[en] Antarctic soils are known to be oligotrophic and of having low buffering capacities. It is expected that this is particularly the case for inland high altitude regions. We hypothesized that the bedrock type and the presence of macrobiota in these soils enforce a high selective pressure on their bacterial communities. To test this, we analysed the bacterial community structure in 52 soil samples from the western Sør Rondane Mountains (Dronning Maud Land, East Antarctica) using the Illumina MiSeq platform in combination with ARISA fingerprinting. The samples were taken along broad environmental gradients in an area covering nearly 1000 km². Ordination and variation partitioning analyses revealed that the total organic carbon content was the most significant variable in structuring the bacterial communities, followed by pH, electric conductivity, bedrock type and the moisture content, while spatial distance was of relatively minor importance. Acidobacteria (Chloracidobacteria) and Actinobacteria (Actinomycetales) dominated gneiss derived mineral soil samples, while Proteobacteria (Sphingomonadaceae), Cyanobacteria, Armatimonadetes and candidate division FBP dominated soil samples with a high total organic carbon content that were mainly situated on granite derived bedrock.
Centre/Unité de recherche :
Centre for Protein Engineering
Disciplines :
Sciences de l’environnement & écologie Microbiologie
Auteur, co-auteur :
Tytgat, Bjorn
Verleyen, Elie
Sweetlove, Maxime
D'hondt, Sofie
Clerck, Pia
Van Ranst, Eric
Peeters, Karolien
Roberts, Steven
Namsaraev, Zorigto
Wilmotte, Annick ; Université de Liège > Département des sciences de la vie > Physiologie et génétique bactériennes
Vyverman, Wim
Willems, Anne
Langue du document :
Anglais
Titre :
Bacterial community composition in relation to bedrock type and macrobiota in soils 1 from the Sør Rondane Mountains, East Antarctica
Date de publication/diffusion :
2016
Titre du périodique :
FEMS Microbiology Ecology
ISSN :
0168-6496
eISSN :
1574-6941
Maison d'édition :
Wiley, Oxford, Royaume-Uni
Volume/Tome :
92
Pagination :
fiw126
Peer reviewed :
Peer reviewed vérifié par ORBi
Intitulé du projet de recherche :
BELDIVA
Organisme subsidiant :
BELSPO - SPP Politique scientifique - Service Public Fédéral de Programmation Politique scientifique F.R.S.-FNRS - Fonds de la Recherche Scientifique Special Research Fund BOF of Ghent University
Aislabie J, Jordan S, Ayton J et al. Bacterial diversity associated with ornithogenic soil of the Ross Sea region, Antarctica. Can J Microbiol 2009;55:21-36.
Bakermans C, Skidmore ML, Douglas S et al. Molecular characterization of bacteria from permafrost of the Taylor Valley, Antarctica. FEMS Microbiol Ecol 2014;89:331-46.
Barton HA, Taylor NM, Kreate MP et al. The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments. Int J Speleol 2007;36:93-104.
Best MG. Igneous and Metamorphic Petrology. 2nd edn. Hoboken, New Jersey, USA: Wiley-Blackwell, 2002.
Borcard D, Legendre P. All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices. Ecol Model 2002;153:51-68.
Borcard D, Legendre P, Avois-Jacquet C et al. Dissecting the spatial structure of ecological data at multiple scales. Ecology 2004;85:1826-32.
Brinkmann M, Pearce DA, Convey P et al. The cyanobacterial community of polygon soils at an inland Antarctic nunatak. Polar Biol 2007;30:1505-11.
Brown MV, Schwalbach MS, Hewson I et al. Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series. Environ Microbiol 2005;7:1466-79.
Bryant DA, Costas AMG, Maresca JA et al. Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic acidobacterium. Science 2007;317:523-6.
Bryce CC, Le Bihan T, Martin SF et al. Rock geochemistry induces stress and starvation responses in the bacterial proteome. Environ Microbiol 2016;18:1110-21.
Cannone N, Ellis-Evans JC, Strachan R et al. Interactions between climate, vegetation and the active layer in soils at two Maritime Antarctic sites. 2006;18:323-33.
Cannone N, Guglielmin M. Influence of vegetation on the ground thermal regime in continental Antarctica. Geoderma 2009;151:215-23.
Carson JK, Campbell L, Rooney D et al. Minerals in soil select distinct bacterial communities in their microhabitats. FEMS Microbiol Ecol 2009;67:381-8.
Cary SC, McDonald IR, Barrett JE et al. On the rocks: the microbiology of Antarctic Dry Valley soils. Nat Rev Microbiol 2010;8: 129-38.
Chong CW, Pearce DA, Convey P et al. Patterns in the distribution of soil bacterial 16S rRNA gene sequences from different regions of Antarctica. Geoderma 2012;181-182:45-55.
Chong C-W, Pearce DA, Convey P. Emerging spatial patterns in Antarctic prokaryotes. Front Microbiol 2015;6, DOI: 10.3389/fmicb.2015.01058.
Chown SL, Convey P. Spatial and temporal variability across life's hierarchies in the terrestrial Antarctic. Philos T Roy Soc B 2007;362:2307-31.
Clarke KR, Somerfield PJ, Gorley RN. Testing of null hypotheses in exploratory community analyses: similarity profiles and biota-environment linkage. J Exp Mar Biol Ecol 2008;366:56-69.
Cleenwerck I, Camu N, Engelbeen K et al. Acetobacter ghanensis sp. nov., a novel acetic acid bacterium isolated from traditional heap fermentations of Ghanaian cocoa beans. Int J Syst Evol Micr 2007;57:1647-52.
Convey P, Gibson JAE, Hillenbrand C-D et al. Antarctic terrestrial life-challenging the history of the frozen continent? Biol Rev Camb Philos 2008;83:103-17.
Corinaldesi C, Danovaro R, Dell'Anno A. Simultaneous recovery of extracellular and intracellular DNA suitable formolecular studies from marine sediments. Appl Environ Microb 2005;71:46-50.
Cowan DA, Makhalanyane TP, Dennis PG et al. Microbial ecology and biogeochemistry of continental Antarctic soils. Front Microbiol 2014;5:154.
Cowan DA, Russell NJ, Mamais A et al. Antarctic Dry Valley mineral soils contain unexpectedly high levels of microbial biomass. Extremophiles 2002;6:431-6.
Cowan DA, Sohm JA, Makhalanyane TP et al. Hypolithic communities: Important nitrogen sources in Antarctic desert soils. Environ Microbiol Rep 2011;3:581-6.
Dana GL, Wharton RA, Jr, Dubayah RA. Solar radiation in theMcmurdo Dry Valleys, Antarctica. Ecosyst Dynamics Polar Desert. 1998;72:9-64.
DeSantis TZ, Hugenholtz P, Larsen N et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microb 2006;72:5069-72.
Dray S, Legendre P, Peres-Neto PR. Spatial modelling: a comprehensive framework for principal coordinate analysis of neighbour matrices (PCNM). Ecol Model 2006;196:483-93.
Edgar RC. Search and clustering orders ofmagnitude faster than BLAST. Bioinformatics 2010;26:2460-1.
Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 2013;10:996-8.
Edgar RC, Haas BJ, Clemente JC et al. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011;27:2194-200.
Edwards U, Rogall T, Blöcker H et al. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 1989;17:7843-53.
Engelbrektson A, Kunin V, Wrighton KC et al. Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J 2010;4:642-7.
Ertz D, Aptroot A, Van de Vijver B et al. Lichens from the Utsteinen Nunatak (Sør Rondane Mountains, Antarctica), with the description of one new species and the establishment of permanent plots. Phytotaxa 2014;191:99.
Fernández-Carazo R, Namsaraev Z, Mano M-J et al. Cyanobacterial diversity for an anthropogenic impact assessment in the Sør Rondane Mountains area, Antarctica. Antarct Sci 2012;24:229-42.
Fierer N, Bradford MA, Jackson RB. Toward an ecological classification of soil bacteria. Ecology 2007;88:1354-64.
Fierer N, Jackson RB. The diversity and biogeography of soil bacterial communities. P Natl Acad Sci USA 2006;103:626-31.
Fisher MM, Triplett EW. Automated Approach for Ribosomal Intergenic Spacer Analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 1999;65:4630-6.
Fossen H. Structural Geology. Cambridge, UK: Cambridge University Press, 2010.
Geyer KM, Altrichter AE, Takacs-Vesbach CD et al. Bacterial community composition of divergent soil habitats in a polar desert. FEMS Microbiol Ecol 2014;89:490-4.
Geyer KM, Altrichter AE, Van Horn DJ et al. Environmental controls over bacterial communities in polar desert soils. Ecosphere 2013;4:art127.
Gorodetskaya IV, Kneifel S, Maahn M et al. Cloud and precipitation properties from ground-based remote sensing instruments in East Antarctica. Cryosph 2015;9:285-304.
Gorodetskaya IV, Van Lipzig NPM, Van Den BroekeMR et al. Meteorological regimes and accumulation patterns at Utsteinen, Dronning Maud Land, East Antarctica: analysis of two contrasting years. J Geophys Res-Atmos 2013;118:1700-15.
Gray ND, McCann CM, Christgen B et al. Soil geochemistry confines microbial abundances across an arctic landscape implications for net carbon exchange with the atmosphere. Biogeochemistry 2014;120:307-17.
Gürtler V, Stanisich VA. New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 1996;142:3-16.
Hall BL, Denton GH, Fountain AG et al. Antarctic lakes suggest millennial reorganizations of Southern Hemisphere atmospheric and oceanic circulation. P Natl Acad Sci USA 2010;107:21355-9.
Hodgson DA, Convey P, Verleyen E et al. The limnology and biology of the Dufek Massif, TransantarcticMountains 82? South. Polar Sci 2010;4:197-214.
Janssen PH. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microb 2006;72:1719-28.
Joseph SJ, Hugenholtz P, Sangwan P et al. Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microb 2003;69:7210-5.
Kim M, Cho A, Lim HS et al. Highly heterogeneous soil bacterial communities around Terra Nova Bay of Northern Victoria Land, Antarctica. PLoS One 2015;10:e0119966.
Kovacs A, Yacoby K, Gophna U. A systematic assessment of automated ribosomal intergenic spacer analysis (ARISA) as a tool for estimating bacterial richness. Res Microbiol 2010;161: 192-7.
Lamprinou V, Skaraki K, Kotoulas G et al. Toxopsis calypsus gen. nov., sp. nov. (Cyanobacteria. Nostocales) from cave "Francthi", Peloponnese, Greece: A morphological and molecular evaluation. Int J Syst Evol Micr 2012;62:2870-7.
Legendre P, Borcard D, Peres-Neto PR. Analyzing beta diversity: partitioning the spatial variation of community composition data. Ecol Monogr 2005;75:435-50.
McDonald D, PriceMN, Goodrich J et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 2012;6:610-8.
Magalhães C, Stevens MI, Cary SC et al. At limits of life: multidisciplinary insights reveal environmental constraints on biotic diversity in continental Antarctica. PLoS One 2012;7: e44578.
Mitchell AC, Lafrenière MJ, Skidmore ML et al. Influence of bedrockmineral composition onmicrobial diversity in a subglacial environment. Geology 2013;41:855-8.
Namsaraev Z, Mano M-J, Fernandez R et al. Biogeography of terrestrial cyanobacteria from Antarctic ice-free areas. Ann Glaciol 2010;51:171-7.
Newsham KK, Pearce DA, Bridge PD. Minimal influence of water and nutrient content on the bacterial community composition of a maritime Antarctic soil. Microbiol Res 2010;165: 523-30.
Niederberger TD, McDonald IR, Hacker AL et al. Microbial community composition in soils of Northern Victoria Land, Antarctica. Environ Microbiol 2008;10:1713-24.
Niederberger TD, Sohm JA, Gunderson TE et al. Microbial community composition of transiently wetted Antarctic Dry Valley soils. Front Microbiol 2015;6:9.
Obbels D, Verleyen E, Mano M-J et al. Bacterial and eukaryotic biodiversity patterns in terrestrial and aquatic habitats in the Sør Rondane Mountains, Dronning Maud Land, East Antarctica. FEMS Microbiol Ecol 2016;32: DOI: 10.1093/femsec/fiw041.
Ohyama Y, Hiruta SI. The terrestrial arthropods of Sor Røndane in eastern Dronning Maud Land, Antarctica, with biogeographical notes. Polar Biol 1995;15:341-7.
Oksanen J, Blanchet FG, Kindt R et al. Vegan: Community Ecology Package. R package version 2.3-0, 2015, https://cran.r-project. org/web/packages/vegan/index.html.
Osanai Y, Nogi Y, Baba S et al. Geologic evolution of the Sør Rondane Mountains, East Antarctica: collision tectonics proposed based on metamorphic processes and magnetic anomalies. Precambrian Res 2013;234:8-29.
Pattyn F, Matsuoka K, Berte J. Glacio-meteorological conditions in the vicinity of the Belgian Princess Elisabeth Station, Antarctica. Antarct Sci 2010;22:79.
Pearce DA, Newsham KK, Thorne MAS et al. Metagenomic analysis of a southern maritime Antarctic soil. Front Microbiol 2012;3:1-13.
Peeters K, Ertz D, Willems A. Culturable bacterial diversity at the Princess Elisabeth Station (Utsteinen, Sør Rondane Mountains, East Antarctica) harbours many newtaxa. Syst Appl Microbiol 2011;34:360-7.
Peres-Neto PR, Legendre P, Dray S et al. Variation partitioning of species data matrices: Estimation and comparison of fractions. Ecology 2006;87:2614-25.
Pointing SB, Chan Y, Lacap DC et al. Highly specialized microbial diversity in hyper-arid polar desert. P Natl Acad Sci USA 2009;106:19964-9.
Popa R, Popa R, Mashall MJ et al. Limitations and benefits of ARISA intra-genomic diversity fingerprinting. J Microbiol Methods 2009;78:111-8.
Pugh PJA, Convey P. Surviving out in the cold: Antarctic endemic invertebrates and their refugia. J Biogeogr 2008;35:2176-86.
R Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing, 2015.
Raymond J, Siefert JL, Staples CR et al. The natural history of nitrogen fixation. Mol Biol Evol 2004;21:541-54.
Schloss PD. The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 2010;6:e1000844.
Schloss PD, Westcott SL, Ryabin T et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microb 2009;75:7537-41.
Sellstedt A, Richau KH. Aspects of nitrogen-fixing actinobacteria, in particular free-living and symbiotic frankia. FEMS Microbiol Lett 2013;342:179-86.
Seneviratne G, Indrasena IK. Nitrogen fixation in lichens is important for improved rockweathering. J Biosci 2006;31:639-43.
Shiraishi K, Osanai Y, Ishizuka H et al. Antarctic Geological Map Series Sheet 35 Sør Rondane Mountains (1:250 000). Tokyo: National Institute of Polar Research, 1997.
Sokol ER, Herbold CW, Lee CK et al. Local and regional influences over soil microbial metacommunities in the Transantarctic Mountains. Ecosphere 2013;4:1-24.
Stomeo F, Makhalanyane TP, Valverde A et al. Abiotic factors influencemicrobial diversity in permanently cold soil horizons of a maritime-associated Antarctic Dry Valley. FEMS Microbiol Ecol 2012;82:326-40.
Tahon G, Tytgat B, Stragier P et al. Analysis of RuBisCO, nifH and pufLM genes in soils near the Princess Elisabeth Station, Sør Rondane Mountains, Antarctica, indicates a large diversity of auto- and phototrophic bacteria. Microb Ecol 2016, DOI: 10.1007/s00248-015-0704-6.
Teixeira LCRS, Peixoto RS, Cury JC et al. Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica. ISME J 2010;4:989-1001.
Tsujimoto M, McInnes SJ, Convey P et al. Preliminary description of tardigrade species diversity and distribution pattern around coastal Syowa Station and inland Sør Rondane Mountains, Dronning Maud Land, East Antarctica. Polar Biol 2014;37:1361-7.
Tytgat B, Verleyen E, Obbels D et al. Bacterial diversity assessment in antarctic terrestrial and aquatic microbial mats: A comparison between bidirectional pyrosequencing and cultivation. PLoS One 2014;9, DOI: 10.1371/journal.pone.0097564.
Van Horn DJ, Van Horn ML, Barrett JE et al. Factors controlling soil microbial biomass and bacterial diversity and community composition in a cold desert ecosystem: Role of geographic scale. PLoS One 2013;8, DOI: 10.1371/journal.pone.0066103.
Vrionis HA, Whyte LG, Miller RV. Life at the poles in the age of global warming: Part 2. Microbe 2013;8:491.
Vyverman W, Verleyen E, Wilmotte A et al. Evidence for widespread endemism among Antarctic micro-organisms. Polar Sci 2010;4:103-13.
Wang Q, Garrity GM, Tiedje JM et al. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microb 2007;73: 5261-7.
Ward N, Challacombe J, Janssen P et al. Three genomes from the phylum Acidobacteria provide insight into their lifestyles in soils. Appl Environ Microb 2009.
Wood SA, Rueckert A, Cowan DA et al. Sources of edaphic cyanobacterial diversity in the Dry Valleys of Eastern Antarctica. ISME J 2008;2:308-20.
Yarwood S, Wick A, Williams M et al. Parent material and vegetation influence soil microbial community structure following 30-years of rock weathering and pedogenesis. Microb Ecol 2014;69:383-94.
Yergeau E, Kang S, He Z et al. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. ISME J 2007a;1:163-79.
Yergeau E, Newsham KK, Pearce DA et al. Patterns of bacterial diversity across a range of Antarctic terrestrial habitats. Environ Microbiol 2007b;9:2670-82.
Zwart G, Hiorns WD, Methé BA et al. Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria. Syst Appl Microbiol 1998;21: 546-56.
