR) spacer mapping, genome comparison, and transcriptomic profiling revealed that phages Bin1, Bin2, and Bin4 infected SOB and MOB. The observation of prophages in the snail endosymbionts and expression of the phage integrase gene suggested the presence of lysogenic infection, and the expression of phage structural protein and lysozyme genes indicated active lytic infection. Furthermore, SOB and MOB appear to employ adaptive CRISPR-Cas systems to target phage DNA. Additional expressed defence systems, such as innate restriction-modification systems and dormancy-inducing toxin-antitoxin systems, may co-function and form multiple lines for anti-viral defence. To counter host defence, phages Bin1, Bin2, and Bin3 appear to have evolved anti-restriction mechanisms and expressed methyltransferase genes that potentially counterbalance host restriction activity. In addition, the high-level expression of the auxiliary metabolic genes narGH, which encode nitrate reductase subunits, may promote ATP production, thereby benefiting phage DNA packaging for replication. CONCLUSIONS This study provides new insights into phage-bacteria interplay in intracellular environments of a deep-sea vent snail. Video Abstract.
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Affiliation(s)
- Kun Zhou
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Hong Kong, China
- Shenzhen University-HKUST Joint Marine Science Ph.D. Program, Shenzhen University, Shenzhen, 518060, China
| | - Ying Xu
- Shenzhen University-HKUST Joint Marine Science Ph.D. Program, Shenzhen University, Shenzhen, 518060, China.
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University (Xiang'an), Xiamen, Fujian, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, China.
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong University of Science and Technology, Hong Kong, China.
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21
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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] [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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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] [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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Lee W, Juniper SK, Perez M, Ju S, Kim S. Diversity and characterization of bacterial communities of five co-occurring species at a hydrothermal vent on the Tonga Arc. Ecol Evol 2021; 11:4481-4493. [PMID: 33976824 PMCID: PMC8093707 DOI: 10.1002/ece3.7343] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 11/06/2022] Open
Abstract
Host-symbiont relationships in hydrothermal vent ecosystems, supported by chemoautotrophic bacteria as primary producers, have been extensively studied. However, the process by which densely populated co-occurring invertebrate hosts form symbiotic relationships with bacterial symbionts remains unclear. Here, we analyzed gill-associated symbiotic bacteria (gill symbionts) of five co-occurring hosts, three mollusks ("Bathymodiolus" manusensis, B. brevior, and Alviniconcha strummeri) and two crustaceans (Rimicaris variabilis and Austinograea alayseae), collected together at a single vent site in the Tonga Arc. We observed both different compositions of gill symbionts and the presence of unshared operational taxonomic units (OTUs). In addition, the total number of OTUs was greater for crustacean hosts than for mollusks. The phylogenetic relationship trees of gill symbionts suggest that γ-proteobacterial gill symbionts have coevolved with their hosts toward reinforcement of host specificity, while campylobacterial Sulfurovum species found across various hosts and habitats are opportunistic associates. Our results confirm that gill symbiont communities differ among co-occurring vent invertebrates and indicate that hosts are closely related with their gill symbiont communities. Considering the given resources available at a single site, differentiation of gill symbionts seems to be a useful strategy for obtaining nutrition and energy while avoiding competition among both hosts and gill symbionts.
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Affiliation(s)
- Won‐Kyung Lee
- Genome Editing Research CenterKorea Research Institute of Bioscience and BiotechnologyDaejeonKorea
| | - S. Kim Juniper
- Department of BiologySchool of Earth and Ocean SciencesUniversity of VictoriaVictoriaBCCanada
| | - Maëva Perez
- Département des Sciences BiologiquesUniversité de MontréalMontrealQCCanada
| | - Se‐Jong Ju
- Korea Institute of Ocean Science & TechnologyBusanKorea
| | - Se‐Joo Kim
- Genome Editing Research CenterKorea Research Institute of Bioscience and BiotechnologyDaejeonKorea
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Goulet TL, Goulet D. Climate Change Leads to a Reduction in Symbiotic Derived Cnidarian Biodiversity on Coral Reefs. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.636279] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Symbiotic relationships enable partners to thrive and survive in habitats where they would either not be as successful, or potentially not exist, without the symbiosis. The coral reef ecosystem, and its immense biodiversity, relies on the symbioses between cnidarians (e.g., scleractinian corals, octocorals, sea anemones, jellyfish) and multiple organisms including dinoflagellate algae (family Symbiodiniaceae), bivalves, crabs, shrimps, and fishes. In this review, we discuss the ramifications of whether coral reef cnidarian symbioses are obligatory, whereby at least one of the partners must be in the symbiosis in order to survive or are facultative. Furthermore, we cover the consequences of cnidarian symbioses exhibiting partner flexibility or fidelity. Fidelity, where a symbiotic partner can only engage in symbiosis with a subset of partners, may be absolute or context dependent. Current literature demonstrates that many cnidarian symbioses are highly obligative and appear to exhibit absolute fidelity. Consequently, for many coral reef cnidarian symbioses, surviving changing environmental conditions will depend on the robustness and potential plasticity of the existing host-symbiont(s) combination. If environmental conditions detrimentally affect even one component of this symbiotic consortium, it may lead to a cascade effect and the collapse of the entire symbiosis. Symbiosis is at the heart of the coral reef ecosystem, its existence, and its high biodiversity. Climate change may cause the demise of some of the cnidarian symbioses, leading to subsequent reduction in biodiversity on coral reefs.
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25
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Sato M, Sasaki A. Evolution and Maintenance of Mutualism between Tubeworms and Sulfur-Oxidizing Bacteria. Am Nat 2021; 197:351-365. [PMID: 33625963 DOI: 10.1086/712780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractTubeworms and sulfur-oxidizing bacteria mutualism, an essential part of the chemosynthetic ecosystem in the deep sea, has several puzzling features. After acquiring sulfur-oxidizing bacteria from the environment, tubeworms become fully dependent on their symbiont bacteria for nutrient intake. Once ingested by the tubeworm larva, no additional symbionts join from the environment, and no symbionts are released until the host tubeworm dies. Despite this very narrow window to acquire symbionts, some tubeworm species can live for >200 years. Such a restricted release of symbionts could lead to a shortage of symbiont bacteria in the environment without which tubeworms could not survive. In our study, we examine the conditions under which this mutualism can persist and whether the host mortality rate evolves toward a low value using a mathematical model for the tubeworm-symbiont bacteria system. Our model reveals that mutualism can persist only when the host mortality rate is within an intermediate range. With cohabitation of multiple symbionts strains in the same host, host mortality rate evolves toward a low value without driving either host or symbiont to extinction when competition among symbionts is weak and their growth within a host is slow. We also find the parameter conditions that lead to unlimited evolutionary escalation of host mortality rate toward coextinction of both tubeworms and symbionts populations (evolutionary double suicide). The generality of this evolutionary fragility in obligate mutualistic systems as well as the contrasting evolutionary robustness in host-parasite systems are discussed.
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Kuroda M, Nagasaki T, Koito T, Hongo Y, Yoshida T, Maruyama T, Tsuchida S, Nemoto S, Inoue K. Possible Roles of Hypotaurine and Thiotaurine in the Vesicomyid Clam Phreagena okutanii. THE BIOLOGICAL BULLETIN 2021; 240:34-40. [PMID: 33730534 DOI: 10.1086/712396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
AbstractVesicomyid clams, which inhabit deep-sea hydrothermal vents and hydrocarbon seeps, are nutritionally dependent on symbiotic, chemoautotrophic bacteria that produce organic matter by using hydrogen sulfide. Vesicomyid clams absorb hydrogen sulfide from the foot and transport it in their hemolymph to symbionts in the gill. However, mechanisms to cope with hydrogen sulfide toxicity are not fully understood. Previous studies on vent-specific invertebrates, including bathymodiolin mussels, suggest that hypotaurine, a precursor of taurine, mitigates hydrogen sulfide toxicity by binding it to bisulfide ion, so as to synthesize thiotaurine. In this study, we cloned cDNAs from the vesicomyid clam Phreagena okutanii for the taurine transporter that transports hypotaurine into cells and for cysteine dioxygenase and cysteine-sulfinate decarboxylase, major enzymes involved in hypotaurine synthesis. Results of reverse-transcription polymerase chain reaction indicate that mRNAs of these three genes are most abundant in the foot, followed by the gill. However, hypotaurine and thiotaurine levels, measured by reverse-phase high-performance liquid chromatography, were low in the foot and high in the gill. In addition, thiotaurine was detected in hemolymph cells. Hypotaurine synthesized in the foot may be transported to the gill after binding to bisulfide ion, possibly by hemolymph cells.
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27
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Hinzke T, Kleiner M, Meister M, Schlüter R, Hentschker C, Pané-Farré J, Hildebrandt P, Felbeck H, Sievert SM, Bonn F, Völker U, Becher D, Schweder T, Markert S. Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis. eLife 2021; 10:58371. [PMID: 33404502 PMCID: PMC7787665 DOI: 10.7554/elife.58371] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 12/05/2020] [Indexed: 12/13/2022] Open
Abstract
The hydrothermal vent tubeworm Riftia pachyptila hosts a single 16S rRNA phylotype of intracellular sulfur-oxidizing symbionts, which vary considerably in cell morphology and exhibit a remarkable degree of physiological diversity and redundancy, even in the same host. To elucidate whether multiple metabolic routes are employed in the same cells or rather in distinct symbiont subpopulations, we enriched symbionts according to cell size by density gradient centrifugation. Metaproteomic analysis, microscopy, and flow cytometry strongly suggest that Riftia symbiont cells of different sizes represent metabolically dissimilar stages of a physiological differentiation process: While small symbionts actively divide and may establish cellular symbiont-host interaction, large symbionts apparently do not divide, but still replicate DNA, leading to DNA endoreduplication. Moreover, in large symbionts, carbon fixation and biomass production seem to be metabolic priorities. We propose that this division of labor between smaller and larger symbionts benefits the productivity of the symbiosis as a whole.
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Affiliation(s)
- Tjorven Hinzke
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany.,Energy Bioengineering Group, University of Calgary, Calgary, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
| | - Mareike Meister
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.,Leibniz Institute for Plasma Science and Technology, Greifswald, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, Greifswald, Germany
| | - Christian Hentschker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jan Pané-Farré
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Petra Hildebrandt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Horst Felbeck
- Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, United States
| | - Florian Bonn
- Institute of Biochemistry, University Hospital, Goethe University School of Medicine Frankfurt, Frankfurt, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Stephanie Markert
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
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Rimskaya-Korsakova N, Fontaneto D, Galkin S, Malakhov V, Martínez A. Geochemistry drives the allometric growth of the hydrothermal vent tubeworm Riftia pachyptila (Annelida: Siboglinidae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The tubeworm Riftia pachyptila is a key primarily producer in hydrothermal vent communities due to the symbiosis with sulphur-oxidizing bacteria, which provide nourishment to the worm from sulphides, oxygen and carbon dioxide. These substances diffuse from the vent water into the bloodstream of the worm through their tentacular crowns, and then to the bacteria, hosted in a specialized organ of the worm, called a trophosome. The uptake rates of these substances depend on the surface/volume relationship of the tentacles. We here describe two morphotypes, ‘fat’ and ‘slim’, respectively, from the basalt sulphide-rich vents at 9 °N and 21 °N at the East Pacific Rise, and the highly sedimented, sulphide-poor vents at 27 °N in the Guaymas Basin. The ‘fat’ morphotype has a thicker body and tube, longer trunk and smaller tentacular crowns, whereas the ‘slim’ morphotype has shorter trunk, thinner body and tube, and presents longer tentacular crowns and has a higher number of tentacular lamellae. Given the dependence on sulphides for the growth of R. pachyptila, as well as high genetic connectivity of the worm’s populations along the studied localities, we suggest that such morphological differences are adaptive and selected to keep the sulphide uptake near to the optimum values for the symbionts. ‘Fat’ and ‘slim’ morphotypes are also found in the vestimentiferan Ridgeia piscesae in similar sulphide-rich and poor environments in the northern Pacific.
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Affiliation(s)
| | - Diego Fontaneto
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), Verbania Pallanza, Italy
| | - Sergey Galkin
- Laboratory of Ocean Benthic Fauna, Shirshov Institute of Oceanology of the Russian Academy of Science, Moscow, Russia
| | - Vladimir Malakhov
- Department of Invertebrate Zoology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alejandro Martínez
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), Verbania Pallanza, Italy
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29
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Metatranscriptomics by
In Situ
RNA Stabilization Directly and Comprehensively Revealed Episymbiotic Microbial Communities of Deep-Sea Squat Lobsters. mSystems 2020; 5:5/5/e00551-20. [PMID: 33024051 PMCID: PMC8534475 DOI: 10.1128/msystems.00551-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Shinkaia crosnieri is an invertebrate that inhabits an area around deep-sea hydrothermal vents in the Okinawa Trough in Japan by harboring episymbiotic microbes as the primary nutrition. To reveal physiology and phylogenetic composition of the active episymbiotic populations, metatranscriptomics is expected to be a powerful approach. However, this has been hindered by substantial perturbation (e.g., RNA degradation) during time-consuming retrieval from the deep sea. Here, we conducted direct metatranscriptomic analysis of S. crosnieri episymbionts by applying in situ RNA stabilization equipment. As expected, we obtained RNA expression profiles that were substantially different from those obtained by conventional metatranscriptomics (i.e., stabilization after retrieval). The episymbiotic community members were dominated by three orders, namely, Thiotrichales, Methylococcales, and Campylobacterales, and the Campylobacterales members were mostly dominated by the Sulfurovum genus. At a finer phylogenetic scale, the episymbiotic communities on different host individuals shared many species, indicating that the episymbionts on each host individual are not descendants of a few founder cells but are horizontally exchanged. Furthermore, our analysis revealed the key metabolisms of the community: two carbon fixation pathways, a formaldehyde assimilation pathway, and utilization of five electron donors (sulfide, thiosulfate, sulfur, methane, and ammonia) and two electron accepters (oxygen and nitrate/nitrite). Importantly, it was suggested that Thiotrichales episymbionts can utilize intercellular sulfur globules even when sulfur compounds are not usable, possibly also in a detached and free-living state. IMPORTANCE Deep-sea hydrothermal vent ecosystems remain mysterious. To depict in detail the enigmatic life of chemosynthetic microbes, which are key primary producers in these ecosystems, metatranscriptomic analysis is expected to be a promising approach. However, this has been hindered by substantial perturbation (e.g., RNA degradation) during time-consuming retrieval from the deep sea. In this study, we conducted direct metatranscriptome analysis of microbial episymbionts of deep-sea squat lobsters (Shinkaia crosnieri) by applying in situ RNA stabilization equipment. Compared to conventional metatranscriptomics (i.e., RNA stabilization after retrieval), our method provided substantially different RNA expression profiles. Moreover, we discovered that S. crosnieri and its episymbiotic microbes constitute complex and resilient ecosystems, where closely related but various episymbionts are stably maintained by horizontal exchange and partly by their sulfur storage ability for survival even when sulfur compounds are not usable, likely also in a detached and free-living state.
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31
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Sass K, Güllert S, Streit WR, Perner M. A hydrogen-oxidizing bacterium enriched from the open ocean resembling a symbiont. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:396-405. [PMID: 32338395 DOI: 10.1111/1758-2229.12847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 03/31/2020] [Accepted: 04/21/2020] [Indexed: 06/11/2023]
Abstract
A new autotrophic hydrogen-oxidizing Chromatiaceae bacterium, namely bacterium CTD079, was enriched from a water column sample at 1500 m water depth in the southern Pacific Ocean. Based on the phylogeny of 16S rRNA genes, it was closely related to a scaly snail endosymbiont (99.2% DNA sequence identity) whose host so far is only known to colonize hydrothermal vents along the Indian ridge. The average nucleotide identity between the genomes of CTD079 and the snail endosymbiont was 91%. The observed differences likely reflect adaptations to their specific habitats. For example, CTD079 encodes additional enzymes like the formate dehydrogenase increasing the organism's spectrum of energy generation pathways. Other additional physiological features of CTD079 included the increase of viral defence strategies, secretion systems and specific transporters for essential elements. These important genome characteristics suggest an adaptation to life in the open ocean.
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Affiliation(s)
- Katharina Sass
- Molecular Biology of Microbial Consortia, Universität Hamburg, Hamburg, Germany
- Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Simon Güllert
- Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Wolfgang R Streit
- Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Mirjam Perner
- Molecular Biology of Microbial Consortia, Universität Hamburg, Hamburg, Germany
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32
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Wang Y, Liu L, Yu M, Zhou S, Fu T, Sun W, Du R, Zhang XH. Carideicomes alvinocaridis gen. nov., sp. nov., a marine bacterium isolated from shrimp gill in a hydrothermal field of Okinawa Trough. Int J Syst Evol Microbiol 2020; 70:1777-1784. [PMID: 32234113 DOI: 10.1099/ijsem.0.003971] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, oval-shaped, non-motile bacterium with no flagella, designated strain SCR17T, was isolated from a shrimp gill habitat in Tangyin hydrothermal field of Okinawa Trough. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SCR17T formed a lineage within the family 'Rhodobacteraceae', and shared 16S rRNA gene sequence similarity of 93.2-96.2 % to the related genera Aquicoccus and Roseivivax. Strain SCR17T was able to grow with 0-14 % (w/v) NaCl (optimum, 9-10 %). The sole respiratory quinone was ubiquinone-10. The major polar lipids of strain SCR17T comprised phosphatidylcholine (PC), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), an unidentified aminolipid (AL), an unidentified phospholipid (PL) and an unidentified lipid (L). The predominant fatty acids (more than 10 % of the total fatty acids) were C18 : 1ω7c or/and C18 : 1ω6c, anteiso-C15 : 0, C16 : 0 and C19 : 0 cyclo ω8c . The genomic DNA G+C content of strain SCR17T was 67.7 mol%. Based on polyphasic taxonomic analyses, strain SCR17T is considered to represent a novel species in a new genus of the family 'Rhodobacteraceae', for which the name Carideicomes alvinocaridis gen. nov., sp. nov. is proposed. The type strain of Carideicomes alvinocaridis is SCR17T (=JCM 33426T=MCCC 1K03732T). The discovery of a novel host-associated bacterium in hydrothermal fields provides an opportunity for the study of host-bacterial symbiosis in extreme environments.
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Affiliation(s)
- Yiting Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Lijun Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Min Yu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Shun Zhou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Tianyu Fu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Wen Sun
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Rui Du
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiao-Hua Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China.,MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
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Goffredi SK, Tilic E, Mullin SW, Dawson KS, Keller A, Lee RW, Wu F, Levin LA, Rouse GW, Cordes EE, Orphan VJ. Methanotrophic bacterial symbionts fuel dense populations of deep-sea feather duster worms (Sabellida, Annelida) and extend the spatial influence of methane seepage. SCIENCE ADVANCES 2020; 6:eaay8562. [PMID: 32284974 PMCID: PMC7124940 DOI: 10.1126/sciadv.aay8562] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 01/09/2020] [Indexed: 06/11/2023]
Abstract
Deep-sea cold seeps are dynamic sources of methane release and unique habitats supporting ocean biodiversity and productivity. Here, we describe newly discovered animal-bacterial symbioses fueled by methane, between two species of annelid (a serpulid Laminatubus and sabellid Bispira) and distinct aerobic methane-oxidizing bacteria belonging to the Methylococcales, localized to the host respiratory crown. Worm tissue δ13C of -44 to -58‰ are consistent with methane-fueled nutrition for both species, and shipboard stable isotope labeling experiments revealed active assimilation of 13C-labeled methane into animal biomass, which occurs via the engulfment of methanotrophic bacteria across the crown epidermal surface. These worms represent a new addition to the few animals known to intimately associate with methane-oxidizing bacteria and may further explain their enigmatic mass occurrence at 150-million year-old fossil seeps. High-resolution seafloor surveys document significant coverage by these symbioses, beyond typical obligate seep fauna. These findings uncover novel consumers of methane in the deep sea and, by expanding the known spatial extent of methane seeps, may have important implications for deep-sea conservation.
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Affiliation(s)
| | - Ekin Tilic
- Scripps Institution of Oceanography, La Jolla, CA, USA
- University of Bonn, Bonn, Germany
| | | | | | | | | | - Fabai Wu
- California Institute of Technology, Pasadena, CA, USA
| | - Lisa A. Levin
- Scripps Institution of Oceanography, La Jolla, CA, USA
| | - Greg W. Rouse
- Scripps Institution of Oceanography, La Jolla, CA, USA
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Miyazaki J, Ikuta T, Watsuji TO, Abe M, Yamamoto M, Nakagawa S, Takaki Y, Nakamura K, Takai K. Dual energy metabolism of the Campylobacterota endosymbiont in the chemosynthetic snail Alviniconcha marisindica. ISME JOURNAL 2020; 14:1273-1289. [PMID: 32051527 PMCID: PMC7174374 DOI: 10.1038/s41396-020-0605-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 01/16/2020] [Accepted: 01/30/2020] [Indexed: 11/09/2022]
Abstract
Some deep-sea chemosynthetic invertebrates and their symbiotic bacteria can use molecular hydrogen (H2) as their energy source. However, how much the chemosynthetic holobiont (endosymbiont-host association) physiologically depends on H2 oxidation has not yet been determined. Here, we demonstrate that the Campylobacterota endosymbionts of the gastropod Alviniconcha marisindica in the Kairei and Edmond fields (kAlv and eAlv populations, respectively) of the Indian Ocean, utilize H2 in response to their physical and environmental H2 conditions, although the 16S rRNA gene sequence of both the endosymbionts shared 99.6% identity. A thermodynamic calculation using in situ H2 and hydrogen sulfide (H2S) concentrations indicated that chemosynthetic symbiosis could be supported by metabolic energy via H2 oxidation, particularly for the kAlv holobiont. Metabolic activity measurements showed that both the living individuals and the gill tissues consumed H2 and H2S at similar levels. Moreover, a combination of fluorescence in situ hybridization, quantitative transcript analyses, and enzymatic activity measurements showed that the kAlv endosymbiont expressed the genes and enzymes for both H2- and sulfur-oxidations. These results suggest that both H2 and H2S could serve as the primary energy sources for the kAlv holobiont. The eAlv holobiont had the ability to utilize H2, but the gene expression and enzyme activity for hydrogenases were much lower than for sulfur-oxidation enzymes. These results suggest that the energy acquisitions of A. marisindica holobionts are dependent on H2- and sulfur-oxidation in the H2-enriched Kairei field and that the mechanism of dual metabolism is controlled by the in situ H2 concentration.
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Affiliation(s)
- Junichi Miyazaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.
| | - Tetsuro Ikuta
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Tomo-O Watsuji
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.,Department of Food and Nutrition, Higashi-Chikushi Junior College, 5-1-1 Shimoitozu, Kitakyusyu, 803-0846, Japan
| | - Mariko Abe
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Masahiro Yamamoto
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Satoshi Nakagawa
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.,Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Kentaro Nakamura
- Department of Systems Innovation, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
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Dick GJ. The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally. Nat Rev Microbiol 2020; 17:271-283. [PMID: 30867583 DOI: 10.1038/s41579-019-0160-2] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The discovery of chemosynthetic ecosystems at deep-sea hydrothermal vents in 1977 changed our view of biology. Chemosynthetic bacteria and archaea form the foundation of vent ecosystems by exploiting the chemical disequilibrium between reducing hydrothermal fluids and oxidizing seawater, harnessing this energy to fix inorganic carbon into biomass. Recent research has uncovered fundamental aspects of these microbial communities, including their relationships with underlying geology and hydrothermal geochemistry, interactions with animals via symbiosis and distribution both locally in various habitats within vent fields and globally across hydrothermal systems in diverse settings. Although 'black smokers' and symbioses between microorganisms and macrofauna attract much attention owing to their novelty and the insights they provide into life under extreme conditions, habitats such as regions of diffuse flow, subseafloor aquifers and hydrothermal plumes have important roles in the global cycling of elements through hydrothermal systems. Owing to sharp contrasts in physical and chemical conditions between these various habitats and their dynamic, extreme and geographically isolated nature, hydrothermal vents provide a valuable window into the environmental and ecological forces that shape microbial communities and insights into the limits, origins and evolution of microbial life.
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Affiliation(s)
- Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA.
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Bacterial Intracellular Sulphur Globules. BACTERIAL ORGANELLES AND ORGANELLE-LIKE INCLUSIONS 2020. [DOI: 10.1007/978-3-030-60173-7_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Micro-organisms and the Microbiome. WHY GUT MICROBES MATTER 2020. [PMCID: PMC7233799 DOI: 10.1007/978-3-030-43246-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The term ‘Micro-organism’ refers to any living thing that is too small to be seen with the naked eye. It covers an astonishing array of life forms that began with the earliest living occupants of our planet. Of the three recognized domains of life, two (Bacteria and Archaea) consist exclusively of micro-organisms. The third (Eukaryota) contains all of the macroscopic, multi-celled organisms that we recognize as plants and animals, but it also includes many micro-organisms. ‘Microbiome’ is a collective term for all of the micro-organisms belonging to these three domains, while the ‘Biome’ comprises all life on earth. For most of earth’s history until the evolution of multicellular Eukaryota around 600 million years ago, however, the earth’s Biome consisted only of micro-organisms (Fig. 1.1). Even now the Microbiome is estimated to represent more than half of the total living matter (biomass) on the planet [1]. Their invisibility makes it easy for us to overlook the vast impact that micro-organisms have on the sustainability of the planet and of life on earth. While this book will focus on the gut-associated Microbiome, it is important that we start with a look at the wider microbial world.
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Abstract
All animals are associated with microorganisms; hence, host-microbe interactions are of fundamental importance for life on earth. However, we know little about the molecular basis of these interactions. Therefore, we studied the deep-sea Riftia pachyptila symbiosis, a model association in which the tubeworm host is associated with only one phylotype of endosymbiotic bacteria and completely depends on this sulfur-oxidizing symbiont for nutrition. Using a metaproteomics approach, we identified both metabolic interaction processes, such as substrate transfer between the two partners, and interactions that serve to maintain the symbiotic balance, e.g., host efforts to control the symbiont population or symbiont strategies to modulate these host efforts. We suggest that these interactions are essential principles of mutualistic animal-microbe associations. The deep-sea tubeworm Riftia pachyptila lacks a digestive system but completely relies on bacterial endosymbionts for nutrition. Although the symbiont has been studied in detail on the molecular level, such analyses were unavailable for the animal host, because sequence information was lacking. To identify host-symbiont interaction mechanisms, we therefore sequenced the Riftia transcriptome, which served as a basis for comparative metaproteomic analyses of symbiont-containing versus symbiont-free tissues, both under energy-rich and energy-limited conditions. Our results suggest that metabolic interactions include nutrient allocation from symbiont to host by symbiont digestion and substrate transfer to the symbiont by abundant host proteins. We furthermore propose that Riftia maintains its symbiont by protecting the bacteria from oxidative damage while also exerting symbiont population control. Eukaryote-like symbiont proteins might facilitate intracellular symbiont persistence. Energy limitation apparently leads to reduced symbiont biomass and increased symbiont digestion. Our study provides unprecedented insights into host-microbe interactions that shape this highly efficient symbiosis.
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Hydrogen Does Not Appear To Be a Major Electron Donor for Symbiosis with the Deep-Sea Hydrothermal Vent Tubeworm Riftia pachyptila. Appl Environ Microbiol 2019; 86:AEM.01522-19. [PMID: 31628148 DOI: 10.1128/aem.01522-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/09/2019] [Indexed: 12/23/2022] Open
Abstract
Use of hydrogen gas (H2) as an electron donor is common among free-living chemolithotrophic microorganisms. Given the presence of this dissolved gas at deep-sea hydrothermal vents, it has been suggested that it may also be a major electron donor for the free-living and symbiotic chemolithoautotrophic bacteria that are the primary producers at these sites. Giant Riftia pachyptila siboglinid tubeworms and their symbiotic bacteria ("Candidatus Endoriftia persephone") dominate many vents in the Eastern Pacific, and their use of sulfide as a major electron donor has been documented. Genes encoding hydrogenase are present in the "Ca Endoriftia persephone" genome, and proteome data suggest that these genes are expressed. In this study, high-pressure respirometry of intact R. pachyptila and incubations of trophosome homogenate were used to determine whether this symbiotic association could also use H2 as a major electron donor. Measured rates of H2 uptake by intact R. pachyptila in high-pressure respirometers were similar to rates measured in the absence of tubeworms. Oxygen uptake rates in the presence of H2 were always markedly lower than those measured in the presence of sulfide, as was the incorporation of 13C-labeled dissolved inorganic carbon. Carbon fixation by trophosome homogenate was not stimulated by H2, nor was hydrogenase activity detectable in these samples. Though genes encoding [NiFe] group 1e and [NiFe] group 3b hydrogenases are present in the genome and transcribed, it does not appear that H2 is a major electron donor for this system, and it may instead play a role in intracellular redox homeostasis.IMPORTANCE Despite the presence of hydrogenase genes, transcripts, and proteins in the "Ca Endoriftia persephone" genome, transcriptome, and proteome, it does not appear that R. pachyptila can use H2 as a major electron donor. For many uncultivable microorganisms, omic analyses are the basis for inferences about their activities in situ However, as is apparent from the study reported here, there are dangers in extrapolating from omics data to function, and it is essential, whenever possible, to verify functions predicted from omics data with physiological and biochemical measurements.
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Thaler AD, Amon D. 262 Voyages Beneath the Sea: a global assessment of macro- and megafaunal biodiversity and research effort at deep-sea hydrothermal vents. PeerJ 2019; 7:e7397. [PMID: 31404427 PMCID: PMC6688594 DOI: 10.7717/peerj.7397] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/02/2019] [Indexed: 11/20/2022] Open
Abstract
For over 40 years, hydrothermal vents and the communities that thrive on them have been a source of profound discovery for deep-sea ecologists. These ecosystems are found throughout the world on active plate margins as well as other geologically active features. In addition to their ecologic interest, hydrothermal vent fields are comprised of metallic ores, sparking a nascent industry that aims to mine these metal-rich deposits for their mineral wealth. Here, we provide the first systematic assessment of macrofaunal and megafaunal biodiversity at hydrothermal vents normalized against research effort. Cruise reports from scientific expeditions as well as other literature were used to characterize the extent of exploration, determine the relative biodiversity of different biogeographic provinces, identify knowledge gaps related to the distribution of research effort, and prioritize targets for additional sampling to establish biodiversity baselines ahead of potential commercial exploitation. The Northwest Pacific, Southwest Pacific, and Southern Ocean biogeographic provinces were identified as high biodiversity using rarefaction of family-level incidence data, whereas the North East Pacific Rise, Northern East Pacific, Mid-Atlantic Ridge, and Indian Ocean provinces had medium biodiversity, and the Mid-Cayman Spreading Center was identified as a province of relatively low biodiversity. A North/South divide in the extent of biological research and the targets of hydrothermal vent mining prospects was also identified. Finally, we provide an estimate of sampling completeness for each province to inform scientific and stewardship priorities.
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Affiliation(s)
- Andrew D Thaler
- Blackbeard Biologic: Science and Environmental Advisors, St. Michaels, MD, USA.,Center for Environmental Science, Horn Point Laboratory, University of Maryland, Cambridge, MD, USA
| | - Diva Amon
- Department of Life Sciences, Natural History Museum, London, UK
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Malakhov VV, Gantsevich MM. Trophosome in the Vestimentiferan Tubeworm Ridgeia piscesae Jones 1985 (Annelida, Siboglinidae) Develops from Cells of the Coelomic Lining. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2019; 485:44-46. [PMID: 31197593 DOI: 10.1134/s0012496619020078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 10/25/2018] [Accepted: 10/25/2018] [Indexed: 11/23/2022]
Abstract
The paper reports the study of the anatomy of early juvenile individuals of the vestimentiferan tubeworm Ridgeia piscesae (Annelida, Siboglinidae). Adult vestimentiferans lack the digestive tract but have the trophosome, whose cells are inhabited by chemoautotrophic bacteria. It has been shown, in 280- to 300-µm early juvenile individuals, that the trophosome develops from cells of the coelomic lining on the gut surface and on the lateral body walls. The observed proto-trophosome structure suggests that the bacteria are first captured by the coelomic cells of the body wall and then transferred to the coelomic cells located on the gut surface.
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Chemosynthetic symbiont with a drastically reduced genome serves as primary energy storage in the marine flatworm Paracatenula. Proc Natl Acad Sci U S A 2019; 116:8505-8514. [PMID: 30962361 PMCID: PMC6486704 DOI: 10.1073/pnas.1818995116] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Animals typically store their primary energy reserves in specialized cells. Here, we show that in the small marine flatworm Paracatenula, this function is performed by its bacterial chemosynthetic symbiont. The intracellular symbiont occupies half of the biomass in the symbiosis and has a highly reduced genome but efficiently stocks up and maintains carbon and energy, particularly sugars. The host rarely digests the symbiont cells to access these stocks. Instead, the symbionts appear to provide the bulk nutrition by secreting outer-membrane vesicles. This is in contrast to all other described chemosynthetic symbioses, where the hosts continuously digest full cells of a small and ideally growing symbiont population that cannot provide a long-term buffering capacity during nutrient limitation. Hosts of chemoautotrophic bacteria typically have much higher biomass than their symbionts and consume symbiont cells for nutrition. In contrast to this, chemoautotrophic Candidatus Riegeria symbionts in mouthless Paracatenula flatworms comprise up to half of the biomass of the consortium. Each species of Paracatenula harbors a specific Ca. Riegeria, and the endosymbionts have been vertically transmitted for at least 500 million years. Such prolonged strict vertical transmission leads to streamlining of symbiont genomes, and the retained physiological capacities reveal the functions the symbionts provide to their hosts. Here, we studied a species of Paracatenula from Sant’Andrea, Elba, Italy, using genomics, gene expression, imaging analyses, as well as targeted and untargeted MS. We show that its symbiont, Ca. R. santandreae has a drastically smaller genome (1.34 Mb) than the symbiont´s free-living relatives (4.29–4.97 Mb) but retains a versatile and energy-efficient metabolism. It encodes and expresses a complete intermediary carbon metabolism and enhanced carbon fixation through anaplerosis and accumulates massive intracellular inclusions such as sulfur, polyhydroxyalkanoates, and carbohydrates. Compared with symbiotic and free-living chemoautotrophs, Ca. R. santandreae’s versatility in energy storage is unparalleled in chemoautotrophs with such compact genomes. Transmission EM as well as host and symbiont expression data suggest that Ca. R. santandreae largely provisions its host via outer-membrane vesicle secretion. With its high share of biomass in the symbiosis and large standing stocks of carbon and energy reserves, it has a unique role for bacterial symbionts—serving as the primary energy storage for its animal host.
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Sigwart JD, Chen C. Comparative Oxygen Consumption of Gastropod Holobionts from Deep-Sea Hydrothermal Vents in the Indian Ocean. THE BIOLOGICAL BULLETIN 2018; 235:102-112. [PMID: 30358445 DOI: 10.1086/699326] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Physiological traits are the foundation of an organism's success in a dynamic environment, yet basic measurements are unavailable for many taxa and even ecosystems. We measured routine metabolism in two hydrothermal vent gastropods, Alviniconcha marisindica (n = 40) and the scaly-foot gastropod Chrysomallon squamiferum (n = 18), from Kairei and Edmond vent fields on the Central Indian Ridge (23-25°S, about 3000 meter depth). No previous studies have measured metabolism in any Indian Ocean vent animals. After recovering healthy animals to the surface, we performed shipboard closed-chamber respirometry experiments to compare oxygen uptake at different temperatures (10, 16, and 25 °C) at surface pressure (1 atm). The physiology of these species is driven by the demands of their chemoautotrophic symbionts. Chrysomallon has very enlarged respiratory and circulatory systems, and endosymbionts are housed in its trophosome-like internal esophageal gland. By contrast, Alviniconcha has chemoautotrophic bacteria within the gill and less extensive associated anatomical adaptations. Thus, we predicted that routine oxygen consumption of Chrysomallon might be higher than that of Alviniconcha. However, oxygen consumption of Chrysomallon was not higher than that of Alviniconcha, and, further, Chrysomallon maintained a steady metabolic demand in two widely separated experimental temperatures, while Alviniconcha did not. We interpret that these findings indicate that (1) the "trophosome" does not fundamentally increase oxygen requirement compared to other gastropod holobionts, and (2) cold temperatures (10 °C) induce a stress response in Alviniconcha, resulting in aberrantly high uptake. While these two large gastropod species co-occur, differences in oxygen consumption may reflect the separate niches they occupy in the vent ecosystem.
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Bellec L, Cambon-Bonavita MA, Cueff-Gauchard V, Durand L, Gayet N, Zeppilli D. A Nematode of the Mid-Atlantic Ridge Hydrothermal Vents Harbors a Possible Symbiotic Relationship. Front Microbiol 2018; 9:2246. [PMID: 30294317 PMCID: PMC6159746 DOI: 10.3389/fmicb.2018.02246] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/03/2018] [Indexed: 12/26/2022] Open
Abstract
Deep-sea hydrothermal vent meiofauna have been the focus of recent research and the discovery of an abundant well-adapted free-living marine nematode on the Mid-Atlantic Ridge offers new perspectives on adaptations to the vent environment. Indeed, knowledge concerning biological interactions of microbes and meiofauna in marine extreme environments is scarce, especially for nematodes. In this study, we used microscopic observations [fluorescence in situ hybridization (FISH) and scanning electron microscopy (SEM)] and metabarcoding of 16S rRNA to characterize the bacterial community of the nematode species Oncholaimus dyvae, an overlooked but ecologically important vent organism. Detection of bacteria in the buccal cavity and on the cuticle (SEM) and epibionts in its intestine (FISH) suggests that O. dyvae harbors its own bacterial community. Molecular results and phylogenetic analysis show that bacteria associated with this species are related to symbiotic lineages typical of hydrothermal vent fauna, such as sulfur-oxidizing bacteria related to Epsilonproteobacteria and Gammaproteobacteria. This multi-approach study suggests a potential symbiotic role of bacteria with its nematode host and opens new research perspectives on vent meiofauna.
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Affiliation(s)
- Laure Bellec
- IFREMER, Centre Brest, REM/EEP/LEP, ZI de la pointe du diable, CS10070, Plouzané, France.,IFREMER, Centre Brest, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (REM/EEP/LM2E), ZI de la pointe du diable, CS10070, Plouzané, France.,CNRS, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France.,Université Bretagne Occidentale (UBO), UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France
| | - Marie-Anne Cambon-Bonavita
- IFREMER, Centre Brest, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (REM/EEP/LM2E), ZI de la pointe du diable, CS10070, Plouzané, France.,CNRS, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France.,Université Bretagne Occidentale (UBO), UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France
| | - Valérie Cueff-Gauchard
- IFREMER, Centre Brest, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (REM/EEP/LM2E), ZI de la pointe du diable, CS10070, Plouzané, France.,CNRS, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France.,Université Bretagne Occidentale (UBO), UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France
| | - Lucile Durand
- IFREMER, Centre Brest, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (REM/EEP/LM2E), ZI de la pointe du diable, CS10070, Plouzané, France.,CNRS, UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France.,Université Bretagne Occidentale (UBO), UMR 6197 - Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), Technopole Brest-Iroise, Plouzané, France
| | - Nicolas Gayet
- IFREMER, Centre Brest, REM/EEP/LEP, ZI de la pointe du diable, CS10070, Plouzané, France
| | - Daniela Zeppilli
- IFREMER, Centre Brest, REM/EEP/LEP, ZI de la pointe du diable, CS10070, Plouzané, France
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Husson B, Sarrazin J, van Oevelen D, Sarradin PM, Soetaert K, Menesguen A. Modelling the interactions of the hydrothermal mussel Bathymodiolus azoricus with vent fluid. Ecol Modell 2018. [DOI: 10.1016/j.ecolmodel.2018.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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46
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Metaorganisms in extreme environments: do microbes play a role in organismal adaptation? ZOOLOGY 2018; 127:1-19. [DOI: 10.1016/j.zool.2018.02.004] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/08/2018] [Accepted: 02/12/2018] [Indexed: 02/06/2023]
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Gignoux-Wolfsohn SA, Aronson FM, Vollmer SV. Complex interactions between potentially pathogenic, opportunistic, and resident bacteria emerge during infection on a reef-building coral. FEMS Microbiol Ecol 2017. [PMID: 28637338 DOI: 10.1093/femsec/fix080] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Increased bacterial diversity on diseased corals can obscure disease etiology and complicate our understanding of pathogenesis. To untangle microbes that may cause white band disease signs from microbes responding to disease, we inoculated healthy Acropora cervicornis corals with an infectious dose from visibly diseased corals. We sampled these dosed corals and healthy controls over time for sequencing of the bacterial 16S region. Endozoicomonas were associated with healthy fragments from 4/10 colonies, dominating microbiomes before dosing and decreasing over time only in corals that displayed disease signs, suggesting a role in disease resistance. We grouped disease-associated bacteria by when they increased in abundance (primary vs secondary) and whether they originated in the dose (colonizers) or the previously healthy corals (responders). We found that all primary responders increased in all dosed corals regardless of final disease state and are therefore unlikely to cause disease signs. In contrast, primary colonizers in the families Pasteurellaceae and Francisellaceae increased solely in dosed corals that ultimately displayed disease signs, and may be infectious foreign bacteria involved in the development of disease signs. Moving away from a static comparison of diseased and healthy bacterial communities, we provide a framework to identify key players in other coral diseases.
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Affiliation(s)
- Sarah A Gignoux-Wolfsohn
- Department of Ecology, Evolution, & Natural Resources School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901-8525, USA
| | - Felicia M Aronson
- Marine Science Center, Northeastern University, Nahant, MA 01908, USA
| | - Steven V Vollmer
- Marine Science Center, Northeastern University, Nahant, MA 01908, USA
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48
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Anderson RE, Reveillaud J, Reddington E, Delmont TO, Eren AM, McDermott JM, Seewald JS, Huber JA. Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents. Nat Commun 2017; 8:1114. [PMID: 29066755 PMCID: PMC5655027 DOI: 10.1038/s41467-017-01228-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/30/2017] [Indexed: 02/01/2023] Open
Abstract
Little is known about evolutionary drivers of microbial populations in the warm subseafloor of deep-sea hydrothermal vents. Here we reconstruct 73 metagenome-assembled genomes (MAGs) from two geochemically distinct vent fields in the Mid-Cayman Rise to investigate patterns of genomic variation within subseafloor populations. Low-abundance populations with high intra-population diversity coexist alongside high-abundance populations with low genomic diversity, with taxonomic differences in patterns of genomic variation between the mafic Piccard and ultramafic Von Damm vent fields. Populations from Piccard are significantly enriched in nonsynonymous mutations, suggesting stronger purifying selection in Von Damm relative to Piccard. Comparison of nine Sulfurovum MAGs reveals two high-coverage, low-diversity MAGs from Piccard enriched in unique genes related to the cellular membrane, suggesting these populations were subject to distinct evolutionary pressures that may correlate with genes related to nutrient uptake, biofilm formation, or viral invasion. These results are consistent with distinct evolutionary histories between geochemically different vent fields, with implications for understanding evolutionary processes in subseafloor microbial populations.
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Affiliation(s)
- Rika E Anderson
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA.
- Department of Biology, Carleton College, Northfield, MN, 55057, USA.
| | - Julie Reveillaud
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Cirad UMR 117, Inra UMR 1309 ASTRE, Cirad Campus International de Baillarguet, Montpellier, France
| | - Emily Reddington
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Great Pond Foundation, Edgartown, MA, 02539, USA
| | - Tom O Delmont
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - A Murat Eren
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Jill M McDermott
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
- Department of Earth and Environmental Sciences, Lehigh University, Bethlehem, PA, 18015, USA
| | - Jeff S Seewald
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Julie A Huber
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
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49
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Liu H, Wang H, Cai S, Zhang H. A Novel ω3-Desaturase in the Deep Sea Giant Tubeworm Riftia pachyptila. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:345-350. [PMID: 28493048 DOI: 10.1007/s10126-017-9753-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 04/28/2017] [Indexed: 06/07/2023]
Abstract
One paradox of the trophic biochemistry of the deep sea giant tubeworm Riftia pachyptila, endemic to hydrothermal vent sites and nourished by polyunsaturated fatty acid (PUFA) deficiency chemolitoautotrophic sulfide-oxidizing bacteria, is the source of their PUFAs. Biosynthesis of PUFA starts with two precursors C18:2n-6 and C18:3n-3, which cannot be biosynthesized by most animals due to lack of ω6- and ω3-desaturase; thus, C18:2n-6 and C18:3n-3 are generally essential fatty acids for animals. Here, we characterized a gene derived from the R. pachyptila located by hydrothermal vent, which encoded a novel ω3-desaturase (Rp3Fad). The gene was identified by searching the R. pachyptila transcriptome database using known ω3-desaturases, and its predicted protein showed 37-45% identical to ω3-desaturases of fungus and microalgae, and only 31% identitical to nematode Caenorhabditis elegans ω3-desaturase. Expression in yeast Saccharomyces cerevisiae showed that the Rp3Fad could desaturate C18:2n-6 and C18:3n-6 into C18:3n-3 and C18:4n-3, respectively, displaying a Δ15 activity similar to plant ω3-desaturase, but it showed no activity towards C20 n-6 PUFA substrates, differing from the well-characterized C. elegans ω3-desaturases. Δ5, Δ6, Δ8, and Δ12 activity were also tested, resulting in no corresponding production. The function of ω3-desaturase identified in R. pachyptila could produce C18:3n - 3 used in synthesis of n - 3 series PUFAs, suggesting an adaption to PUFA deficiency environment in deep sea hydrothermal vent.
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Affiliation(s)
- Helu Liu
- Institute of Deep Sea Science and Engineering, Chinese Academy of Science, Sanya, 572000, China
| | - Hui Wang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Science, Sanya, 572000, China
| | - Shanya Cai
- Institute of Deep Sea Science and Engineering, Chinese Academy of Science, Sanya, 572000, China
| | - Haibin Zhang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Science, Sanya, 572000, China.
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50
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Heywood JL, Chen C, Pearce DA, Linse K. Bacterial communities associated with the Southern Ocean vent gastropod, Gigantopelta chessoia: indication of horizontal symbiont transfer. Polar Biol 2017. [DOI: 10.1007/s00300-017-2148-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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