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Mitchell JH, Freedman AH, Delaney JA, Girguis PR. Co-expression analysis reveals distinct alliances around two carbon fixation pathways in hydrothermal vent symbionts. Nat Microbiol 2024; 9:1526-1539. [PMID: 38839975 DOI: 10.1038/s41564-024-01704-y] [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: 06/18/2023] [Accepted: 04/19/2024] [Indexed: 06/07/2024]
Abstract
Most autotrophic organisms possess a single carbon fixation pathway. The chemoautotrophic symbionts of the hydrothermal vent tubeworm Riftia pachyptila, however, possess two functional pathways: the Calvin-Benson-Bassham (CBB) and the reductive tricarboxylic acid (rTCA) cycles. How these two pathways are coordinated is unknown. Here we measured net carbon fixation rates, transcriptional/metabolic responses and transcriptional co-expression patterns of Riftia pachyptila endosymbionts by incubating tubeworms collected from the East Pacific Rise at environmental pressures, temperature and geochemistry. Results showed that rTCA and CBB transcriptional patterns varied in response to different geochemical regimes and that each pathway is allied to specific metabolic processes; the rTCA is allied to hydrogenases and dissimilatory nitrate reduction, whereas the CBB is allied to sulfide oxidation and assimilatory nitrate reduction, suggesting distinctive yet complementary roles in metabolic function. Furthermore, our network analysis implicates the rTCA and a group 1e hydrogenase as key players in the physiological response to limitation of sulfide and oxygen. Net carbon fixation rates were also exemplary, and accordingly, we propose that co-activity of CBB and rTCA may be an adaptation for maintaining high carbon fixation rates, conferring a fitness advantage in dynamic vent environments.
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2
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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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3
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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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4
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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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5
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Breusing C, Schultz DT, Sudek S, Worden AZ, Young CR. High‐contiguity genome assembly of the chemosynthetic gammaproteobacterial endosymbiont of the cold seep tubeworm
Lamellibrachia barhami. Mol Ecol Resour 2020. [PMCID: PMC7540712 DOI: 10.1111/1755-0998.13220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Symbiotic relationships between vestimentiferan tubeworms and chemosynthetic Gammaproteobacteria build the foundations of many hydrothermal vent and hydrocarbon seep ecosystems in the deep sea. The association between the vent tubeworm Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone has become a model system for symbiosis research in deep‐sea vestimentiferans, while markedly fewer studies have investigated symbiotic relationships in other tubeworm species, especially at cold seeps. Here we sequenced the endosymbiont genome of the tubeworm Lamellibrachia barhami from a cold seep in the Gulf of California, using short‐ and long‐read sequencing technologies in combination with Hi‐C and Dovetail Chicago libraries. Our final assembly had a size of ~4.17 MB, a GC content of 54.54%, 137X coverage, 4153 coding sequences, and a checkm completeness score of 97.19%. A single scaffold contained 99.51% of the genome. Comparative genomic analyses indicated that the L. barhami symbiont shares a set of core genes and many metabolic pathways with other vestimentiferan symbionts, while containing 433 unique gene clusters that comprised a variety of transposases, defence‐related genes and a lineage‐specific CRISPR/Cas3 system. This assembly represents the most contiguous tubeworm symbiont genome resource to date and will be particularly valuable for future comparative genomic studies investigating structural genome evolution, physiological adaptations and host‐symbiont communication in chemosynthetic animal‐microbe symbioses.
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Affiliation(s)
- Corinna Breusing
- Monterey Bay Aquarium Research Institute Moss Landing CA USA
- National Oceanography Centre Southampton UK
| | - Darrin T. Schultz
- Monterey Bay Aquarium Research Institute Moss Landing CA USA
- Department of Biomolecular Engineering and Bioinformatics University of California Santa Cruz Santa Cruz CA USA
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute Moss Landing CA USA
| | - Alexandra Z. Worden
- Monterey Bay Aquarium Research Institute Moss Landing CA USA
- GEOMAR Helmholtz Centre for Ocean Research Kiel Germany
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6
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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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7
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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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8
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Teske A, McKay LJ, Ravelo AC, Aiello I, Mortera C, Núñez-Useche F, Canet C, Chanton JP, Brunner B, Hensen C, Ramírez GA, Sibert RJ, Turner T, White D, Chambers CR, Buckley A, Joye SB, Soule SA, Lizarralde D. Characteristics and Evolution of sill-driven off-axis hydrothermalism in Guaymas Basin - the Ringvent site. Sci Rep 2019; 9:13847. [PMID: 31554864 PMCID: PMC6761151 DOI: 10.1038/s41598-019-50200-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/09/2019] [Indexed: 01/17/2023] Open
Abstract
The Guaymas Basin spreading center, at 2000 m depth in the Gulf of California, is overlain by a thick sedimentary cover. Across the basin, localized temperature anomalies, with active methane venting and seep fauna exist in response to magma emplacement into sediments. These sites evolve over thousands of years as magma freezes into doleritic sills and the system cools. Although several cool sites resembling cold seeps have been characterized, the hydrothermally active stage of an off-axis site was lacking good examples. Here, we present a multidisciplinary characterization of Ringvent, an ~1 km wide circular mound where hydrothermal activity persists ~28 km northwest of the spreading center. Ringvent provides a new type of intermediate-stage hydrothermal system where off-axis hydrothermal activity has attenuated since its formation, but remains evident in thermal anomalies, hydrothermal biota coexisting with seep fauna, and porewater biogeochemical signatures indicative of hydrothermal circulation. Due to their broad potential distribution, small size and limited life span, such sites are hard to find and characterize, but they provide critical missing links to understand the complex evolution of hydrothermal systems.
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Affiliation(s)
- Andreas Teske
- University of North Carolina at Chapel Hill, Department of Marine Sciences, Chapel Hill, USA.
| | - Luke J McKay
- University of North Carolina at Chapel Hill, Department of Marine Sciences, Chapel Hill, USA.,Montana State University, Center for Biofilm Engineering, Bozeman, USA
| | - Ana Christina Ravelo
- University of California at Santa Cruz, Department of Ocean Sciences, Santa Cruz, USA
| | - Ivano Aiello
- San Jose State University, Moss Landing Marine Laboratory, Moss Landing, USA
| | - Carlos Mortera
- Universidad Nacional Autónoma de México, Instituto de Geofísica, Mexico City, Mexico
| | | | - Carles Canet
- Universidad Nacional Autónoma de México, Instituto de Geofísica, Mexico City, Mexico.,Universidad Nacional Autónoma de México, Centro de Ciencias de la Atmósfera, Mexico City, Mexico
| | - Jeffrey P Chanton
- Florida State University, Department of Earth, Ocean and Atmospheric Sciences, Tallahassee, USA
| | - Benjamin Brunner
- The University of Texas at El Paso, Department of Geological Sciences, El Paso, USA
| | | | - Gustavo A Ramírez
- University of North Carolina at Chapel Hill, Department of Marine Sciences, Chapel Hill, USA
| | - Ryan J Sibert
- University of Georgia, Department of Marine Sciences, Athens, USA
| | - Tiffany Turner
- University of North Carolina at Chapel Hill, Department of Marine Sciences, Chapel Hill, USA
| | - Dylan White
- University of North Carolina at Chapel Hill, Department of Marine Sciences, Chapel Hill, USA
| | - Christopher R Chambers
- University of North Carolina at Chapel Hill, Department of Marine Sciences, Chapel Hill, USA
| | - Andrew Buckley
- University of North Carolina at Chapel Hill, Department of Marine Sciences, Chapel Hill, USA
| | - Samantha B Joye
- University of Georgia, Department of Marine Sciences, Athens, USA
| | - S Adam Soule
- Woods Hole Oceanographic Institution, Geology & Geophysics Department, Woods Hole, USA
| | - Daniel Lizarralde
- Woods Hole Oceanographic Institution, Geology & Geophysics Department, Woods Hole, USA
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9
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Buckley A, MacGregor B, Teske A. Identification, Expression and Activity of Candidate Nitrite Reductases From Orange Beggiatoaceae, Guaymas Basin. Front Microbiol 2019; 10:644. [PMID: 30984153 PMCID: PMC6449678 DOI: 10.3389/fmicb.2019.00644] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/14/2019] [Indexed: 11/13/2022] Open
Abstract
Orange filamentous Beggiatoaceae form massive microbial mats on hydrothermal sediments in Guaymas Basin; these bacteria are considered to oxidize sulfide with nitrate and nitrite as electron acceptors. From a previously analyzed genome of an orange Beggiatoaceae filament, three candidate genes for enzymes with nitrite-reducing function - an orange octaheme cytochrome, a nirS nitrite reductase, and a nitrite/tetrathionate-reducing octaheme cytochrome - were cloned and expressed in Escherichia coli. The expressed and purified orange cytochrome showed reduced nitrite-reducing activity compared to the multifunctional native protein obtained from microbial mats. The nirS gene product showed in vitro but no in-gel nitrite-reducing activity; and the nitrite/tetrathionate-reducing octaheme cytochrome was capable of reducing both nitrite and tetrathionate in vitro. Phylogenetic analysis shows that the orange Beggiatoaceae nirS, in contrast to the other candidate nitrite reductases, does not form monophyletic lineages with its counterparts in other large sulfur-oxidizing bacteria, and most likely represents a recent acquisition by lateral gene transfer. The nitrite/tetrathionate-reducing enzyme of the orange Beggiatoaceae is related to nitrite- and tetrathionate reductases harbored predominantly by Gammaproteobacteria, including obligate endosymbionts of hydrothermal vent tubeworms. Thus, the orange Guaymas Basin Beggiatoaceae have a repertoire of at least three different functional enzymes for nitrite reduction. By demonstrating the unusual diversity of enzymes with a potential role in nitrite reduction, we show that bacteria in highly dynamic, sulfide-rich hydrothermal vent habitats adapt to these conditions that usually prohibit nitrate and nitrite reduction. In the case of the orange Guaymas Beggiatoaceae, classical denitrification appears to be replaced by different multifunctional enzymes for nitrite and tetrathionate reduction; the resulting ecophysiological flexibility provides a new key to the dominance of these Beggiatoaceae in hydrothermal hot spots.
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Affiliation(s)
- Andrew Buckley
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Barbara MacGregor
- Department of Earth Sciences, College of Science and Engineering, University of Minnesota, Minneapolis, MN, United States
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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10
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Seston SL, Beinart RA, Sarode N, Shockey AC, Ranjan P, Ganesh S, Girguis PR, Stewart FJ. Metatranscriptional Response of Chemoautotrophic Ifremeria nautilei Endosymbionts to Differing Sulfur Regimes. Front Microbiol 2016; 7:1074. [PMID: 27486438 PMCID: PMC4949241 DOI: 10.3389/fmicb.2016.01074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/27/2016] [Indexed: 12/26/2022] Open
Abstract
Endosymbioses between animals and chemoautotrophic bacteria are ubiquitous at hydrothermal vents. These environments are distinguished by high physico-chemical variability, yet we know little about how these symbioses respond to environmental fluctuations. We therefore examined how the γ-proteobacterial symbionts of the vent snail Ifremeria nautilei respond to changes in sulfur geochemistry. Via shipboard high-pressure incubations, we subjected snails to 105 μM hydrogen sulfide (LS), 350 μM hydrogen sulfide (HS), 300 μM thiosulfate (TS) and seawater without any added inorganic electron donor (ND). While transcript levels of sulfur oxidation genes were largely consistent across treatments, HS and TS treatments stimulated genes for denitrification, nitrogen assimilation, and CO2 fixation, coincident with previously reported enhanced rates of inorganic carbon incorporation and sulfur oxidation in these treatments. Transcripts for genes mediating oxidative damage were enriched in the ND and LS treatments, potentially due to a reduction in O2 scavenging when electron donors were scarce. Oxidative TCA cycle gene transcripts were also more abundant in ND and LS treatments, suggesting that I. nautilei symbionts may be mixotrophic when inorganic electron donors are limiting. These data reveal the extent to which I. nautilei symbionts respond to changes in sulfur concentration and species, and, interpreted alongside coupled biochemical metabolic rates, identify gene targets whose expression patterns may be predictive of holobiont physiology in environmental samples.
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Affiliation(s)
| | - Roxanne A Beinart
- Department of Organismic and Evolutionary Biology, Harvard University Cambridge, MA, USA
| | - Neha Sarode
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Abigail C Shockey
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA
| | - Piyush Ranjan
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Sangita Ganesh
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University Cambridge, MA, USA
| | - Frank J Stewart
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
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11
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Williams TJ, Cavicchioli R. Marine metaproteomics: deciphering the microbial metabolic food web. Trends Microbiol 2014; 22:248-60. [PMID: 24731505 DOI: 10.1016/j.tim.2014.03.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 03/12/2014] [Accepted: 03/12/2014] [Indexed: 10/25/2022]
Abstract
Metaproteomics can be applied to marine systems to discover metabolic processes in the ocean. This review describes current breakthroughs regarding marine microbes in the areas of microbial procurement of nutrients, important and previously unrecognized metabolic processes, functional roles for proteins with previously unknown functions, and intricate networks of metabolic interactions between symbiotic microbes and their hosts. By recognizing that metaproteomics empowers our understanding of the roles that marine microbes play in global biogeochemical cycles, the achievements to date from this advancing field highlight the enormous potential that the future holds.
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Affiliation(s)
- Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales 2052, Australia.
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12
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Liao L, Wankel SD, Wu M, Cavanaugh CM, Girguis PR. Characterizing the plasticity of nitrogen metabolism by the host and symbionts of the hydrothermal vent chemoautotrophic symbioses Ridgeia piscesae. Mol Ecol 2013; 23:1544-1557. [PMID: 24237389 DOI: 10.1111/mec.12460] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 06/26/2013] [Accepted: 06/27/2013] [Indexed: 11/30/2022]
Abstract
Chemoautotrophic symbionts of deep sea hydrothermal vent tubeworms are known to provide their hosts with all their primary nutrition. While studies have examined how chemoautotrophic symbionts provide the association with nitrogen, fewer have examined if symbiont nitrogen metabolism varies as a function of environmental conditions. Ridgeia piscesae tubeworms flourish at Northeastern Pacific vents, occupy a range of microhabitats, and exhibit a high degree of morphological plasticity [e.g. long-skinny (LS) and short-fat (SF) phenotypes] that may relate to environmental conditions. This plasticity affords an opportunity to examine whether symbiont nitrogen metabolism varies among host phenotypes. LS and SF R. piscesae were recovered from the Axial and Main Endeavour Field hydrothermal vents. Nitrate and ammonium were quantified in Ridgeia blood, and the expression of key nitrogen metabolism genes, as well as stable nitrogen isotope ratios, was quantified in host branchial plume and symbiont-containing tissues. Nitrate and ammonium were abundant in the blood of both phenotypes though environmental ammonium concentrations were, paradoxically, lowest among individuals with the highest blood ammonium. Assimilatory nitrate reductase transcripts were always below detection, though in both LS and SF R. piscesae symbionts, we observed elevated expression of dissimilatory nitrate reductase genes, as well as symbiont and host ammonium assimilation genes. Site-specific differences in expression, along with tissue stable isotope analyses, suggest that LS and SF Ridgeia symbionts are engaged in both dissimilatory nitrate reduction and ammonia assimilation to varying degrees. As such, it appears that environmental conditions -not host phenotype-primarily dictates symbiont nitrogen metabolism.
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Affiliation(s)
- Li Liao
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge, MA, 02138-2020, USA; SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, 200136, China
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13
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Pérez-Rodríguez I, Bohnert KA, Cuebas M, Keddis R, Vetriani C. Detection and phylogenetic analysis of the membrane-bound nitrate reductase (Nar) in pure cultures and microbial communities from deep-sea hydrothermal vents. FEMS Microbiol Ecol 2013; 86:256-67. [PMID: 23889124 DOI: 10.1111/1574-6941.12158] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 05/17/2013] [Accepted: 06/04/2013] [Indexed: 11/28/2022] Open
Abstract
Over the past few years the relevance of nitrate respiration in microorganisms from deep-sea hydrothermal vents has become evident. In this study, we surveyed the membrane-bound nitrate reductase (Nar) encoding gene in three different deep-sea vent microbial communities from the East Pacific Rise and the Mid-Atlantic Ridge. Additionally, we tested pure cultures of vent strains for their ability to reduce nitrate and for the presence of the NarG-encoding gene in their genomes. By using the narG gene as a diagnostic marker for nitrate-reducing bacteria, we showed that nitrate reductases related to Gammaproteobacteria of the genus Marinobacter were numerically prevalent in the clone libraries derived from a black smoker and a diffuse flow vent. In contrast, NarG sequences retrieved from a community of filamentous bacteria located about 50 cm above a diffuse flow vent revealed the presence of a yet to be identified group of enzymes. 16S rRNA gene-inferred community compositions, in accordance with previous studies, showed a shift from Alpha- and Gammaproteobacteria to Epsilonproteobacteria as the vent fluids become warmer and more reducing. Based on these findings, we argue that Nar-catalyzed nitrate reduction is likely relevant in temperate and less reducing environments where Alpha- and Gammaproteobacteria are more abundant and where nitrate concentrations reflect that of background deep seawater.
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Affiliation(s)
- Ileana Pérez-Rodríguez
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA; Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
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14
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Metatranscriptomics reveal differences in in situ energy and nitrogen metabolism among hydrothermal vent snail symbionts. ISME JOURNAL 2013; 7:1556-67. [PMID: 23619306 PMCID: PMC3721115 DOI: 10.1038/ismej.2013.45] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 01/31/2013] [Accepted: 02/11/2013] [Indexed: 01/04/2023]
Abstract
Despite the ubiquity of chemoautotrophic symbioses at hydrothermal vents, our understanding of the influence of environmental chemistry on symbiont metabolism is limited. Transcriptomic analyses are useful for linking physiological poise to environmental conditions, but recovering samples from the deep sea is challenging, as the long recovery times can change expression profiles before preservation. Here, we present a novel, in situ RNA sampling and preservation device, which we used to compare the symbiont metatranscriptomes associated with Alviniconcha, a genus of vent snail, in which specific host-symbiont combinations are predictably distributed across a regional geochemical gradient. Metatranscriptomes of these symbionts reveal key differences in energy and nitrogen metabolism relating to both environmental chemistry (that is, the relative expression of genes) and symbiont phylogeny (that is, the specific pathways employed). Unexpectedly, dramatic differences in expression of transposases and flagellar genes suggest that different symbiont types may also have distinct life histories. These data further our understanding of these symbionts' metabolic capabilities and their expression in situ, and suggest an important role for symbionts in mediating their hosts' interaction with regional-scale differences in geochemistry.
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15
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Bright M, Eichinger I, von Salvini-Plawen L. The metatrochophore of a deep-sea hydrothermal vent vestimentiferan (Polychaeta: Siboglinidae). ORG DIVERS EVOL 2012; 13:163-188. [PMID: 26074729 PMCID: PMC4461187 DOI: 10.1007/s13127-012-0117-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 11/03/2012] [Indexed: 01/02/2023]
Abstract
Vestimentiferans (Siboglinidae, Polychaeta) live as juveniles and adults in an obligate mutualistic association with thiotrophic bacteria. Since their development is aposymbiotic, metatrochophores of vestimentiferans from the East Pacific Rise colonizing deep-sea hydrothermal vents are infected with the specific symbiont, develop the trophosome, and reduce their digestive system. To gain insight into the anatomy and ultrastructure and to compare this stage with metatrochophores from other siboglinids, we serial sectioned and reconstructed three specimens using light and transmission electron microscopy. The metatrochophore was composed of a prostomium, a small peristomium, two chaetigers (or two chaetigers and one additional segment without chaetae), and a minute pygidium. A digestive system and an intraepidermal nervous system were developed. Larval organs such as the prototroch, the neurotroch, and an apical organ were present, along with juvenile/adult organs such as tentacles, uncini, pyriform glands, and the anlage of the nephridial organ. We propose that in vestimentiferans, the vestimentum is the head arising from the prostomium, peristomium, and the anterior part of the first chaetiger. In frenulates, in contrast, the head is composed on the one hand of the cephalic lobe arising from the prostomium and on the other of the forepart developing from the peristomium and the anterior part of the first chaetiger. In frenulates the muscular septum between the forepart and trunk develops later than the first two chaetigers. Since this septum has no counterpart in vestimentiferans, the forepart-trunk border of frenulates is not considered homologous with the vestimentum-trunk border in vestimentiferans. The obturacular region in vestimentiferans does not appear to be a body region but rather the head appendages arising from the first chaetiger. In contrast, the tentacles in frenulates are prostomial head appendages. In both taxa, the trunk is the posterior part of the first chaetiger, and the opisthosoma is the following chaetigers and the pygidium. Comparisons with other polychaetes suggest that two larval segments are autapomorphic for the monophyletic Siboglinidae.
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Affiliation(s)
- Monika Bright
- Department of Marine Biology, University of Vienna, Althanstr. 14, 1090 Vienna, Austria
| | - Irmgard Eichinger
- Department of Marine Biology, University of Vienna, Althanstr. 14, 1090 Vienna, Austria
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16
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Kleiner M, Petersen JM, Dubilier N. Convergent and divergent evolution of metabolism in sulfur-oxidizing symbionts and the role of horizontal gene transfer. Curr Opin Microbiol 2012; 15:621-31. [DOI: 10.1016/j.mib.2012.09.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 09/17/2012] [Accepted: 09/19/2012] [Indexed: 10/27/2022]
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17
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Nyholm SV, Song P, Dang J, Bunce C, Girguis PR. Expression and putative function of innate immunity genes under in situ conditions in the symbiotic hydrothermal vent tubeworm Ridgeia piscesae. PLoS One 2012; 7:e38267. [PMID: 22701617 PMCID: PMC3372519 DOI: 10.1371/journal.pone.0038267] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 05/05/2012] [Indexed: 11/19/2022] Open
Abstract
The relationships between hydrothermal vent tubeworms and sulfide-oxidizing bacteria have served as model associations for understanding chemoautotrophy and endosymbiosis. Numerous studies have focused on the physiological and biochemical adaptations that enable these symbioses to sustain some of the highest recorded carbon fixation rates ever measured. However, far fewer studies have explored the molecular mechanisms underlying the regulation of host and symbiont interactions, specifically those mediated by the innate immune system of the host. To that end, we conducted a series of studies where we maintained the tubeworm, Ridgeia piscesae, in high-pressure aquaria and examined global and quantitative changes in gene expression via high-throughput transcriptomics and quantitative real-time PCR (qPCR). We analyzed over 32,000 full-length expressed sequence tags as well as 26 Mb of transcript sequences from the trophosome (the organ that houses the endosymbiotic bacteria) and the plume (the gas exchange organ in contact with the free-living microbial community). R. piscesae maintained under conditions that promote chemoautotrophy expressed a number of putative cell signaling and innate immunity genes, including pattern recognition receptors (PRRs), often associated with recognizing microbe-associated molecular patterns (MAMPs). Eighteen genes involved with innate immunity, cell signaling, cell stress and metabolite exchange were further analyzed using qPCR. PRRs, including five peptidoglycan recognition proteins and a Toll-like receptor, were expressed significantly higher in the trophosome compared to the plume. Although PRRs are often associated with mediating host responses to infection by pathogens, the differences in expression between the plume and trophosome also implicate similar mechanisms of microbial recognition in interactions between the host and symbiont. We posit that regulation of this association involves a molecular "dialogue" between the partners that includes interactions between the host's innate immune system and the symbiont.
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Affiliation(s)
- Spencer V. Nyholm
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
- * E-mail: (SVN); (PRG)
| | - Pengfei Song
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Jeanne Dang
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Corey Bunce
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Peter R. Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail: (SVN); (PRG)
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