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Koito T, Ito Y, Suzuki A, Tame A, Ikuta T, Suzuki M, Mitsunobu S, Sugimura M, Inoue K. Difference in sulfur regulation mechanism between tube-dwelling and free-moving polychaetes sympatrically inhabiting deep-sea hydrothermal chimneys. ZOOLOGICAL LETTERS 2023; 9:18. [PMID: 37789380 PMCID: PMC10548688 DOI: 10.1186/s40851-023-00218-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 08/03/2023] [Indexed: 10/05/2023]
Abstract
The environment around deep sea hydrothermal vents is characterized by an abundance of sulfur compounds, including toxic hydrogen sulfide. However, numerous communities of various invertebrates are found in it. It is suggested that invertebrates in the vicinity of hydrothermal vents detoxify sulfur compounds by biosynthesis of taurine-related compounds in the body. On the other hand, the vent endemic polychaete Alvinella pompejana has spherocrystals composed of sulfur and other metals in its digestive tract. It was considered that the spherocrystals contribute to the regulation of sulfur in body fluids. Paralvinella spp. and Polynoidae. gen. sp. live sympatrically and in areas most affected by vent fluid. In this study, we focused on the digestive tract of Paralvinella spp. and Polynoidae. gen. sp. to examine whether they have spherocrystals. We also investigated the possible involvement of bacteria in the digestive tract in spherulization. Examination with a scanning electron microscope (SEM) equipped with Energy Disperse X-ray Spectroscopy (EDS) detected spherocrystals containing sulfur and iron in the digestive tract of Paralvinella spp. In contrast, such spherocrystals were not observed in that of Polynoidae. gen. sp. although sulfur is detected there by inductively coupled plasma-optical emission spectrometry (ICP-OES). Meta-16S rRNA analysis indicated that the floras of the digestive tracts of the two species were very similar, suggesting that enteric bacteria are not responsible for spherocrystal formation. Analysis of taurine-related compounds indicated that the digestive tissues of Polynoidae. gen. sp. contain a higher amount of hypotaurine and thiotaurine than those of Paralvinella spp. Therefore, the two sympatric polychaetes use different strategies for controlling sulfur, i.e., Paralvinella spp. forms spherocrystals containing elemental sulfur and iron in the digestive tract, but Polynoidae. gen. sp. accumulates taurine-related compounds instead of spherocrystals. Such differences may be related to differences in their lifestyles, i.e., burrow-dweller or free-moving, or may have been acquired phylogenetically in the evolutionary process.
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Affiliation(s)
- Tomoko Koito
- Department of Marine Science and Resources, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan.
| | - Yusuke Ito
- Department of Marine Science and Resources, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Akihiko Suzuki
- Department of Marine Science and Resources, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
- Present Address: National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Akihiro Tame
- Marine Works Japan, Ltd., 3-54-1 Oppamahigashi, Yokosuka, Kanagawa, 237-0063, Japan
| | - Tetsuro Ikuta
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Miwa Suzuki
- Department of Marine Science and Resources, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Satoshi Mitsunobu
- Department of Science and Technology for Biological Resources and Environment, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
| | - Makoto Sugimura
- Enoshima Aquarium, 2-19-1 Katase, Fujisawa, Kanagawa, 251-0035, Japan
| | - Koji Inoue
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-Shi, Chiba, 277-8564, Japan
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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] [Grants] [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.
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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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Oortwijn T, de Fouw J, Petersen JM, van Gils JA. Sulfur in lucinid bivalves inhibits intake rates of a molluscivore shorebird. Oecologia 2022; 199:69-78. [PMID: 35486255 DOI: 10.1007/s00442-022-05170-3] [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: 08/02/2021] [Accepted: 03/28/2022] [Indexed: 11/25/2022]
Abstract
A forager's energy intake rate is usually constrained by a combination of handling time, encounter rate and digestion rate. On top of that, food intake may be constrained when a forager can only process a maximum amount of certain toxic compounds. The latter constraint is well described for herbivores with a limited tolerance to plant secondary metabolites. In sulfidic marine ecosystems, many animals host chemoautotrophic endosymbionts, which store sulfur compounds as an energy resource, potentially making their hosts toxic to predators. The red knot Calidris canutus canutus is a molluscivore shorebird that winters on the mudflats of Banc d'Arguin, where the most abundant bivalve prey Loripes orbiculatus hosts sulfide-oxidizing bacteria. In this system, we studied the potential effect of sulfur on the red knots' intake rates, by offering Loripes with various sulfur content to captive birds. To manipulate toxicity, we starved Loripes for 10 days by removing them from their symbiont's energy source sulfide. As predicted, we found lower sulfur concentrations in starved Loripes. We also included natural variation in sulfur concentrations by offering Loripes collected at two different locations. In both cases lower sulfur levels in Loripes resulted in higher consumption rates in red knots. Over time the red knots increased their intake rates on Loripes, showing their ability to adjust to a higher intake of sulfur.
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Affiliation(s)
- Tim Oortwijn
- Department Coastal Systems (COS), NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg (Texel), The Netherlands.
| | - Jimmy de Fouw
- Department Coastal Systems (COS), NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg (Texel), The Netherlands
- Faculty of Science, Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jillian M Petersen
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Jan A van Gils
- Department Coastal Systems (COS), NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg (Texel), The Netherlands
- Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103, 9700 CC, Groningen, The Netherlands
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Becker-Kerber B, de Barros GEB, Paim PSG, Prado GMEM, da Rosa ALZ, El Albani A, Laflamme M. In situ filamentous communities from the Ediacaran (approx. 563 Ma) of Brazil. Proc Biol Sci 2021; 288:20202618. [PMID: 33402067 DOI: 10.1098/rspb.2020.2618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Precambrian filamentous microfossils are common and diverse. Nevertheless, their taxonomic assignment can be difficult owing to their overall simple shapes typically lacking in diagnostic features. Here, we report in situ communities of well-preserved, large filamentous impressions from the Ediacaran Itajaí Basin (ca 563 Ma) of Brazil. The filaments are uniserial (unbranched) and can reach up to 200 µm in width and up to 44 mm in length. They occur as both densely packed or sparsely populated surfaces, and typically show a consistent orientation. Although simple in shape, their preferred orientation suggests they were tethered to the seafloor, and their overall flexibility (e.g. bent, folded and twisted) supports a biological (rather than sedimentary) affinity. Biometric comparisons with modern filamentous groups further support their biological affinity, suggesting links with either large sulfide-oxidizing bacteria (SOB) or eukaryotes. Other morphological and palaeoecological characteristics further corroborates their similarities with modern large filamentous SOB. Their widespread occurrence and association with complex Ediacaran macrobiota (e.g. frondose organisms, Palaeopascichnus) suggest that they probably played an important role in the ecological dynamics of these early benthic communities by providing firm substrates for metazoans to inhabit. It is further hypothesized that the dynamic redox condition in the latest Ediacaran, with the non-continuous rise in oxygen concentration and periods of hypoxia, may have created ideal conditions for SOB to thrive.
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Affiliation(s)
- Bruno Becker-Kerber
- Programa de Pós-Graduação em Ecologia e Recursos Naturais, Universidade Federal de São Carlos, Washington Luiz, 325 km, São Carlos (SP) 13565-905, Brazil.,Unité Mixte de Recherche (UMR), Centre National de la Recherche Scientifique (CNRS), IC2MP 7285, University of Poitiers, 86073 Poitiers, France
| | - Gabriel Eduardo Baréa de Barros
- Programa de Pós-Graduação em Biologia Comparada, Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Universidade de São Paulo (USP), Avenue Bandeirantes, 3900-Vila Monte Alegre, 14049-900, Ribeirão Preto, São Paulo, Brazil
| | - Paulo Sergio Gomes Paim
- Programa de Pós-Graduação em Geologia, Universidade do Vale do Rio dos Sinos, 93.022-750, São Leopoldo (RS), Brazil
| | - Gustavo M E M Prado
- Programa de Pós Graduação em Geoquímica e Geotectônica, Instituto de Geociências, Universidade de São Paulo (USP), Avenue Bandeirantes, 3900-Vila Monte Alegre, 14049-900, Ribeirão Preto, São Paulo, Brazil
| | | | - Abderrazak El Albani
- Unité Mixte de Recherche (UMR), Centre National de la Recherche Scientifique (CNRS), IC2MP 7285, University of Poitiers, 86073 Poitiers, France
| | - Marc Laflamme
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario, Canada L5 L 1C6
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Metabolic Adaptation to Sulfur of Hyperthermophilic Palaeococcus pacificus DY20341 T from Deep-Sea Hydrothermal Sediments. Int J Mol Sci 2020; 21:ijms21010368. [PMID: 31935923 PMCID: PMC6981617 DOI: 10.3390/ijms21010368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/26/2019] [Accepted: 12/29/2019] [Indexed: 11/30/2022] Open
Abstract
The hyperthermo-piezophilic archaeon Palaeococcus pacificus DY20341T, isolated from East Pacific hydrothermal sediments, can utilize elemental sulfur as a terminal acceptor to simulate growth. To gain insight into sulfur metabolism, we performed a genomic and transcriptional analysis of Pa. pacificus DY20341T with/without elemental sulfur as an electron acceptor. In the 2001 protein-coding sequences of the genome, transcriptomic analysis showed that 108 genes increased (by up to 75.1 fold) and 336 genes decreased (by up to 13.9 fold) in the presence of elemental sulfur. Palaeococcus pacificus cultured with elemental sulfur promoted the following: the induction of membrane-bound hydrogenase (MBX), NADH:polysulfide oxidoreductase (NPSOR), NAD(P)H sulfur oxidoreductase (Nsr), sulfide dehydrogenase (SuDH), connected to the sulfur-reducing process, the upregulation of iron and nickel/cobalt transfer, iron–sulfur cluster-carrying proteins (NBP35), and some iron–sulfur cluster-containing proteins (SipA, SAM, CobQ, etc.). The accumulation of metal ions might further impact on regulators, e.g., SurR and TrmB. For growth in proteinous media without elemental sulfur, cells promoted flagelin, peptide/amino acids transporters, and maltose/sugar transporters to upregulate protein and starch/sugar utilization processes and riboflavin and thiamin biosynthesis. This indicates how strain DY20341T can adapt to different living conditions with/without elemental sulfur in the hydrothermal fields.
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Ponnudurai R, Sayavedra L, Kleiner M, Heiden SE, Thürmer A, Felbeck H, Schlüter R, Sievert SM, Daniel R, Schweder T, Markert S. Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont. Stand Genomic Sci 2017; 12:50. [PMID: 28878861 PMCID: PMC5581435 DOI: 10.1186/s40793-017-0266-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/23/2017] [Indexed: 11/30/2022] Open
Abstract
Bathymodiolus thermophilus, a mytilid mussel inhabiting the deep-sea hydrothermal vents of the East Pacific Rise, lives in symbiosis with chemosynthetic Gammaproteobacteria within its gills. The intracellular symbiont population synthesizes nutrients for the bivalve host using the reduced sulfur compounds emanating from the vents as energy source. As the symbiont is uncultured, comprehensive and detailed insights into its metabolism and its interactions with the host can only be obtained from culture-independent approaches such as genomics and proteomics. In this study, we report the first draft genome sequence of the sulfur-oxidizing symbiont of B. thermophilus, here tentatively named Candidatus Thioglobus thermophilus. The draft genome (3.1 Mb) harbors 3045 protein-coding genes. It revealed pathways for the use of sulfide and thiosulfate as energy sources and encodes the Calvin-Benson-Bassham cycle for CO2 fixation. Enzymes required for the synthesis of the tricarboxylic acid cycle intermediates oxaloacetate and succinate were absent, suggesting that these intermediates may be substituted by metabolites from external sources. We also detected a repertoire of genes associated with cell surface adhesion, bacteriotoxicity and phage immunity, which may perform symbiosis-specific roles in the B. thermophilus symbiosis.
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Affiliation(s)
- Ruby Ponnudurai
- Institute of Pharmacy, Ernst Moritz Arndt University, Greifswald, Germany
| | - Lizbeth Sayavedra
- Max Planck Institute for Marine Microbiology, Department of Symbiosis, Bremen, Germany
| | - Manuel Kleiner
- Department of Geoscience, University of Calgary, Calgary, Canada
| | - Stefan E Heiden
- Institute of Pharmacy, Ernst Moritz Arndt University, Greifswald, Germany
| | - Andrea Thürmer
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg August University, Göttingen, Germany
| | - Horst Felbeck
- Scripps Institution of Oceanography, La Jolla, CA USA
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, Ernst Moritz Arndt University, Greifswald, Germany
| | - Stefan M Sievert
- Woods Hole Oceanographic Institution, Biology Department, Woods Hole, MA USA
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg August University, Göttingen, Germany
| | - Thomas Schweder
- Institute of Pharmacy, Ernst Moritz Arndt University, Greifswald, Germany.,Institute of Marine Biotechnology, Walther-Rathenau-Straße 49A, 17489 Greifswald, Germany
| | - Stephanie Markert
- Institute of Pharmacy, Ernst Moritz Arndt University, Greifswald, Germany.,Institute of Marine Biotechnology, Walther-Rathenau-Straße 49A, 17489 Greifswald, Germany
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Dang H, Chen CTA. Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment. Front Microbiol 2017; 8:1246. [PMID: 28769878 PMCID: PMC5509916 DOI: 10.3389/fmicb.2017.01246] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 06/20/2017] [Indexed: 11/15/2022] Open
Abstract
Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth’s biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and “omics” studies in this field.
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Affiliation(s)
- Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
| | - Chen-Tung A Chen
- Department of Oceanography, National Sun Yat-sen UniversityKaohsiung, Taiwan
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Zhou Y, He Y, Wang C, Zhang X. Characterization of miRNAs from hydrothermal vent shrimp Rimicaris exoculata. Mar Genomics 2015; 24 Pt 3:371-8. [DOI: 10.1016/j.margen.2015.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 09/13/2015] [Accepted: 09/13/2015] [Indexed: 10/23/2022]
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Draft Genome Sequence of the Endosymbiont “
Candidatus
Ruthia magnifica” UCD-CM (Phylum
Proteobacteria
). GENOME ANNOUNCEMENTS 2014; 2:2/4/e00717-14. [PMID: 25035337 PMCID: PMC4102874 DOI: 10.1128/genomea.00717-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Here, we present the draft genome of the endosymbiont “Candidatus Ruthia magnifica” UCD-CM, a member of the phylum Proteobacteria, found from the gills of a deep-sea giant clam, Calyptogena magnifica. The assembly consists of 1,160,249 bp contained in 18 contigs.
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Forget NL, Kim Juniper S. Free-living bacterial communities associated with tubeworm (Ridgeia piscesae) aggregations in contrasting diffuse flow hydrothermal vent habitats at the Main Endeavour Field, Juan de Fuca Ridge. Microbiologyopen 2013; 2:259-75. [PMID: 23401293 PMCID: PMC3633350 DOI: 10.1002/mbo3.70] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 12/19/2012] [Accepted: 01/07/2013] [Indexed: 02/01/2023] Open
Abstract
We systematically studied free-living bacterial diversity within aggregations of the vestimentiferan tubeworm Ridgeia piscesae sampled from two contrasting flow regimes (High Flow and Low Flow) in the Endeavour Hydrothermal Vents Marine Protected Area (MPA) on the Juan de Fuca Ridge (Northeast Pacific). Eight samples of particulate detritus were recovered from paired tubeworm grabs from four vent sites. Most sequences (454 tag and Sanger methods) were affiliated to the Epsilonproteobacteria, and the sulfur-oxidizing genus Sulfurovum was dominant in all samples. Gammaproteobacteria were also detected, mainly in Low Flow sequence libraries, and were affiliated with known methanotrophs and decomposers. The cooccurrence of sulfur reducers from the Deltaproteobacteria and the Epsilonproteobacteria suggests internal sulfur cycling within these habitats. Other phyla detected included Bacteroidetes, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes, Verrucomicrobia, and Deinococcus–Thermus. Statistically significant relationships between sequence library composition and habitat type suggest a predictable pattern for High Flow and Low Flow environments. Most sequences significantly more represented in High Flow libraries were related to sulfur and hydrogen oxidizers, while mainly heterotrophic groups were more represented in Low Flow libraries. Differences in temperature, available energy for metabolism, and stability between High Flow and Low Flow habitats potentially explain their distinct bacterial communities.
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Affiliation(s)
- Nathalie L Forget
- Department of Biology, University of Victoria, 3800 Finnerty Rd, Victoria, British Columbia, Canada V8P 5C2.
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Physiological homogeneity among the endosymbionts of Riftia pachyptila and Tevnia jerichonana revealed by proteogenomics. ISME JOURNAL 2011; 6:766-76. [PMID: 22011719 DOI: 10.1038/ismej.2011.137] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The two closely related deep-sea tubeworms Riftia pachyptila and Tevnia jerichonana both rely exclusively on a single species of sulfide-oxidizing endosymbiotic bacteria for their nutrition. They do, however, thrive in markedly different geochemical conditions. A detailed proteogenomic comparison of the endosymbionts coupled with an in situ characterization of the geochemical environment was performed to investigate their roles and expression profiles in the two respective hosts. The metagenomes indicated that the endosymbionts are genotypically highly homogeneous. Gene sequences coding for enzymes of selected key metabolic functions were found to be 99.9% identical. On the proteomic level, the symbionts showed very consistent metabolic profiles, despite distinctly different geochemical conditions at the plume level of the respective hosts. Only a few minor variations were observed in the expression of symbiont enzymes involved in sulfur metabolism, carbon fixation and in the response to oxidative stress. Although these changes correspond to the prevailing environmental situation experienced by each host, our data strongly suggest that the two tubeworm species are able to effectively attenuate differences in habitat conditions, and thus to provide their symbionts with similar micro-environments.
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Roeselers G, Newton ILG, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM. Complete genome sequence of Candidatus Ruthia magnifica. Stand Genomic Sci 2010; 3:163-73. [PMID: 21304746 PMCID: PMC3035367 DOI: 10.4056/sigs.1103048] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The hydrothermal vent clam Calyptogena magnifica (Bivalvia: Mollusca) is a member of the Vesicomyidae. Species within this family form symbioses with chemosynthetic Gammaproteobacteria. They exist in environments such as hydrothermal vents and cold seeps and have a rudimentary gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. The C. magnifica symbiont, Candidatus Ruthia magnifica, was the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced (Newton et al. 2007). Here we expand upon the original report and provide additional details complying with the emerging MIGS/MIMS standards. The complete genome exposed the genetic blueprint of the metabolic capabilities of the symbiont. Genes which were predicted to encode the proteins required for all the metabolic pathways typical of free-living chemoautotrophs were detected in the symbiont genome. These include major pathways including carbon fixation, sulfur oxidation, nitrogen assimilation, as well as amino acid and cofactor/vitamin biosynthesis. This genome sequence is invaluable in the study of these enigmatic associations and provides insights into the origin and evolution of autotrophic endosymbiosis.
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Affiliation(s)
- Guus Roeselers
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
- Radboud University, Department of Microbiology, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Irene L. G. Newton
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
- Department of Biological Sciences, 106 Central St, Wellesley, MA 02482, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Thomas A. Auchtung
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
| | - Geoffrey F. Dilly
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
| | - Rachel J. Dutton
- Harvard Medical School, Department of Microbiology and Molecular Genetics, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Meredith C. Fisher
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
| | - Kristina M. Fontanez
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
| | - Evan Lau
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
| | - Frank J. Stewart
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
| | - Paul M. Richardson
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Kerrie W. Barry
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Elizabeth Saunders
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - John C. Detter
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Dongying Wu
- University of California, Davis Genome Center, Genome and Biomedical Sciences Facility, Room 5311, 451 East Health Sciences Drive, Davis, CA 95616–8816, USA
| | - Jonathan A. Eisen
- University of California, Davis Genome Center, Genome and Biomedical Sciences Facility, Room 5311, 451 East Health Sciences Drive, Davis, CA 95616–8816, USA
| | - Colleen M. Cavanaugh
- Harvard University, Department of Organismic and Evolutionary Biology, 16 Divinity Avenue, Biolabs 4080, Cambridge, MA 02138, USA
- Corresponding author
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Haymon RM, Koski RA, Sinclair C. Fossils of hydrothermal vent worms from cretaceous sulfide ores of the samail ophiolite, oman. Science 2010; 223:1407-9. [PMID: 17746052 DOI: 10.1126/science.223.4643.1407] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Fossil worm tubes of Cretaceous age preserved in the Bayda massive sulfide deposit of the Samail ophiolite, Oman, are apparently the first documented examples of fossils embedded in massive sulfide deposits from the geologic record. The geologic setting of the Bayda deposit and the distinctive mineralogic and textural features of the fossiliferous samples suggest that the Bayda sulfide deposit and fossil fauna are remnants of a Cretaceous sea-floor hydrothermal vent similar to modern hot springs on the East Pacific Rise and the Juan de Fuca Ridge.
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Stahl DA, Lane DJ, Olsen GJ, Pace NR. Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Science 2010; 224:409-11. [PMID: 17741220 DOI: 10.1126/science.224.4647.409] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Ribosomal RNA (rRNA) sequences were used to establish the phylogenetic affiliations of symbioses in which prokaryotes appear to confer sulfur-based chemoautotrophy on their invertebrate hosts. Two submarine hydrothermal vent animals, the vestimentiferan tube worm Riftia pachyptila and the clam Calyptogena magnifica, and a tidal-flat bivalve, Solemya velum, were inspected. 5S rRNA's were extracted from symbiont-bearing tissues, separated into unique forms, and their nucleotide sequences determined and related to other 5S rRNA's in a phylogenetic tree analysis. The prokaryotic symbionts are related to one another and affiliated with the same narrow phylogenetic grouping as Escherichia coli and Pseudomonas aeruginosa. The sequence comparisons suggest that Riftia is more closely related to the bivalves than their current taxonomic status would suggest.
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Duplessis MR, Ziebis W, Gros O, Caro A, Robidart J, Felbeck H. Respiration strategies utilized by the gill endosymbiont from the host lucinid Codakia orbicularis (Bivalvia: Lucinidae). Appl Environ Microbiol 2004; 70:4144-50. [PMID: 15240294 PMCID: PMC444781 DOI: 10.1128/aem.70.7.4144-4150.2004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The large tropical lucinid clam Codakia orbicularis has a symbiotic relationship with intracellular, sulfide-oxidizing chemoautotrophic bacteria. The respiration strategies utilized by the symbiont were explored using integrative techniques on mechanically purified symbionts and intact clam-symbiont associations along with habitat analysis. Previous work on a related symbiont species found in the host lucinid Lucinoma aequizonata showed that the symbionts obligately used nitrate as an electron acceptor, even under oxygenated conditions. In contrast, the symbionts of C. orbicularis use oxygen as the primary electron acceptor while evidence for nitrate respiration was lacking. Direct measurements obtained by using microelectrodes in purified symbiont suspensions showed that the symbionts consumed oxygen; this intracellular respiration was confirmed by using the redox dye CTC (5-cyano-2,3-ditolyl tetrazolium chloride). In the few intact chemosymbioses tested in previous studies, hydrogen sulfide production was shown to occur when the animal-symbiont association was exposed to anoxia and elemental sulfur stored in the thioautotrophic symbionts was proposed to serve as an electron sink in the absence of oxygen and nitrate. However, this is the first study to show by direct measurements using sulfide microelectrodes in enriched symbiont suspensions that the symbionts are the actual source of sulfide under anoxic conditions.
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Affiliation(s)
- Melinda R Duplessis
- Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California 92093-0202, USA.
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Won YJ, Hallam SJ, O'Mullan GD, Pan IL, Buck KR, Vrijenhoek RC. Environmental acquisition of thiotrophic endosymbionts by deep-sea mussels of the genus bathymodiolus. Appl Environ Microbiol 2004; 69:6785-92. [PMID: 14602641 PMCID: PMC262266 DOI: 10.1128/aem.69.11.6785-6792.2003] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Deep-sea Bathymodiolus mussels, depending on species and location, have the capacity to host sulfur-oxidizing (thiotrophic) and methanotrophic eubacteria in gill bacteriocytes, although little is known about the mussels' mode of symbiont acquisition. Previous studies of Bathymodiolus host and symbiont relationships have been based on collections of nonoverlapping species across wide-ranging geographic settings, creating an apparent model for vertical transmission. We present genetic and cytological evidence for the environmental acquisition of thiotrophic endosymbionts by vent mussels from the Mid-Atlantic Ridge. Open pit structures in cell membranes of the gill surface revealed likely sites for endocytosis of free-living bacteria. A population genetic analysis of the thiotrophic symbionts exploited a hybrid zone where two Bathymodiolus species intergrade. Northern Bathymodiolus azoricus and southern Bathymodiolus puteoserpentis possess species-specific DNA sequences that identify both their symbiont strains (internal transcribed spacer regions) and their mitochondria (ND4). However, the northern and southern symbiont-mitochondrial pairs were decoupled in the hybrid zone. Such decoupling of symbiont-mitochondrial pairs would not occur if the two elements were transmitted strictly vertically through the germ line. Taken together, these findings are consistent with an environmental source of thiotrophic symbionts in Bathymodiolus mussels, although an environmentally "leaky" system of vertical transmission could not be excluded.
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Affiliation(s)
- Yong-Jin Won
- Monterey Bay Aquarium Research Institute, Moss Landing, California 95039-0628, USA
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17
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Lebata MJ. Oxygen, sulphide and nutrient uptake of the mangrove mud clam Anodontia edentula (Family: Lucinidae). MARINE POLLUTION BULLETIN 2001; 42:1133-1138. [PMID: 11763226 DOI: 10.1016/s0025-326x(01)00113-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Oxygen, sulphide and nutrient (ammonia, nitrite and phosphate) uptake of Anodontia edentula was measured. Oxygen and sulphide were measured from sealed containers provided with 1 l fresh mangrove mud (sulphide source) and seawater (oxygen source) with two treatments (with and without clam) at 16 replicates each. Oxygen, sulphide and other parameters were measured at days 1 (initial), 3 and 5 (final). Nutrients were measured from containers filled with 1.5 l wastewater from a milkfish broodstock tank with two treatments (with and without clam) at eight replicates each. Ammonia, NO2 and P04 were measured at days 0 (initial) 3, 6, 9 and 12 (final). Results showed significantly decreasing oxygen and sulphide concentrations in treatment with clams (ANOVA, p < 0.001). A significantly higher ammonia concentration (ANOVA, p < 0.05) was observed in treatment with clams while no significant difference was observed in nitrite and phosphate between the two treatments. A decreasing ammonia and an increasing nitrite trend was also observed in both treatments starting at day 3.
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Affiliation(s)
- M J Lebata
- Aquaculture Department, Southeast Asian Fisheries Development Center, Tigbauan, Iloilo, Philippines.
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18
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Metzler DE, Metzler CM, Sauke DJ. Electron Transport, Oxidative Phosphorylation, and Hydroxylation. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50021-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Maina JN, Maloiy GMO. Adaptations of a tropical swamp worm, alma emini, for subsistence in a H2S-rich habitat: evolution of endosymbiotic bacteria, sulfide metabolizing bodies, and novel processes of elimination of neutralized sulfide complexes. J Struct Biol 1998; 122:257-66. [PMID: 9774530 DOI: 10.1006/jsbi.1998.4000] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The epithelial cell lining of the respiratory groove of Alma emini, an oligochaete glossoscolecid worm that lives in a hydrogen sulfide (H2S)-rich tropical swamp, was investigated by transmission electron microscopy to determine the underlying structural adaptations which enable the worm to subsist in a highly inimical habitat. The epithelium of the respiratory groove is made up of squamous cells with a highly amplified free epithelial surface. The cells are tightly packed with electron dense sulfur metabolizing bodies (SMBs) and contain endosymbiotic bacteria. Presence of sulfur in the electron dense SMBs was confirmed by X-ray microanalysis. Certain eukaryotic cells with prominent filopodia-like cytoplasmic extensions were observed under the epithelial cells and in the muscle tissue. The cells contained numerous heteromorphic endosymbiotic bacteria and scattered SMBs. Both the SMBs and the bacteria are reckoned to be involved in scavenging and detoxifying H2S. The removal of sulfide complexes was observed to occur through excision of blebs formed by epithelial cell membrane elaborations and by exocytosis of crystalline-like particles. These adaptive stratagems generally correspond with those that have been adopted by many marine and hydrothermal vent organisms that occupy sulfide-rich biomes. The congruent adaptive stratagems and ultrastructural morphologies in such a diverse community of organisms have been imposed by a common need to neutralize the insidious effects of H2S in their environments. Copyright 1998 Academic Press.
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Affiliation(s)
- JN Maina
- The Medical School, The University of the Witwatersrand, 7 York Road, Parktown, Johannesburg, 2193, South Africa
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Mével G, Faidy C, Prieur D. Distribution, activity, and diversity of heterotrophic nitrifiers originating from East Pacific deep-sea hydrothermal vents. Can J Microbiol 1996. [DOI: 10.1139/m96-024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nitrifiers (bacteria, n = 160) were enriched and isolated from samples of hydrothermal waters, sediments, invertebrate tissues, and chimney rocks collected from two East Pacific deep-sea hydrothermal vents (2000 m): the 13°N site and the Guaymas Basin. They were nitrite producers and seemed be widely and uniformly distributed in various parts of hydrothermal ecosystem. These bacteria grew and nitrified better heterotrophically than autotrophically and they possessed characteristics of heterotrophic nitrifiers. All were aerobic, mesophilic gram-negative rods with a unfermentative metabolism and 88% were nitrate reducers or denitrifiers. They were characterized by a high physiological and nutritional diversity, and because of their ability to ammonify, nitrify, and reduce nitrate, they could largely contribute to the nitrogen cycle in hydrothermal sites.Key words: hydrothermal vents, heterotrophic bacteria, nitrifying activity.
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Ben-Mlih F, Marty JC, Fiala-Médioni A. Fatty acid composition in deep hydrothermal vent symbiotic bivalves. J Lipid Res 1992. [DOI: 10.1016/s0022-2275(20)41337-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Lutz RA, Fritz LW, Cerrato RM. A comparison of bivalve (Calyptogena magnifica) growth at two deep-sea hydrothermal vents in the eastern Pacific. ACTA ACUST UNITED AC 1988. [DOI: 10.1016/0198-0149(88)90050-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Amino acid compositions of periostracal proteins from molluscs living in the vicinity of deep sea hydrothermal vents: an unusual methionine-rich structural protein. ACTA ACUST UNITED AC 1987. [DOI: 10.1016/0305-0491(87)90278-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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26
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Bonar DB, Weiner RM, Colwell RR. Microbial-invertebrate interactions and potential for biotechnology. MICROBIAL ECOLOGY 1986; 12:101-110. [PMID: 24212460 DOI: 10.1007/bf02153225] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
As the interactions between marine invertebrates and their bacterial commensals and symbionts are better understood, the application of biotechnology will enhance both environmental and economic benefit. In the immediate future, marine bacteria, either selected or genetically engineered, will play a significant role in enhancing the development of selected invertebrates in aquaculture and in the field. Luck may also favor discovery of mechanisms to suppress the development of biofouling species, perhaps by making it possible to coat submerged surfaces with bacterial films designed to repell larvae and/or interfere with larval morphogenesis. In any case, the future is appealing.
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Affiliation(s)
- D B Bonar
- Department of Zoology, University of Maryland, 20742, College Park, Maryland, USA
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Berg CJ, Krzynowek J, Alatalo P, Wiggin K. Sterol and fatty acid composition of the clam, Codakia orbicularis, with chemoautotrophic symbionts. Lipids 1985; 20:116-20. [PMID: 3982234 DOI: 10.1007/bf02534217] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Codakia orbicularis may obtain nutrients from chemoautolithotrophic bacteria. The chemical composition of the C. orbicularis was investigated because of this unusual source of nutrition, and because it is a human food source in the Caribbean. The lipid fraction of these molluscs is discussed in detail. Polyunsaturated fatty acids account for only 11-15% of the total fatty acids, and non-methylene interrupted dienes are present as high as 9.5%. Cholesterol represents about 45% of the total sterols present.
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Powell MA, Somero GN. Blood Components Prevent Sulfide Poisoning of Respiration of the Hydrothermal Vent Tube Worm Riftia pachyptila. Science 1983; 219:297-9. [PMID: 17798280 DOI: 10.1126/science.219.4582.297] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Respiration of plume tissue of the hydrothermal vent tube worm Riftia pachyptila is insensitive to sulfide poisoning in contrast to tissues of animals that do not inhabit vents. Permeability barriers may not be responsible for this insensitivity since plume homogenates are also resistant to sulfide poisoning. Cytochrome c oxidase of plume, however, is strongly inhibited by sulfide at concentrations less than 10 microM. Factors present in blood, but not in cytosol, prevent sulfide from inhibiting cytochrome c oxidase. Avoidance of sulfide poisoning of respiration in Riftia pachyptila thus appears to involve a blood-borne factor having a higher sulfide affinity than that of cytochrome c oxidase, with the result that appreciable amounts of free sulfide are prevented from accumulating in the blood and entering the intracellular compartment.
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30
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Felbeck H. Sulfide oxidation and carbon fixation by the gutless clamSolemya reidi: an animal-bacteria symbiosis. J Comp Physiol B 1983. [DOI: 10.1007/bf00689721] [Citation(s) in RCA: 90] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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