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.
Similar content being viewed by others
References
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
MacLean D, Jones JD, Studholme DJ (2009) Application of ‘next-generation’ sequencing technologies to microbial genetics. Nat Rev Microbiol 7:287–296
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
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
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
Zhou J, Deng Y, Luo F, He Z, Tu Q, Zhi X (2010) Functional molecular ecological networks. MBio 1:e00169–10
Faust K, Raes J (2012) Microbial interactions: from networks to models. Nat Rev Microbiol 10:538–550
Degnan PH, Ochman H (2012) Illumina-based analysis of microbial community diversity. ISME J 6:183–194
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
Ugolini FC, Bockheim JG (2008) Antarctic soils and soil formation in a changing environment: a review. Geoderma 144:1–8
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
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
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
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.
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
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
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
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
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
Chen VB, Davis IW, Richardson DC (2009) KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program. Protein Sci 11:2403–2409
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
Feldmann RM, Woodbume MO (1988) Geology and paleontology of Seymour Island, Antarctic Peninsula. Geological Society of America, Boulder
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
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
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
Mahajan GB, Balachandran L (2012) Antibacterial agents from actinomycetes—a review. Front Biosci 4:240–253
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
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
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
Spain AM, Krumholz LR, Elshahed MS (2009) Abundance, composition, diversity and novelty of soil Proteobacteria. ISME J 3:992–1000
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
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
Sessitsch A, Howieson JG, Perret X, Antoun H, Martínez-Romero E (2002) Advances in Rhizobium research. Crit Rev Plant Sci 21:323–378
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
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
Cottee-Jones HEW, Whittaker RJ (2012) The keystone species concept: a critical appraisal. Front Biogeogr 4:117–127
Wassermann S, Faust K (1994) Social network analysis. Cambridge University Press, Cambridge
Deng Y, Jiang YH, Yang Y, He Z, Luo F, Zhou J (2012) Molecular ecological network analyses. BMC Bioinform 13:113
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
Corresponding author
Electronic Supplementary Material
Below is the link to the electronic supplementary material.
Table S1
(DOCX 170 kb)
Rights and permissions
About this article
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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00248-014-0510-6