Elevational Patterns in Archaeal Diversity on Mt. Fuji

PLoS ONE

Volumn 7, Issue 9, 2012, Pages

  Singh, Dharmesh ^a   Takahashi, Koichi ^b   Adams, Jonathan M ^a  

^a Seoul National University   (South Korea)

^b SHINSHU UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; ARCHAEAL DNA; NITRATE; POTASSIUM; RNA 16S;

ALTITUDE; ARCHAEON; ARTICLE; BOOTSTRAPPING; COMMUNITY ECOLOGY; DATA BASE; DESERT; DNA SEQUENCE; ECOLOGICAL NICHE; EURYARCHAEOTA; EVOLUTIONARY ADAPTATION; FOREST; GENE AMPLIFICATION; GEOGRAPHIC ELEVATION; GEOLOGY; JAPAN; MESOPHILE; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROCLIMATE; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PYROSEQUENCING; SOIL MICROFLORA; SOLAR RADIATION; SPECIES DIVERSITY; SPECIES RICHNESS; TAXONOMY; THAUMARCHAEOTA; TOPOGRAPHY; VOLCANIC ASH;

ALTITUDE; ARCHAEA; JAPAN; PHYLOGENY; RNA, RIBOSOMAL, 16S;

ARCHAEA; BACTERIA (MICROORGANISMS); EURYARCHAEOTA;

EID: 84866134338     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0044494     Document Type: Article

References (76)

1. Woese CR, Fox GE, (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 74: 5088-5090.
2. Woese CR, Kandler O, Wheelis ML, (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A 87: 4576-4579.
3. DeLong EF, (1998) Everything in moderation: Archaea as 'non-extremophiles'. Current Opinion in Genetics & Development 8: 649-654.
4. Ehrhardt CJ, Haymon RM, Lamontagne MG, Holden PA, (2007) Evidence for hydrothermal Archaea within the basaltic flanks of the East Pacific Rise. Environmental Microbiology 9: 900-912.
5. Delong EF, (1992) Archaea in Coastal Marine Environments. Proceedings of the National Academy of Sciences of the United States of America 89: 5685-5689.
6. Fuhrman JA, McCallum K, Davis AA, (1992) Novel major archaebacterial group from marine plankton. Nature 356: 148-149.
7. Boetius A, Ravenschlag K, Schubert CJ, Rickert D, Widdel F, et al. (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407: 623-626.
8. Orphan VJ, House CH, Hinrichs KU, McKeegan KD, DeLong EF, (2002) Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. Proceedings of the National Academy of Sciences of the United States of America 99: 7663-7668.
9. Li L, Kato C, Horikoshi K, (1999) Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench. Marine Biotechnology 1: 391-400.
10. Schleper C, Holben W, Klenk HP, (1997) Recovery of Crenarchaeotal ribosomal DNA sequences from freshwater-lake sediments. Applied and Environmental Microbiology 63: 321-323.
11. Hershberger KL, Barns SM, Reysenbach AL, Dawson SC, Pace NR, (1996) Wide diversity of Crenarchaeota. Nature 384: 420.
12. Abreu C, Jurgens G, De Marco P, Saano A, Bordalo AA, (2001) Crenarchaeota and Euryarchaeota in temperate estuarine sediments. J Appl Microbiol 90: 713-718.
13. Jurgens G, Glockner FO, Amann R, Saano A, Montonen L, et al. (2000) Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization. Fems Microbiology Ecology 34: 45-56.
14. Bintrim SB, Donohue TJ, Handelsman J, Roberts GP, Goodman RM, (1997) Molecular phylogeny of archaea from soil. Proceedings of the National Academy of Sciences of the United States of America 94: 277-282.
15. Buckley DH, Graber JR, Schmidt TM, (1998) Phylogenetic analysis of nonthermophilic members of the kingdom Crenarchaeota and their diversity and abundance in soils. Applied and Environmental Microbiology 64: 4333-4339.
16. Oline DK, Schmidt SK, Grant MC, (2006) Biogeography and landscape-scale diversity of the dominant crenarchaeota of soil. Microbial Ecology 52: 480-490.
17. Jurgens G, Lindstrom K, Saano A, (1997) Novel group within the kingdom Crenarchaeota from boreal forest soil. Applied and Environmental Microbiology 63: 803-805.
18. Sandaa RA, Enger O, Torsvik V, (1999) Abundance and diversity of Archaea in heavy-metal-contaminated soils. Appl Environ Microbiol 65: 3293-3297.
19. Takai K, Moser DP, DeFlaun M, Onstott TC, Fredrickson JK, (2001) Archaeal diversity in waters from deep South African gold mines. Applied and Environmental Microbiology 67: 5750-5760.
20. Friedrich MW, Schmitt-Wagner D, Lueders T, Brune A, (2001) Axial differences in community structure of Crenarchaeota and Euryarchaeota in the highly compartmentalized gut of the soil-feeding termite Cubitermes orthognathus. Applied and Environmental Microbiology 67: 4880-4890.
21. Furlong MA, Singleton DR, Coleman DC, Whitman WB, (2002) Molecular and culture-based analyses of prokaryotic communities from an agricultural soil and the burrows and casts of the earthworm Lumbricus rubellus. Applied and Environmental Microbiology 68: 1265-1279.
22. Robertson CE, Harris JK, Spear JR, Pace NR, (2005) Phylogenetic diversity and ecology of environmental Archaea. Current Opinion in Microbiology 8: 638-642.
23. Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P, (2008) Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nature Reviews Microbiology 6: 245-252.
24. Brochier-Armanet C, Forterre P, Gribaldo S, (2011) Phylogeny and evolution of the Archaea: one hundred genomes later. Current Opinion in Microbiology 14: 274-281.
25. Auguet JC, Barberan A, Casamayor EO, (2010) Global ecological patterns in uncultured Archaea. Isme Journal 4: 182-190.
26. Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, et al. (2011) Examining the global distribution of dominant archaeal populations in soil. Isme Journal 5: 908-917.
27. Nicol GW, Leininger S, Schleper C, Prosser JI, (2008) The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environmental Microbiology 10: 2966-2978.
28. Zhang LM, Wang M, Prosser JI, Zheng YM, He JZ, (2009) Altitude ammonia-oxidizing bacteria and archaea in soils of Mount Everest. Fems Microbiology Ecology 70: 208-217.
29. Angel R, Soares MIM, Ungar ED, Gillor O, (2010) Biogeography of soil archaea and bacteria along a steep precipitation gradient. Isme Journal 4: 553-563.
30. Currie DJ, Paquin V, (1987) Large-Scale Biogeographical Patterns of Species Richness of Trees. Nature 329: 326-327.
31. Lomolino MV, (2001) Elevational gradients of species-density: historical and prospective views. Global Ecology and Biogeography 10: 3-13.
32. McCain CM, (2005) Elevational gradients in diversity of small mammals. Ecology 86: 366-372.
33. Adams JM (2009) Species richness: patterns in the diversity of life. Chichester: Springer in association with Praxis. xvii, 380 p., [316] plates p.
34. Huston MA (1994) Biological diversity: the coexistence of species on changing landscapes. Cambridge: Cambridge University Press. xix, 681 p. p.
35. Brown JH, (2001) Mammals on mountainsides: elevational patterns of diversity. Global Ecology and Biogeography 10: 101-109.
36. Hu JH, Xie F, Li C, Jiang JP (2011) Elevational Patterns of Species Richness, Range and Body Size for Spiny Frogs. Plos One 6.
37. Fierer N, McCain CM, Meir P, Zimmermann M, Rapp JM, et al. (2011) Microbes do not follow the elevational diversity patterns of plants and animals. Ecology.
38. Bryant JA, Lamanna C, Morlon H, Kerkhoff AJ, Enquist BJ, et al. (2008) Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity. Proceedings of the National Academy of Sciences of the United States of America 105: 11505-11511.
39. Singh D, Takahashi K, Kim M, Chun J, Adams JM, (2012) A hump-backed trend in bacterial diversity with elevation on mount fuji, Japan. Microbial ecology 63: 429-437.
40. Kan JJ, Clingenpeel S, Macur RE, Inskeep WP, Lovalvo D, et al. (2011) Archaea in Yellowstone Lake. Isme Journal 5: 1784-1795.
41. Ohsawa M, (1984) Differentiation of Vegetation Zones and Species Strategies in the Subalpine Region of Mt Fuji. Vegetatio 57: 15-52.
42. Manerkar MA, Seena S, Barlocher F, (2008) Q-RT-PCR for assessing archaea, bacteria, and fungi during leaf decomposition in a stream. Microbial Ecology 56: 467-473.
43. Buee M, De Boer W, Martin F, van Overbeek L, Jurkevitch E, (2009) The rhizosphere zoo: An overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors. Plant and Soil 321: 189-212.
44. He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM, et al. (2007) Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ Microbiol 9: 2364-2374.
45. Jia ZJ, Conrad R, (2009) Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environmental Microbiology 11: 1658-1671.
46. Lehtovirta LE, Prosser JI, Nicol GW, (2009) Soil pH regulates the abundance and diversity of Group 1.1c Crenarchaeota. FEMS Microbiol Ecol 70: 367-376.
47. Leininger S, Urich T, Schloter M, Schwark L, Qi J, et al. (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806-809.
48. Angelov A, Liebl W, (2006) Insights into extreme thermoacidophily based on genome analysis of Picrophilus torridus and other thermoacidophilic archaea. Journal of Biotechnology 126: 3-10.
49. Ochsenreiter T, Selezi D, Quaiser A, Bonch-Osmolovskaya L, Schleper C, (2003) Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16 S RNA surveys and real time PCR. Environmental Microbiology 5: 787-797.
50. Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk HP, et al. (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environmental Microbiology 7: 1985-1995.
51. Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, et al. (2008) A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proceedings of the National Academy of Sciences of the United States of America 105: 2134-2139.
52. Tourna M, Stieglmeier M, Spang A, Konneke M, Schintlmeister A, et al. (2011) Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proceedings of the National Academy of Sciences of the United States of America 108: 8420-8425.
53. Kim JG, Jung MY, Park SJ, Rijpstra WIC, Sinninghe Damste JS, et al. (2012) Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I.1b from an agricultural soil. Environmental Microbiology 14: 1528-1543.
54. Masuzawa T, Nishitani S, (1991) Seasonal changes in the soil temperature over a three-year period at the timberline on Mt. Fuji. Reports of Faculty of Science, Shizuoka University 25: 69-78.
55. Miehe G, Miehe S, (1994) Zur oberen Waldgrenze in tropischen Gebirgen. Phytocoenologia 24: 53-110.
56. Winiger M, (1981) Zur thermisch-hygrischen Gliederung des Mount Kenya. Erdkunde 35: 248-263.
57. Korner C, Bannister P, Mark AF, (1986) Altitudinal Variation in Stomatal Conductance, Nitrogen-Content and Leaf Anatomy in Different Plant Life Forms in New-Zealand. Oecologia 69: 577-588.
58. Jung MY, Park SJ, Min D, Kim JS, Rijpstra WIC, et al. (2011) Enrichment and Characterization of an Autotrophic Ammonia-Oxidizing Archaeon of Mesophilic Crenarchaeal Group I.1a from an Agricultural Soil. Applied and Environmental Microbiology 77: 8635-8647.
59. Martens-Habbena W, Berube PM, Urakawa H, de la TorreJR, Stahl DA, (2009) Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461: 976-U234.
60. Stehr G, Bottcher B, Dittberner P, Rath G, Koops HP, (1995) The Ammonia-Oxidizing Nitrifying Population of the River Elbe Estuary. Fems Microbiology Ecology 17: 177-186.
61. Park HD, Noguera DR, (2007) Characterization of two ammonia-oxidizing bacteria isolated from reactors operated with low dissolved oxygen concentrations. Journal of Applied Microbiology 102: 1401-1417.
62. Di HJ, Cameron KC, Shen JP, Winefield CS, O'Callaghan M, et al. (2010) Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions. FEMS Microbiol Ecol 72: 386-394.
63. Verhamme DT, Prosser JI, Nicol GW, (2011) Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms. Isme Journal 5: 1067-1071.
64. 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. Applied and Environmental Microbiology 74: 1620-1633.
65. Chen XP, Zhu YG, Xia Y, Shen JP, He JZ, (2008) Ammonia-oxidizing archaea: important players in paddy rhizosphere soil? Environmental Microbiology 10: 1978-1987.
66. Herrmann M, Saunders AM, Schramm A, (2008) Archaea dominate the ammonia-oxidizing community in the rhizosphere of the freshwater macrophyte Littorella uniflora. Applied and Environmental Microbiology 74: 3279-3283.
67. Hur M, Kim Y, Song HR, Kim JM, Choi YI, et al. (2011) Effect of genetically modified poplars on soil microbial communities during the phytoremediation of waste mine tailings. Appl Environ Microbiol 77: 7611-7619.
68. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities. Applied and Environmental Microbiology 75: 7537-7541.
69. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, et al. (2012) Introducing EzTaxon-e: a prokaryotic 16 S rRNA Gene sequence database with phylotypes that represent uncultured species. International Journal of Systematic and Evolutionary Microbiology 62: 716-721.
70. Magurran AE (2004) Measuring biological diversity: Oxford:Blackwell Science. 100 p.
71. Lozupone C, Knight R, (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 71: 8228-8235.
72. Stamatakis A, (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
73. Clarke KR, Gorley RN (2006) Primer v6: User Manual/Tutorials: Primer-E Ltd: Plymouth, UK.
74. Legendre P, Lapointe FJ, Casgrain P, (1994) Modeling brain evolution from behavior: A permutational regression approach. Evolution 48: 1487-1499.
75. Sarle WS (1990) The VARCLUS Procedure. SAS/STAT User's Guide: Cary NC: SAS Institute, Inc.
76. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.