Hostname: page-component-586b7cd67f-vdxz6 Total loading time: 0 Render date: 2024-11-20T08:32:12.886Z Has data issue: false hasContentIssue false
  • English
  • Français

The impacts of deglaciation and human activity on the taxonomic structure of prokaryotic communities in Antarctic soils on King George Island

Published online by Cambridge University Press:  05 October 2018

E.V. Pershina ,
E.A. Ivanova ,
E.V. Abakumov  and
E.E. Andronov
E.V. Pershina*
Affiliation:
All-Russia Research Institute for Agricultural Microbiology, Podbelsky Highway 3, Saint Petersburg, Russia Saint Petersburg State University, Universitetskaya Embankment 7/9, Saint Petersburg, Russia
E.A. Ivanova
Affiliation:
All-Russia Research Institute for Agricultural Microbiology, Podbelsky Highway 3, Saint Petersburg, Russia Saint Petersburg State University, Universitetskaya Embankment 7/9, Saint Petersburg, Russia V.V. Dokuchaev Soil Institute, Pyzhevskiy Lane 7 (b.2), Moscow, Russia
E.V. Abakumov
Affiliation:
Saint Petersburg State University, Universitetskaya Embankment 7/9, Saint Petersburg, Russia
E.E. Andronov
Affiliation:
All-Russia Research Institute for Agricultural Microbiology, Podbelsky Highway 3, Saint Petersburg, Russia Saint Petersburg State University, Universitetskaya Embankment 7/9, Saint Petersburg, Russia V.V. Dokuchaev Soil Institute, Pyzhevskiy Lane 7 (b.2), Moscow, Russia
*
*[email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

The soil microbiome was investigated at environmentally distinct locations on King George Island in the South Shetland Islands (Antarctic Peninsula) using 16 S rRNA gene pyrosequencing. The taxonomic composition of the soil prokaryotes (bacteria and archaea) was evaluated at three sites representing human-disturbed soils (Bellingshausen Station) and soils undergoing different stages of deglaciation (fresh and old moraines located near Ecology Glacier). The taxonomic analysis revealed 20 bacterial and archaeal phyla, among which Proteobacteria (29.6%), Actinobacteria (25.3%), Bacteroidetes (15.8%), Cyanobacteria (11.2%), Acidobacteria (4.9%) and Verrucomicrobia (4.5%) comprised most of the microbiome. In a beta-diversity analysis, the samples formed separate clusters. The Bellingshausen Station samples were characterized by an increased amount of Nostoc sp. and Janibacter sp. Although the deglaciation history had less of an effect on the soil microbiome, the early stages of deglaciation (Sample 1) had a higher proportion of bacteria belonging to the families Xanthomonadaceae, Sphingomonadaceae and Nocardioidaceae, whereas the older moraines (Sample 2) were enriched with Chthoniobacteriacae and N1423WL. Solirubrobacteriales, Gaiellaceae and Chitinophagaceae bacteria were present in both stages of deglaciation, characterized by genus-level differences. Taxonomic analysis of the abundant operational taxonomic units (OTUs) revealed both endemic (Marisediminicola antarctica, Hymenobacter glaciei) and cosmopolitan bacterial species in the microbiomes.

Keywords

16 S rRNA amplicon pyrosequencingAntarctic morainesanthropogenic impactmicrobiome
Type
Biological Sciences
Information
Antarctic Science , Volume 30 , Issue 5 , October 2018 , pp. 278 - 288
Copyright
© Antarctic Science Ltd 2018 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Bates, S.T., Berg-Lyons, D., Caporaso, J.G., Walters, W.A., Knight, R. & Fierer, N. 2011. Examining the global distribution of dominant archaeal populations in soil. The ISME Journal, 5, 10.1038/ismej.2010.171.Google Scholar
Bockheim, J.G., ed. 2015. The soils of Antarctica. Cham, Switzerland: Springer, 322 pp.Google Scholar
Bolter, M. 2001. Soil development and soil biology on King George Island, Maritime Antarctic. Polish Polar Research, 2, 10.2478/v10183-011-0002-z.Google Scholar
Bottos, E.M., Scarrow, J.W., Archer, S.D.J., McDonald, I.R. & Cary, S.C. 2014. Bacterial community structures of Antarctic soils. In Cowan, D.A., ed. Antarctic terrestrial microbiology: physical and biological properties of Antarctic soils. Heidelberg: Springer, 9–33.Google Scholar
Bowman, J.P. & Nichols, D.S. 2005. Novel members of the family Flavobacteriaceae from Antarctic maritime habitats including Subsaximicrobium wynnwilliamsii gen. nov., sp. nov., Subsaximicrobium saxinquilinus sp. nov., Subsaxibacter broadyi gen. nov., sp. nov., Lacinutrix copepodicola gen. nov., sp. nov., and novel species of the genera Bizionia, Gelidibacter and Gillisia . International Journal of Systematic and Evolutionary Microbiology, 55, 10.1099/ijs.0.63527-0.Google Scholar
Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7, 10.1038/nmeth0510-335.Google Scholar
Chong, C.W., Pearce, D.A., Convey, P., Yew, W.C. & Tan, I.K.P. 2012. Patterns in the distribution of soil bacterial 16S rRNA gene sequences from different regions of Antarctica. Geoderma, 181–182, 10.1016/j.geoderma.2012.02.017.Google Scholar
Chong, C.W., Tan, G.Y.A., Wong, R.C.S., Riddle, M.J. & Tan, I.K.P. 2009. DGGE fingerprinting of bacteria in soils from eight ecologically different sites around Casey Station, Antarctica. Polar Biology, 32, 10.1007/s00300-009-0585-6.Google Scholar
De Gannes, V., Bekele, I., Dipchansingh, D., Wuddivira, M.N., De Cairies, S., Boman, M. & Hickey, W.J. 2016. Microbial community structure and function of soil following ecosystem conversion from native forests to teak plantation forests. Frontiers in Microbiology, 7, 10.3389/fmicb.2016.01976.Google Scholar
DeSantis, T.Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., Huber, T., Dalevi, D., Hu, P. & Andersen, G.L. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology, 72, 10.1128/AEM.03006-05.Google Scholar
Fierer, N. & Jackson, R.B. 2006. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences of the United States of America, 103, 10.1073/pnas.0507535103.Google Scholar
Fierer, N., Leff, J.W., Adams, B.J., Nielsen, U.N., Bates, S.T., Lauber, C.L., Owens, S., Gilbert, J.A., Wall, D.H. & Caporaso, J.G. 2012. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proceedings of the National Academy of Sciences of the United States of America, 109, 10.1073/pnas.1215210110.Google Scholar
Foong, C.P., Ling, C.M.W.V. & González, M. 2010. Metagenomic analyses of the dominant bacterial community in the Fildes Peninsula, King George Island (South Shetland Islands). Polar Science, 4, 10.1016/j.polar.2010.05.010.Google Scholar
Fukuda, W., Chino, Y., Araki, S., Kondo, Y., Imanaka, H., Kanai, T., Atomi, H. & Imanaka, T. 2014. Polymorphobacter multimanifer gen. nov., sp. nov., a polymorphic bacterium isolated from Antarctic white rock. International Journal of Systematic and Evolutionary Microbiology, 64, 10.1099/ijs.0.050005-0.Google Scholar
González-Rocha, G., Muñoz-Cartes, G., Canales-Aguirre, C.B., Lima, C.A., Domínguez-Yévenes, M., Bello-Toledo, H. & Hernández, C.E. 2017. Diversity structure of culturable bacteria isolated from the Fildes Peninsula (King George Island, Antarctica): a phylogenetic analysis perspective. PLoS ONE, 12(6), e0179390.Google Scholar
Hughes, K.A. 2014. Threats to soil communities: human impacts. In Cowan, D.A., ed. Antarctic terrestrial microbiology: physical and biological properties of Antarctic soils. Heidelberg: Springer, 263–277.Google Scholar
Janssen, P.H. 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Applied and Environmental Microbiology, 72, 10.1128/AEM.72.3.1719-1728.2006.Google Scholar
Jia, L., Feng, X., Zheng, Z., Han, L., Hou, X., Lu, Z. & Lv, J. 2015. Polymorphobacter fuscus sp. nov., isolated from permafrost soil, and emended description of the genus Polymorphobacter . International Journal of Systematic and Evolutionary Microbiology, 65, 10.1099/ijsem.0.000514.Google Scholar
Johnson, R.M., Madden, J.M. & Swafford, J.R. 1972. Taxonomy of Antarctic bacteria from soils and air primarily of the McMurdo Station and Victoria Land Dry Valleys region. Antarctic Research Series Terrestrial Biology III, 30, 10.1029/AR030p0035.Google Scholar
Larsbrink, J., Zhu, Y., Kharade, S.S., Kwiatkowski, K.J., Eijsink, V.G.H., Koropatkin, N.M., McBride, M.J. & Pope, P.B. 2016. A polysaccharide utilization locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin. Biotechnology for Biofuels, 9, 10.1186/s13068-016-0674-z.Google Scholar
Li, H.R., Yu, Y., Luo, W. & Zeng, Y.X. 2010. Marisediminicola antarctica gen. nov., sp. nov., an actinobacterium isolated from the Antarctic. International Journal of Systematic and Evolutionary Microbiology, 60, 10.1099/ijs.0.018754-0.Google Scholar
Lim, Y.K., Kweon, O.J., Kim, H.R., Kim, T.H. & Lee, M.K. 2017. First case of bacteremia caused by Janibacter hoylei . APMIS, 125, 10.1111/apm.12693.Google Scholar
Liu, Q., Liu, H.C., Zhang, J.L., Zhou, Y.G. & Xin, Y.H. 2015. Nocardioides glacieisoli sp. nov., isolated from a glacier. International Journal of Systematic and Evolutionary Microbiology, 65, 10.1099/ijsem.0.000658.Google Scholar
Lozupone, C. & Knight, R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology, 71, 10.1128/AEM.71.12.8228-8235.2005.Google Scholar
Myung, I.S., Lee, Y.K., Jeong, I.H., Moon, S.Y., Lee, S.W. & Shim, H.S. 2007. A new disease, bacterial black rot of Korean radish, caused by Acidovorax konjaci . Molecular Biology and Evolution, 24, 10.5197/j.2044-0588.2010.022.026.Google Scholar
Niederberger, T.D., Sohm, J.A., Gunderson, T.E., Parker, A.E., Tirindelli, J., Capone, D.G., Carpenter, E.J. & Cary, S.C. 2015. Microbial community composition of transiently wetted Antarctic Dry Valley soils. Frontiers in Microbiology, 6, 10.3389/fmicb.2015.00009.Google Scholar
Pan, Q., Wang, F., Zhang, Y., Cai, M., He, J. & Yang, H. 2013. Denaturing gradient gel electrophoresis fingerprinting of soil bacteria in the vicinity of the Chinese Great Wall Station, King George Island, Antarctica. Journal of Environmental Sciences, 25, 10.1016/S1001-0742(12)60229-0.Google Scholar
Peter, H.U., Buesser, C., Mustafa, O. & Pfeiffer, S. 2008. Risk assessment for the Fildes Peninsula and Ardley Island, and development of management plans for their designation as Specially Protected or Specially Managed Areas. Dessau-Roßlau: Umweltbundesamt, 344 pp. https://umweltbundesamt.de/publikationen/risk-assessment-for-fildes-peninsula-ardley-island.Google Scholar
Richter, I., Herbold, C.W., Lee, C.K., McDonald, I.R., Barrett, J.E. & Cary, S.C. 2014. Influence of soil properties on archaeal diversity and distribution in the McMurdo Dry Valleys, Antarctica. FEMS Microbiology Ecology, 89, 10.1111/1574-6941.12322.Google Scholar
Shivaji, S., Chaturvedi, P., Begum, Z., Pindi, P.K., Manorama, R., Padmanaban, D.A., Shouche, Y.S., Pawar, S., Vaishampayan, P., Dutt, C.B.S. & Datta, G.N. 2009. Janibacter hoylei sp. nov., Bacillus isronensis sp. nov. and Bacillus aryabhattai sp. nov., isolated from cryotubes used for collecting air from the upper atmosphere. International Journal of Systematic and Evolutionary Microbiology, 59, 10.1099/ijs.0.002527-0.Google Scholar
Simas, F.N.B., Schaeffer, C.E.G.R., Michel, R.F.M., Francelimo, M.R. & Bockheim, J.G. 2015. Soils of the South Orkney and South Shetland islands, Antarctica. In Bockheim, J.G., ed. The soils of Antarctica. Cham, Switzerland: Springer, 227–274.Google Scholar
Siple, C.A. & Darling, P.A. 1941. Bacteria of Antarctica. Journal of Bacteriology, 42, 83–98.Google Scholar
Strunecký, O., Elster, J. & Komárek, J. 2012. Molecular clock evidence for survival of Antarctic cyanobacteria (Oscillatoriales, Phormidium autumnale) from Paleozoic times. FEMS Microbiology Ecology, 82, 10.1111/j.1574-6941.2012.01426.x.Google Scholar
Teixeira, L.C.R.S., Peixoto, R.S., Cury, J.C., Sul, W.J., Pellizari, V.H., Tiedje, J. & Rosado, A.S. 2010. Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica. The ISME Journal, 4, 10.1002/9781118297674.ch105.Google Scholar
Tindall, B. 2004. Prokaryotic diversity in the Antarctic: the tip of the iceberg. Microbial Ecology, 47, 10.1007/s00248-003-1050-7.Google Scholar
Vincent, W.F. 2000. Evolutionary origins of Antarctic microbiota: invasion, selection and endemism. Antarctic Science, 12, 10.1017/S0954102000000420.Google Scholar
Wang, N.F., Zhang, T., Zhang, F., Wang, E.T., He, J.F., Ding, H., Zhang, B.T., Liu, J., Ran, X.B. & Zang, J.Y. 2015. Diversity and structure of soil bacterial communities in the Fildes Region (maritime Antarctica) as revealed by 454 pyrosequencing. Frontiers in Microbiology, 6, 10.3389/fmicb.2015.01188.Google Scholar
Wang, Q., Garrity, G.M., Tiedje, J.M. & Cole, J.R. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73, 10.1128/AEM.00062-07.Google Scholar
Weidler, G.W., Gerbl, F.W. & Stan-Lotter, H. 2008. Crenarchaeota and their role in the nitrogen cycle in a subsurface radioactive thermal spring in the Austrian Central Alps. Applied and Environmental Microbiology, 74, 10.1128/AEM.02602-07.Google Scholar
Yan, W., Ma, H., Shi, G., Li, Y., Sun, B., Xiao, X. & Zhang, Y. 2017. Independent shifts of abundant and rare bacterial populations across East Antarctica glacial foreland. Frontiers in Microbiology, 8, 10.3389/fmicb.2017.01534.Google Scholar
Zdanowski, M.K., Zmuda-Baranowska, M.J., Borsuk, P., Światecki, A., Górniak, D., Wolicka, D., Jankowska, K.M. & Grzesiak, J. 2013. Culturable bacteria community development in postglacial soils of Ecology Glacier, King George Island, Antarctica. Polar Biology, 36, 10.1007/s00300-012-1278-0.Google Scholar
Supplementary material: PDF

Pershina et al. supplementary material

Table S1 and Figure S1

Download Pershina et al. supplementary material(PDF)
PDF 2.3 MB