Archaeal diversity in a terrestrial acidic spring field revealed by a novel PCR primer targeting archaeal 16S rRNA genes

FEMS Microbiology Letters

Volumn 319, Issue 1, 2011, Pages 34-43

  Kato, Shingo ^a   Itoh, Takashi ^b   Yamagishi, Akihiko ^a  

^a TOKYO UNIVERSITY OF PHARMACY AND LIFE SCIENCES   (Japan)

^b RIKEN BIORESOURCE CENTER   (Japan)

Author keywords

16S rRNA gene; Archaea; PCR; Terrestrial acidic hot spring; Thermoacidophiles; Thermoplasma

Indexed keywords

RNA 16S;

ACIDITY; ARCHAEAL GENE; ARCHAEBACTERIUM; BACTERIUM CULTURE; CRENARCHAEOTA; GENETIC SIMILARITY; GENETIC VARIABILITY; HYPERTHERMOPHILE; LETTER; LOW TEMPERATURE; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; THERMAL SPRING; THERMOPLASMATALES; UNINDEXED SEQUENCE; WATER SAMPLING; WATER TEMPERATURE;

ARCHAEA; BASE SEQUENCE; BIODIVERSITY; DNA PRIMERS; DNA, ARCHAEAL; GEOLOGIC SEDIMENTS; HOT SPRINGS; HYDROGEN-ION CONCENTRATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S;

ARCHAEA; CRENARCHAEOTA; EURYARCHAEOTA; KORARCHAEOTA; THERMOPLASMA; THERMOPLASMATA;

EID: 79955006053     PISSN: 03781097     EISSN: 15746968     Source Type: Journal    
DOI: 10.1111/j.1574-6968.2011.02267.x     Document Type: Letter

References (57)

1. Altschul SF, Gish W, Miller W, Meyers EW & Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
2. Amann RI, Ludwig W & Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59: 143-169.
3. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ & Weightman AJ (2006) New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microb 72: 5734-5741.
4. Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE & Banfield JF (2006) Lineages of acidophilic archaea revealed by community genomic analysis. Science 314: 1933-1935.
5. Baker GC, Smith JJ & Cowan DA (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Meth 55: 541-555.
6. Barns SM, Fundyga RE, Jeffries MW & Pace NR (1994) Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. P Natl Acad Sci USA 91: 1609-1613.
7. Barns SM, Delwiche CF, Palmer JD & Pace NR (1996) Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. P Natl Acad Sci USA 93: 9188-9193.
8. Brochier-Armanet C, Boussau B, Gribaldo S & Forterre P (2008) Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol 6: 245-252.
9. Brock TD, Brock KM, Belly RT & & Weiss RL (1972) Sulfolobus: a new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Arch Microbiol 84: 54-68.
10. Brosius J, Dull TJ, Sleeter DD & Noller HF (1981) Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol 148: 107-127.
11. Bult CJ, White O, Olsen GJ et al. (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273: 1058-1073.
12. Casanueva A, Galada N, Baker G, Grant W, Heaphy S, Jones B, Yanhe M, Ventosa A, Blamey J & Cowan D (2008) Nanoarchaeal 16S rRNA gene sequences are widely dispersed in hyperthermophilic and mesophilic halophilic environments. Extremophiles 12: 651-656.
13. DeLong EF (1992) Archaea in coastal marine environments. P Natl Acad Sci USA 89: 5685-5689.
14. Dojka MA, Hugenholtz P, Haack SK & Pace NR (1998) Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microb 64: 3869-3877.
15. Eder W, Ludwig W & Huber R (1999) Novel 16S rRNA gene sequences retrieved from highly saline brine sediments of Kebrit Deep, Red Sea. Arch Microbiol 172: 213-218.
16. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
17. Elkins JG, Podar M, Graham DE et al. (2008) A korarchaeal genome reveals insights into the evolution of the Archaea. P Natl Acad Sci USA 105: 8102-8107.
18. Garcia-Moyano A, Gonzalez-Toril E, Aguilera A & Amils R (2007) Prokaryotic community composition and ecology of floating macroscopic filaments from an extreme acidic environment, Rio Tinto (SW, Spain). Syst Appl Microbiol 30: 601-614.
19. Hansel CM, Fendorf S, Jardine PM & Francis CA (2008) Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Appl Environ Microb 74: 1620-1633.
20. Hohn MJ, Hedlund BP & Huber H (2002) Detection of 16S rDNA sequences representing the novel phylum 'Nanoarchaeota': indication for a wide distribution in high temperature biotopes. Syst Appl Microbiol 25: 551-554.
21. Huber G, Spinnler C, Gambacorta A & Stetter KO (1989) Metallosphaera sedula gen. and sp. nov. represents a new genus of aerobic, metal-mobilizing, thermoacidophilic archaebacteria. Syst Appl Microbiol 12: 38-47.
22. Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC & Stetter KO (2002) A new phylum of archaea represented by a nanosized hyperthermophilic symbiont. Nature 417: 63-67.
23. Itoh T (2003) Taxonomy of nonmethanogenic hyperthermophilic and related thermophilic archaea. J Biosci Bioeng 96: 203-212.
24. Itoh T, Suzuki K & Nakase T (1998) Thermocladium modestius gen. nov., sp. nov., a new genus of rod-shaped, extremely thermophilic crenarchaeote. Int J Syst Bacteriol 48: 879-887.
25. Itoh T, Suzuki K, Sanchez PC & Nakase T (1999) Caldivirga maquilingensis gen. nov., sp. nov., a new genus of rod-shaped crenarchaeote isolated from a hot spring in the Philippines. Int J Syst Bacteriol 49: 1157-1163.
26. Itoh T, Suzuki K & Nakase T (2002) Vulcanisaeta distributa gen. nov., sp. nov., and Vulcanisaeta souniana sp. nov., novel hyperthermophilic, rod-shaped crenarchaeotes isolated from hot springs in Japan. Int J Syst Evol Micr 52: 1097-1104.
27. Itoh T, Nomura N & Sako Y (2003a) Distribution of 16S rRNA introns among the family Thermoproteaceae and their evolutionary implications. Extremophiles 7: 229-233.
28. Itoh T, Suzuki K, Sanchez PC & Nakase T (2003b) Caldisphaera lagunensis gen. nov., sp. nov., a novel thermoacidophilic crenarchaeote isolated from a hot spring at Mt Maquiling, Philippines. Int J Syst Evol Micr 53: 1149-1154.
29. Itoh T, Yoshikawa N & Takashina T (2007) Thermogymnomonas acidicola gen. nov., sp. nov., a novel thermoacidophilic, cell wall-less archaeon in the order Thermoplasmatales, isolated from a solfataric soil in Hakone, Japan. Int J Syst Evol Micr 57: 2557-2561.
30. Jackson CR, Langner HW, Donahoe-Christiansen J, Inskeep WP & McDermott TR (2001) Molecular analysis of microbial community structure in an arsenite-oxidizing acidic thermal spring. Environ Microbiol 3: 532-542.
31. Jennifer EB, McArthur JV & Lawrence JS (2002) Recovery of novel bacterial diversity from a forested wetland impacted by reject coal. Environ Microbiol 4: 764-769.
32. Kato S, Kobayashi C, Kakegawa T & Yamagishi A (2009a) Microbial communities in iron-silica-rich microbial mats at deep-sea hydrothermal fields of the Southern Mariana Trough. Environ Microbiol 11: 2094-2111.
33. Kato S, Yanagawa K, Sunamura M et al. (2009b) Abundance of Zetaproteobacteria within crustal fluids in back-arc hydrothermal fields of the Southern Mariana Trough. Environ Microbiol 11: 3210-3222.
34. Kato S, Takano Y, Kakegawa T et al. (2010) Biogeography and biodiversity in sulfide structures of active and inactive vents at deep-sea hydrothermal fields of the Southern Mariana Trough. Appl Environ Microb 76: 2968-2979.
35. Kimura H, Ishibashi J, Masuda H, Kato K & Hanada S (2007) Selective phylogenetic analysis targeting 16S rRNA genes of hyperthermophilic archaea in the deep-subsurface hot biosphere. Appl Environ Microb 73: 2110-2117.
36. Lane DJ (1991) 16S/23s rRNA sequencing. John Wiley & Sons, Chichester, UK.
37. Loy A, Arnold R, Tischler P, Rattei T, Wagner M & Horn M (2008) probeCheck - a central resource for evaluating oligonucleotide probe coverage and specificity. Environ Microbiol 10: 2894-2898.
38. Massana R, Murray AE, Preston CM & DeLong EF (1997) Vertical distribution and phylogenetic characterization of marine planktonic archaea in the Santa Barbara channel. Appl Environ Microb 63: 50-56.
39. Ng C-C, Chang C-C & Shyu Y-T (2005) Archaeal community revealed by 16S rRNA and fluorescence in situ hybridization in a sulphuric hydrothermal hot spring, northern Taiwan. World J Microb Biot 21: 933-939.
40. Ohba T, Sawa T, Taira N, Ohwada M, Morikawa N & Kazahaya K (2007) Chemical evolution of volcanic fluid present in the hydrothermal system developed on the central cones of Hakone volcano caldera. Reports of Hot Springs Research Institute of Kanagawa Prefecture 39: 1-42 (in Japanese).
41. Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276: 734-740.
42. Prokofeva M, Miroshnichenko M, Kostrikina N, Chernyh N, Kuznetsov B, Tourova T & Bonch-Osmolovskaya E (2000) Acidilobus aceticus gen. nov., sp. nov., a novel anaerobic thermoacidophilic archaeon from continental hot vents in Kamchatka. Int J Syst Evol Micr 50: 2001-2008.
43. Reysenbach A-L (2001) Class IV. Thermoplasmata class. nov. Bergey's Manual of Systematic Bacteriology, 2nd edn (Boone DR & Castenholz RW, eds), pp. 335-340. Springer, New York.
44. Reysenbach AL, Ehringer M & Hershberger K (2000) Microbial diversity at 83°C in calcite springs, Yellowstone National Park: another environment where the Aquificales and 'Korarchaeota' coexist. Extremophiles 4: 61-67.
45. Robertson CE, Harris JK, Spear JR & Pace NR (2005) Phylogenetic diversity and ecology of environmental Archaea. Curr Opin Microbiol 8: 638-642.
46. Rowe OF, Sánchez-España J, Hallberg KB & Johnson DB (2007) Microbial communities and geochemical dynamics in an extremely acidic, metal-rich stream at an abandoned sulfide mine (Huelva, Spain) underpinned by two functional primary production systems. Environ Microbiol 9: 1761-1771.
47. Schleper C, Jurgens G & Jonuscheit M (2005) Genomic studies of uncultivated archaea. Nat Rev Microbiol 3: 479-488.
48. Schloss PD & Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microb 71: 1501-1506.
49. Segerer A, Neuner A, Kristjansson JK & Stetter KO (1986) Acidianus infernus gen. nov., sp. nov., and Acidianus brierleyi comb. nov: facultatively aerobic, extremely acidophilic thermophilic sulfur-metabolizing archaebacteria. Int J Syst Bacteriol 36: 559-564.
50. Segerer AH, Trincone A, Gahrtz M & Stetter KO (1991) Stygiolobus azoricus gen. nov., sp. nov. represents a novel genus of anaerobic, extremely thermoacidophilic archaebacteria of the order Sulfolobales. Int J Syst Bacteriol 41: 495-501.
51. Shimizu S, Akiyama M, Naganuma T, Fujioka M, Nako M & Ishijima Y (2007) Molecular characterization of microbial communities in deep coal seam groundwater of northern Japan. Geobiology 5: 423-433.
52. Spear JR, Walker JJ, McCollom TM & Pace NR (2005) Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. P Natl Acad Sci USA 102: 2555-2560.
53. Takai K & Horikoshi K (1999) Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 152: 1285-1297.
54. Takai K & Sako Y (1999) A molecular view of archaeal diversity in marine and terrestrial hot water environments. FEMS Microbiol Ecol 28: 177-188.
55. Wilson M, Siering P, White C, Hauser M & Bartles A (2008) Novel Archaea and Bacteria dominate stable microbial communities in North America's largest hot spring. Microb Ecol 56: 292-305.
56. Woese C (1987) Bacterial evolution. Microbiol Rev 51: 221-271.
57. Zillig W, Stetter K, Schafer W, Janekovic D, Wunderl S, Holz I & Palm P (1981) Thermoproteales: a novel type of extremely thermoacidophilic anaerobic archaebacteria isolated from icelandic solfataras. Zbl Bakt Mik Hyg I C 2: 205-227.