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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Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402.
Arp AJ, Childress JJ . (1983). Sulfide binding by the blood of the hydrothermal vent tube worm Riftia pachyptila. Science 219: 295–297.
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA et al. (2008). The RAST server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
Bhakdi S, Tranum-Jensen J . (1991). Alpha-toxin of Staphylococcus aureus. Microbiol Rev 55: 733–751.
Ballal A, Manna AC . (2010). Control of thioredoxin reductase gene (trxB) transcription by SarA in Staphylococcus aureus. J Bacteriol 192: 336–345.
Blum J, Fridovich I . (1984). Enzymatic defenses against oxygen toxicity in the hydrothermal vent animals Riftia pachyptila and Calyptogena magnifica. Arch Biochem Biophys 228: 617–620.
Bright M, Bulgheresi S . (2010). A complex journey: transmission of microbial symbionts. Nat Rev 8: 218–230.
Bright M, Sorgo A . (2003). Ultrastructural reinvestigation of the trophosome of adults of Riftia pachyptila (Annelida, Siboglinidae). Invertebr Biol 122: 345–366.
Cary SC, Warren W, Anderson E, Giovannoni SJ . (1993). Identification and localization of bacterial endosymbionts in hydrothermal vent taxa with symbiont-specific polymerase chain reaction amplification and in situ hybridization techniques. Mol Mar Biol Biotechnol 2: 51–62.
Cavanaugh CM, Gardiner SL, Jones ML, Jannasch HW, Waterbury JB . (1981). Prokaryotic cells in the hydrothermal vent tube worm Riftia pachyptila Jones: possible chemoautotrophic symbionts. Science 213: 340–342.
Childress JJ, Fisher CR, Favuzzi JA, Kochevar RE, Sanders NK, Alayse AM . (1991). Sulfide-driven autotrophic balance in the bacterial symbiont-containing hydrothermal vent tubeworm, Riftia pachyptila Jones. Biol Bull 180: 135–153.
Cowen JP, Fornari DJ, Shank TM, Love B, Glazer B, Treuch AH et al. (2007). Volcanic eruptions at East Pacific Rise near 9°50′N. EOS Trans Am Geophys Un 88: 81–83.
Dahl C, Schulte A, Stockdreher Y, Hong C, Grimm F, Sander J et al. (2008). Structural and molecular genetic insight into a widespread sulfur oxidation pathway. J Mol Biol 384: 1287–1300.
Di Meo CA, Wilbur AE, Holben WE, Feldman RA, Vrijenhoek RC, Cary SC . (2000). Genetic variation among endosymbionts of widely distributed vestimentiferan tubeworms. Appl Environ Microbiol 66: 651–658.
Distel DL, Felbeck H . (1988). Pathways of inorganic carbon fixation in the endosymbiont-bearing lucinid clam Lucinoma aequizonata. J Exp Zool 247: 1–10.
Distel DL, Lane DJ, Olsen GJ, Giovannoni SJ, Pace B, Pace NR et al. (1988). Sulfur-oxidizing bacterial endosymbionts: analysis of phylogeny and specificity by 16S rRNA sequences. J Bacteriol 170: 2506–2510.
Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Duran C et al. (2010) Geneious v5.3, Available from http://www.geneious.com/.
Edwards DB, Nelson DC . (1991). DNA-DNA solution hybridization studies of the bacterial symbionts of hydrothermal vent tube worms (Riftia pachyptila and Tevnia jerichonana). Appl Environ Microbiol 57: 1082–1088.
Felbeck H . (1981). Chemoautotrophic potential of the hydrothermal vent tube worm Riftia pachyptila Jones (Vestimentifera). Science 213: 336–338.
Felbeck H, Jarchow J . (1998). Carbon release from purified chemoautotrophic bacterial symbionts of the hydrothermal vent tubeworm Riftia pachyptila. Physiol Biochem Zool 71: 294–302.
Felbeck H, Somero GN . (1982). Primary production in deep-sea hydrothermal vent organisms: roles of sulfide-oxidizing bacteria. Trends Biochemical Sci 7: 201–204.
Feldman RA, Black MB, Cary CS, Lutz RA, Vrijenhoek RC . (1997). Molecular phylogenetics of bacterial endosymbionts and their vestimentiferan hosts. Mol Mar Biol Biotechnol 6: 268–277.
Fisher CR, Childress JJ . (1984). Substrate oxidation by trophosome tissue from Riftia pachyptila Jones (phylum pogonophora). Mar Biol Lett 5: 171–183.
Fisher CR, Childress JJ, Minich E . (1989). Autotrophic carbon fixation by the chemoautotrophic symbionts of Riftia pachyptila. Biol Bull 177: 372–385.
Girguis PR, Childress JJ . (2006). Metabolite uptake, stoichiometry and chemoautotrophic function of the hydrothermal vent tubeworm Riftia pachyptila: responses to environmental variations in substrate concentrations and temperature. J Exp Biol 209: 3516–3528.
Girguis PR, Raymond WL, Desaulniers N, Childress JJ, Pospesel M et al. (2000). Fate of nitrate acquired by the tubeworm Riftia pachyptila. Appl Environ Microbiol 66: 2783–2790.
Hand SC . (1987). Trophosome ultrastructure and the characterization of isolated bacteriocytes from invertebrate-sulfur bacteria symbioses. Biol Bull 173: 260–276.
Harmer TL, Rotjan RD, Nussbaumer AD, Bright M, Ng AW, DeChaine EG et al. (2008). Free-living tube worm endosymbionts found at deep-sea vents. Appl Environ Microbiol 74: 3895–3898.
Haymon RM, Fornari DJ, Von Damm KL, Lilley MD, Perfit MR, Edmond JM et al. (1993). Volcanic eruption of the mid-ocean ridge along the East Pacific Rise crest at 9°45-52′N: Direct submersible observations of seafloor phenomena associated with an eruption event in April, 1991. Earth Planet Sc Lett 119: 85–101.
Helmann JD, Wu MF, Gaballa A, Kobel PA, Morshedi MM, Fawcett P et al. (2003). The global transcriptional response of Bacillus subtilis to peroxide stress is coordinated by three transcriptional factors. J Bacteriol 185: 243–253.
Hentschel U, Felbeck H . (1993). Nitrate respiration in the hydrothermal vent worm Riftia pachyptila. Nature 366: 338–340.
Hessler RR, Smithey WM, Boudrias MA, Keller CH, Lutz RA, Childress JJ . (1988). Temporal change in megafauna at the Rose Garden hydrothermal vent (Galapagos Rift; eastern tropical Pacific). Deep Sea Res 35: 1681–1709.
Inglis TJJ, Robertson T, Woods DE, Dutton N, Chang BJ . (2003). Flagellum-mediated adhesion by Burkholderia pseudomallei precedes invasion of Acanthamoeba astronyxis. Infect Immun 71: 2280–2282.
Johnson KS . (1988). Chemical and biological interactions in the Rose Garden hydrothermal field, Galapagos spreading center. Deep Sea Res Pt A 35: 1723–1744.
Jones ML . (1981a). Riftia pachyptila, new genus, new species, the vestimentiferan worm from the Galápagos Rift geothermal vents (Pogonophora). Proc Biol Soc Wash 93: 1295–1313.
Jones ML . (1981b). Riftia pachyptila Jones: observations on the vestimentiferan worm from the Galápagos Rift. Science 213: 333–336.
Jones ML . (1985). On the Vestimentifera, new phylum: six new species and other taxa from hydrothermal vents and elsewhere. Bull Biol Soc Wash 6: 117–158.
Krehenbrink M, Oppermann-Sanio FB, Steinbüchel A . (2002). Evaluation of non-cyanobacterial genome sequences for occurrence of genes encoding proteins homologous to cyanophycin synthetase and cloning of an active cyanophycin synthetase from Acinetobacter sp. strain DSM 587. Arch Microbiol 177: 371–380.
Le Bris N, Govenar B, Le Gall C, Fisher CR . (2006). Variability of physico-chemical conditions in 9°N EPR diffuse flow vent habitat. Mar Chem 98: 167–182.
Le Bris N, Sarradin PM, Pennec S . (2001). A new deep-sea probe for in situ pH measurement in the environment of hydrothermal vent biological communities. Deep Sea Res Pt I 48: 1941–1951.
Lee RW, Childress JJ . (1994). Assimilation of inorganic nitrogen by marine invertebrates and their chemoautotrophic and methanotrophic symbionts. Appl Environ Microbiol 60: 1852–1858.
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376–380.
Markert S, Arndt C, Felbeck H, Becher D, Sievert SM, Hügler M et al. (2007). Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila. Science 315: 247–250.
Markert S, Gardebrecht A, Felbeck H, Sievert SM, Klose J, Becher D et al. (2011). Status quo in physiological proteomics of the uncultured Riftia pachyptila endosymbiont. Proteomics 11: 3106–3117.
Moore TS, Shank TM, Nuzzio DB, Luther III GW . (2009). Time-series chemical and temperature habitat characterization of diffuse flow hydrothermal sites at 9°50′N East Pacific Rise. Deep Sea Res Pt II: Topical Stud Oceanograph 56: 1616–1621.
Mullineaux LS, Fisher CR, Peterson CH, Schaeffer SW . (2000). Tubeworm succession at hydrothermal vents: use of biogenic cues to reduce habitat selection error? Oecologia 123: 275–284.
Needleman SB, Wunsch CD . (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443–453.
Nees HA, Lutz RA, Shank TM, Luther GW . (2009). Pre- and post-eruption diffuse flow variability among tubeworm habitats at 9°50′ north on the East Pacific Rise. Deep Sea Res II 56: 1607–1615.
Nussbaumer AD, Fisher CR, Bright M . (2006). Horizontal endosymbiont transmission in hydrothermal vent tubeworms. Nature 441: 345–348.
Pflugfelder B, Fisher CR, Bright M . (2005). The color of the trophosome: elemental sulfur distribution in the endosymbionts of Riftia pachyptila (Vestimentifera; Siboglinidae). Mar Biol 146: 895–901.
Pleijel F, Dahlgren TG, Rouse GW . (2009). Progress in systematics: from Siboglinidae to Pogonophora and Vestimentifera and back to Siboglinidae. Comp Rend Biol 332: 140–148.
Pospesel MA, Hentschel U, Felbeck H . (1998). Determination of nitrate in the blood of the hydrothermal vent tubeworm Riftia pachyptila using a bacterial nitrate reduction assay. Deep Sea Res Pt I Oceanograph Res Papers 45: 2189–2200.
Rickard D, Luther III GW . (2007). Chemistry of iron sulfides. Chem Rev 107: 514–562.
Robidart JC, Bench SR, Feldman RA, Novoradovsky A, Podell SB, Gaasterland T et al. (2008). Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics. Environ Microbiol 3: 121–126.
Shank TM, Fornari DJ, Von Damm KL, Lilley MD, Haymon RM, Lutz RA . (1998). Temporal and spatial patterns of biological community development at nascent deep-sea hydrothermal vents (9°50′ N, East Pacific Rise). Deep Sea Res II 45: 465–515.
Shank TM, Govenar B, Buckman K, Fornari DJ, Soule SA, Luther GW et al. (2006). Initial biological, chemical and geological observations after the 2005–6 volcanic eruption on the East Pacific Rise. EOS Trans Am Geophys Un 87, Fall Meet. Suppl., Abstract V13C-04..
Sorgo A, Gaill F, Lechaire JP, Arndt C, Bright M . (2002). Glycogen storage in the Riftia pachyptila trophosome: contribution of host and symbionts. Mar Ecol Prog Ser 231: 115–120.
Stewart FJ, Cavanaugh CM . (2006). Symbiosis of thioautotrophic bacteria with Riftia pachyptila. Prog Mol Subcell Biol 41: 197–225.
Stewart V, Lu Y, Darwin AJ . (2002). Periplasmic nitrate reductase (NapABC enzyme) supports anaerobic respiration by Escherichia coli K-12. J Bacteriol 184: 1314–1323.
Thornhill DJ, Fielmann KT, Santos SR, Halanych KM . (2008). Siboglinid-bacteria endosymbiosis: a model system for studying symbiotic mechanisms. Commun Integr Biol 1: 163–166.
Toft C, Anderson SGE . (2010). Evolutionary microbial genomics: insights into bacterial host adaptation. Nat Rev Genet 11: 465–475.
Tolstoy M, Cowen JP, Bakter ET, Fornari DJ, Rubin KH, Shank TM et al. (2006). A sea-floor spreading event captured by seismometers. Science 314: 1920–1922.
Von Damm KL . (2000). Chemistry of hydrothermal vent fluids from 9°–10° N, East Pacific Rise. ‘Time zero’, the immediate posteruptive period. J Geophys Res 105: 203–222.
Von Damm KL, Oosting SE, Kozlowski R, Buttermore LG, Colodner DC, Edmonds HN et al. (1995). Evolution of East Pacific Rise hydrothermal vent fluids following a volcanic eruption. Nature 357: 47–50.
Waters VL, Crosa JH . (1991). Colicin V virulence plasmids. Microbiol Rev 55: 437–450.
Ziegler K, Diener A, Herpin C, Richter R, Deutzmann R, Lockau W . (1998). Molecular characterization of cyanophycin synthetase, the enzyme catalyzing the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin). Eur J Biochem 254: 154–159.
Acknowledgements
We are grateful to the captains, crews and pilots of R/V Atlantis and DSV Alvin for their outstanding help in obtaining the samples. The cruises were funded through Grant OCE-0452333 of the US National Science Foundation (NSF) to SMS. Cruise participation of NLB was funded by Ifremer. Development of chemical sensors was supported by Ifremer and CNRS. This work was supported by Grant SCHW 595/3-3 of the Deutsche Forschungsgemeinschaft (DFG) to TS and by the German Federal Ministry of Education and Research (BMBF; reference 03F0480A/B). SMS was supported through NSF and a senior fellowship awarded by the Alfried Krupp Wissenschaftskolleg Greifswald (Germany).
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Gardebrecht, A., Markert, S., Sievert, S. et al. Physiological homogeneity among the endosymbionts of Riftia pachyptila and Tevnia jerichonana revealed by proteogenomics. ISME J 6, 766–776 (2012). https://doi.org/10.1038/ismej.2011.137
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DOI: https://doi.org/10.1038/ismej.2011.137
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