Soil bacterial community abundance and diversity in ice-free areas of Keller Peninsula, Antarctica

Applied Soil Ecology

Volumn 61, Issue , 2012, Pages 7-15

  Roesch, Luiz F W ^a   Fulthorpe, Roberta R ^b   Pereira, Antonio B ^a   Pereira, Clarissa K ^a   Lemos, Leandro N ^a   Barbosa, Anthony D ^a   Suleiman, Afnan K A ^a   Gerber, Alexandra L ^c   Pereira, Marcos G ^d   Loss, Arcângelo ^d   da Costa, Elias M ^d  

^a UNIVERSIDADE FEDERAL DO PAMPA   (Brazil)

^b UNIVERSITY OF TORONTO   (Canada)

^c LABORATÓRIO NACIONAL DE COMPUTAÇÃO CIENTÍFICA   (Brazil)

^d FEDERAL RURAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

Author keywords

16SrRNA; Antarctic microbiome; Microbially influenced global change; Pyrosequencing

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 84863768631     PISSN: 09291393     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.apsoil.2012.04.009     Document Type: Article

References (41)

1. Angel R., Soares M., Ungar E., Gillor O. Biogeography of soil archaea and bacteria along a steep precipitation gradient. ISME J. 2010, 4(4):553-563.
2. Bergmann G., et al. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol. Biochem. 2011, 43(7):1450-1455.
3. Berry D., Ben Mahfoudh K., Wagner M., Loy A. Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Appl. Environ. Microbiol. 2011, 77(21):7846-7849.
4. Campbell I.B, Claridge G.G.C. Antarctica: Soils, Weathering Processes and Environment 1987, Elsevier, Amsterdam, The Netherlands.
5. Caporaso J.G., et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 2010, 7(5):335-336.
6. Cary S.C., McDonald I.R., Barrett J.E., Cowan D.A. On the rocks: the microbiology of Antarctic Dry Valley soils. Nat. Rev. Microbiol. 2010, 8:129-138.
7. Chu H., et al. Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ. Microbiol. 2010, 12(11):2998-3006.
8. Convey P. Antarctic ecosystems. Encyclopedia of Biodiversity 2007, Elsevier, San Diego, USA, http://dx.doi.org/10.1016/B0-12-226865-2/00014-6. 2nd ed. (online). S.A. Levin (Ed.).
9. Embrapa Manual de Métodos de Análises de Solos 1997, Rio de Janeiro, 212 pp. 2nd ed.
10. Faith D.P. Conservation evaluation and phylogenetic diversity. Biol. Conserv. 1992, 61(1):1-10.
11. Fierer N., Jackson R. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. U.S.A. 2006, 103(3):626-631.
12. Fierer N., Strickland M., Liptzin D., Bradford M., Cleveland C. Global patterns in belowground communities. Ecol. Lett. 2009, 12(11):1238-1249.
13. Francelino M.R., et al. Geomorphology and soils distribution under paraglacial conditions in an ice-free area of Admiralty Bay, King George Island, Antarctica. Catena 2011, 85(3):194-204.
14. Fulthorpe R., Roesch L., Riva A., Triplett E. Distantly sampled soils carry few species in common. ISME J. 2008, 2(9):901-910.
15. Ganzert L., Lipski A., Hubberten H., Wagner D. The impact of different soil parameters on the community structure of dominant bacteria from nine different soils located on Livingston Island, South Shetland Archipelago, Antarctica. FEMS Microbiol. Ecol. 2011, 76:476-491.
16. Giongo A., et al. PANGEA: pipeline for analysis of next generation amplicons. ISME J. 2010, 4(7):852-861.
17. Hamady M., Walker J.J., Harris J.K., Gold N.J., Knight R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat. Methods 2008, 5(3):235-237.
18. Headland R.K. A Chronology of Antarctic Exploration. Quaritch, London, A Synopsis of Events and Activities from the Earliest Times until the International Polar Years, 2007-2009 2009, 722 pp.
19. Janssen P. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 2006, 72(3):1719-1728.
20. Larkin M.A, et al. Clustal W and clustal X version 2.0. Bioinformatics 2007, 23(21):2947-2948.
21. Lauber C., Hamady M., Knight R., Fierer N Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 2009, 75(15):5111-5120.
22. Lee C.K., Barbier B.A., Bottos E.M., McDonald I.R., Cary S.C. The inter-valley soil comparative survey: the ecology of Dry Valley edaphic microbial communities. ISME J. 2011, (E-pub ahead of print). 10.1038/ismej.2011.170.
23. Lemos L., Fulthorpe R., Triplett E., Roesch L Rethinking microbial diversity analysis in the high throughput sequencing era. J. Microbiol. Methods 2011, 86(1):42-51.
24. Marschner H., Römheld V., Ossenberg-Neuhaus H Rapid methods for measuring changes in pH and reducing processes along roots of intact plants. Z. Pflanzenphysiol. Bd. 1982, 105:407-416.
25. Mitchell R., et al. Is vegetation composition or soil chemistry the best predictor of the soil microbial community?. Plant Soil 2010, 333(1-2):417-430.
26. Nei M., Kumar S. Molecular Evolution and Phylogenetics 2000, Oxford University Press, New York.
27. Niederberger T.D., McDonald I.R., Hacker A.L., Soo R.M., Barrett J.E., Wall D.H., Cary S.C. Microbial community composition in soils of Northern Victoria Land, Antarctica. Environ. Microbiol. 2008, 10(7):1713-1724.
28. Ochyra R., Smith R.I.L., Bednarek-Ochyra H. The Illustrated Moss Flora of Antarctica 2008, Cambridge University Press, Cambridge, UK, 704 pp.
29. Øvstedal D.O., Smith R.I.L. Lichens of Antarctica and South Georgia. A Guide to Their Identification and Ecology 2001, Cambridge University Press, Cambridge, UK, 424 pp.
30. Pereira A.B., Spielman A., Amartins M.F.N., Francelino M.R. Plant communities from ice-free areas of Keller Peninsul, King George Island, Antarctica. Oecol. Bras. 2007, 10(1):14-22.
31. Roesch L.F., et al. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 2007, 1:283-290.
32. Rousk J., et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 2010, 4(10):1340-1351.
33. Schloss P.D., Westcott S.L., Ryabin T., et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009, 75:7537-7541.
34. Shannon P., et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13(11):2498-2504.
35. Simas F.N.B., et al. Genesis, properties and classification of Cryosols from Admiralty Bay, maritime Antarctica. Geoderma 2008, 144(1-2):116-122.
36. Tamura K., et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28(10):2731-2739.
37. Teixeira L., et al. Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica. ISME J. 2010, 4(8):989-1001.
38. Ugolini F.C., Bockheim J.G. Antarctic soils and soil formation in a changing environment: a review. Geoderma 2008, 144:1-8.
39. Uroz S., Buee M., Murat C., Frey-Klett P., Martin F Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ. Microbiol. Rep. 2010, 2(2):281-288.
40. Wall D.H., Virginia R.A. Controls on soil biodiversity: insights from extreme environments. Appl. Soil Ecol. 1999, 13(2):137-150.
41. Wang Q., Garrity G.M., Tiedje J.M., Cole JR Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 2007, 73(16):5261-5267.