Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels

eLife

Volumn 4, Issue September, 2015, Pages

  Sayavedra, Lizbeth ^a   Kleiner, Manuel ^a   Ponnudurai, Ruby ^b   Wetzel, Silke ^a   Pelletier, Eric ^c,d,j   Barbe, Valerie ^c   Satoh, Nori ^e   Shoguchi, Eiichi ^e   Fink, Dennis ^a   Breusing, Corinna ^f   Reusch, Thorsten B H ^f   Rosenstiel, Philip ^g   Schilhabel, Markus B ^g   Becher, Dörte ^b,h   Schweder, Thomas ^b,h   Markert, Stephanie ^b,h   Dubilier, Nicole ^a,i   Petersen, Jillian M ^a,k  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^b UNIVERSITY OF GREIFSWALD   (Germany)

^c CENTRE NATIONAL DE SÉQUENÇAGE   (France)

^d Metabolic Genomics Group   (France)

^e OKINAWA INSTITUTE OF SCIENCE AND TECHNOLOGY GRADUATE UNIVERSITY   (Japan)

^f GEOMAR HELMHOLTZ CENTRE FOR OCEAN RESEARCH KIEL   (Germany)

^g UNIVERSITY HOSPITAL SCHLESWIG HOLSTEIN   (Germany)

^h Institute of Marine Biotechnology   (Germany)

ⁱ UNIVERSITY OF BREMEN   (Germany)

^j UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

^k UNIVERSITY OF VIENNA   (Austria)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA EXTRACTION; GENE DUPLICATION; GENE EXPRESSION; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; HORIZONTAL GENE TRANSFER; HYDROTHERMAL VENT; LIQUID CHROMATOGRAPHY; METAGENOME; MICROBIAL GENOME; PHYLOGENY; POLYMERASE CHAIN REACTION; PROTEOMICS; SINGLE NUCLEOTIDE POLYMORPHISM; SYMBIONT; SYNTENY; TRANSCRIPTOMICS; VIBRIO; YERSINIA; ANIMAL; AQUATIC SPECIES; BACTERIAL GENOME; BACTERIUM; BIOSYNTHESIS; BIVALVE; CHEMISTRY; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENETICS; GROWTH, DEVELOPMENT AND AGING; MICROBIOLOGY; MOLECULAR GENETICS; SYMBIOSIS;

BACTERIAL DNA; BACTERIAL TOXIN; PROTEOME; SEA WATER;

ANIMALS; AQUATIC ORGANISMS; BACTERIA; BACTERIAL TOXINS; BIVALVIA; DNA, BACTERIAL; GENE EXPRESSION PROFILING; GENOME, BACTERIAL; HYDROTHERMAL VENTS; MOLECULAR SEQUENCE DATA; PROTEOME; SEAWATER; SEQUENCE ANALYSIS, DNA; SYMBIOSIS;

EID: 84945966892     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.07966.001     Document Type: Article

References (176)

1. Achaz G, Coissac E, Netter P, Rocha EPC. 2003. Associations between inverted repeats and the structural evolution of bacterial genomes. Genetics 164:1279-1289.
2. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25:3389-3402. doi: 10.1093/nar/25.17.3389.
3. Anantharaman K, Breier JA, Sheik CS, Dick GJ. 2012. Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria. Proceedings of the National Academy of Sciences of USA 110:330-335. doi: 10.1073/pnas.1215340110.
4. Backert S, Meyer TF. 2006. Type IV secretion systems and their effectors in bacterial pathogenesis. Current Opinion in Microbiology 9:207-217. doi: 10.1016/j.mib.2006.02.008.
5. Badger MR, Bek EJ. 2008. Multiple RuBisCO forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle. Journal of Experimental Botany 59:1525-1541. doi: 10.1093/jxb/erm297.
6. Bailly X, Olivieri I, De Mita S, Cleyet-Marel J-C, Bé na G. 2006. Recombination and selection shape the molecular diversity pattern of nitrogen-fixing Sinorhizobium sp. associated to Medicago. Molecular Ecology 15:2719-2734. doi: 10.1111/j.1365-294X.2006.02969.x.
7. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR. 2004. The Pfam protein families database. Nucleic Acids Research 32:D138-D141. doi: 10.1093/nar/gkh121.
8. Benz J, Meinhart A. 2014. Antibacterial effector/immunity systems: it's just the tip of the iceberg. Current Opinion in Microbiology 17:1-10. doi: 10.1016/j.mib.2013.11.002.
9. Bettencourt R, Roch P, Stefanni S, Rosa D, Colaço A, Serrão Santos R. 2007. Deep sea immunity: unveiling immune constituents from the hydrothermal vent mussel Bathymodiolus azoricus. Marine Environmental Research 64:108-127. doi: 10.1016/j.marenvres.2006.12.010.
10. Bhavsar AP, Guttman JA, Finlay BB. 2007. Manipulation of host-cell pathways by bacterial pathogens. Nature 449:827-834. doi: 10.1038/nature06247.
11. Boeckmann B. 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Research 31:365-370. doi: 10.1093/nar/gkg095.
12. Bradford MM. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Analytical Biochemistry 72:248-254.
13. Brinkhoff T, Giebel H-A, Simon M. 2008. Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Archives of Microbiology 189:531-539. doi: 10.1007/s00203-008-0353-y.
14. Buchan A, González JM, Moran MA. 2005. Overview of the marine roseobacter lineage. Applied and Environment Microbiology 71:5665-5677. doi: 10.1128/AEM.71.10.5665-5677.2005.
15. Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD. 2014. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Research 42:D459-D471. doi: 10.1093/nar/gkt1103.
16. Cavanaugh CM, Robinson JJ. 1996. CO2 fixation in chemoautotroph-invertebrate symbioses: expression of form I and form II RuBisCO. In: Lidstrom ME, Tabita FR, editors. Microbial growth on C1 compounds: Springer Netherlands. p. 285-292.
17. Cavanaugh CM, McKiness ZP, Newton ILG, Stewart FJ. 2006. Marine chemosynthetic symbioses. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E, editors. The Prokaryotes: Springer New York. p. 475-507.
18. Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J, Hoff K, Kessner D, Tasman N, Shulman N, Frewen B, Baker TA, Brusniak MY, Paulse C, Creasy D, Flashner L, Kani K, Moulding C, Seymour SL, Nuwaysir LM, Lefebvre B, Kuhlmann F, Roark J, Rainer P, Detlev S, Hemenway T, Huhmer A, Langridge J, Connolly B, Chadick T, Holly K, Eckels J, Deutsch EW, Moritz RL, Katz JE, Agus DB, MacCoss M, Tabb DL, Mallick P. 2012. A cross-platform toolkit for mass spectrometry and proteomics. Nature Biotechnology 30:918-920. doi: 10.1038/nbt.2377.
19. Christie-Oleza JA, Piña-Villalonga JM, Bosch R, Nogales B, Armengaud J. 2012. Comparative proteogenomics of twelve Roseobacter exoproteomes reveals different adaptive strategies among these marine bacteria. Molecular & Cellular Proteomics 11:M111.013110. doi: 10.1074/mcp.M111.013110.
20. Clayton AL, Oakeson KF, Gutin M, Pontes A, Dunn DM, von Niederhausern AC, Weiss RB, Fisher M, Dale C. 2012. A novel human-infection-derived bacterium provides insights into the evolutionary origins of mutualistic insect-bacterial symbioses. PLOS Genetics 8:e1002990. doi: 10.1371/journal.pgen.1002990.
21. Cossart P, Sansonetti PJ. 2004. Bacterial invasion: the paradigms of enteroinvasive pathogens. Science 304:242-248. doi: 10.1126/science.1090124.
22. Coustau C, Renaud F, Maillard C, Pasteur N, Delay B. 1991. Differential susceptibility to a trematode parasite among genotypes of the Mytilus edulis/galloprovincialis complex. Genetics Research 57:207-212. doi: 10.1017/ S0016672300029359.
23. da Silva PM, Magalhã es AR, Barracco MA. 2002. Effects of Bucephalus sp. (Trematoda: Bucephalidae) on Perna perna mussels from a culture station in Ratones Grande Island, Brazil. Journal of Invertebrate Pathology 79:154-162. doi: 10.1016/S0022-2011(02)00026-5.
24. Dale C, Moran NA. 2006. Molecular interactions between bacterial symbionts and their hosts. Cell 126:453-465. doi: 10.1016/j.cell.2006.07.014.
25. Dale C, Young SA, Haydon DT, Welburn SC. 2001. The insect endosymbiont Sodalis glossinidius utilizes a type III secretion system for cell invasion. Proceedings of the National Academy of Sciences of USA 98:1883-1888. doi: 10.1073/pnas.021450998.
26. Davies RL, Campbell S, Whittam TS. 2002. Mosaic structure and molecular evolution of the leukotoxin operon (lktCABD) in Mannheimia (Pasteurella) haemolytica, Mannheimia glucosida, and Pasteurella trehalosi. Journal of Bacteriology 184:266-277. doi: 10.1128/JB.184.1.266-277.2002.
27. Davis JJ, Olsen GJ. 2010. Characterizing the native codon usages of a genome: an axis projection approach. Molecular Biology and Evolution 28:211-221. doi: 10.1093/molbev/msq185.
28. De Wit P, Pespeni MH, Ladner JT, Barshis DJ, Seneca F, Jaris H, Therkildsen NO, Morikawa M, Palumbi SR. 2012. The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis. Molecular Ecology Resources 12:1058-1067. doi: 10.1111/1755-0998.12003.
29. DeChaine EG, Bates AE, Shank TM, Cavanaugh CM. 2006. Off-axis symbiosis found: characterization and biogeography of bacterial symbionts of Bathymodiolus mussels from Lost City hydrothermal vents. Environmental Microbiology 8:1902-1912. doi: 10.1111/j.1462-2920.2005.01113.x.
30. Degnan PH, Moran NA. 2008. Diverse phage-encoded toxins in a protective insect endosymbiont. Applied and Environmental Microbiology 74:6782-6791. doi: 10.1128/AEM.01285-08.
31. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673-679. doi: 10.1093/bioinformatics/btm009.
32. Distel DL, Lee HK, Cavanaugh CM. 1995. Intracellular coexistence of methano- and thioautotrophic bacteria in a hydrothermal vent mussel. Proceedings of the National Academy of Sciences of USA 92:9598-9602. doi: 10.1073/ pnas.92.21.9598.
33. Dmytrenko O, Russell SL, Loo WT, Fontanez KM, Liao L, Roeselers G, Sharma R, Stewart FJ, Newton IL, Woyke T, Wu D, Lang JM, Eisen JA, Cavanaugh CM. 2014. The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. BMC Genomics 15:924. doi: 10.1186/1471-2164-15-924.
34. Dobrindt U, Hochhut B, Hentschel U, Hacker J. 2004. Genomic islands in pathogenic and environmental microorganisms. Nature Reviews Microbiology 2:414-424. doi: 10.1038/nrmicro884.
35. Douglas AE. 2014. The symbiotic habit.
36. Dubilier N, Bergin C, Lott C. 2008. Symbiotic diversity in marine animals: the art of harnessing chemosynthesis. Nature Reviews Microbiology 6:725-740. doi: 10.1038/nrmicro1992.
37. Duperron S, Bergin C, Zielinski F, Blazejak A, Pernthaler A, McKiness ZP, DeChaine E, Cavanaugh CM, Dubilier N. 2006. A dual symbiosis shared by two mussel species, Bathymodiolus azoricus and Bathymodiolus puteoserpentis (Bivalvia: Mytilidae), from hydrothermal vents along the northern Mid-Atlantic Ridge. Environmental Microbiology 8:1441-1447.
38. Duperron S, Halary S, Lorion J, Sibuet M, Gaill F. 2008. Unexpected co-occurrence of six bacterial symbionts in the gills of the cold seep mussel Idas sp. (Bivalvia: Mytilidae). Environmental Microbiology 10:433-445. doi: 10.1111/ j.1462-2920.2007.01465.x.
39. Duperron S, Gaudron SM, Rodrigues CF, Cunha MR, Decker C, Olu K. 2013. An overview of chemosynthetic symbioses in bivalves from the North Atlantic and Mediterranean sea. Biogeosciences 10:3241-3267. doi: 10.5194/bg-10-3241-2013.
40. Elias JE, Gygi SP. 2007. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nature Methods 4:207-214. doi: 10.1038/nmeth1019.
41. Emanuelsson O, Brunak S, von Heijne G, Nielsen H. 2007. Locating proteins in the cell using TargetP, SignalP and related tools. Nature Protocols 2:953-971. doi: 10.1038/nprot.2007.131.
42. Eng JK, McCormack AL, Yates JR III. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Journal of the American Society for Mass Spectrometry 5:976-989. doi: 10.1016/1044-0305(94)80016-2.
43. Eymann C, Dreisbach A, Albrecht D, Bernhardt J, Becher D, Gentner S, Tam le T, Büttner K, Buurman G, Scharf C, Venz S, Völker U, Hecker M. 2004. A comprehensive proteome map of growing Bacillus subtilis cells. Proteomics 4:2849-2876. doi: 10.1002/pmic.200400907.
44. Finn RD, Clements J, Eddy SR. 2011. HMMER web server: interactive sequence similarity searching. Nucleic Acids Research 39:W29. doi: 10.1093/nar/gkr367.
45. Fisher CR, Brooks JM, Vodenichar JS, Zande JM, Childress JJ, Burke RA Jr. 1993. The co-occurrence of methanotrophic and chemoautotrophic sulfur-oxidizing bacterial symbionts in a deep-sea mussel. Marine Ecology 14:277-289. doi: 10.1111/j.1439-0485.1993.tb00001.x.
46. Florens L, Carozza MJ, Swanson SK, Fournier M, Coleman MK, Workman JL, Washburn MP. 2006. Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods 40:303-311. doi: 10.1016/j.ymeth.2006.07.028.
47. Fontanez KM, Cavanaugh CM. 2014. Evidence for horizontal transmission from multilocus phylogeny of deep-sea mussel (Mytilidae) symbionts: horizontal transmission of mussel symbionts. Environmental Microbiology 16:3608-3621. doi: 10.1111/1462-2920.12379.
48. Galagan JE. 2014. Genomic insights into tuberculosis. Nature Reviews Genetics 15:307-320. doi: 10.1038/nrg3664.
49. Gardebrecht A, Markert S, Sievert SM, Felbeck H, Thürmer A, Albrecht D, Wollherr A, Kabisch J, Le Bris N, Lehmann R, Daniel R, Liesegang H, Hecker M, Schweder T. 2012. Physiological homogeneity among the endosymbionts of Riftia pachyptila and Tevnia jerichonana revealed by proteogenomics. The ISME Journal 6:766-776. doi: 10.1038/ismej.2011.137.
50. Gebruk AV, Chevaldonné P, Shank T, Lutz RA, Vrijenhoek RC. 2000. Deep-sea hydrothermal vent communities of the Logatchev area (14°45'N, Mid-Atlantic Ridge): diverse biotopes and high biomass. Journal of the Marine Biological Association of the UK 80:383-393. doi: 10.1017/S0025315499002088.
51. Goffredi SK, Yi H, Zhang Q, Klann JE, Struve IA, Vrijenhoek RC, Brown CT. 2014. Genomic versatility and functional variation between two dominant heterotrophic symbionts of deep-sea Osedax worms. The ISME Journal 8:908-924. doi: 10.1038/ismej.2013.201.
52. Gogarten JP, Townsend JP. 2005. Horizontal gene transfer, genome innovation and evolution. Nature Reviews Microbiology 3:679-687. doi: 10.1038/nrmicro1204.
53. Goodrich-Blair H, Clarke DJ. 2007. Mutualism and pathogenesis in Xenorhabdus and Photorhabdus: two roads to the same destination. Molecular Microbiology 64:260-268. doi: 10.1111/j.1365-2958.2007.05671.x.
54. Haglund CM, Welch MD. 2011. Pathogens and polymers: microbe-host interactions illuminate the cytoskeleton. The Journal of Cell Biology 195:7-17. doi: 10.1083/jcb.201103148.
55. Halary S, Riou V, Gaill F, Boudier T, Duperron S. 2008. 3D FISH for the quantification of methane- and sulphuroxidizing endosymbionts in bacteriocytes of the hydrothermal vent mussel Bathymodiolus azoricus. The ISME Journal 2:284-292. doi: 10.1038/ismej.2008.3.
56. Harada M, Yoshida T, Kuwahara H, Shimamura S, Takaki Y, Kato C, Miwa T, Miyake H, Maruyama T. 2009. Expression of genes for sulfur oxidation in the intracellular chemoautotrophic symbiont of the deep-sea bivalve Calyptogena okutanii. Extremophiles 13:895-903. doi: 10.1007/s00792-009-0277-8.
57. Harmer TL, Rotjan RD, Nussbaumer AD, Bright M, Ng AW, DeChaine EG, Cavanaugh CM. 2008. Free-living tube worm endosymbionts found at deep-sea vents. Applied and Environmental Microbiology 74:3895-3898. doi: 10. 1128/AEM.02470-07.
58. Hart MM, Forsythe J, Oshowski B, Bücking H, Jansa J, Kiers ET. 2013. Hiding in a crowd-does diversity facilitate persistence of a low-quality fungal partner in the mycorrhizal symbiosis? Symbiosis 59:47-56. doi: 10.1007/ s13199-012-0197-8.
59. Heinz E, Williams TA, Nakjang S, Noë l CJ, Swan DC, Goldberg AV, Harris SR, Weinmaier T, Markert S, Becher D, Bernhardt J, Dagan T, Hacker C, Lucocq JM, Schweder T, Rattei T, Hall N, Hirt RP, Embley TM. 2012. The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution. PLOS Pathogens 8:e1002979. doi: 10.1371/journal.ppat.1002979.
60. Hentschel U, Steinert M, Hacker J. 2000. Common molecular mechanisms of symbiosis and pathogenesis. Trends in Microbiology 8:226-231. doi: 10.1016/S0966-842X(00)01758-3.
61. Hopkins SH. 1957. B. Parasitism. Geological society of america memoirs: Geological Society of America. p. 413-428.
62. Hueck CJ. 1998. Type III protein secretion systems in bacterial pathogens of animals and plants. Microbiology and Molecular Biology Reviews 62:379-433.
63. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. 2009. InterPro: the integrative protein signature database. Nucleic Acids Research 37:D211-D215. doi: 10.1093/nar/gkn785.
64. Jackson AP, Thomas GH, Parkhill J, Thomson NR. 2009. Evolutionary diversification of an ancient gene family (rhs) through C-terminal displacement. BMC Genomics 10:584. doi: 10.1186/1471-2164-10-584.
65. Jiggins FM, Hurst GDD, Yang Z. 2002. Host-symbiont conflicts: positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae. Molecular Biology and Evolution 19:1341-1349.
66. Kadar E, Bettencourt R, Costa V, Santos RS, Lobo-da-Cunha A, Dando P. 2005. Experimentally induced endosymbiont loss and re-acquirement in the hydrothermal vent bivalve Bathymodiolus azoricus. Journal of Experimental Marine Biology and Ecology 318:99-110.
67. Kaebernick M, Neilan BA, Börner T, Dittmann E. 2000. Light and the transcriptional response of the Microcystin biosynthesis gene cluster. Applied and Environmental Microbiology 66:3387-3392. doi: 10.1128/AEM.66.8.3387- 3392.2000.
68. Käll L, Storey JD, MacCoss MJ, Noble WS. 2008. Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. Journal of Proteome Research 7:29-34. doi: 10.1021/pr700600n.
69. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. 2011. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Research 40:D109-D114. doi: 10.1093/nar/gkr988.
70. Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30:3059-3066. doi: 10.1093/nar/gkf436.
71. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647-1649. doi: 10.1093/bioinformatics/bts199.
72. Kelley LA, Sternberg MJE. 2009. Protein structure prediction on the Web: a case study using the Phyre server. Nature Protocols 4:363-371. doi: 10.1038/nprot.2009.2.
73. Kleiner M, Petersen JM, Dubilier N. 2012a. Convergent and divergent evolution of metabolism in sulfur-oxidizing symbionts and the role of horizontal gene transfer. Current Opinion in Microbiology 15:621-631. doi: 10.1016/j. mib.2012.09.003.
74. Kleiner M, Wentrup C, Lott C, Teeling H, Wetzel S, Young J, Chang YJ, Shah M, VerBerkmoes NC, Zarzycki J, Fuchs G, Markert S, Hempel K, Voigt B, Becher D, Liebeke M, Lalk M, Albrecht D, Hecker M, Schweder T, Dubilier N. 2012b. Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use. Proceedings of the National Academy of Sciences of USA 109:E1173-E1182. doi: 10.1073/pnas.1121198109.
75. Kobayashi I. 2001. Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Research 29:3742-3756. doi: 10.1093/nar/29.18.3742.
76. Koskiniemi S, Lamoureux JG, Nikolakakis KC, t'Kint de Roodenbeke C, Kaplan MD, Low DA, Hayes CS. 2013. Rhs proteins from diverse bacteria mediate intercellular competition. Proceedings of the National Academy of Sciences of USA 110:7032-7037. doi: 10.1073/pnas.1300627110.
77. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. 2001. Predicting transmembrane protein topology with a hidden markov model: application to complete genomes1. Journal of Molecular Biology 305:567-580. doi: 10.1006/jmbi.2000.4315.
78. Kung VL, Khare S, Stehlik C, Bacon EM, Hughes AJ, Hauser AR. 2012. An rhs gene of Pseudomonas aeruginosa encodes a virulence protein that activates the inflammasome. Proceedings of the National Academy of Sciences of USA 109:1275-1280. doi: 10.1073/pnas.1109285109.
79. Kuwahara H, Yoshida T, Takaki Y, Shimamura S, Nishi S, Harada M, Matsuyama K, Takishita K, Kawato M, Uematsu K, Fujiwara Y, Sato T, Kato C, Kitagawa M, Kato I, Maruyama T. 2007. Reduced genome of the thioautotrophic intracellular symbiont in a deep-sea clam, Calyptogena okutanii. Current Biology 17:881-886. doi: 10.1016/j.cub. 2007.04.039.
80. Kwak JS, Jeong H-G, Satchell KJF. 2011. Vibrio vulnificus rtxA1 gene recombination generates toxin variants with altered potency during intestinal infection. Proceedings of the National Academy of Sciences of USA 108:1645-1650. doi: 10.1073/pnas.1014339108.
81. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Research 35:3100-3108. doi: 10.1093/nar/gkm160.
82. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357-359. doi: 10. 1038/nmeth.1923.
83. Lauenstein G, Harmon M, Gottholm B. 1993. National status and trends program: monitoring site descriptions (1984-1990) for the national mussel watch and benthic surveillance projects: National Oceanic and Atmospheric Administration. NOAA technical memorandum NOS ORCA-70. 1-358.
84. Lavik G, Stührmann T, Brüchert V, Van der Plas A, Mohrholz V, Lam P, Mußmann M, Fuchs BM, Amann R, Lass U, Kuypers MM. 2009. Detoxification of sulphidic African shelf waters by blooming chemolithotrophs. Nature 457:581-584. doi: 10.1038/nature07588.
85. Li W, Godzik A. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658-1659. doi: 10.1093/bioinformatics/btl158.
86. Lindsay JA, Ruzin A, Ross HF, Kurepina N, Novick RP. 1998. The gene for toxic shock toxin is carried by a family of mobile pathogenicity islands in Staphylococcus aureus. Molecular Microbiology 29:527-543. doi: 10.1046/j.1365- 2958.1998.00947.x.
87. LinhartováI, Bumba L, Mašín J, Basler M, Osička R, Kamanová J, ProcházkováK, Adkins I, Hejnová-HolubováJ, SadílkováL, MorováJ, Sebo P. 2010. RTX proteins: a highly diverse family secreted by a common mechanism. FEMS Microbiology Reviews 34:1076-1112. doi: 10.1111/j.1574-6976.2010.00231.x.
88. Liu X, Sheng J, Iii RC. 2011. Fatty acid production in genetically modified cyanobacteria. Proceedings of the National Academy of Sciences of USA 108:6899-6904. doi: 10.1073/pnas.1103014108.
89. Liu Z, Müller J, Li T, Alvey RM, Vogl K, Frigaard NU, Rockwell NC, Boyd ES, Tomsho LP, Schuster SC, Henke P, Rohde M, Overmann J, Bryant DA. 2013. Genomic analysis reveals key aspects of prokaryotic symbiosis in the phototrophic consortium "Chlorochromatium aggregatum". Genome Biology 14:R127. doi: 10.1186/gb-2013-14-11-r127.
90. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25:0955.
91. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, Buchner A, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüssmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, LenkeM, Ludwig T, Bode A, Schleifer KH. 2004. ARB: a software environment for sequence data. Nucleic Acids Research 32:1363-1371. doi: 10.1093/nar/gkh293.
92. Ma K, Vitek O, Nesvizhskii AI. 2012. A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet. BMC Bioinformatics 13:S1. doi: 10.1186/1471-2105-13-S16-S1.
93. Markert S, Arndt C, Felbeck H, Becher D, Sievert SM, Hügler M, Albrecht D, Robidart J, Bench S, Feldman RA, Hecker M, Schweder T. 2007. Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila. Science 315:247-250. doi: 10.1126/science.1132913.
94. Markert S, Gardebrecht A, Felbeck H, Sievert SM, Klose J, Becher D, Albrecht D, Thürmer A, Daniel R, Kleiner M, Hecker M, Schweder T. 2011. Status quo in physiological proteomics of the uncultured Riftia pachyptila endosymbiont. Proteomics 11:3106-3117. doi: 10.1002/pmic.201100059.
95. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC. 2011. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Research 40:D115-D122. doi: 10.1093/nar/gkr1044.
96. McClure R, Balasubramanian D, Sun Y, Bobrovskyy M, Sumby P, Genco CA, Vanderpool CK, Tjaden B. 2013. Computational analysis of bacterial RNA-Seq data. Nucleic Acids Research 41:e140-e140. doi: 10.1093/nar/ gkt444.
97. McFall-Ngai M, Hadfield MG, Bosch TC, Carey HV, Domazet-Lǒso T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF, Hentschel U, King N, Kjelleberg S, Knoll AH, Kremer N, Mazmanian SK, Metcalf JL, Nealson K, Pierce NE, Rawls JF, Reid A, Ruby EG, Rumpho M, Sanders JG, Tautz D, Wernegreen JJ. 2013. Animals in a bacterial world, a new imperative for the life sciences. Proceedings of the National Academy of Sciences of USA 110:3229-3236. doi: 10.1073/pnas.1218525110.
98. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. 2010. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20:1297-1303. doi: 10.1101/gr.107524.110.
99. Meyer F. 2003. GenDB-an open source genome annotation system for prokaryote genomes. Nucleic Acids Research 31:2187-2195. doi: 10.1093/nar/gkg312.
100. Melvin JA, Scheller EV, Miller JF, Cotter PA. 2014. Bordetella pertussis pathogenesis: current and future challenges. Nature Reviews Microbiology 12:274-288. doi: 10.1038/nrmicro3235.
101. Meusch D, Gatsogiannis C, Efremov RG, Lang AE, Hofnagel O, Vetter IR, Aktories K, Raunser S. 2014. Mechanism of Tc toxin action revealed in molecular detail. Nature 508:61-65. doi: 10.1038/nature13015.
102. Minguez L, Buronfosse T, Giambé rini L. 2012. Different host exploitation strategies in two zebra mussel-trematode systems: Adjustments of host life history traits. PLOS ONE 7:e34029. doi: 10.1371/journal.pone.0034029.
103. Moebius N, Üzüm Z, Dijksterhuis J, Lackner G, Hertweck C. 2014. Active invasion of bacteria into living fungal cells. eLife 3:e03007. doi: 10.7554/eLife.03007.
104. Moreira D, López-García P. 2003. Are hydrothermal vents oases for parasitic protists? Trends in Parasitology 19:556-558. doi: 10.1016/j.pt.2003.09.013.
105. Murillo AA, Ramírez-Flandes S, DeLong EF, Ulloa O. 2014. Enhanced metabolic versatility of planktonic sulfuroxidizing γ-proteobacteria in an oxygen-deficient coastal ecosystem. Aquatic Microbiology 1:18. doi: 10.3389/ fmars.2014.00018.
106. Muyzer G, Teske A, Wirsen CO, Jannasch HW. 1995. Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Archives of Microbiology 164:165-172. doi: 10.1007/BF02529967.
107. Newton I, Girguis P, Cavanaugh C. 2008. Comparative genomics of vesicomyid clam (Bivalvia: Mollusca) chemosynthetic symbionts. BMC Genomics 9:585. doi: 10.1186/1471-2164-9-585.
108. Newton IL, 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. 2007. The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315:998-1000. doi: 10.1126/science.1138438.
109. Ochman H, Lawrence JG, Groisman EA. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304. doi: 10.1038/35012500.
110. Ogier JC, Pagès S, Bisch G, Chiapello H, Mé digue C, Rouy Z, Teyssier C, Vincent S, Tailliez P, Givaudan A, Gaudriault S. 2014. Attenuated virulence and genomic reductive evolution in the entomopathogenic bacterial symbiont species, Xenorhabdus poinarii. Genome Biology and Evolution 6:1495-1513. doi: 10.1093/gbe/evu119.
111. Ohno M, Mé nez R, Ogawa T, Danse JM, Shimohigashi Y, Fromen C, Ducancel F, Zinn-justin S, Le du MH, Boulain JC, Tamiya T, Mé nez A. 1998. Molecular evolution of snake toxins: is the functional diversity of snake toxins associated with a mechanism of accelerated evolution? Progress in Nucleic Acid Research and Molecular Biology 59:307-364.
112. Oliver KM, Russell JA, Moran NA, Hunter MS. 2003. Facultative bacterial symbionts in aphids confer resistance to parasitic wasps. Proceedings of the National Academy of Sciences of USA 100:1803-1807. doi: 10.1073/pnas. 0335320100.
113. Oliver KM, Moran NA, Hunter MS. 2005. Variation in resistance to parasitism in aphids is due to symbionts not host genotype. Proceedings of the National Academy of Sciences of USA 102:12795-12800. doi: 10.1073/pnas. 0506131102.
114. Oliver KM, Degnan PH, Burke GR, Moran NA. 2010. Facultative symbionts in aphids and the horizontal transfer of ecologically important traits. Annual Review of Entomology 55:247-266. doi: 10.1146/annurev-ento-112408-085305.
115. Paerl H. 2008. Nutrient and other environmental controls of harmful cyanobacterial blooms along the freshwater-marine continuum. In: Hudnell HK, editor. Cyanobacterial harmful algal blooms: state of the science and research needs, Springer New York. p. 217-237.
116. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research 25:1043-1055. doi: 10. 1101/gr.186072.114.
117. Partida-Martinez LP, Groth I, Schmitt I, Richter W, Roth M, Hertweck C. 2007. Burkholderia rhizoxinica sp. nov. and Burkholderia endofungorum sp. nov., bacterial endosymbionts of the plant-pathogenic fungus Rhizopus microsporus. International Journal of Systematic and Evolutionary Microbiology 57:2583-2590. doi: 10.1099/ijs.0.64660-0.
118. Pernthaler A, Pernthaler J, Amann R. 2002. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Applied and Environmental Microbiology 68:3094-3101. doi: 10.1128/AEM. 68.6.3094-3101.2002.
119. Petersen J, Dubilier N. 2014. Gene swapping in the dead zone. eLife 3. doi: 10.7554/eLife.04600.
120. Petersen JM, Dubilier N. 2009. Methanotrophic symbioses in marine invertebrates: methanotrophic symbioses in marine invertebrates. Environmental Microbiology Reports 1:319-335. doi: 10.1111/j.1758-2229.2009.00081.x.
121. Petersen JM, Zielinski FU, Pape T, Seifert R, Moraru C, Amann R, Hourdez S, Girguis PR, Wankel SD, Barbe V, Pelletier E, Fink D, Borowski C, Bach W, Dubilier N. 2011. Hydrogen is an energy source for hydrothermal vent symbioses. Nature 476:176-180. doi: 10.1038/nature10325.
122. Petersen JM, Wentrup C, Verna C, Knittel K, Dubilier N. 2012. Origins and evolutionary flexibility of chemosynthetic symbionts from deep-sea animals. The Biological Bulletin 223:123-137.
123. Ponting CP, Schultz J, Milpetz F, Bork P. 1999. SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Research 27:229-232. doi: 10.1093/nar/27.1.229.
124. Poole SJ, Diner EJ, Aoki SK, Braaten BA, t'Kint de Roodenbeke C, Low DA, Hayes CS. 2011. Identification of functional toxin/Immunity genes linked to contact-dependent growth inhibition (CDI) and rearrangement hotspot (Rhs) systems. PLOS Genetics 7:e1002217. doi: 10.1371/journal.pgen.1002217.
125. Powell EN, Barber RD, Kennicutt MC II, Ford SE. 1999. Influence of parasitism in controlling the health, reproduction and PAH body burden of petroleum seep mussels. Deep Sea Research Part I Oceanographic Research Papers 46:2053-2078. doi: 10.1016/S0967-0637(99)00035-7.
126. Pruesse E, Peplies J, Glöckner FO. 2012. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823-1829. doi: 10.1093/bioinformatics/bts252.
127. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41:D590-D596. doi: 10.1093/nar/gks1219.
128. Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841-842. doi: 10.1093/bioinformatics/btq033.
129. R Development Core Team. 2011. R: a language and environment for statistical computing.
130. Rasko DA, Myers GS, Ravel J. 2005. Visualization of comparative genomic analyses by BLAST score ratio. BMC Bioinformatics 6:2. doi: 10.1186/1471-2105-6-2.
131. Reams AB, Neidle EL. 2004. Selection for gene clustering by tandem duplication. Annual Review of Microbiology 58:119-142. doi: 10.1146/annurev.micro.58.030603.123806.
132. Richter M, Lombardot T, Kostadinov I, Kottmann R, Duhaime MB, Peplies J, Glöckner FO. 2008. JCoast-a biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes. BMC Bioinformatics 9:177. doi: 10.1186/1471-2105-9-177.
133. Riou V, Duperron S, Halary S, Dehairs F, Bouillon S, Martins I, Colaço A, Serrão Santos R. 2010. Variation in physiological indicators in Bathymodiolus azoricus (Bivalvia: Mytilidae) at the Menez Gwen Mid-Atlantic Ridge deep-sea hydrothermal vent site within a year. Marine Environmental Research 70:264-271. doi: 10.1016/j. marenvres.2010.05.008.
134. Rissman AI, Mau B, Biehl BS, Darling AE, Glasner JD, Perna NT. 2009. Reordering contigs of draft genomes using the Mauve aligner. Bioinformatics 25:2071-2073. doi: 10.1093/bioinformatics/btp356.
135. Robidart JC, Bench SR, Feldman RA, Novoradovsky A, Podell SB, Gaasterland T, Allen EE, Felbeck H. 2008. Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics. Environmental Microbiology 10:727-737. doi: 10.1111/j.1462-2920.2007.01496.x.
136. Rocha EPC, Danchin A. 2002. Base composition bias might result from competition for metabolic resources. Trends in Genetics 18:291-294. doi: 10.1016/S0168-9525(02)02690-2.
137. Roig FJ, Gonzalez-Candelas F, Amaro C. 2010. Domain organization and evolution of multifunctional autoprocessing repeats-in-toxin (MARTX) Toxin in Vibrio vulnificus. Applied and Environmental Microbiology 77:657-668. doi: 10.1128/AEM.01806-10.
138. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574. doi: 10.1093/bioinformatics/btg180.
139. Rouchet R, Vorburger C. 2014. Experimental evolution of parasitoid infectivity on symbiont-protected hosts leads to the emergence of genotype specificity. Evolution 68:1607-1616. doi: 10.1111/evo.12377.
140. Russell JA, Weldon S, Smith AH, Kim KL, Hu Y, Łukasik P, Doll S, Anastopoulos I, Novin M, Oliver KM. 2013. Uncovering symbiont-driven genetic diversity across North American pea aphids. Molecular Ecology 22:2045-2059. doi: 10.1111/mec.12211.
141. Sakiyama T, Ueno H, Homma H, Numata O, Kuwabara T. 2006. Purification and characterization of a hemolysin-like protein, Sll1951, a nontoxic member of the RTX protein family from the Cyanobacterium Synechocystis sp. Strain PCC 6803. Journal of Bacteriology 188:3535-3542. doi: 10.1128/JB.188.10.3535-3542.2006.
142. Sakiyama T, Araie H, Suzuki I, Shiraiwa Y. 2011. Functions of a hemolysin-like protein in the cyanobacterium Synechocystis sp. PCC 6803. Archives of Microbiology 193:565-571. doi: 10.1007/s00203-011-0700-2.
143. Sarrazin J, Sarradin P-M, Allais A-G, Momareto Cruise Participants X. 2006. MoMARETO: a cruise dedicated to the spatio-temporal dynamics and the adaptations of hydrothermal vent fauna on the Mid-Atlantic Ridge. InterRidge News 15:24-33.
144. Satchell KJF. 2007. MARTX, multifunctional autoprocessing repeats-in-toxin toxins. Infection and Immunity 75:5079-5084. doi: 10.1128/IAI.00525-07.
145. Satchell KJF. 2011. Structure and function of MARTX toxins and other large repetitive RTX proteins. Annual Review of Microbiology 65:71-90. doi: 10.1146/annurev-micro-090110-102943.
146. Schmid M, Sieber R, Zimmermann Y-S, Vorburger C. 2012. Development, specificity and sublethal effects of symbiont-conferred resistance to parasitoids in aphids. Functional Ecology 26:207-215. doi: 10.1111/j.1365- 2435.2011.01904.x.
147. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13:2498-2504. doi: 10.1101/gr.1239303.
148. Snyder AK, Rio RVM. 2013. Interwoven biology of the Tsetse holobiont. Journal of Bacteriology 195:4322-4330. doi: 10.1128/JB.00487-13.
149. Soucy SM, Huang J, Gogarten JP. 2015. Horizontal gene transfer: building the web of life. Nature Reviews Genetics 16:472-482. doi: 10.1038/nrg3962.
150. Srinivasan M, Moon YB. 1999. A comprehensive clustering algorithm for strategic analysis of supply chain networks. Computers & Industrial Engineering 36:615-633. doi: 10.1016/S0360-8352(99)00155-2.
151. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688. doi: 10.1093/bioinformatics/btl446.
152. Steele-Mortimer O, Brumell JH, Knodler LA, Mé resse S, Lopez A, Finlay BB. 2002. The invasion-associated type III secretion system of Salmonella enterica serovar Typhimurium is necessary for intracellular proliferation and vacuole biogenesis in epithelial cells. Cellular Microbiology 4:43-54. doi: 10.1046/j.1462-5822.2002.00170.x.
153. Strous M, Kraft B, Bisdorf R, Tegetmeyer HE. 2012. The binning of metagenomic contigs for microbial physiology of mixed cultures. Frontiers in Microbiology 3. doi: 10.3389/fmicb.2012.00410.
154. SunamuraM, Higashi Y, Miyako C, Ishibashi J, Maruyama A. 2004. Two bacteria phylotypes are predominant in the Suiyo Seamount hydrothermal plume. Applied and Environmental Microbiology 70:1190-1198. doi: 10.1128/ AEM.70.2.1190-1198.2004.
155. Takeuchi T, Kawashima T, Koyanagi R, Gyoja F, Tanaka M, Ikuta T, Shoguchi E, Fujiwara M, Shinzato C, Hisata K, Fujie M, Usami T, Nagai K, Maeyama K, Okamoto K, Aoki H, Ishikawa T, Masaoka T, Fujiwara A, Endo K, Endo H, Nagasawa H, Kinoshita S, Asakawa S, Watabe S, Satoh N. 2012. Draft genome of the pearl oyster pinctada fucata: a platform for understanding bivalve biology. DNA Research 19:117-130. doi: 10.1093/dnares/dss005.
156. Tatusov RL. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Research 28:33-36. doi: 10.1093/nar/28.1.33.
157. Van Dover C. 2000. The ecology of deep-sea hydrothermal vents. Princeton, NJ: Princeton University Press.
158. Van Dover CL, German CR, Speer KG, Parson LM, Vrijenhoek RC. 2002. Evolution and biogeography of deep-sea vent and seep invertebrates. Science 295:1253-1257. doi: 10.1126/science.1067361.
159. Vogl K, Wenter R, Dreßen M, Schlickenrieder M, Plöscher M, Eichacker L, Overmann J. 2008. Identification and analysis of four candidate symbiosis genes from "Chlorochromatium aggregatum", a highly developed bacterial symbiosis. Environmental Microbiology 10:2842-2856. doi: 10.1111/j.1462-2920.2008.01709.x.
160. von Cosel R. 2002. A new species of bathymodioline mussel (Mollusca, Bivalvia, Mytilidae) from Mauritania (West Africa), with comments on the genus Bathymodiolus Kenk & Wilson, 1985. Zoosystema 24:259-272.
161. Wagner-Döbler I, Biebl H. 2006. Environmental biology of the marine Roseobacter lineage. Annual Review of Microbiology 60:255-280. doi: 10.1146/annurev.micro.60.080805.142115.
162. Walsh DA, Zaikova E, Howes CG, Song YC, Wright JJ, Tringe SG, Tortell PD, Hallam SJ. 2009. Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science 326:578-582. doi: 10.1126/science. 1175309.
163. Ward ME, Shields JD, Van Dover CL. 2004. Parasitism in species of Bathymodiolus (Bivalvia: Mytilidae) mussels from deep-sea seep and hydrothermal vents. Diseases of Aquatic Organisms 62:1-16. doi: 10.3354/dao062001.
164. Wardle WJ. 1988. A Bucephalid Larva, Cercaria pleuromerae n. sp. (Trematoda: Digenea), parasitizing a deepwater Bivalve from the Gulf of Mexico. The Journal of Parasitology 74:692-694. doi: 10.2307/3282191.
165. Waterfield NR, Bowen DJ, Fetherston JD, Perry RD. 2001. The tc genes of Photorhabdus: a growing family. Trends in Microbiology 9:185-191. doi: 10.1016/S0966-842X(01)01978-3.
166. Wentrup C, Wendeberg A, Schimak M, Borowski C, Dubilier N. 2014. Forever competent: deep-sea bivalves are colonized by their chemosynthetic symbionts throughout their lifetime. Environmental Microbiology 16:3699-3713. doi: 10.1111/1462-2920.12597.
167. West SA, Kiers ET, Pen I, Denison RF. 2002. Sanctions and mutualism stability: when should less beneficial mutualists be tolerated? Journal of Evolutionary Biology 15:830-837. doi: 10.1046/j.1420-9101.2002.00441.x.
168. Wittkop T, Emig D, Lange S, Rahmann S, Albrecht M, Morris JH, Böcker S, Stoye J, Baumbach J. 2010. Partitioning biological data with transitivity clustering. Nature Methods 7:419-420. doi: 10.1038/nmeth0610-419.
169. Won Y, Young C, Lutz R, Vrijenhoek R. 2003a. Dispersal barriers and isolation among deep-sea mussel populations (Mytilidae: Bathymodiolus) from eastern Pacific hydrothermal vents. Molecular Ecology 12:169-184. doi: 10. 1046/j.1365-294X.2003.01726.x.
170. Won YJ, Hallam SJ, O'Mullan GD, Pan IL, Buck KR, Vrijenhoek RC. 2003b. Environmental acquisition of thiotrophic endosymbionts by deep-sea mussels of the genus Bathymodiolus. Applied and Environmental Microbiology 69:6785. doi: 10.1128/AEM.69.11.6785-6792.2003.
171. Wood AP, Aurikko JP, Kelly DP. 2004. A challenge for 21st century molecular biology and biochemistry: what are the causes of obligate autotrophy and methanotrophy? FEMS Microbiology Reviews 28:335-352. doi: 10.1016/j. femsre.2003.12.001.
172. Wright JJ, Konwar KM, Hallam SJ. 2012. Microbial ecology of expanding oxygen minimum zones. Nature Reviews Microbiology 10:381-394. doi: 10.1038/nrmicro2778.
173. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L. 2012. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biology Direct 7:18. doi: 10.1186/1745-6150-7-18.
174. Zhou J, Bruns MA, Tiedje JM. 1996. DNA recovery from soils of diverse composition. Applied and Environmental Microbiology 62:316-322.
175. Zielinski FU, Pernthaler A, Duperron S, Raggi L, Giere O, Borowski C, Dubilier N. 2009. Widespread occurrence of an intranuclear bacterial parasite in vent and seep bathymodiolin mussels. Environmental Microbiology 11:1150-1167. doi: 10.1111/j.1462-2920.2008.01847.x.
176. Zuleta LF, Cunha Cde O, de Carvalho FM, Ciapina LP, Souza RC, Mercante FM, de Faria SM, Baldani JI, Straliotto R, Hungria M, de Vasconcelos AT. 2014. The complete genome of Burkholderia phenoliruptrix strain BR3459a, a symbiont of Mimosa flocculosa: highlighting the coexistence of symbiotic and pathogenic genes. BMC Genomics 15:535. doi: 10.1186/1471-2164-15-535.