Metagenomic comparison of two thiomicrospira lineages inhabiting contrasting deep-sea hydrothermal environments

PLoS ONE

Volumn 5, Issue 10, 2010, Pages

  Brazelton, William J ^a   Baross, John A ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG; GENE PRODUCT; HYDROGEN SULFIDE; PROTEIN SOX; SULFATE; TRANSPOSASE; UNCLASSIFIED DRUG;

ARTICLE; CARBON FIXATION; CONTROLLED STUDY; DEEP SEA SPECIES; GENE ACTIVITY; GENE FUSION; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC CONSERVATION; GENOME ANALYSIS; HYDROTHERMAL VENT; METAGENOMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; OXIDATION; PACIFIC OCEAN; PHYLOGENETIC TREE; PROPHAGE; SEQUENCE HOMOLOGY; SPECIES HABITAT; SULFUR OXIDATION; THIOMICROSPIRA; THIOMICROSPIRA CRUNOGENA; BACTERIAL GENE; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; GENOMICS; MARINE BIOLOGY; PHYLOGENY; PISCIRICKETTSIACEAE;

THIOMICROSPIRA; THIOMICROSPIRA CRUNOGENA; THIOMICROSPIRA CRUNOGENA XCL-2; THIOTRICHALES;

GENES, BACTERIAL; GENOMICS; MARINE BIOLOGY; PHYLOGENY; PISCIRICKETTSIACEAE;

EID: 78149422269     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0013530     Document Type: Article

References (33)

1. Jannasch HW (1995) Microbial Interactions With Hydrothermal Fluids. In: Humphris SE, et al., eds. Seafloor hydrothermal systems: physical, chemical, biological, and geological interactions. Geophysical monograph 91. Washington, D.C.: American Geophysical Union. pp 273-296.
2. Kelley DS, Karson JA, Fruh-Green GL, Yoerger DR, Shank TM, et al. (2005) A serpentinite-hosted ecosystem: the Lost City hydrothermal field. Science 307: 1428-1434. doi:10.1126/science.1102556.
3. Fruh-Green GL, Bernasconi SM, Butterfield DA, Kelley DS (2004) Sulfur isotope geochemistry of the Lost City hydrothermal vent fluids. Eos Trans AGU 85: Abstract B13A-0199.
4. DeChaine EG, Bates AE, Shank TM, Cavanaugh CM (2006) Off-axis symbiosis found: Characterization and biogeography of bacterial symbionts of Bath-ymodiolus mussels from Lost City hydrothermal vents. Environ Microbiol 8:1902-1912. doi:10.1111/j.1462-2920.2005.01113.x.
5. Schrenk MO, Kelley DS, Bolton SA, Baross JA (2004) Low archaeal diversity linked to subseafloor geochemical processes at the Lost City Hydrothermal Field, Mid-Atlantic Ridge. Environ Microbiol 6: 1086-1095.
6. Brazelton WJ, Ludwig KA, Sogin ML, Andreishcheva EN, Kelley DS, et al.(2010) Archaea and bacteria with surprising microdiversity show shifts in dominance over 1000-year time scales in hydrothermal chimneys. Proc Nat Acad Sci U S A 107: 1612-1617.
7. Brazelton WJ, Schrenk MO, Kelley DS, Baross JA (2006) Methane- and sulfur- metabolizing microbial communities dominate the Lost City hydrothermal field ecosystem. Appl Environ Microbiol 72: 6257-6270. doi:10.1128/AEM.00574-06.
8. Brinkhoff T, Muyzer G (1997) Increased species diversity and extended habitat range of sulfur-oxidizing Thiomicrospira spp. Appl Environ Microbiol 63: 3789-3796.
9. Jannasch HW, Wirsen CC, Nelson DC, Robertson LA (1985) Thiomicrospira crunogena sp. nov., a Colorless, Sulfur-Oxidizing Bacterium from a Deep-Sea Hydrothermal Vent. Int J Syst Bacteriol 35: 422-424. doi:10.1099/00207713-35-4-422.
10. Proskurowski G, Lilley MD, Seewald JS, Fruh-Green GL, Olson EJ, et al. (2008) Abiogenic hydrocarbon production at lost city hydrothermal field. Science 319: 604-607. doi:10.1126/science.1151194.
11. Ruby EG, Jannasch HW (1982) Physiological-Characteristics of Thiomicrospira sp. Strain L-12 Isolated from Deep-Sea Hydrothermal Vents. J Bacteriol 149: 161-165.
12. Scott KM, Sievert SM, Abril FN, Ball LA, Barrett CJ, et al. (2006) The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. PLoS Biol 4: e383. doi:10.1371/journal.pbio.0040383.
13. Ahmad A, Barry JP, Nelson DC (1999) Phylogenetic Affinity of a Wide, Vacuolate, Nitrate-Accumulating Beggiatoa sp. from Monterey Canyon, California, with Thioploca spp. Appl Environ Microbiol 65: 270-277.
14. Edmond J, Measures C, Mangum B, Grant B, Sclater F, et al. (1979) On the formation of metal-rich deposits at ridge crests. Earth Planet Sci Lett 46: 19-30. doi:10.1016/0012-821X(79)90062-1.
15. Wirsen CO, Brinkhoff T, Kuever J, Muyzer G, Molyneaux S, et al. (1998) Comparison of a new Thiomicrospira strain from the Mid-Atlantic Ridge with known hydrothermal vent isolates. Appl Environ Microbiol 64: 4057-4059.
16. Butterfield DA, Seyfried WE, Lilley MD (2003) Composition and evolution of hydrothermal fluids. Energy and Mass Transfer in Marine Hydrothermal Systems. Berlin: Dahlem University Press. pp 127.
17. Brazelton WJ, Baross JA (2009) Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm. ISME J 3: 1420-1424.
18. Barton HA, Taylor NM, Lubbers BR, Pemberton AC (2006) DNA extraction from low-biomass carbonate rock: An improved method with reduced contamination and the low-biomass contaminant database. J Microbiol Methods 66: 21-31. doi:10.1016/j.mimet.2005.10.005.
19. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27: 4636-4641.
20. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
21. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, et al. (2000) Artemis: sequence visualization and annotation. Bioinformatics 16: 944-945.
22. Ludwig KA, Kelley DS, Butterfield DA, Nelson BK, Fruh-Green G (2006) Formation and evolution of carbonate chimneys at the Lost City Hydrothermal Field. Geochim Cosmochim Acta 70:3625-3645. doi:10.1016/j.gca.2006.04.016.
23. Ghosh W, Mallick S, DasGupta SK (2009) Origin of the Sox multienzyme complex system in ancient thermophilic bacteria and coevolution of its constituent proteins. Res Microbiol 160:409-420. doi:10.1016/j.resmic.2009.07.003.
24. Javor BJ, Wilmot DB, Vetter RD (1990) Ph-Dependent Metabolism of Thiosulfate and Sulfur Globules in the Chemolithotrophic Marine Bacterium Thiomicrospira crunogena. Arch Microbiol 154: 231-238.
25. Dulov L, Lein A, Dubinina G, Pimenov N (2005) Microbial processes at the Lost City vent field, Mid-Atlantic Ridge. Microbiol 74: 97-103. doi:10.1007/s11021-005-0035-6.
26. Dobrinski KP, Boller AJ, Scott KM (2010) Expression and function of four carbonic anhydrase homologs in the deep-sea chemolithoautotroph Thiomicrospira crunogena. Appl Env Microbiol 76: 3561-3567.
27. Dobrinski KP, Longo DL, Scott KM (2005) The carbon-concentrating mechanism of the hydrothermal vent chemolithoautotroph Thiomicrospira crunogena. J Bacteriol 187: 5761-5766.
28. Nishihara H, Igarashi Y, Kodama T (1991) Hydrogenovibrio marinus gen. nov., sp. nov., a Marine Obligately Chemolithoautotrophic Hydrogen-Oxidizing Bacterium. Int J Syst Bacteriol 41: 130-133. doi:10.1099/00207713-41-1-130.
29. Campbell BJ, Engel AS, Porter ML, Takai K (2006) The versatile e-proteobacteria: key players in sulphidic habitats. Nat Rev Micro 4: 458-468. doi:10.1038/nrmicro1414.
30. Bradley AS, Hayes JM, Summons RE (2009) Extraordinary C-13 enrichment of diether lipids at the Lost City Hydrothermal Field indicates a carbon-limited ecosystem. Geochim Cosmochim Acta 73: 102-118. doi:10.1016/j.gca.2008.10.005.
31. Konstantinidis KT, DeLong EF (2008) Genomic patterns of recombination, clonal divergence and environment in marine microbial populations. ISME J 2: 1052-1065.
32. Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504.
33. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797. doi:10.1093/nar/gkh340.