Thermoanaerobaculum aquaticum gen. nov., sp. nov., the first cultivated member of acidobacteria subdivision 23, isolated from a hot spring

International Journal of Systematic and Evolutionary Microbiology

Volumn 63, Issue PART 11, 2013, Pages 4149-4157

  Losey, Nathaniel A ^a   Stevenson, Bradley S ^a   Busse, Hans Jürgen ^b   Damsté, Jaap S Sinninghe ^c   Rijpstra, W Irene C ^c   Rudd, Stephen ^d   Lawson, Paul A ^a  

^a UNIVERSITY OF OKLAHOMA   (United States)

^b UNIVERSITY OF VETERINARY MEDICINE   (Austria)

^c ROYAL NETHERLANDS INSTITUTE FOR SEA RESEARCH   (Netherlands)

^d Hot Springs Diagnostic Associates   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARDIOLIPIN; FRESH WATER; ISOPRENOID; PHOSPHATIDYLETHANOLAMINE; PHOSPHATIDYLGLYCEROL; POLYAMINE; PYRUVIC ACID; QUINONE DERIVATIVE; RNA 16S;

ACIDOBACTERIA; ARTICLE; BACTERIAL CELL; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM ISOLATION; CONTROLLED STUDY; CULTIVATED SPECIES; FATTY ACID ANALYSIS; GENE SEQUENCE; GROWTH RATE; LIPID COMPOSITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHASE CONTRAST MICROSCOPY; PHYLOGENY; PRIORITY JOURNAL; THERMAL SPRING; THERMOANAEROBACULUM AQUATICUM;

ACIDOBACTERIA; BACTERIA (MICROORGANISMS); NEGIBACTERIA;

EID: 84887029270     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.051425-0     Document Type: Article

References (51)

1. Araujo, J. F., de Castro, A. P., Costa, M. M., Togawa, R. C., Júnior, G. J., Quirino, B. F., Bustamante, M. M., Williamson, L., Handelsman, J. & Kruger, R. H. (2012). Characterization of soil bacterial assemblies in Brazilian savanna-like vegetation reveals acidobacteria dominance. Microb Ecol 64, 760-770.
2. Armstrong, P. A., Lyons, W. B. & Gaudette, H. E. (1979). Application of formaldoxime colorimetric method for the determination of manganese in the pore waters of anoxic marine sediments. Estuaries 2, 198-201.
3. Barns, S. M., Takala, S. L. & Kuske, C. R. (1999). Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl Environ Microbiol 65, 1731-1737.
4. Barns, S. M., Cain, E. C., Sommerville, L. & Kuske, C. R. (2007). Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl Environ Microbiol 73, 3113-3116.
5. Bligh, E. G. & Dyer, W. J. (1959). A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37, 911-917.
6. Bryant, D. A., Costas, A. M., Maresca, J. A., Chew, A. G., Klatt, C. G., Bateson, M. M., Tallon, L. J., Hostetler, J., Nelson, W. C. & other authors (2007). Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic acidobacterium. Science 317, 523-526.
7. Busse, H.-J. & Auling, G. (1988). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11, 1-8
8. Cline, J. D. (1969). Spectrophotometric determination of hydrogen sulfide in natural waters. Limnol Oceanogr 14, 454-458.
9. Coates, J. D., Ellis, D. J., Gaw, C. V. & Lovley, D. R. (1999). Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer. Int J Syst Bacteriol 49, 1615-1622.
10. Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T. & other authors (2009). The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37, D141-D145.
11. Dedysh, S. N., Kulichevskaya, I. S., Serkebaeva, Y. M., Mityaeva, M. A., Sorokin, V. V., Suzina, N. E., Rijpstra, W. I. C. & Sinninghe Damsté, J. S. (2012). Bryocella elongata gen. nov., sp. nov., a member of subdivision 1 of the Acidobacteria isolated from a methanotrophic enrichment culture, and emended description of Edaphobacter aggregans Koch et al. 2008. Int J Syst Evol Microbiol 62, 654-664.
12. DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P. & Andersen, G. L. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72, 5069-5072.
13. Eichler, B. & Pfennig, N. (1988). A new purple sulfur bacterium from stratified freshwater lakes, Amoebobacter purpureus sp. nov. Arch Microbiol 149, 395-400.
14. Eichorst, S. A., Breznak, J. A. & Schmidt, T. M. (2007). Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria. Appl Environ Microbiol 73, 2708-2717.
15. Foesel, B. U., Rohde, M. & Overmann, J. (2013). Blastocatella fastidiosa gen. nov., sp. nov., isolated from semiarid savanna soil the first described species of Acidobacteria subdivision 4. Syst Appl Microbiol 36, 82-89.
16. Fukunaga, Y., Kurahashi, M., Yanagi, K., Yokota, A. & Harayama, S. (2008). Acanthopleuribacter pedis gen. nov., sp. nov., a marine bacterium isolated from a chiton, and description of Acanthopleuribacteraceae fam. nov., Acanthopleuribacterales ord. nov., Holophagaceae fam. nov., Holophagales ord. nov. and Holophagae classis nov. in the phylum 'Acidobacteria'. Int J Syst Evol Microbiol 58, 2597-2601.
17. Hanaichi, T., Sato, T., Iwamoto, T., Malavasi-Yamashiro, J., Hoshino, M. & Mizuno, N. (1986). A stable lead by modification of Sato's method. J Electron Microsc (Tokyo) 35, 304-306.
18. Hosoya, R., Yokoyama, Y., Hamana, K. & Itoh, T. (2006). Polyamine analysis within the eubacterial thirteen phyla Acidobacteria, Actinobacteria, Chlorobi, Chloroflexi, Chyrsiogenetes, Deferribacteres, Fibrobacteres, Firmicutes, Fusobacteria, Gemmatimonadetes, Nitropirae, Planctomycetes, and Verrucomicrobia. Microbiol Cult Collect 22, 21-33.
19. Hutson, R. A., Thompson, D. E. & Collins, M. D. (1993). Genetic interrelationships of saccharolytic Clostridium botulinum types B, E and F and related clostridia as revealed by small-subunit rRNA gene sequences. FEMS Microbiol Lett 108, 103-110.
20. Izumi, H., Nunoura, T., Miyazaki, M., Mino, S., Toki, T., Takai, K., Sako, Y., Sawabe, T. & Nakagawa, S. (2012). Thermotomaculum hydrothermale gen. nov., sp. nov., a novel heterotrophic thermophile within the phylum Acidobacteria from a deep-sea hydrothermal vent chimney in the Southern Okinawa Trough. Extremophiles 16, 245-253.
21. Janssen, P. H. (2006). Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 72, 1719-1728.
22. Kishimoto, N., Kosako, Y. & Tano, T. (1991). Acidobacterium capsulatum gen. nov., sp. nov.: an acidophilic chemoorganotrophic bacterium containing menaquinone from acidic mineral environment. Curr Microbiol 22, 1-7.
23. Koch, I. H., Gich, F., Dunfield, P. F. & Overmann, J. (2008). Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soils. Int J Syst Evol Microbiol 58, 1114-1122.
24. Kulichevskaya, I. S., Suzina, N. E., Liesack, W. & Dedysh, S. N. (2010). Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the Acidobacteria. Int J Syst Evol Microbiol 60, 301-306.
25. Kulichevskaya, I. S., Kostina, L. A., Valásková, V., Rijpstra, W. I. C., Sinninghe Damsté, J. S., de Boer, W. & Dedysh, S. N. (2012). Acidicapsa borealis gen. nov., sp. nov. and Acidicapsa ligni sp. nov., subdivision 1 Acidobacteria from Sphagnum peat and decaying wood. Int J Syst Evol Microbiol 62, 1512-1520.
26. Lau, M. C., Aitchison, J. C. & Pointing, S. B. (2009). Bacterial community composition in thermophilic microbial mats from five hot springs in central Tibet. Extremophiles 13, 139-149.
27. Lawson, P. A., Gharbia, S. E., Shah, H. N. & Clark, D. R. (1989). Recognition of Fusobacterium nucleatum subgroups Fn-1, Fn-2 and Fn-3 by ribosomal RNA gene restriction patterns. FEMS Microbiol Lett 53, 41-45.
28. Liesack, W., Bak, F., Kreft, J. U. & Stackebrandt, E. (1994). Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds. Arch Microbiol 162, 85-90.
29. Lipman, D. J. & Pearson, W. R. (1985). Rapid and sensitive protein similarity searches. Science 227, 1435-1441.
30. Lovley, D. R. & Phillips, E. J. (1986). Organic matter mineralization with reduction of ferric iron in anaerobic sediments. Appl Environ Microbiol 51, 683-689.
31. Lovley, D. R. & Phillips, E. J. (1988). Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese. Appl Environ Microbiol 54, 1472-1480.
32. Mannisto, M. K., Rawat, S., Starovoytov, V. & Haggblom, M. M. (2011). Terriglobus saanensis sp. nov., an acidobacterium isolated from tundra soil. Int J Syst Evol Microbiol 61, 1823-1828.
33. Marks, C. R., Stevenson, B. S., Rudd, S. & Lawson, P. A. (2012). Nitrospira-dominated biofilm within a thermal artesian spring: a case for nitrification-driven primary production in a geothermal setting. Geobiology 10, 457-466.
34. McDonald, D., Price, M. N., Goodrich, J., Nawrocki, E. P., DeSantis, T. Z., Probst, A., Andersen, G. L., Knight, R. & Hugenholtz, P. (2012). An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610-618.
35. Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G + C content of deoxyribonucleic acid by high performance liquid chromatography. Int J Syst Bacteriol 39, 159-167.
36. Okamura, K., Kawai, A., Yamada, T. & Hiraishi, A. (2011). Acidipila rosea gen. nov., sp. nov., an acidophilic chemoorganotrophic bacterium belonging to the phylum Acidobacteria. FEMS Microbiol Lett 317, 138-142.
37. Pankratov, T. A. & Dedysh, S. N. (2010). Granulicella paludicola gen. nov., sp. nov., Granulicella pectinivorans sp. nov., Granulicella aggregans sp. nov. and Granulicella rosea sp. nov., acidophilic, polymer-degrading acidobacteria from Sphagnum peat bogs. Int J Syst Evol Microbiol 60, 2951-2959.
38. Pankratov, T. A., Kirsanova, L. A., Kaparullina, E. N., Kevbrin, V. V. & Dedysh, S. N. (2012). Telmatobacter bradus gen. nov., sp. nov., a cellulolytic facultative anaerobe from subdivision 1 of the Acidobacteria, and emended description of Acidobacterium capsulatum Kishimoto et al. 1991. Int J Syst Evol Microbiol 62, 430-437.
39. Porter, K. G. & Feig, Y. S. (1980). The use of DAPI for identifying and counting aquatic microflora. Limnol Oceanogr 25, 943-948.
40. Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J. & Glockner, F. O. (2007). SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35, 7188-7196.
41. Rios-Hernandez, L. A., Gieg, L. M. & Suflita, J. M. (2003). Biodegradation of an alicyclic hydrocarbon by a sulfate-reducing enrichment from a gas condensate-contaminated aquifer. Appl Environ Microbiol 69, 434-443.
42. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
43. Sinninghe Damsté, J. S., Rijpstra, W. I. C., Hopmans, E. C., Weijers, J. W. H., Foesel, B. U., Overmann, J. & Dedysh, S. N. (2011). 13,16 Dimethyl octacosanedioic acid (iso-diabolic acid), a common membrane-spanning lipid of Acidobacteria subdivisions 1 and 3. Appl Environ Microbiol 77, 4147-4154.
44. Stolz, A., Busse, H.-J. & Kampfer, P. (2007). Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 57, 572-576.
45. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28, 2731-2739.
46. Tanner, R. S. (2002). Cultivation of bacteria and fungi. In Manual of Environmental Microbiology, 3rd edn, pp. 69-78. Edited by C. J. Hurst, R. L. Crawford, A. L. Mills, J. L. Garland, L. D. Stetzenbach & D. A. Lipson. Washington, DC: American Society for Microbiology.
47. Tindall, B. J. (1990a). Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66, 199-202.
48. Tindall, B. J. (1990b). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13, 128-130.
49. Větrovský, T. Baldrian, P.(2013). The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. PLoS ONE 8, e57923.
50. Widdel, F. & Hansen, T. A. (1992). The dissimilatory sulfateand sulfur-reducing bacteria. In The Prokaryotes, 2nd edn, pp. 583-624. Edited by A. Balows, H. G. Truper, M. Dworkin, W. Harder & K. H. Schleifer. New York: Springer.
51. Zimmermann, J., Gonzalez, J. M., Saiz-Jimenez, C. & Ludwig, W. (2005). Detection and phylogenetic relationships of highly diverse uncultured acidobacterial communities in Altamira cave using 23S rRNA sequence analyses. Geomicrobiol J 22, 379-388.