Microbial Ecology

, Volume 63, Issue 2, pp 429–437 | Cite as

A Hump-Backed Trend in Bacterial Diversity with Elevation on Mount Fuji, Japan

  • Dharmesh Singh
  • Koichi Takahashi
  • Mincheol Kim
  • Jongsik Chun
  • Jonathan M. Adams
Soil Microbiology


Little is known of how bacterial diversity in soils varies with elevation. One previous study found a decline with elevation, whereas another found no trend. We chose Mount Fuji of Japan as a geologically and topographically simple mountain system. Samples were taken at elevational intervals, between the base of the mountain at 1,000 m and its summit at 3,700 m. Polymerase chain reaction-amplified soil DNA for the bacterial 16S gene targeting V1–V3 region was pyrosequenced using the 454 Roche machine, and taxonomically classified with reference to a bioinformatic database. There was a significant “peak” in total bacterial diversity at around 2,500 m above the tree line with a decline towards the highest elevations around 3,700 m near the summit. Individual bacterial phyla show distinct trends—increase, decrease, or a mid-elevational “bulge” in diversity. Bacterial diversity does not parallel woody plant or herbaceous plant diversity. We suggest that beyond the tree and vegetation line, the more extreme temperature fluctuations, stronger UV, lack of nutrients, and more frequent disturbance of the loose substrate of these slopes allows less competition and greater bacterial species diversity due to “lottery” recruitment. However, at the highest elevations, the physiological challenges are so extreme that fewer bacterial species are capable of surviving.


Bacterial Community Proteobacteria Actinobacteria Bacterial Diversity Bacteroidetes 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



DS is supported by the Korean Government Scholarship Program, Ministry of Education, Science, and Technology, South Korea.

Supplementary material

248_2011_9900_MOESM1_ESM.xls (36 kb)
Supplementary Table S1 Geographic and climatic information about the samples (XLS 36.5 kb)
248_2011_9900_MOESM2_ESM.xls (34 kb)
Supplementary Table S2 Diversity indices (XLS 34.0 kb)
248_2011_9900_MOESM3_ESM.xls (35 kb)
Supplementary Table S3 Relative average abundance of all bacterial phyla (XLS 35.0 kb)
248_2011_9900_MOESM5_ESM.gif (15 kb)
Supplementary Figure 1

Relationship between soil pH and bacterial diversity (GIF 15.1 kb)

248_2011_9900_MOESM4_ESM.eps (18.6 mb)
High resolution image (EPS 18.6 mb)


  1. 1.
    Adams JM (2009) Species richness: patterns in the diversity of life. Springer, Berlin, p 353, Praxis divisionCrossRefGoogle Scholar
  2. 2.
    Brown JH (2001) Mammals on mountainsides: elevational patterns of diversity. Glob Ecol Biogeogr 10:101–109CrossRefGoogle Scholar
  3. 3.
    Bryant JA, Lamanna C, Morlon H, Keroff AJ, Enquist BJ, Green JL (2008) Microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. Proceedings of the National Academy of Sciences (USA) 105:11505–11511CrossRefGoogle Scholar
  4. 4.
    Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336PubMedCrossRefGoogle Scholar
  5. 5.
    Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW (2007) EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Micro 57:2259–2261CrossRefGoogle Scholar
  6. 6.
    Chun J, Kim KY, Lee JH, Choi Y (2010) The analysis of oral microbial communities of wild-type and toll-like receptor 2-deficient mice using a 454 GS FLX Titanium pyrosequencer. BMC Microbiol 10:101PubMedCrossRefGoogle Scholar
  7. 7.
    Connell JH (1970) A predator–prey system in the Marine Intertidal Region. I. Balanus glandula and several predatory species of Thais. Ecological Monographs 40:49–78CrossRefGoogle Scholar
  8. 8.
    Currie DJ, Paquin V (1987) Large-scale biogeographical patterns of species richness in trees. Nature 329:326–327CrossRefGoogle Scholar
  9. 9.
    Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences (USA) 105:626–631CrossRefGoogle Scholar
  10. 10.
    Fierer N, McCain CM, Meir P, Zimmermann M, Rapp JM, Silaman MR, Knight R (2011) Microbes do not follow the elevational diversity patterns of plants and animals. Ecology 92:797–804PubMedCrossRefGoogle Scholar
  11. 11.
    Fujimura, I (1971) The climate and weather of Mt. Fuji. In: Report of the scientific survey of Mt. Fuji: Fuji-kyuko Ltd, Tokyo. pp. 211–345 (in Japanese)Google Scholar
  12. 12.
    Gaston KJ (2000) Global patterns in biodiversity. Nature 405:220–227PubMedCrossRefGoogle Scholar
  13. 13.
    Grime JP (2001) Plant strategies, vegetation processes, and ecosystem properties, 2nd edn. Wiley, New YorkGoogle Scholar
  14. 14.
    Hamady M, Lozupone C, Knight R (2009) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4:17–27PubMedCrossRefGoogle Scholar
  15. 15.
    Huston MA (1994) Biological diversity: the coexistence of species on changing landscapes. Cambridge University Press, Cambridge, pp. 708Google Scholar
  16. 16.
    Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75:5111–5120PubMedCrossRefGoogle Scholar
  17. 17.
    Lomolino MV (2001) Elevational gradients of species-density: historical and prospective views. Glob Ecol Biogeogr 10:3–13CrossRefGoogle Scholar
  18. 18.
    Lozupone CA, Knight R (2005) UniFrac: a new method for comparing microbial communities. Applied Environmental Microbiology 71:8228–8235Google Scholar
  19. 19.
    Lozupone CA, Knight R (2007) Global patterns in bacterial diversity. Proceedings of the National Academy of Sciences (USA) 104:11436–11440CrossRefGoogle Scholar
  20. 20.
    Kalra YP (1995) Determination of pH of soils by different methods: collaborative study. J AOAC INTERNATIONAL 78:310–324Google Scholar
  21. 21.
    Koerner C (2003) Alpine plant life: functional plant ecology of high mountain ecosystems. Springer, BerlinGoogle Scholar
  22. 22.
    McCain CM (2005) Elevational gradients in diversity of small mammals. Ecology 86:366–372CrossRefGoogle Scholar
  23. 23.
    Mt. Fuji Volcano Disaster Management Conference (2002) Available from: Japanese government report (in Japanese)
  24. 24.
    Nemergut DR, Costello EK, Hamady M, Lozupone C, Jiang L, Schmidt SK, Fierer N, Townsend AR, Cleveland CC, Stanish L, Knight R (2010) Global patterns in the biogeography of bacterial taxa. Environ Microbiol 13:135–144CrossRefGoogle Scholar
  25. 25.
    Ohsawa M (1984) Differentiation of vegetation zones and species strategies in the subalpine region of Mt Fuji. Vegetation 57:15–52CrossRefGoogle Scholar
  26. 26.
    Renaud PE, Webb T, Bjørgesæter A, Karakassis I, Kędra M, Kendall M, Labrune C, Lampadariou N, Somerfield P, Włodarska-Kowalczuk M et al (2009) Continental-scale patterns in benthic invertebrate diversity: insights from the MarBEF database. Mar Ecol Prog Ser 382:239–252CrossRefGoogle Scholar
  27. 27.
    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. Appl Environ Microbiol 75:7537–7541PubMedCrossRefGoogle Scholar
  28. 28.
    Terborgh J (1977) Bird species diversity on an Andean elevational gradient. Ecology 58:1007–1019CrossRefGoogle Scholar
  29. 29.
    Unno T, Jang J, Han D, Kim JH, Sadowsky MJ, Kim OS, Chun J, Hur HG (2010) Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in Watersheds. Environ Sci Technol 44:7777–7782PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Dharmesh Singh
    • 1
  • Koichi Takahashi
    • 2
  • Mincheol Kim
    • 1
  • Jongsik Chun
    • 1
  • Jonathan M. Adams
    • 1
  1. 1.Department of Biological Sciences, College of Natural SciencesSeoul National UniversitySeoulSouth Korea
  2. 2.Department of Biology, Faculty of ScienceShinshu UniversityMatsumotoJapan

Personalised recommendations