Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lo'ihi, Hawai'l

Frontiers in Microbiology

Volumn 4, Issue MAR, 2013, Pages

  Singer, Esther ^a   Heidelberg, John F ^a   Dhillon, Ashita ^b   Edwards, Katrina J ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b GENZYME CORPORATION   (United States)

Author keywords

Hydrothermal vents; Iron oxidation; Loihi seamount; Molybdopterin oxidoreductase; Rubisco; Sulfide oxidation; Zetaproteobacteria

Indexed keywords

BACTERIA (MICROORGANISMS); LEPTOSPIRILLUM; PROTEOBACTERIA;

EID: 84875945150     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2013.00052     Document Type: Article

References (49)

1. Acinas, S. G., Sarma-Rupavtarm, R., Klepac-Ceraj, V., and Polz, M. F. (2005). PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl. Environ. Microbiol. 71, 8966-8969.
2. Aziz, R. K., Bartels, D., Best, A. A., Dejongh, M., Disz, T., Edwards, R. A., etal. (2008). The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75
3. Badger, M. R., and Bek, E. J. (2007). Multiple Rubisco forms in proteobac-teria: their functional significance in relation to CO2 acquisition by the CBB cycle. J. Exp. Bot. 59, 1525-1541.
4. Bagos, P. G., Nikolaou, E. P., Liakopou-los, T. D., and Tsirigos, K. D. (2010). Combined prediction of Tat and Sec signal peptides with hidden Markov models. Bioinformatics 26, 2811-2817.
5. Beaumont, H. J. E., Hommes, N. G., Sayavedra-Soto, L. A., Arp, D. J., Arciero, D. M., Hooper, A. B., etal. (2002). Nitrite reductase of Nitrosomonas europaea is not essential for production of gaseous nitrogen oxides and confers tolerance to nitrite. J. Bacteriol. 184, 2557-2560.
6. Beller, H., Chain, P., Letain, T., Chakicherla, A., Larimer, F., Richardson, P., etal. (2006). The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacil-lus denitrificans. J. Bacteriol. 188, 1473-1488.
7. Bird, L., Bonnefoy, V., and Newman, D. (2011). Bioenergetic challenges of microbial iron metabolisms. Trends Microbiol. 19, 330-340.
8. Carver, T. J., Rutherford, K. M., Berri-man, M., Rajandream, M. A., Bar-rell, B. G., and Parkhill, J. (2005). ACT: the Artemis comparison tool. Bioinformatics 21, 3422-3423.
9. Chandler, D., Fredrickson, J., and Brockman, E (1997). Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol. Ecol. 6, 475-482.
10. Chevreux, B., Wetter, T., and Suhai, S. (1999). Genome sequence assembly using trace signals and additional sequence information, in Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB), 45-56.
11. Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., etal. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25, 1422-1423.
12. Cutruzzola, E (1999). Bacterial nitric oxide synthesis. Biochim. Biophys. Acta 1411, 231-249.
13. Dang, H., Chen, R., Wang, L., Shao, S., Dai, L., Ye, Y., etal. (2011). Molecular characterization of putative biocorroding microbiota with a novel niche detection of Epsilon- and Zetaproteobacteria in Pacific Ocean coastal seawaters. Environ. Microbiol. 13, 3059-3074.
14. Davis, A., Clague, D., Zierenberg, R., Wheat, C., and Cousens, B. (2003). Sulfide formation related to changes in the hydrothermal system on Loihi Seamount, Hawaii, following the seismic event in 1996. Can. Mineral. 41, 457-472.
15. Drummond, A. J., Ashton, B., Bux-ton, S., Cheung, M., Cooper, A., Duran, C., etal. (2011). Geneious v. 5.4.6. Available at: http://www.geneious.com
16. Edwards, K. J., Bach, W., Mccollom, T. M., and Rogers, D. R. (2004). Neu-trophilic iron-oxidizing bacteria in the ocean: their habitats, diversity, and roles in mineral deposition, rock alteration, and biomass production in the deep-sea. Geomicrobiol J. 21, 393-404.
17. Edwards, K. J., Bond, P. L., Druschel, G. K., McGuire, M. M., Hamers, R. J., and Banfield, J. E (2000). Geochem-ical and biological aspects of sulfide mineral dissolution: lessons from Iron Mountain, California. Chem. Geol. 169, 383-397.
18. Edwards, K., Rogers, D., Wirsen, C., and McCollom, T. (2003). Isolation and characterization of novel psychrophilic, neutrophilic, Fe-oxidizing, chemolithoautotrophic α-and γ-Proteobacteria from the deep sea. Appl Environ. Microbiol. 69, 2906-2913.
19. Emerson, D. (2012). Biogeochemistry and microbiology of microaerobic Fe(II) oxidation. Biochem. Soc. Trans. 40, 1211-1216.
20. Emerson, D., and Merrill Floyd, M. (2005). Enrichment and isolation of iron-oxidizing bacteria at neutral pH. Methods Enzymol. 397, 112-123.
21. Emerson, D., and Moyer, C. (2002). Neutrophilic Fe-oxidizing bacteria are abundant at the Loihi Seamount hydrothermal vents and play a major role in Fe oxide deposition. Appl. Environ. Microbiol. 68, 3085.
22. Emerson, D., and Moyer, C. L. (2010). Microbiology of seamounts: common patterns observed in community structure. Oceanography 23, 148-163.
23. Emerson, D., Rentz, J. A., Lilburn, T. G., Davis, R. E., Aldrich, H., Chan, C., etal. (2007). A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities. PLoS ONE 2:e667. doi: 10.1371/journal.pone.0000667
24. Gardebrecht, A., Markert, S., Sievert, S., Felbeck, H., Thürmer, A., Albrecht, D.,etal. (2011). Physiological homogeneity among the endosymbionts of Riftia pachyptila and Tevnia jeri-chonana revealed by proteogenomics. ISMEJ. 6, 766-776.
25. Glazer, B., and Rouxel, O. (2009). Redox speciation and distribution within diverse iron-dominated microbial habitats at Loihi Seamount. Geomicrobiol .J. 26, 606-622.
26. Goltsman, D. S. A., Denef, V. J., Singer, S. W., Verberkmoes, N. C., Lefs-rud, M., Mueller, R. S., etal. (2009). Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing Leptospirillum rubarum (Group II) and Leptospirillum fer-rodiazotrophum (Group III) bacteria in acid mine drainage biofilms. Appl Environ. Microbiol. 75, 4599-4615.
27. Guindon, S., and Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696-704.
28. Handley, K. M., Boothman, C., Mills, R. A., Pancost, R. D., and Lloyd, J. R. (2010). Functional diversity of bacteria in a ferruginous hydrothermal sediment. ISME J. 4, 1193-1205.
29. Jones, C. M., Stres, B., Rosenquist, M., and Hallin, S. (2008). Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification. Mol Biol Evol. 25, 1955-1966.
30. Kämpf, C., and Pfennig, N. (1980). Capacity of Chromatiaceae for chemotrophic growth. Specific respiration rates of Thiocystis violacea and Chromatium vinosum. Arch. Microbiol. 127, 125-135.
31. Karl, D., McMurtry, G., Malahoff, A., and Garcia, M. (1988). Loihi Seamount, Hawaii: a mid-plate volcano with a distinctive hydrothermal system. Nature 336, 532-535.
32. McAllister, S. M., Davis, R. E., McBeth, J. M., Tebo, B. M., Emerson, D., and Moyer, C. L. (2011). Biodiversity and emerging biogeography of the neutrophilic iron-oxidizing Zetaproteobacteria. Appl Environ. Microbiol. 77, 5445-5457.
33. Mehta, T., Coppi, M. V., Childers, S. E., andLovley, D. R. (2005). Outer membrane c-type cytochromes required for Fe(III) and Mn(IV) oxide reduction in Geobacter sulfurreducens. Appl Environ. Microbiol. 71, 8634-8641.
34. Meyer-Dombard, D. R., Amend, J. P., and Osburn, M. R. (2012). Microbial diversity and potential for arsenic and iron biogeochemical cycling at an arsenic rich, shallow-sea hydrothermal vent (Tutum Bay, Papua New Guinea). Chem. Geol. 1-11.
35. Moore, D. D., and Dowhan, D. (2002). Preparation and analysis of DNA, in Current Protocols in Molecular Biology (John Wiley & Sons, Inc) 2.0.1-2.0.3.
36. Moyer, C. L., Dobbs, F. C., and Karl, D. M. (1995). Phylogenetic diversity of the bacterial community from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl. Environ. Microbiol. 61, 1555-1562.
37. Nakai, K., and Horton, P. (1999). PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci. 24, 34-36.
38. Overbeek, R. (2005). The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33, 5691-5702.
39. Rassa, A. C., Mcallister, S. M., Safran, S. A., and Moyer, C. L. (2009). Zeta-Proteobacteria dominate the colonization and formation of microbial mats in low-temperature hydrothermal vents at Loihi Seamount, Hawaii. Geomicrobiol .J. 26, 623-638.
40. Rinaldo, S., and Cutruzzola, E (2007). Nitrite reductases in denitrification, in Biology of the Nitrogen Cycle, eds H. Bothe, S. J. Ferguson, and W. E. Newton (Amsterdam: Elsevier), 37-54.
41. Schmieder, R., and Edwards, R. (2011). Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863-864.
42. Sedwick, P. N., McMurtry, G. M., and Macdougall, J. D. (1992). Chemistry of hydrothermal solutions from Peles vents, Loihi Seamount, Hawaii. Geochim. Cosmochim. Acta 56, 3643-3667.
43. Shen, H.-B., and Chou, K.-C. (2010). Gneg-mPLoc: a top-down strategy to enhance the quality of predicting subcellular localization of Gram-negative bacterial proteins. J. Theor. Biol. 264, 326-333.
44. Singer, E., Emerson, D., Webb, E. A., Barco, R. A., Kuenen, J. G., Nelson, W C, etal. (2011). Maripro-fundus ferrooxydans PV-1 the first genome of a marine Fe(II) oxidizing Zetaproteobacterium. PLoS ONE 6:e25386. doi: 10.1371/journal.pone. 0025386
45. Sun, S., Chen, J., Li, W., Altin-tas, I., Lin, A., Peltier, S., etal. (2011). Community cyberinfrastruc-ture for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res. 39, D546-D551.
46. Treangen, T. J., Sommer, D. D., Angly, E E., Koren, S., and Pop, M. (2011). Next generation sequence assembly with AMOS. Curr. Protoc. Bioinformatics Chapter 11:Unit 11.8.
47. Weiss, J. V., Rentz, J. A., Plaia, T., Neubauer, S. C., Merrill-Floyd, M., Lilburn, T., etal. (2007). Characterization of neutrophilic Fe(II)-oxidizing bacteria isolated from the rhizosphere of wetland plants and description of Ferritrophicum radici-colagen. nov. sp. nov., and Sideroxy-dans paludicola sp. nov. Geomicrobiol. J. 24, 559-570.
48. Wessel, P., Sandwell, D. T., and Kim, S.-S. (2010). The global seamount census. Oceanography 23, 24-33.
49. Wheat, C., Jannasch, H., Plant, J., Moyer, C., Sansone, F., and McMurtry, G. (2000). Continuous sampling of hydrothermal fluids from Loihi Seamount after the 1996 event. J. Geophys. Res. 105, 19353-19367.