Skip to main content

Advertisement

SpringerLink
Log in

Generalized Soil Thaumarchaeota Community in Weathering Rock and Saprolite

  • Environmental Microbiology
  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

Relatively little is known of the archaeal communities associated with endolithic environments, compared to other microbial groups such as bacteria and fungi. Analyzing the pyrosequenced archaeal 16S ribosomal RNA (rRNA) gene V1–V3 region, we investigated the archaeal community associated with aboveground-exfoliated weathering layers of a granite gneiss, and of the saprolite derived from this rock at 1 m depth below the soil surface, in a forested hilly area south of Seoul, South Korea. In both these sites, an archaeal community dominated by the phylum Thaumarchaeota was identified. The archaeal community in all cases closely resembled that of the surface layer of acidic soils in temperate climates of Korea. It appears that there is no clear distinction in archaeal community composition between a soil and a rock and a saprolite despite a tremendous difference in the concentration of total nitrogen and organic carbon. Of the chemical properties we measured, pH was the best predictor of the archaeal community composition and relative abundance of thaumarchaeal subphyla. These findings reinforce the view that soil archaea are mostly generalists, whose ecology is not closely dependent on nitrogen concentration or soil organic matter status, the presence of living roots, or the abundant presence of any other biota.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. Friedmann EI, Ocampo R (1976) Endolithic blue green algae in the dry valleys: primary producers in the antarctic desert ecosystem. Science 193:1247–1249

    Article  CAS  PubMed  Google Scholar 

  2. Hughes KA, Lawley B (2003) A novel Antarctic microbial endolithic community within gypsum crusts. Environ Microbiol 5:555–565

    Article  PubMed  Google Scholar 

  3. Siebert J, Hirsch P, Hoffmann B, Gliesche CG, Peissl K, Jendrach M (1996) Cryptoendolithic microorganisms from Antarctic sandstone of Linnaeus Terrace (Asgard Range): diversity, properties and interactions. Biodivers Conserv 5(11):1337–1363

    Article  Google Scholar 

  4. Hirsch PFEW, Eckhardt FEW, Palmer RJ Jr (1995) Fungi active in weathering of rock and stone monuments. Can J Bot 73(S1):1384–1390

    Article  Google Scholar 

  5. Gerrath JF, Gerrath JA, Larson DW (1995) A preliminary account of endolithic algae of limestone cliffs of the Niagara Escarpment. Can J Bot 73(5):788–793

    Article  Google Scholar 

  6. Walker JJ, Pace NR (2007) Phylogenetic composition of rocky mountain endolithic microbial ecosystems. Appl Environ Microbiol 73(11):3497–3504

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  7. Pointing SB, Chan Y, Lacap DC, Lau MCY, Jurgens JA, Farrell RL (2009) Highly specialized microbial diversity in hyper-arid polar desert. Proc Natl Acad Sci U S A 106(47):19964–19969

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  8. Yung CCC, Chan Y, Lacap DC, Pérez-Ortega S, de los Rios-Murillo A, Lee CK, Cary SC, Pointing SB (2014) Characterization of chasmoendolithic community in Miers Valley, McMurdo Dry Valleys, Antarctica. Microb Ecol 68(2):351–359

    PubMed  Google Scholar 

  9. Smith MC, Bowman JP, Scott FJ, Line MA (2000) Sublithic bacteria associated with Antarctic quartz stones. Antarct Sci 12(02):177–184

    Article  Google Scholar 

  10. de la Torre JR, Goebel BM, Friedmann EI, Pace NR (2003) Microbial diversity of cryptoendolithic communities from the McMurdo Dry Valleys, Antarctica. Appl Environ Microbiol 69(7):3858–3867

    Article  PubMed Central  PubMed  Google Scholar 

  11. Horath T, Bachofen R (2009) Molecular characterization of an endolithic microbial community in dolomite rock in the central Alps (Switzerland). Microb Ecol 58:290–306

    Article  CAS  PubMed  Google Scholar 

  12. Ziolkowski LA, Mykytczuk NCS, Omelon CR, Johnson H, Whyte LG, Slater GF (2013) Arctic gypsum endoliths: a biogeochemical characterization of a viable and active microbial community. Biogeosci Discuss 10:2269–2304

    Article  Google Scholar 

  13. Robinson CK, Wierzchos J, Black C, Crits-Christoph A, Ma B, Ravel J et al (2014) Microbial diversity and the presence of algae in halite endolithic communities are correlated to atmospheric moisture in the hyper arid zone of the Atacama Desert. Environmental Microbiology. doi:10.1111/1462-2920.12364

    PubMed  Google Scholar 

  14. Korea Meteorological Administration (2011) Climatological normal of Korea 1981∼2010. http://www.kma.go.kr/.

  15. Hur M, Kim Y, Song HR, Kim JM, Choi YI, Yi H (2011) Effect of genetically modified poplars on soil microbial communities during the phytoremediation of waste mine tailings. Appl Environ Microbiol 77:7611–7619

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  16. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  17. R Core Team. (2013) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/.

  18. Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser I, Schuster SC, Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806–809

    Article  CAS  PubMed  Google Scholar 

  19. He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM, Xu MG, Di H (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(9):2364–2374

    Article  CAS  PubMed  Google Scholar 

  20. Tripathi BM, Kim M, Lai-Hoe A, Shukor NAA, Rahim RA, Go R, Adams JM (2013) PH dominates variation in tropical soil archaeal diversity and community structure. FEMS Microbiol Ecol 86:303–311

    Article  CAS  PubMed  Google Scholar 

  21. Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N (2010) Examining the global distribution of dominant archaeal populations in soil. ISME J 5(5):908–917

    Article  PubMed Central  PubMed  Google Scholar 

  22. Hu HW, Zhang LM, Dai Y, Di HJ, He JZ (2013) pH-dependent distribution of soil ammonia oxidizers across a large geographical scale as revealed by high-throughput pyrosequencing. J Soils Sediments 13(8):1439–1449

    Article  Google Scholar 

  23. Kundu K, Bergmann I, Hahnke S, Klocke M, Sharma S, Sreekrishnan TR (2013) Carbon source—a strong determinant of microbial community structure and performance of an anaerobic reactor. J Biotechnol 168:616–624

    Article  CAS  PubMed  Google Scholar 

  24. 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. doi:10.1111/j.1574-6941.2009.00748.x

    Article  CAS  PubMed  Google Scholar 

  25. Bonan G (2002) Ecological climatology: concepts and applications. Cambridge University Press, Cambridge

    Google Scholar 

  26. Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, Tischler P, Spieck E, Streit W, Stahl DA, Wagner M, Schleper C (2010) Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol 18(8):331–340

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by a grant from the National Research Foundation (NRF) grant funded by the Korean government, Ministry of Education, Science and Technology (MEST) (NRF-2013-031400). We particularly thank Prof. Jongsik Chun of the Chunlab Inc. (EzTaxon-e database) for providing us with their archaeal reference database. Ke Dong was supported by the SNU Global Scholarship Program.

Author information

Authors and Affiliations

  1. College of Natural Sciences, Seoul National University, Seoul, 151-742, South Korea

    Ke Dong, Woo-Sung Kim, Binu Mani Tripathi & Jonathan Adams

  2. Laboratory of Geographical Ecology, College of Natural Sciences, Seoul National University, Room 320, Building 502, Seoul, 151-742, South Korea

    Jonathan Adams

Authors
  1. Ke Dong
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Woo-Sung Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Binu Mani Tripathi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jonathan Adams
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jonathan Adams.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

Supplementary Fig. S1

(DOCX 1049 kb)

Supplementary Fig. S2

(DOCX 300 kb)

Supplementary Table S3

(DOCX 18 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Dong, K., Kim, WS., Tripathi, B.M. et al. Generalized Soil Thaumarchaeota Community in Weathering Rock and Saprolite. Microb Ecol 69, 356–360 (2015). https://doi.org/10.1007/s00248-014-0526-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-014-0526-y

Keywords

Search

Navigation