Skip to main content

Advertisement

Log in

Distribution and Interaction Patterns of Bacterial Communities in an Ornithogenic Soil of Seymour Island, Antarctica

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

Abstract

Next-generation, culture-independent sequencing offers an excellent opportunity to examine network interactions among different microbial species. In this study, soil bacterial communities from a penguin rookery site at Seymour Island were analyzed for abundance, structure, diversity, and interaction networks to identify interaction patterns among the various taxa at three soil depths. The analysis revealed the presence of eight phyla distributed in different proportions among the surface layer (0–8 cm), middle layer (20–25 cm), and bottom (35–40 cm). The bottom layer presented the highest values of bacterial richness, diversity, and evenness when compared to surface and middle layers. The network analysis revealed the existence of a unique pattern of interactions in which the soil microbial network formed a clustered topology, rather than a modular structure as is usually found in biological communities. In addition, specific taxa were identified as important players in microbial community structure. Furthermore, simulation analyses indicated that the loss of potential keystone groups of microorganisms might alter the patterns of interactions within the microbial community. These findings provide new insights for assessing the consequences of environmental disturbances at the whole-community level in Antarctica.

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

Access this article

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

Instant access to the full article PDF.

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Roesch LFW, Fulthorpe RR, Riva A, Casella G, Hadwin AKM, Kent AD, Daroub SH, Camargo FA, Farmerie WG, Triplett EW (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290

    PubMed Central  CAS  PubMed  Google Scholar 

  2. MacLean D, Jones JD, Studholme DJ (2009) Application of ‘next-generation’ sequencing technologies to microbial genetics. Nat Rev Microbiol 7:287–296

    PubMed  Google Scholar 

  3. Logares R, Haverkamp TH, Kumar S, Lanzén A, Nederbragt AJ, Quince C, Kauserud H (2012) Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches. J Microbiol Methods 91:106–113

    Article  CAS  PubMed  Google Scholar 

  4. 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 75:5111–5120

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Nacke H, Thürmer A, Wollherr A, Will C, Hodac L, Herold N, Schöning I, Schrumpf M, Daniel R (2011) Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS One 6:e17000

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  6. Zhou J, Deng Y, Luo F, He Z, Tu Q, Zhi X (2010) Functional molecular ecological networks. MBio 1:e00169–10

    PubMed Central  PubMed  Google Scholar 

  7. Faust K, Raes J (2012) Microbial interactions: from networks to models. Nat Rev Microbiol 10:538–550

    Article  CAS  PubMed  Google Scholar 

  8. Degnan PH, Ochman H (2012) Illumina-based analysis of microbial community diversity. ISME J 6:183–194

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. Roesch LFW, Fulthorpe RR, Pereira AB, Pereira CK, Lemos LN, Barbosa AD, Suleimana AKA, Gerber AL, Pereira MG, Loss A, Costa EM (2012) Soil bacterial community abundance and diversity in ice-free areas of Keller Peninsula, Antarctica. Appl Soil Ecol 61:7–15

    Article  Google Scholar 

  10. Ugolini FC, Bockheim JG (2008) Antarctic soils and soil formation in a changing environment: a review. Geoderma 144:1–8

    Article  CAS  Google Scholar 

  11. Simas FNB, Schaefer CEGR, Melo VF, Albuquerque-Filho MR, Michel RFM, Pereira VV, Gomes MRM, Costa LM (2007) Ornithogenic cryosols from Maritime Antarctica: phosphatization as a soil forming process. Geoderma 138:191–203

    Article  CAS  Google Scholar 

  12. Aislabie J, Jordan S, Ayton J, Klassen JL, Barker GM, Turner S (2009) Bacterial diversity associated with ornithogenic soil of the Ross Sea region, Antarctica. Can J Microbiol 55:21–36

    Article  CAS  PubMed  Google Scholar 

  13. Kim OS, Chae N, Lim HS, Cho A, Kim JH, Hong SG, Oh J (2012) Bacterial diversity in ornithogenic soils compared to mineral soils on King George Island, Antarctica. J Microbiol 50:1081–1085

    Article  CAS  PubMed  Google Scholar 

  14. Souza KKD, Schaefer CEGR, Simas FNB, Spinola DN, Paula MD Soil formation in Seymour Island, Weddell Sea, Antarctica, Geomorphology http://dx.doi.org/10.1016/j.geomorph.2014.03.047.

  15. 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  PubMed Central  CAS  PubMed  Google Scholar 

  16. Lupatini M, Suleiman AKA, Jacques RJS, Antoniolli ZI, Ferreira AS, Kuramae EE, Roesch LFW (2014) Network topology reveals high connectance levels and few key microbial genera within soils. Front Env Sci 2:1–11

    Article  Google Scholar 

  17. Huse SM, Welch DM, Morrison HG, Sogin ML (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 12:1889–1898

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Lemos LN, Fulthorpe RR, Triplett EW, Roesch LFW (2011) Rethinking microbial diversity analysis in the high throughput sequencing era. J Microbiol Methods 86:42–51

    Article  CAS  PubMed  Google Scholar 

  19. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. Chen VB, Davis IW, Richardson DC (2009) KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program. Protein Sci 11:2403–2409

    Article  Google Scholar 

  21. Bastian, M, Heymann, S, Jacomy, M (2009) Gephi: an open source software for exploring and manipulating networks. In International AAAI conference on weblogs and social media: San Jose, California

  22. Feldmann RM, Woodbume MO (1988) Geology and paleontology of Seymour Island, Antarctic Peninsula. Geological Society of America, Boulder

    Google Scholar 

  23. Yergeau E, Newsham KK, Pearce DA, Kowalchuk GA (2007) Patterns of bacterial diversity across a range of Antarctic terrestrial habitats. Environ Microbiol 9:2670–2682

    Article  CAS  PubMed  Google Scholar 

  24. Le Blanc JC, Goncalves ER, Mohn WW (2008) Global response to desiccation stress in the soil actinomycete Rhodococcus jostii RHA1. Appl Environ Microbiol 74:2627–2636

    Article  Google Scholar 

  25. Essoussi I, Boujmil R, Nouioui I, Abbassi-Ghozzi I, Hamza A, Boudabous A, Gtari M (2011) Genetic diversity and esterase-profiling of Actinobacteria isolated from Sahara desert stones and monuments. Geomicrobiol J 29:23–28

    Article  Google Scholar 

  26. Mahajan GB, Balachandran L (2012) Antibacterial agents from actinomycetes—a review. Front Biosci 4:240–253

    Article  Google Scholar 

  27. Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF, Dv S (2007) Genomics of actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev 71:495–548

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  28. Acosta-Martínez V, Dowd SE, Sun Y, Allen VG (2008) Tag encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem 40:2762–2770

    Article  Google Scholar 

  29. Rampelotto PH, de Siqueira FA, Barboza AD, Roesch LF (2013) Changes in diversity, abundance, and structure of soil bacterial communities in Brazilian Savanna under different land use systems. Microb Ecol 66:593–607

    Article  PubMed  Google Scholar 

  30. Spain AM, Krumholz LR, Elshahed MS (2009) Abundance, composition, diversity and novelty of soil Proteobacteria. ISME J 3:992–1000

    Article  CAS  PubMed  Google Scholar 

  31. Niederberger TD, McDonald IR, Hacker AL, Soo RM, Barrett JE, Wall DH, Cary SC (2008) Microbial community composition in soils of Northern Victoria Land, Antarctica. Environ Microbiol 10:1713–1724

    Article  CAS  PubMed  Google Scholar 

  32. Teixeira LC, Peixoto RS, Cury JC, Sul WJ, Pellizari VH, Tiedje J, Rosado AS (2010) Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica. ISME J 4:989–1001

    Article  PubMed  Google Scholar 

  33. Sessitsch A, Howieson JG, Perret X, Antoun H, Martínez-Romero E (2002) Advances in Rhizobium research. Crit Rev Plant Sci 21:323–378

    Article  CAS  Google Scholar 

  34. Mendes LW, Kuramae EE, Navarrete A, van Veen J, Tsai SM (2014) Taxonomical and functional microbial community selection in soybean rhizosphere. ISME J. doi:10.1038/ismej.2014.17

    Google Scholar 

  35. Chong CW, Convey P, Pearce DA, Tan IKP (2012) Assessment of soil bacterial communities on Alexander Island (in the maritime and continental Antarctic transitional zone). Polar Biol 35:387–399

    Article  Google Scholar 

  36. Cottee-Jones HEW, Whittaker RJ (2012) The keystone species concept: a critical appraisal. Front Biogeogr 4:117–127

    Google Scholar 

  37. Wassermann S, Faust K (1994) Social network analysis. Cambridge University Press, Cambridge

    Book  Google Scholar 

  38. Deng Y, Jiang YH, Yang Y, He Z, Luo F, Zhou J (2012) Molecular ecological network analyses. BMC Bioinform 13:113

    Article  Google Scholar 

Download references

Acknowledgments

The authors acknowledge the National Council for Scientific and Technological Development (CNPq, Brazil) and the Coordination for the Improvement of Higher Education Personnel (CAPES, Brazil) for their financial support. This work was supported by the INCT-APA (CNPq process no. 574018/2008-5, FAPERJ E-26/170.023/2008), and supported by the Ministry of Science and Technology, and the secretariat for the Marine Resources Interministerial Committee (SECIRM).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Luiz Fernando Wurdig Roesch.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

Table S1

(DOCX 170 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Rampelotto, P.H., Barboza, A.D.M., Pereira, A.B. et al. Distribution and Interaction Patterns of Bacterial Communities in an Ornithogenic Soil of Seymour Island, Antarctica. Microb Ecol 69, 684–694 (2015). https://doi.org/10.1007/s00248-014-0510-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-014-0510-6

Keywords

Navigation